A HISTORICAL OVERVIEW OF THE SCIENCE AND PHILOSOPHY OF EVOLUTION

 

A HISTORICAL OVERVIEW OF THE SCIENCE AND PHILOSOPHY OF EVOLUTION

INTRODUCTION:     

Philosophers pursued the concept of evolution for thousands of years.  Many different ideas were explored and discarded until biologists blended the thoughts of Gregor Mendel and Charles Darwin into a theory called the modern synthesis in the first half of the twentieth century.  While it attracted considerable support in the scientific community, it is now being challenged by new discoveries in microbiology.  The following overview follows the changes in thinking over the years.  At this time, the accumulation of books and papers on evolution constitute a huge body of literature and no overview can possibly be all inclusive.  Hopefully, this overview reviews enough pertinent documents to adequately demonstrate how evolutionary concepts have changed over the years.

Much of the voluminous literature on evolution contains a mix of philosophy, theology, and science, and some is quite contentious.  Except for period before Darwin, this overview, so far as possible, focuses mostly on the science.  However, a compete separation between evolution science and philosophy is not possible because evolution began as philosophy and even today some new hypothesis continue to come from philosophers rather than from scientists.  Also, philosophers continue critiquing the logic of evolutionary theory. The overview does not include theological papers and books because science cannot evaluate the validity of theological views on evolution.

Collectively, the scientific literature does not provide conclusive support for Darwinian evolution (the modern synthesis). The reader can decide whether scientific observations and experiments establish evolution as a “fact” as is frequently claimed.  Science usually follows a path of hypothesis to theory to law.  Calling evolution a “fact” suggests it is somehow different from experimental sciences such as physics and chemistry.  One obvious difference is the limited ability to perform confirming experiments. Hence, the conventional scientific progression from hypothesis to theory to law is not possible.

Collectively, the scientific references included in this overview do show that the textbook and media version of evolution is not entirely consistent with the scientific literature.  Far from being a clearly defined, established “fact”, Darwinian evolution was never based on a consensus and the diversity of opinions in the scientific community keeps expanding.

The textbook version of what is called the modern synthesis (Darwinian evolution) is rather absolute.  Evolution is a fact, macroevolution is simply an accumulation of microevolution over billions of years, and the entire scientific community supports it.  The scientific literature is less certain.  Numerous scientists have published books and papers challenging one or more aspects of Darwinism, and many are calling for revision or replacement.  There are staunch defenders of the as is modern synthesis, but they tend to be educators and philosophers rather than scientific researchers.  Not only is there no consensus supporting the as is modern synthesis, there is not even a common understanding of exactly what it is or how it was developed.  Some say it always included random mutation as well as Darwinism and Meldelism, and some say it did not.

The current situation is not surprising because the modern synthesis was established before the chemical and physical nature of the cell and the genome was understood.  The structure of the DNA molecule and the genetic code contained therein was not recognized and understood until years after the synthesis was established. Furthermore, since the discovery of DNA over half century ago, incredible discoveries about the details of life have been made.  Therefore, the scientific literature contains extensive discussion about whether the modern synthesis is consistent with all of the knowledge gained since it was established.

This overview follows the timeline of the related literature, beginning a couple of thousand years ago.  Key papers and books were reviewed, as well as many less significant references that bring novel views to the discussion.  The survey of publications is far from complete however, because the number of books and papers on evolution is immense.  Hopefully, the ones that were reviewed include most of the pertinent points related to the extended scientific discussion on evolution.

Overview of Literature:

Darwin’s Assumptions:

Darwin based Origin of Species on a number of assumptions; the initial spontaneous generation of life, evolution of all life forms from a common ancestor, the potential for unlimited variation in a long sequence of offspring, very gradual changes from generation of generation, more offspring than the environment could support, and selection of survivors by the environment (natural selection).

The various assumptions Darwin made in Origin all appeared previously in the literature, but not collectively.  Darwin’s book attracted attention because he integrated them into “one long argument” collectively supporting them as an explanation for the presence of the extreme variety of life on earth.  Although Origin sold well and promoted extensive discussion, the scientific community did not accept all of Darwin’s assumptions. They immediately spotted the obvious flaw in his vision of variation (blending inheritance), and were extremely doubtful of natural selection. For the next sixty years, various alternate theories were published.  The only assumption in Origins that gained some acceptance at the time was that of a common ancestor.  Even that was not universally accepted, since some scientists believed, as did Lamarck, that life may have spontaneously begun more than once.  Today, some scientists still suspect that may be true. Serious scientific resistance to most of Darwin’s work continued for many decades following the publication of Origins.

The Fossils

Darwin knew that the fossil record did not support his assumption of slow variations in animal forms over long periods of time, but he assumed that was because of insufficient fossil samples. He further assumed that supporting fossil evidence would eventually be found.   However, the many fossils collected since his time has not produced a consensus supporting Darwin’s assumption.  Some evolutionists claim there are now enough transition fossils to prove common origin.  Others claim there are not and challenge the proposed transitions. Lifeforms preserved in the fossil record often appear suddenly without any apparent ancestors, as in the Cambrian explosion, and are then often unchanged for very long periods of time.  When there is change, it usually occurs relatively quickly.

To address that apparent inconsistency in the fossil record, Gould and Eldridge proposed the concept of “punctuated equilibrium” in 1972.  They postulated that evolution usually proceeds very slowly, but is rapid at times (punctuated). Presumably, the reason is that significant change can only occur in small populations because in large populations interbreeding with like creatures will minimize variation.  Therefore, evolution can only move rapidly in small populations produced by mass extinctions or geographic isolation.  Because it then proceeds rapidly and the population is small, chances of any intermediate individuals being preserved in the fossil record is small. Today, current literature clearly shows there is still no scientific consensus on whether or not the fossil record is consistent with Darwinian evolution.

Original Life Form:

Darwin did not attempt to explain the origin of the first life form that evolved into all the many plants and animals found on earth.  He did, however, speculate that it may have formed spontaneously, in a “warm little pond”, from inanimate materials.  Today, many evolutionists believe that is what happened, and many careers and many millions of dollars have been and are being expended pursuing a way in which that might have happened.  In the USA, the National Science Foundation continues to award generous grants for experiments searching for the origin of life.  Some of the research has produced some basic organic molecules from inorganic compounds.  However, that basic organic material is an extremely long way from a living cell and even further from a life form that can reproduce.

The Miller Urey experiment, once considered a classical origin of life experiment and included in many textbooks, has subsequently been discredited. As stated by Joseph A. Kuhn: “Unfortunately, the experimental conditions of a low-oxygen, nitrogen-rich reducing environment has been refuted by many. The experiment actually produces a racemic mixture of amino acids that would inhibit the production of useful proteins.”

An increasing number of scientists, such as organic chemist James Tour, are beginning to believe that current origin of life research is futile because the modern synthesis cannot explain it.  Their thinking is that the origin of life may require information as well as material and energy.

Genetics:

When Gregor Mendel’s work on genetics was rediscovered in 1900, it initially cast further doubt on Darwinism.  Genetics did not appear to be compatible with the assumptions of very small increments of change and the potential for unlimited variation.  Instead, genetics demonstrated very noticeable increments of change and offered no mechanism for the addition of complexity.

Not until the 1930’s, when natural selection began to become became part of an overall evolutionary hypothesis called the modern synthesis, did Darwin receive significant recognition.  Though usually described as a synthesis of Darwinian evolution and Mendelian genetics, the synthesis also included, in a limited form, De Vries mutation theory.  It assumed life could spontaneously experience sudden changes, rather than only gradual change as assumed by Darwin.  Macro (large scale) evolution, which accommodated the concept of a common ancestor, was recognized (by some) as not possible with only Darwinian natural selection and Mendelian genetics.  Therefore, to accommodate the assumption of a common ancestor, the assumption of random mutation had to be included even though there was no understanding of a physical process that could cause such mutation.  As obvious as this may seem, papers continue to be published on the history of the modern synthesis, and not all agree on if or when mutation became a part of it. There continues to be a lot of focus on the work of Fisher, Haldane, and Wright in developing population genetics, which attempted to explain how various combinations of Mendelian genetic factors could produce the appearance of very gradual change rather than only discrete increments of change. However, population genetics only proves that Mendel’s work does not contradict Darwin’s. It does not offer and explanation for the development of complexity, so the concept of mutation had to be included in the modern synthesis.

By the 1950s, evolutionists had solidified the basis of the modern synthesis.  Standing variation (all the information contained in existing genes) and random mutations provided the opportunity for variation, and natural selection determined which variants survived and produced the most offspring.  Mutations added complexity. This process was thought responsible for the development of all living organisms on earth from a common ancestor in accordance with Darwin’s tree of life (the only illustration in Origins).  Spontaneous generation of the first life form and the cause of mutant variations were not explained.  The modern synthesis received considerable, but not unanimous support.  Some scientists were uncomfortable with the unexplained mutation process, and continued to offer alternatives. At the time, the unexplained origin of life received less attention, but was also a continuing topic of debate.

DNA:

When the structure of the DNA molecule was discovered in 1953, evolutionists were finally able to propose a physical process supporting mutation.  Errors made during duplication of DNA molecules were thought to provide a continuous series of random mutations.  Most random mutations would be harmful or benign, but occasional beneficial mutations were thought to explain the evolution of all life from a common ancestor.  The details of exactly how random errors produced novel and complex advances received limited attention. The general concept was that a continuous series of very small, beneficial mutations in the DNA molecule could produce absolutely any viable life form if time was unlimited. 

Other Sources of Variation;

While the modern synthesis was founded on the very general concept of mutation of genes as the source of variation supporting macroevolution, subsequent discoveries have and are discovering many different types of mutation.  When the structure of the DNA molecule was discovered (subsequent to the establishment of the modern synthesis) evolutionists assumed that random modifications (deletions, insertions, substitutions, or duplications) of that molecule explained macroevolution.  Subsequently, other sources of change have been discovered.

One other such source of variability is epigenetics.  Long strands of DNA often have multiple, but not identical, genes for the same feature. Of those multiple genes, some are turned off and some are turned on.  The “switch” is a small, additional molecule attached to the DNA strand, and on or off is determined by the presence or absence of this extra molecule.  Under certain conditions, the status of these switches can be changed outside of the reproduction process.  Therefore, some variation in higher life forms is possible outside of Mendelian genetics.

Microbiologists also discovered genetic networks. When microbiologists first began decoding DNA, they thought only a few percent of the genes distributed along the DNA molecule contained currently useful information.  They considered most of the other DNA to be “junk DNA” that was evolutionary residue and no longer required to form and maintain lifeforms.  That was because the genes they could most easily relate to a function were genes that directed the production of protein and biological structure.  Subsequently, it was learned that most if not all of the ‘junk DNA” contains information that is critical for life.  There are genes that contain the information for directly producing living structure and there are other genes that (along with or in conjunction with the epigenome and gene networks) regulate the production genes.  That regulation is required to organize the physical structure of the developing lifeform.

Continuing discoveries have shown that even the cell itself contains important information not included in either the DNA or the epigenome.  The concept of cellular regulatory circuits then emerged.  Considering that cells have to determine where and when to produce various different materials, perhaps the additional complexity should have been expected.  What is becoming quite clear is that DNA itself cannot produce life. During reproduction, new life begins with a complete cell which is an incredibly complex structure maintained by a system with many interacting components. The exact process the cells use to produce a complex body plan is still not understood.  The current production of literature pursuing this area of biology is voluminous.

Thus, the understanding of the structure and transfer of genetic information has changed greatly over the years since Darwin.  Beginning with the rediscovery of Mendel’s work, biologists have identified numerous ways that genetic information can be altered and passed from one generation to the next.

Standing Variation:

All of the known ways, however, only exchange and reorganize existing information.  They can cause color, size, and specific shape to change, but they may not be able to produce entirely new features.  There is currently no generally accepted, conclusive proof that a frog could evolve from a fish.  The only way currently known biological process could produce novel features is by a lengthy, and perhaps highly improbable, sequence of mutations (random errors).  Various scientists are therefore challenging the ability of the modern synthesis to explain macroevolution.

Improbability:

Some, using the estimated rate of mutations, have conducted probability analysis showing that the slow process of random mutation could not have produced complex lifeform in the time that the earth has existed. The rate of uncorrected mutation is low, and the DNA code is incredibly complex.  Therefore, some statistical studies show that the probability of random error producing a new species in the time that life has existed on earth is extremely low.  Others, applying the concept of irreducible complexity, claim that information as well as material and energy were required.

All Combination’s not Necessary:

Others claim that the probability calculations are invalid because a completely unique DNA structure and gene network is not required to develop a particular lifeform. They claim that not all combinations of mutations have to be tried. They point to the absence of random geometry in existing lifeforms. They also point to literature showing that very similar lifeforms sometimes have very different genetic structure.  That proves that alternate genes can do same job.  

Micro versus Macro and Complexity:

Much of the literature addresses microevolution and macroevolution, and is not consistent with the textbook version of evolution. Generally, but not always, the literature defines microevolution as small changes within a species. Common examples of microevolution are the many breeds of dogs, and the classic text book examples: the spotted moth and Darwin’s finches.  Macroevolution is the appearance of new, novel features that eventually bring about major changes of form.  Some scientists believe a very long sequence of micro evolutionary steps can produce macroevolution (ex: development of an amphibian from a fish). That is, macroevolution is simply and accumulation of microevolution over very long periods of time, as presented in biology textbooks. Others believe that microevolution and macroevolution must be based on fundamentally different processes. The continuing accumulation of literature on micro and macro evolution is voluminous, and there is no consensus on the process of macroevolution.

Since science has not resolved the debate over micro and macro evolution, various philosophers continue to prepare papers and books on the topic.  Some, based on a process of logic, conclude that microevolution cannot explain macroevolution, while others pursue a thought process that leads to unqualified support for the modern synthesis as is.  The complexity of the questions also attracts the attention of other scientists and engineers.  Physicists, chemists, electrical engineers, and computer scientists are contributing to the debate.  Their inputs are often critical of the modern synthesis, and maintain that it cannot explain the development of complex biological systems.  Defenders of the modern synthesis typically include various biologists, zoologists, and especially paleontologists. In general, supporters view the issue from the fossil record and the presumed family tree, and attempt to explain away, with various arguments, the discontinuities in the fossil record.  Critics look at the emerging complexity of the living cell and genetic material, and question the ability of random mutation and natural selection to produce it.

According to the modern synthesis, macroevolution can only occur if an appreciable string of favorable mutations accumulate in the DNA code. Single mutations will usually be disastrous or neutral.  If not disastrous or neutral, any single mutation can only have negligible, if any, favorable effect and is therefore unlikely to be preserved by natural selection. A significant, favorable change therefore requires a fortuitous accumulation of a combination of   neutral or marginally favorable mutations that collectively produce a significant favorable variation.  Natural selection can then spread this favorable change throughout the surviving members of the species.

However, an error in DNA duplication during cell division usually does not become a mutation to support evolution because the cell includes correction mechanisms. It checks DNA duplications for accuracy, and repairs errors. Therefore, the probability of a not immediately beneficial mutations accumulating in the DNA is very small. This repair process presents a challenge to the assumption that random, not immediately beneficial mutations accumulate to eventually produce macroevolution.

As advances in microbiology during the last half of the twentieth century discovered ever increasing complexity in biological structure, more frequent questions about the validity of the modern synthesis began to arise.  Some evolutionists began calling for an extended evolutionary synthesis which would account for discoveries made since the modern synthesis was established.  Today, the issue is contentious within the scientific community.  Some evolutionists still believe the modern synthesis is valid as is, while others believe it is, at least partially, obsolete.  Since the modern synthesis is currently still the established paradigm, especially in education and philosophy, questioning it sometimes jeopardizes careers in academic institutions.  Doubters are also often subjected to academic ostracism and media ridicule. However, peer reviewed scientific literature does contain many dissenting opinions.  The often heard claim that only creationists reject the modern synthesis is not accurate.

Current challenges to the modern synthesis are frequently based on complexity.  The claim is that a process solely dependent upon standing variation, random mutation, and natural selection could not produce the complex features found in higher lifeforms.  The rational is that a complex feature either works or it does not work. Said another way, the biological structure that performs a complex function provides no benefit until it is complete.  Partially complete structures provide no benefit so natural selection cannot preserve them. A classic example is the rotary motor that powers the flagellum that propels bacteria such as Escherichia coli. A flagellum without the motor would not provide propulsion and natural selection could not preserve it. Similarly, a motor without flagellum could not be preserved.

Evolutionists counter this argument by defining two evolutionary processes; direct and indirect.  In direct evolution, a random mutation produces a slight benefit.  That gives the lifeform a reproductive advantage.  Subsequent mutations provide further enhancement, and the advantageous feature develops further.  An example might be random lengthening of the vertebrae in the giraffe’s neck.  Each increment of added length adds browsing opportunities so the animal is better nourished and better able to survive and reproduce.

In indirect evolution, the first step is completely independent, direct evolution of multiple features that provide entirely different functions.  Successive, beneficial mutations in each independent evolutionary path refine the respective structural features until they are both somewhat advanced.  Then, there is a serendipitous event that permits two or more independently evolved features to combine to perform a new and completely unrelated function.  An often cited example is again the bacterial flagellum, a rotary device that provides propulsion and movement.  Critics of the modern synthesis say that the flagellum is irreducibly complex.  It is not functional and not beneficial until all of the parts present; therefore a succession of random mutation could not have produced it.  Defenders of the modern synthesis say that all of the parts could have evolved independently, for other unknown purposes, by random mutation and natural selection.  Then, by indirect evolution, the various parts, such as motor and flagellum, could have somehow combined to produce the rotary flagellum.

Complexity:

As microbiologists continue to reveal the incredible complexity of cell structure, the concept of “irreducible complexity” appears more and more frequently.  It posits that complex structures and functions in advanced lifeforms could not have resulted from a lengthy sequence of random errors because individual components of complex system have no evolutionally benefit until the entire system is complete.  Therefore, natural selection could propagate the complex system once it existed, and perhaps improve it, but it could not produce individual components before they had a useful application. Michael Behe, a microbiologist, has produced numerous publications promoting the concept of irreducible complexity. One of the first examples he cited is the rotary bacterial propulsion system described previously.  Behe has produced lengthy arguments claiming that the individual components of this biological motor could not possibly have been shaped by natural selection. Behe and others have produced numerous books challenging the belief that random error and natural selection could have produced various complex biological systems.

Another complex example is biological gears. Gears in an animal structure either work or they don’t.  They cannot evolve slowly in small increments by natural selection before they are complete and useful. Yet there is at least one animal that includes fully functional gears in its structure. The small hopping insect Issus Coleoptratus has toothed gears on the joints of its hind legs that precisely synchronize kicks as it jumps.

Therefore, a growing number of scientists are supporting the concept of irreducible complexity, and it is presenting a serious challenge to the modern synthesis.  Some scientists are beginning to suspect the universe consists of material, energy, and information because the specific, complex information required supporting advanced lifeforms cannot be produced by only a combination of random mutation and natural selection.  Some scientists also think that information, as well as material derived from energy, is required to produce the 98 natural elements.

Some microbiologists promoting the concept of irreducible complexity extended it to assume intelligent design.  Concluding that information, along with energy and material, was needed to produce life, they argue that science can identify underlying intelligence in biological systems, just as an anthropologist can determine if a pile of rocks were arranged by natural, random processes or by intelligent activity.  Traditional (modern synthesis based) evolutionists are highly critical of the concept of intelligent design, and group supporters with creationists.  Intelligent design supporters, however, insist that the concept of irreducible complexity is strictly science based.  Unfortunately, much of the associated literature has become a very contentious debate rather than an objective search for a better understanding of the origin of life and the development of complex, existing lifeforms. The fundamental dispute may present a philosophical impasse: can the universe contain information but not intelligence?

Two Major Weak Points:

As is, the modern synthesis is still burdened by the two major weak points: 1) there is no commonly accepted hypothesis explaining the spontaneous origin of life, and 2) there is no commonly accepted hypothesis for the specific process of macroevolution or any irrefutable evidence proving that it has actually happened.  All evidence that is offered, such as the fossil record, is inferential.  Some evolutionists, and especially those in the academic community, continue to believe that macroevolution is nothing more than accumulated microevolution, while many other scientists offer evidence suggesting that macroevolution requires a different process than microevolution.  A massive amount of literature has been and is accumulating on this issue, and thus far, none of it indicates the questions will be resolved soon. Given these two major deficiencies, the claim that evolution is a “fact” is not supported by existing, peer reviewed scientific literature.

Other Problems:

Researchers have found numerous other problems that cannot be explained by the modern synthesis and continue to find more.  The modern synthesis appears too simplistic, and does not provide an adequate explanation for the development of complex body forms, the origin of sex, and the splitting of species. Some have concluded that epigenetics, rather than genetics, is the main driver of the evolution that does occur. Researchers that built the world’s largest evolutionary tree concluded that species arise because of chance mutations, not natural selection. Recently developed DNA based trees of life show that Darwin’s simplistic tree is completely wrong and they challenge the concept of a common ancestor.

Some have concluded that epigenetics rather than genetics is the main driver of evolutionary development, and that epigenetics may be altered by both the environment and stress during meiosis. Others have concluded that the hypothesis of junk DNA is wrong, that duplicate genes have important functions, and that genes are merely recipes for producing proteins and do not define structure. Information in cell, not in the DNA, is required to develop and embryo.

Some research has shown that the cell is completely independent of the DNA, is incredibly complex, and must be inherited. DNA alone cannot produce life. The means by which the cell interprets the information in the DNA has not yet been explained. Other researchers are suggesting that the cell stores biological information in read write system and that both the organism and the environment can change it. Others have shown that complexity can increase as information is lost rather than gained.

A common observation found in publications critical of the modern synthesis is that Darwin and the authors of the modern synthesis offered no real explanation for the origin of species. Natural selection explains the survival of the fittest but it does not explain the arrival of the fittest.

A review of historical and current literature shows that many of the current challenges to the modern synthesis are the same as the challenges to Origins over a century ago. Today however, those objections are supported by data from various areas of research rather than just alternate hypothesis.

Four Groups:

While the media usually portrays the contentious evolution debate as contest between evolutionists and creationist’s, there are actually at least four groups involved; staunch supporters of the modern synthesis,  promoters of an extended evolutionary synthesis,  advocates for intelligent design, and creationists. Creationist arguments cannot be evaluated from the standpoint of science, and are therefore not included in this historical summary. The positions of the other three groups can, their differences are substantial, and there is currently no indication those differences will be resolved in the near future. However, the frequently made claim that all serious scientists support Darwinian evolution in the form of the modern synthesis is clearly not supported by the literature.  Rather, and ever growing number of papers and books are challenging the modern synthesis, either in part or completely.

Two Faces of Evolution:

There are currently, therefore, two faces of evolution. The is the public face, presented by academia, textbooks, and the media. Simply stated, it claims the modern synthesis, as is, is established “fact”. It is true that is very well established in society and that it has therefore prevailed in numerous court cases about what can and cannot be taught in high schools. It is also so well rooted in academia that it can derail the careers of scientists arrogant enough to challenge the modern synthesis. The “hidden” face, which seriously questions the scientific viability of the modern synthesis, is hidden in plain sight. It exists in peer reviewed scientific publications available to anyone who is curious. Because the contradictions are so serious and obvious, it has also been appearing more and more frequently in numerous popular books marketed to the general public.  Eventually, the many problems with the current modern synthesis may become obvious to all.  However, if the history of past conflicts in science is relevant to this conflict, at least one, and perhaps more, generations of scientists and educators will have to leave this world before that can happen. In theory, science is perfectly objective. Not all scientists, however, are.

Future posts well provide information on supporting literature.

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A Sample of the Literature

 in Chronological Order

(With comments, summary, excerpts, or copy of abstract)

 

BEFORE DARWIN:

The basic concepts of evolution first appeared thousands of years ago.  The Greek philosopher Anaximander (610—546 BC) believed that one type of animal could descend from another, and Empedocles (490-430 BC) even thought that they could be made up of various combinations of pre-existing parts.  Empedocles (490–432 BC) attempted to develop a comprehensive concept for the development of animal life in a manner that suggested evolution by natural selection.  The Roman philosopher Titus Lucretius Carus (99-55 B.C.E.) wrote De Rerum Natura ("On the Nature of Things"). Lucretius envisioned an "evolutionary" theory similar to that of Empedocles. Species formed by the chance combination of elements. Natural selection caused the extinction of unfit organisms, and those organisms that survived did so because of their strength, speed, or cunning.  However, he did not believe in the continuing evolution of species.  He thought that the process of evolution was now over, and species were fixed.

Muslim philosopher and scientist Nasir al-Din al-Tusi, in a work called Akhlaq-i-Nasri that he prepared in the thirteenth century, documented a basic theory of evolution.  He imagined that atoms evolved into minerals, and minerals evolved into living organisms (first plants, then animals).  He described how animals develop various advantageous features, depending upon what environment they are in.  His text includes the following claim:  "The organisms that can gain the new features faster are more variable. As a result, they gain advantages over other creatures. ... The bodies are changing as a result of the internal and external interactions."

French naturalist Comte de Buffon (Count Buffon, 1707–1788) questioned the fixity of species and suggested a transmutationist theory with a similarity to Darwinian evolution.  Buffon noted that despite similar environments, different regions have distinct plants and animals.  This is now considered to be the first principle of biogeography. He suggested that species may have both "improved" and "degenerated" after dispersing from a common place of origin.  In volume 14 of Histoire naturelle, générale et particulière , he proposed that all the world's quadrupeds had developed from an original set of just thirty-eight quadrupeds.  Therefore, some consider him a "transformist" that preceded Darwin.

 

In 1744, Carl Linnaeus proposed that all life began with just a few starting species, and that all life then on earth were formed by a succession of hybrids. 

Pierre-Louis Moreau de Maupertuis published the basic concepts of genetics and evolution in 1745 and 1751.  He suggested that traits from both parents determine the combination of traits found in individual members of a species, a basic concept of modern genetics. In addition, he understood the concept of genetic fitness, the idea that only those traits that offer advantages would be passed on from generation to generation.  Later, Darwin called this idea natural selection.

In 1794, geologist James Hutton proposed the concept of natural selection, with the least fit members of a species succumbing to the environment and the best fit reproducing most successfully.

The physician, naturalist, and philosopher Erasmus Darwin, grandfather of Charles Darwin, published the book Zoonomia (The Laws of Organic Life) in 1795.  He believed that life originated with a single common ancestor, and speculated about how one species might be transformed into another.  He assumed the “the strongest and most active animal should propagate the species, which should thence become improved.”

French biologist Jean-Baptiste Lamarck published his theory of the transmutation of species (Philosophie Zoologique) in 1809. Lamarck believed that simple life forms appeared spontaneously, and had inherent capability to develop further complexity.  He further believed that they could alter their form with lifetime activities and that they could pass those alterations to their offspring.

In Lamarckian adaption, the organism modified its habits and ultimately its makeup in response to environmental conditions. Changes in habit resulted in permanent alterations of the organisms over time, and such modifications were passed along to offspring. The process was called “the inheritance of acquired characteristics.”   For example, he believed that each generation of giraffes developed slightly longer necks because giraffes stretched their necks to browse on tall treetops. Lamarck did not imagine a single common ancestor.  He thought that simple life forms arose spontaneously now and then and gradually evolved into the various higher lifeforms that inhabit the earth.  Pasteur did not establish the law of biogenesis until after Lamarck’s died and Darwin published Origins of Species. Therefore, belief in the spontaneous generation of life was still fairly common at the time of Lamarck.

William Wells published an accurate description of the natural selection process in 1818. Darwin was unaware of Well’s work when he published the first edition of Origin of Species, but acknowledged Wells work in later editions.

In 1831, the Scottish horticulturalist Patrick Matthew published a clear statement of the law of natural selection in an appendix to his book Naval Timber and Arboriculture in 1831. Also in 1831, Geoffroy Saint-Hilaire produced a paper with the title Memoir on the Degree to Which the Environment Influences Animal Form. He suggested that the environment could cause the sudden production of a new species from an existing species.  Albert von Kolliker revived Geoffroy's theory in 1864.

Robert Edmond Grant and Charles Lyell believed all lifeforms had the capacity to transform into other species. They claimed that that progression of lifeforms in the geologic record appeared to support this belief.  However, they did not propose a mechanism for the transformation of species.  Grant believed that all species, plants and animals, had a common origin, and was one of Darwin’s professors at the University of Edinburgh.

In 1835 Edward Blyth described how wild animals appear with slight variations, and speculated about how what is now called natural selection would operate on the variations.  He saw natural selection as analogous to artificial selection used by breeders to produce domestic animals with desired features.  By 1837 Blyth realized that some variations might be better suited to the environment than the original species.

The subcellular structures that would later be called chromosomes were first observed by Carl Nageli in 1843, but their function was unknown.  In 1882, Walter Flemming published a book explaining how chromosomes were doubled in the process of cell division.

In the Oracle of Reason (1841-1843), Charles Southwell and William Chilton published a serial article entitled “Theory of Regular Gradation.”   It was a theory of serial species change and development, or transmutation, as evolution was called at the time.

In 1844, geologist Robert Chambers published (anonymously) a bestselling book entitled Vestiges of the Natural History of Creation.  It claimed that life had appeared spontaneously, and that low forms of life then evolved into higher forms, including man. Supposedly, as an embryo developed, it passed through the final fetal forms of each of its ancestors.  Therefore, all that was needed to achieve a higher form was a longer gestation period.  The book was highly controversial, and some thought that may have made Darwin reluctant to publish his book, which existed in rough draft as early as 1839.

DARWIN:

In 1858, Charles Darwin and Alfred Russel Wallace presented a joint paper on evolution by natural selection. The following year, Darwin published On The Origin of Species.   Due in no small part to energetic promotion by Thomas Huxley (widely known as Darwin’s bulldog), Origin attracted considerable attention both in the scientific community and the general, and sold much better than expected.  Additional copies were printed to meet the demand.

Darwin combined some basic observations with a number of assumptions.  On his voyage to South America and the Galapagos Islands, Darwin observed very noticeable variety in the animals. He was particularly interested in the variety of woodpeckers on the different islands.  As a naturalist, he was familiar with variations in plants and animals caused by selective breeding, so he wondered if there was a natural process similar to selective breeding that could cause progressive increments of change in wild plants and animals.

Eventually, he adopted the concept of natural selection.  He proposed, as did Hutton and Wells, that small changes, from generation to generation, could cause plants and animals to become more or less able to survive and reproduce in their environment.  Those best adapted to their environment would survive and produce more offspring, so the average form of their species would shift to the better adapted form. 

Darwin has no idea what caused the generation to generation variations, or that they might be limited. In spite of his familiarity with the limitations of selective breeding of plants and animals, he assumed incremental variations were unlimited.  He thought that a succession of small incremental changes, occurring over long periods of time, could produce new species.  One of his notebooks contains the famous sketch that was subsequently labeled a “tree if life”, and the only illustration contained in Origin of Species is a more refined drawing of that idea. The trunk of the tree is the common lifeform, and the branches and twigs are the variety of lifeforms presumed to have evolved over millions of years.

His first assumption (unlimited variation) facilitated his second assumption (common ancestors).  If there were no limits on generation to generation variability, then, given enough time and appropriate environmental conditions, any lifeform could eventually evolve into another.  A fish could, if exposed to a suitable succession of changing environments over many millions of years, become a lizard, and a lizard could eventually become a mouse.  Ultimately, all of life could have one single common ancestor.

The core idea in Origin of Species (common ancestors) eventually caught on among biologists.  Most, however, did not believe that natural selection could be responsible for transforming one species into another.  Complete acceptance of the assumptions in Origin of Species was hindered because it offered no plausible physical explanation for the source of variation.  Further, it assumed that the variation that did occur from one generation to the next was due to blending the traits of male and female parents.  Biologists such as Fleming Jenkin quickly noted that was impossible.  If features were blended from generation to generation, then the population would stabilize at an average form.  Transition from one species to another was impossible if variations were blended.  In 1868, eleven years after Origin of Species, Darwin attempted to rectify the problem by publishing his theory of pangenesis.  It assumed the acquisition of environmentally induced variations that could be passed on to offspring.  This assumption had been made previously by Hippocrates (Hippocrates, VII, 471-75) and Lamarck.  Darwin attempted to adapt it to his theory of evolution but was unable to explain exactly how it worked.

Darwin stated the following at the beginning of Chapter 22 in his 1875 edition of The variation of animals and plants under domestication; “These several considerations alone render it probable that variability of every kind is directly [somatically-mediated] or indirectly [germinally-mediated] caused by changed conditions of life. Or, to put the case under another point of view, if it were possible to expose all the individuals of a species during many generations to absolutely uniform conditions of life, there would be no variability.”  Obviously, Darwin accepted some of the fundamental ideas presented by Lamarck. In the first edition of Origin, Darwin had stated; "Variability is governed by many complex laws - by correlation of growth, by use and disuse, and by the direct action of the physical conditions of life".

Darwin was able to believe that variation was unlimited because he was not aware of the work of a contemporary; Gregor Mendel.  Through careful and extensive experiments, Mendel established the foundation for the science of genetics.  Mendel presented his results at a Brno Society for Natural History meeting in 1865 and published his paper "Research on Plant Hybrids" in the 1866 issue of the Society's Proceedings. However, his work remained unnoticed until decades later.  The principles of genetics clearly established that generational variability is not unlimited.  The possibilities are strictly and specifically limited by the code in the genes (standing variation).  Selective breeders knew that.  No matter how many generations of peas they subjected to selective breeding, the final generation was still peas. No matter how many years they selectively breed horses, pigeons, and dogs to develop desired features, and no matter how much they changed, they are still horses and dogs. Darwin did study selective breeding, especially of pigeons, but still assumed that, over time, variation is unlimited.

Without understanding the source or nature of variation, Darwin assumed that an unlimited number of small and favorable variations would be available to allow the simplest lifeform to advance to the most complex along his envisioned tree of life.

AFTER DARWIN:

While Origins was a best seller, it was not initially accepted by the scientific community. It actually took nearly century for Darwinian evolution to become mainstream science.

Reviews of Origins:

In the year following the publication of Origin, Asa Gray published a critical review; (Asa Gray Review: The Origin of Species, American Journal of Science and Arts, March, 1860).  Thinking that Darwin’s work was not original, Gray wrote : “That the existing kinds of animals and plants, or many of them, may be derived from other and earlier kinds, in the lapse of time, is by no means a novel proposition. Not to speak of ancient speculations of the sort, it is the well-known Lamarckian theory”.  In addition, Gray elaborated on four specific objections to Origin. First, Gray asserted that Darwin’s claims were not consistent with the fossil record.  Second, he claimed Darwin presented no convincing evidence for a common ancestor.  Third, he challenged Darwin’s assumptions concerning hybrids and sterility.  Forth, he stated that Darwin presented no convincing explanation for the origin of complex organs.  He conceded that, once established, natural selection might improve complex lifeforms, but said that Darwin’s attempts to explain their origin reminded him of Lamarck.

Richard Owen also reviewed Origin in 1860 (Darwin, On the Origin of Species. The Edinburgh Review, Volume 111). Some thought Owen's review disproved Darwin’s theory of evolution.  One of Owen's chief charges was that Darwin had failed to bring any new facts to light, effectively basing his theory on imagination rather than observation. The argument raged through the scientific community and the popular press for years. Owen agreed that evolution occurred, but thought it was more complex than outlined in Origin. Some think Owen anticipated the issues that appeared later with the development of evolutionary developmental biology.  https://www.abebooks.com/first-edition/Darwin-Origin-Species-Edinburgh-Review-Volume/18305390508/bd

In 1867, Fleeming Jenkin reviewed the second edition of Origin of Species.  He argued that limited variation precluded the possibility of a common ancestor for all existing species and that natural selection could not produce new, complex, biological organs with new functions.  He further pointed out that, if the theory of blending inheritance was true, then the effect of any one variation in the parent would be halved in the offspring and from a long term point of view blending inheritance would tend to result in stable uniform species, not evolving varieties

Competing Theories:

Following the publication of Origin of Species, many scientists accepted the general concepts of evolution, but did not believe the cause was natural selection.  They also did not accept Darwin’s concept of variation and did not necessarily believe that it only occurred in small increments.  As a result of these objections, a number of anti-Darwinian theories, such as orthogenesis and Lamarckism were proposed. Many professional biologists seriously considered or actively promoted alternatives to Darwinism throughout the last later decades of the 19^th century.

In 1868, Ernst Haeckel published  Natürliche Schöpfungsgeschichte: Gemeinverständliche Wissenschaftliche Vorträge über die Entwickelungslehre  (The History of Creation: Or the Development of the Earth and Its Inhabitants by the Action of Natural Causes).  Haeckel believed that each stage of embryonic development in higher lifeforms resembled the adult forms of a succession of ancestors in their family tree.  For example, the human embryo initially resembles that of a fish.  In subsequent stages, it resembles that of a reptile, an amphibian, a generic mammal, and finally a human.  Haeckel produced drawing of these stages of development that were used textbooks as recently as 2010.  However, they are now widely recognized to be incorrect.

Edward Drinker Cope‘s “On the Origin of Genera" (1868), held that while natural selection may preserve superficial variations, it cannot explain the formation of genera.   Cope thought a "steady progressive development of organization" resulted from "a continual crowding backward of the successive steps of individual development".   He thought an embryo could continue its growth with a new stage of development beyond that of its parents. The additional growth stage could take it to a higher level of organization and later generations could inherit this higher level Evolution was thus a continuous advance of organization.

George Jackson Mivart published On the Genesis of Species (1871) and Man and Apes (1873).  Both publications claimed Darwinism was insufficient to explain how a sequence of small changes could develop a complex living organism.  He reasoned that a small change that had no immediate advantage could not be preserved by natural selection.  He did not challenge common ancestry, but believed that natural selection could not develop earths many lifeforms.  He thought that something more than natural selection, perhaps some “innate force”, was needed.  He also argued, at length, that natural selection could not possibly explain convergent evolution (development of similar complex features in unrelated lifeforms) because it should be highly improbable but there are many common examples.

Samuel Butler published Life and Habit in 1878 and Unconscious Memory in 1871.  Since Origins did not explain the mechanism of heredity or the source of variation, and Darwin’s later publication on pangenesis did not gain acceptance, Butler promoted a theory of heredity loosely based on the thinking of Lamarck.  He thought there was a chemical connection between memory and heredity and that this caused lifetime experiences to effect variation from generation to generation.  A similar hypothesis was developed independently in France by The´odule Ribot and also in Germany by Ewald Hering, (Über das Gedächtniss als eine Allgemeine Function der Organisirten Materie, 1870).

During this period of uncertainty, even the direction of evolution was questioned.  E. Ray Lankester, (Degeneration. A chapter in Darwinism, I880) proposed that species degenerated when they encountered a less challenging lifestyle.  Apparently primitive lifeforms could not therefore be assumed to be fundamentally primitive.  They may have advanced to a higher state at one time, and later degenerated.  Lankester gave numerous examples of animals that he believed had degenerated thru loss of limbs and organs.  This greatly confused apparent relationships when current animals were studied.  E. W. MacBride took the concept to the extreme.  He proposed that all the invertebrates were degenerate offshoots of the main stream vertebrates.

Although he didn’t coin the term, Carl von Nageli presented the basic concepts of orthogenesis in Mechanisch-physiologische Theorie der Abstammungslehre (Mechanical-physiological theory of descent) Nägeli in 1884.  He thought that Darwinism did not explain the causes of evolutionary transformations, but only assumed that "the causes of the manifold variability are to be found in climatic and nutritional influences". Nageli observed that haphazard environmental circumstances would cause animals to be different if early evolution were repeated. 
There might, for example, be no mammals, and he thought that unthinkable.  Nägeli introduced the concept of "interior forces", which determined the form of the living organism.  Those forces were thought to operate independent of the environment.  Basically, his thinking was similar to that of Lamarck.

William Bateson compiled Materials for the Study of Variation: Treated with Especial Regard to Discontinuity in the Origin of Species (1984) to show that there are continuous and discontinuous biological variations.  One type of example is when an expected body-part has been replaced by another.  He studies included bees with legs instead of antennae; crayfish with extra oviducts; and humans with extra ribs.  Bateson challenged Darwin’s theory of natural selection, claiming that it could not explain the origin of species. While Darwin hypothesized that natural selection caused species to evolve via the very gradual accumulation of small beneficial characters, Bateson, argued that evolution sometimes occurs in large jumps (saltationism). Bateson’s work was reviewed by Samantha Hauserman in 2014. https://embryo.asu.edu/pages/william-bateson-1861-1926  Further information on Bateson is available at https://worddisk.com/wiki/William_Bateson/

N Y Danileveky’s book Darwinism was published shortly after his death in 1885.  The book summarized the criticisms against Darwinism that had appeared in the literature during the previous twenty years.  In the conclusion, Danilevsky listed fifteen scientific problems which he believed made both natural selection and evolution impossible. They were as follows:

1.      Animals were chosen for breeding and plants for cultivation because of their innate ability to vary.  Thus any analogy between artificial and natural selection was invalid.

2.      Domesticated animals, if allowed, reverted to their original wild type.  Darwin himself had mentioned this and thus implied that the species type retained some irrepressible force whatever influences it might have been subjected to under domestication.

3.      The conclusion that natural selection was that much stronger then artificial selection, as nature was then man, was a pure sophism. Nature could  not build machines.

4.      Divergence between domestic types never reached the same scale as differences between species.

5.      The importance of selection was grossly exaggerated.  The most important and the largest variations that appeared in domestic animals were not the result of selection but of a spontaneous saltation.

6.      From these previous points Danileveky concluded that the analogy between artificial and natural selection suggested by Darwin’s theory lost its validity, or was , at any rate, reduced to the smallest proportions.

7.      The struggle for survival lacked extreme intensity, consistency and unity of direction, the qualities necessary for the action of selection.

8.      The intensity and general presence in time and place of the struggle for survival was over estimated by Darwin.

9.      Crossing had to annihilate any variations. The struggle for survival did exist and i.t was to Darwin that we had to give the credit for pointing it out but it did not have the power of selection,. It was a bio-geographical principle, explaining the geographical distribution of organisms but not having any biological significance.

10.  The existence of useless, harmless or purely morphological characteristics could not be explained by the theory of selection.

11.  If the world had developed according to Darwinian principles then it would be entirely different from the contemporary world.

12.  It natural selection existed, then transitional forms should have been found but there were none.

13.  There was insufficient paleontological evidence.

14.  There was no evidence that when an old species died out a new one was formed at the same time.

15.  The length of time necessary for the Darwinian process was far in excess of the period of time that the earth had existed.

Subsequently, N Strakhov, an associate of Danileveky’s, published an article entitled “A Complete Refutation of Darwinism” in 1887.

Hugo de Vries published Intracellular Pangenesis in 1889.  He attempted to expand and explain Darwin’s pangenesis theory, but his ideas were never widely accepted and eventually disproved.

Initially, German biologist August Weismann accepted the Lamarckian theory of the inheritance of acquired characteristics.  Weismann began lecturing on his germ plasma theory in 1883.  Later, Weismann realized that if genetic recombination was the only means of introducing heritable variations that limited the amount of variation possible.  Unable to explain the source of novel genetic variations, he considered an evolutionary change of the germ plasm.  He did not, however, suggest any physical cause for such evolutionary change. 

After 1893, all of Weismann’s publications accepted natural selection as the sole evolutionary mechanism.  However, he recognized that Darwin failed to identify a credible source for the origin of variation.  Based on the progress of cytology (the medical and scientific study of cells) in the 1870s, he knew that two distinct germ cells come together during sexual reproduction.  He assumed random combinations of germ cells provided a significant s source of variation.  He assumed the germ plasm alone (no ordinary body fluid) was responsible for transmitting the information of heredity. Therefore, the body of an organism contained but could never affect this germinal material and hence could not affect its offspring. This implied that Lamarckism was wrong since characteristics that were acquired by an organism during its lifetime could not be transmitted to its offspring. With a modified source of variation and a defense of natural selection, his germ-plasma theory became known as neo Darwinism.

During the eclipse of Darwinism, James Mark Baldwin (A New Factor in Evolution, The American Naturalist. 30 (354): 441–451, 1896, and. Organic Selection, Science 5 (121): 634–636, 1897) proposed that an organism with the ability to learn new behaviors to adapt to environmental change will have greater reproductive success.  That ability therefore affects the gene pool of the population through natural selection.  Called the Baldwin effect, it appears similar to Lamarckism but does not assume inheritance of acquired characteristics.

German zoologist Theodore Eimer (On Orthogenesis and the Impotence of Natural Selection in Species Formation, 1898), held that orthogenesis, (directed evolution) disproved August Weismann’s claim that all existing characters of animals have some utility.  Eimer believed organic growth and physiological causes made organisms develop in definite directions whether or not resulting features had any utility.  Natural selection cannot prevent the appearance of predetermined characters. This was consistent with the theory of saltation which held that development of new forms is controlled by internal forces.

By the end of the century, biologists were close to rejecting natural selection.  They believed that forces arising during development were paramount, and that these forces were sporadic, operating as sudden transformations, or saltations.  They also reconsidered Lamarck’s concept of the inheritance of acquired characters. Then, the rediscovery of Mendel’s work further confounded the situation.

1900

Mendel rediscovered:

Three biologists, working independently, published rediscoveries of Mendelian laws of inheritance in 1900. They were Hugo DeVries, Carl Correns and Erich von Tschermak.  When Mendel’s work was rediscovered and then verified, there was an obvious problem.  If reproduction was controlled by discreetly distinct genes rather than some process of continuous variation, natural selection could not modify lifeforms beyond the limits of the genetic code.  A fish might evolve into different shapes and sizes and colors, but it could not evolve into a lizard.  All animals could not have evolved from a common ancestor unless all of the information (genes) necessary for that to happen was initially present in the common ancestor.  At the time, the rediscovery of Mendelian genetics appeared to disprove Darwinian evolution.

Then, in 1901, the geneticist Hugo de Vries observed sudden new forms in his plant experiments.   Not realizing that he was looking at unique hybrids, he assumed that the new forms had evolved spontaneously. He then concluded that all plants and animals could experience sudden changes in form and that that was the origin of new species. Rejecting Darwin’s idea that species evolved with many small changes over long periods of time, he published his two-volume The Mutation Theory (1900–1903) in which he was the first to use the term “mutation”, which he derived from the Latin “mutantem”. For a time, many biologists supported deVries theory of sudden, spontaneous changes in form (mutations).   Basically, the concept was the same as proposed by Geoffroy Saint-Hilaire in 1831. In the first decade of the 20th century, mutationism became a rival to Darwinism and was supported by notable geneticists such as Thomas Hunt Morgan. As late as 1940, geneticist Richard Goldschmidt again argued for single-step speciation by sudden and spontaneous mutation in an attempt to explain the discontinuities in the fossil record

In 1902, Theodor Boveri observed the connection between chromosomes and the rules of inheritance previously discovered by Mendel.  Walter Sutton independently discovered the connections between chromosomes and Mendelian genetics at about the same time.  His "The Chromosomes in Heredity" was published in 1903.  Sutton suggested that "the association of paternal and maternal chromosomes in pairs and their subsequent separation during the reduction division...may constitute the physical basis of the Mendelian law of heredity”.  The suggestion was controversial until 1915 when Thomas Hunt Morgan, initially skeptical, verified Suttons work with studies of the fruit fly Drosophila melanogaster.

Sutton, working with marine life forms, had also become familiar with the process of "reduction division" (later called meiosis), which gives rise to reproductive germ cells, or gametes. In meiosis, the number of chromosomes is reduced by half in sperm and egg cells, with the original number restored in the zygote, or fertilized egg, during reproduction. This process was consistent with Mendel's conclusions.  The Boveri-Sutton Chromosome Theory, as it came to be known, was discussed and debated during the first years of the twentieth century. It was embraced by some but strongly rejected by others. By 1915 Thomas Hunt Morgan, initially a strong skeptic, laid the controversy to rest with studies of the fruit fly Drosophila melanogaster.

In 1910, and earlier work by DeVries became available to the scientific community: Intracellular Pangenesis, Hugo De Vries, translated by C. Stuart Gager, Open Court Publishing Co., 1910.  Devries had published the book in German in 1889.  It proposed a modified version of Darwin’s pangenesis hypothesis. De Vries believed Darwin’s gemmules could not move from body cells to sexual cells.  He thought they could only move within the cell, from nucleus to the cytoplasm.  He changed the term gemmule to pangene, which others later shortened to gene.

The Arrival of the Fit,  John Burroughs , The North American Review, Feb., 1915, Vol. 201, No. 711 (Feb., 1915), pp. 197- 201, https://www.jstor.org/stable/25108368. This was an early claim that Darwinism and Mendelism combined are still inadequate. Excerpt: “It has been aptly said that while Darwin's theory of natural selection may account for the survival of the fittest, it does not account for the arrival of the fittest. The arrival of the fittest, sooner or later, seems in some way guaranteed by tendencies that are beyond the hit-and-miss method of natural selection.”

Geologist and paleontologist Henry Fairfield Osborn (The Origin and Evolution of Life, 1916) initially supported Edward Drinker Cope's neo-Lamarckism, but later adopted organic selection, also known as the Baldwin effect.  He thought mutation and natural selection do not create any modifications in life forms.  He believed in orthogenesis, and developed his own theory for variation.  He assumed a physiochemical process caused aristogenes operated as bio-mechanisms in the gene plasm to create new forms,

Reginald R. Gates published The Mutation Theory and the Species-Concept in The American Naturalist in Oct. 1917.  Citing many examples of plants and animals, he claimed there were two types of variability; continuous and dependent on environmental stress and discontinuous and independent of environment.  Therefore, Darwin’s theory of variation based on small increments of change was correct, but incomplete.  Overall, Gates believed that variation was due to various combinations of local adaptation, mutation, and orthogenesis.

D’Arcy Wentworth Thompson published On Growth and Form in 1917.  The voluminous book displays many mathematical patterns in plants and animals and, as Fodor and Palmarini pointed out in What Darwin got Wrong, Thompson’s work implies something is missing from Darwin’s theories.  There is evidence of biological optimization indicating there are geometric and physical constraints on metabolic processes.   There must be natural laws that limit possible configurations, and the driving force cannot have been natural selection because natural selection could not have tried all the many possible options.

The American Naturalist Vol. LII. June-July, 1918 Nos. 618-619 The Role Of Reproduction In Evolution, Professor E. M. East. Excerpt: “In neither kingdom was sex developed as a more rapid means of multiplication, since, as Mlaupas showed, a single infusion (a type of microscopic animal) may become the progenitor of some 50,000 individuals during the time necessary for one pair to conjugate. Some other requirement was fulfilled; and fulfilled adequately if we may judge by the number of times sexual differentiation arose and the tenacity with which it was retained.”

In 1919, de Vries published The Present Position Of The Mutation Theory in Nature (Nov 6).  The paper claimed that, since he published his mutation theory sixteen years earlier, all new evidence supported his theory. In his words, “Thus we see that the broad arguments for the mutation theory are continually increasing in number, whereas the criticisms are more and more directed against special cases.”   de Vries elaborated as follows: “Darwin assumed that species originate by the gradual accumulation of infinitesimal, ordinarily invisible variations on account of their utility in the struggle for life. The difficulties inherent in this conception have led to the theory of mutation, which supposes that the production of species and varieties proceeds by small but distinct steps, each step corresponding to one or more unit-characters. It is only after their appearance that the environment can decide about their utility. . .. It explained the appearance of the numerous useless qualities of animals and plants, and eliminated the objection that the first almost imperceptible changes could scarcely have any beneficial significance for their bearers. It developed the doctrine of two essential types of variability, which are now called fluctuating variability and mutability. The first of these describes the small but always present differences among individuals of the same stock, whereas the second is the way in which varieties are known to arise in horticulture and arboriculture.”  Thus, 60 years after Darwin published Origin, there were still prominent biologists who did not accept his work.

The Evolution of the Cell, E. A. Minchin, The American Naturalist , Jan., 1916, Vol. 50, No. 589 (Jan., 1916), pp. 5-38. Excerpt: “I propose in this address to deal with an aspect of cytology which appears to me not to have received as yet the attention which it deserves, namely, the evolution of the cell itself and of its complex organization as revealed by the investigation of cytologists. Up to the present time the labors of professed cytologists have been directed almost entirely towards the study of the cell in its most perfect form as it occurs in the Metazoa and the higher plants. Many cytologists appear indeed to regard the cell, as they know it in the Metazoa and Metaphyta, as the beginning of all things, the primordial unit in the evolution of living beings. For my part I would as soon postulate the special creation of man as believe that the Metazoan cell, with its elaborate organization and its extraordinarily perfected method of nuclear division by karyokinesis, represents the starting-point of the evolution of life.”

1920- 1950

Further challenges:

By the 1920s, genetics was steadily undermining Lamarckism by appearing to show there is no way for acquired characters to be incorporated into fixed units of heredity (genes).  Variation was also understood to be effectively random, as Darwin had supposed.  Mutations were not directed.

The Russian biologist Leo S. Berg (Nomogenesis; or, Evolution Determined by Lawaeckel, 1922) acquired a large collection of empirical data which appeared to contradict Darwinism.  Berg claimed that variation was not random, but constrained within specific limits.  He further claimed that these limits left hardly any opportunity for natural selection to alter lifeforms.  Berg believed in a process of directed mutation, and claimed the fossil record supported that conclusion.

The British zoologist and evolutionist Sir Gavin de Beer published the book, Embryology and Evolution in 1930.  The book vigorously rejected the embryonic concept of recapitulation promoted by Haeckel, and included illustrations illustrating Haeckel errors. De Beer elaborated further on Haeckel’s errors in Embryos and Ancestors copyrighted in 1940, 1951, and 1958.  However, Haeckel’s illustrations purporting that the sequences of embryological development supported evolution continued to be used in biology textbooks.

.The Modern Synthesis:

Throughout the first few decades of the twentieth century, there appeared to be a fundamental conflict between Darwinism and Mendalism.  According to Mendalism, variations were caused by random recombination of existing genes.  The total number of possible combinations was known as the standing variation of a species, and was fixed. Darwinism, however, required unlimited variation to eventually permit many very different lifeforms to descend from a common ancestor.

To resolve the conflict, biologist merged the two branches of science (evolution and genetics) into one called the modern synthesis (AKA neo-Darwinism).  The fix was implemented by reintroducing the concept of mutations, or spontaneous errors.  While genetics limited the ultimate extent of generational variability, the modern synthesis presumed mistakes could enter the genetic code during reproduction.  Given the accumulation of enough errors (mutations) over millions of years, unlimited variation could still occur.  Thus, although a path of evolution determined by a lengthy sequence of random errors would certainly be much messier, Darwin’s assumption of unlimited change was still assumed to be possible.  However, the assumption of random errors accounting for the apparent conflict between Darwinism and Mendelism  was made without any understanding of the chemistry of genetics.  That was not achieved until decades later with the discovery and interpretation of the DNA molecule.

Ronald Fisher’s book The Genetical Theory of Natural Selection (1930) is credited with showing that heredity concept of Gregor Mendel and the slow variation and natural selection concept of Darwin and Wallace were not necessarily incompatible.  By that time it was known that physical features could be influenced by more than one gene.  Using mathematical models and statistics, Fisher showed that small variations could appear due to complex combinations of genes and that natural selection could select for advantageous genes and alter the genotype of a population.  Fisher developed what is today called population genetics.  Contributions by J.B.S. Haldane and Sewall Wright to the theory of population genetics were also very significant.

Fisher blended Darwinism, Mendelism and mutationism and developed mathematic models to show that natural selection could be the driving force for evolution. Excerpt: “The other biological theories which have been put forward, either as auxiliaries, or as the sole means of organic evolution, are not quite in the same position.  For advocates of Natural Selection have not failed to point out, what was evidently the chief attraction of the theory to Darwin and Wallace, that it proposes to give an account of the means of modification in the organic world by reference only to 'known ', or independently demonstrable, causes. The alternative theories of modification rely, avowedly, on hypothetical properties of living matter which are inferred from the facts of evolution themselves. Yet, although this distinction has often been made clear, its logical cogency could never be fully developed in the absence of a separate investigation of the independently demonstrable modes of causation which are claimed as its basis. The present book, with all the limitations of a first attempt, is at least an attempt to consider the theory of Natural Selection on its own merits.”

The paleontologist Robert Broom (Evolution. Is there intelligence behind it? South African Journal of Science 30: 1–19, 1933) studied Darwinism, Lamarckism, and mutationism and concluded that they, by themselves, could not explain evolution and the fossil record.  He determined that some intelligent force must also be involved in the formation of life.  He also held the unique view that evolution was over.  He did not expect further change.

In 1935, Conway Zirkle traced the idea of pangenesis all the way back to Hippocrates:  The Inheritance of Acquired Characters and the Provisional Hypothesis of Pangenesis. American Naturalist 69: 417-445.

Theodosius Dobzhansky published the first edition of Genetics and the Origin of Species in 1937. He addressed the problems with Darwinian evolution and discussed how they might be resolved using modern discoveries in genetics.  He proposed that evolution might produce a new species in three steps: 1) development of raw material by chromosomal recombination and mutation, 2) changes in the frequency and combinations of genes in a population, and 3) fixation of the change(s) by reproductive isolation.

The work of Fisher, Haldane, Wright, Dobzhansky and many others finally solidified a unified theory of evolution based on the theories of Darwin and Mendel and deVries concept of mutation.  Contrary to some historical accounts of evolution, this was the first time scientists achieved a near consensus on a unified theory of evolution (the modern synthesis).  Although it is almost universally represented as a synthesis of the work of Darwin and Mendel, it actual required more than that.  The mutation theory of deVries and others also had to be included (but on a very small scale).  Mendel did not consider mutation, and mutation theory had to replace Darwin’s theory of unlimited variation.  Darwin’s theory of natural selection was retained as a key component of the modern synthesis.

While the modern synthesis established a general concept for the origin of new species, it offered no explanation for exactly how one species might split into two until Ernst Mayr published Systematics and the Origin of Species in 1942. Mayr approached the problem by redefining species. He wrote that a species is not just a group of similar individuals, but a group that can only breed among itself.  Mayer envisioned a new species beginning with geographical isolation combined with genetic drift that, due to natural selection, eventually inhibited interbreeding with the original population. 

Also in 1942, J. Huxley published Evolution: The Modern Synthesis.  This comprehensive 645 page book is credited with documenting the blending of Darwinism and Menedlism to form the Modern Synthesis. Over the years, there were numerous reprinting’s and a third edition (800 pages) was published in 1974. Then, it was reissued again in 2010.  It established the modern synthesis as the favored evolutionary paradigm in biology.

1950

Macro vs micro:                       

As the work of Darwin and Mendel was merged to form neo Darwinism, the terms macroevolution and micro evolution were established.  Macroevolution is frequently defined as the development of new taxonomic groups (kingdom, phylum or division, class, order, family, genus, species).  Development of all known species from common ancestors in conformance with Darwin’s tree of life is thought to display macroevolution.  Microevolution is correspondingly defined as the variation of life forms that can be explained by the laws of genetics (standing variation).  Thus defined, microevolution is undisputed.  Numerous examples of microevolution have been observed in both the laboratory and in nature.  The most common familiar example of microevolution is the dog.  Selective breeding has created tremendous variation, but all dogs still belong to a single species.  No information that that was not in the original DNA of the wolf was required to produce the various breeds of dogs.  Said another way, all dog breeds were produced by genetic recombination and selective breeding.  No mutations were required.

Whether macroevolution has ever occurred is not so easily proved. Decades of experiments forcing random errors in the DNA of tens of thousands of generations of fruit flies produced many deformed fruit flies, but all the offspring have been fruit flies.  Similarly, decades of experiments with bacteria have produced bacteria with unique characteristic, but they are all bacteria.

However, macroevolution is not defined consistently in the literature.  Evolutions sometimes argue that macroevolution is just an accumulation of microevolution over time. Thus, proof of microevolution proves macroevolution.  This definition of macro and micro evolution is based on the same logic as Darwin’s initial assumption; the generation to generation variation of lifeforms is unlimited.  According to Mendelian genetics, the assumption is wrong.  The assumption of beneficial mutation has to be introduced to make the assumption possible.

On close inspection, proposed examples of macroevolution usually turn out to be examples of microevolution.  The classic examples of evolution presented in biology textbooks, Darwin’s finches and the spotted moth, are examples of microevolution.  No new species was created.  The variation that occurred was caused by standing variation in the DNA. No mutation was required. More recent observations even showed that these variations are reversible, clearly proving that all observed variations were within the existing DNA of the ancestors.

Macro evolution requires variation due to mutation of the DNA.  Since errors are rare, and since DNA errors that do occur are usually repaired by specialized molecular machinery in the cell, macro evolution cannot occur quickly.  Experiments have been conducted with short life cycle species, such as fruit flies and bacteria, in attempts to force macroevolution.  DNA has been mutated with harsh environments, such as radiation.  Decades of such research with fruit flies and bacteria have not produced a new species. 

An exception is hybridization.  Hybrids are usually sterile (like a mule) but hybrids capable of reproduction have appeared in the plant kingdom.  By definition, such an event produces a new species instantly, without mutations.  But the new species is the result of a new combination of genetic code, not of mutation and natural selection.  Some plant species that seemed to appear spontaneously were viable hybrids of existing plant species (ex: deVries primroses).  In the animal kingdom, the red wolf is believed to be a hybrid of a wolf and a coyote. Unlike the mule, it is capable of reproducing.

Even before the discovery of the double helix of DNA, Barbara McClintock discovered flexibility in the genetic code.  Working with corn, she discovered “transposition”, the ability of chromosomes to reorganize by moving segments from one location to another.  She subsequently published the paper (1950) The origin and behavior of mutable loci in maize. Further research by others discovered the ability of very simple organisms to exchange or combine DNA directly, without sexual reproduction. Horizontal gene transfer moves genetic code directly from one cell to another. During the process of symbiogenesis, simple organisms merge to form one new one.

Gregor Mendel & His Precursors, Conway Zirkle, Isis, Vol. 42, No. 2 (Jun., 1951), pp. 97-104, the paper reviews the exceptional nature of Mendel’s work. Excerpt: “Mendel's paper is truly remarkable. We are struck at once with its notable economy of effort. There seems to have been no waste motion either in designing the experiments, in collecting the data, or in interpreting the results. Mendel chose the proper genus (Pisum) for his investigation, conducted his researches cleanly, and seemed to have known just what he should expect to discover. His work is beautifully unified and complete, more so, in fact, than that of the three biologists who discovered him, de Vries, Correns, and von Tschermak”.

Francesco D'Amato (1953) The Problem of the Origin of Spontaneous Mutations, Caryologia, 5:1, 1-13, The paper explains why natural radiation does not explain mutations, and states: “In conclusion, spontaneous mutation could be interpreted as a kind of response to special metabolic or physiological conditions.  Cells or tissues might not be protected against an increase in the concentration of some metabolites normally present in the organism (or the organ), or they might suffer from the chemical action of new compounds formed in special physiological conditions as a consequence of internal and/ or external influences. Another possibility is that cells or tissues be not able to withstand, in certain physiological conditions, the doses of metabolites normally present in the organism (or organ), the result then being a kind of autointoxication at physiological doses.”

A production of amino acids under possible primitive earth conditions, Stanley Miller and Harold Urey, Science 1953;117:528–529. The often cited results of this experiment became embedded in textbooks as a possible explanation for the origin of life. The authors produced amino acids in a flask containing basic chemicals and subjected to electric spark (simulating lightening).  The experiment is no longer an attractive explanation for the spontaneous generation of life because the early earth’s atmosphere is now known to have been different than assumed in the experiment and there is no accepted hypothesis of life forming spontaneously from amino acids.

Discovery of DNA:

While the modern synthesis was viewed as a complete model of evolution, it still offered no physical explanation for the chemistry of standing variation (population of existing genes).  Biologists knew there were genes that caused life to develop according to Mendel’s laws, and some suspected that the genetic information was contained in the chromosomes, but there was no understanding of how the cell stored the information.  It was not until 1953 that Crick and Watson discovered the unique biological structure of the DNA molecule, AKA the double helix. Shortly thereafter, the arrangement of atoms in the DNA molecule was presumed to form a code that defined genes.

Evelyn M. Witkin’s article Mutations and Evolution appeared in the October 1957 Issue of The Atlantic.  It cites experiments with bacteria to prove that mutation and adaption to environmental change are the basis of evolution. The experiments exposed a large population of bacteria to a high concentration of an antibiotic. Initially, multiplication slowed dramatically, but after a few days, rapid growth was again observed.  Witkin posed two hypotheses to explain the observation. 1) “The first is that a small number of initially sensitive bacteria were modified as a direct result of the action of streptomycin, thereby acquiring permanent resistance.” And 2) “The second possibility is that the resistant individuals had already acquired the properties necessary for resistance before coming into contact with streptomycin, as a result of a mutation during the normal division of the sensitive population.”

Witkin’s article claimed that if the fist were true, that “would be an example of an adaptive hereditary change caused by the environment, as Darwin envisaged the origin of most hereditary variations.”  Alternately, if the second were true, “the role of the antibiotic would be entirely passive, providing conditions that favor selectively the multiplication of those rare individuals present in the population that are already equipped, by virtue of the previous occurrence of a chance rearrangement of a particular gene, to withstand its inhibitory action.”  The article went on to state that many experiments conducted over 15 years had proved the second hypothesis was correct, and that mutations had produced a small number of streptomycin resistant members of the population before the bacteria was exposed to the antibiotic.  This was presumed to prove that a random accumulation of neutral mutations can produce variations that turn out to be beneficial when the environment changes.

This first glimpse into microbiology hinted at the incredible complexity the future would uncover.  Darwinism however, adapted to the discovery of DNA.  The splitting and subsequent reconstruction of the helix during reproduction was seen as a means of introducing mutations.  Biologists assumed that errors made while constructing the new DNA molecules could, if not immediately catastrophic, be preserved as latent errors in the genetic code.  A single error would not likely cause great variation, but subsequent errors could accumulate.  Sometime, in the very distant future, and accumulation of errors might combine to produce a beneficial variation that would be preserved by natural selection.  Thus, Darwin’s assumption of unlimited variation became more complicated, but was still possible.  Neo-Darwinism (the modern synthesis) continued into the age of microbiology.  Neo Darwinism and the modern syntheses are often used interchangeably in the literature, even though they were different historically.

When Darwin sketched his tree of life, he based it on physical similarities of animals.  He assumed that animals with common features had a common ancestor with that feature. When neo Darwinism was later established, biologists continued building on the tree of life in the same way as previously unknown species were discovered.  However, when biologists we able to read genetic code, it became apparent that the established tree of life was not valid.  Attempts to rearrange the tree using common genetics eventually led to a bush rather than a tree, and then to a web.

1960

Genetic Regulatory Mechanisms in the Synthesis of Proteins, Francois Jacob and Jacques Monod,  J. Mol. Biol. 3, 318-356,  1960. This paper announced the discovery of regulatory genes. Primary genes just control the rate of protein synthesis. The regulator genes themselves are controlled by cytoplasmic components that can repress or activate the regulator genes Abstract: “The synthesis of enzymes in bacteria follows a double genetic control. The so-called structural genes determine the molecular organization of the proteins. Other, functionally specialized, genetic determinants, called regulator and operator genes, control the rate of protein synthesis through the intermediacy of cytoplasmic components or repressors. The repressors can be either inactivated (induction) or activated (repression) by certain specific metabolites. This system of regulation appears to operate directly at the level of the synthesis by the gene of a short lived intermediate, or messenger, which becomes associated with the ribosomes where protein synthesis takes place.”

Natural selection as the process of accumulating genetic information in adaptive evolution, Motoo Kimura, Genet. Res., Camb. (1961), 2, pp. 127-140.  The paper assumes that natural selection creates genetic information and attempts to calculate information gain for higher life forms. Excerpt: “The purposes of the present paper are threefold. First, a method will be proposed by which the rate of accumulation of genetic information in the process of adaptive evolution may be measured. Secondly, for the first time, an approximate estimate of the actual amount of genetic information in higher animals will be derived which might have been accumulated since the beginning of the Cambrian epoch (500 million years), and thirdly, there is a discussion of problems involved in the storage and transformation of the genetic information thus acquired.”

At the 1966 Philadelphia Wistar Symposium, chaired by Nobel Laureate Sir Peter Medawar, mathematicians and scientists from related fields met to determine whether Neo-Darwinism is mathematically feasible.  The general consensus was that it is not. (Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, Wistar Institute Press, 1966, No. 5) https://www.pathlights.com/ce_encyclopedia/Encyclopedia/20hist12.htm

Information transmission In Evolution, Lee M. Spetner, IEEE Transactions On Information Theory, Vol.  IT=14 No.1, 1968, Abstract: “On the basis of a model previously established for the random-mutation portion of the synthetic theory of evolution, an investigation is made of the information that can be transmitted from the environment to the evolving species. The probability that a given adaptive character is produced decreases with increasing information measure of the adaptive character. The average information transmitted in any one evolutionary step is defined as the product of the information and its probability of transmission. The average information turns out to be very small for a reasonable number of trials and reasonable gene size. This is consistent with the conjecture that evolution proceeds in small steps, and the size of a step can be discussed quantitatively in terms of the amount of adaptive information that is being transmitted into the species.”

Carl Woese published The Genetic Code: the Molecular Basis for Genetic Expression in 1967.  Woese had found that Darwin’s tree of life was not supported by the code in DNA.  His research showed that evolutionary relationships between organisms were entirely different that Darwin had assumed and that the true relationships indicated a convoluted bush rather than a tree.  He also determined that different species can exchange portions of DNA (horizontal gene transfer) so that evolution that does occur is not solely dependent on ancestry and environment.

The Reception in Russia of Darwinian Doctrines Concerning Evolution, by Sarah Swilwurne White, PhD Thesis, Imperial College of Science & Technology, London University, March, 1968. Excerpt from abstract: “There are two important reasons for studying the reception of Darwinian concepts in Russia in the 19th century. First, very little is generally known in England about Russian biology and geology of that century and the period is especially interesting since it precedes that of modern Soviet science. Second, the differences and similarities of the reception of Darwinism in Russia with its reception elsewhere throw light on the general progress of acceptance and rejection of a scientific theory.”

Evolutionary rate at the molecular level, Motoo Kimura, (Nature, February 1968): Kimura proposed that, at the molecular level, natural selection has little effect on evolution.  Most mutations become fixed by genetic drift rather than selection.  Kimura stated: "This neutral theory claims that the overwhelming majority of evolutionary changes at the molecular level are not caused by selection acting on advantageous mutants, but by random fixation of selectively neutral or very nearly neutral mutants through the cumulative effect of sampling drift (due to finite population number) under continued input of new mutations".  If true, then when DNA sequence diversity between species is examined, then there should be more diversity in functionally less important sequences because natural selection could not eliminate them. A couple of decades later, Kimura followed up with a paper claiming genetic research was supporting his theory (The neutral theory of molecular evolution: A review of recent evidence, Japanese Journal of Genetics, 1991).

The Analysis of Selection in Experimental Populations, William H. Dumouchel and Wyatt W. Anderson, Genetics 58: 435449, 1968, Excerpt from abstract: “ Many laboratory experiments have been devised to test various aspects of the theory. The demonstration that some of the genetic changes in nature could be reproduced in experimental populations opened the way for a many-faceted attack on the genetic processes in evolution. We will consider the problem of measuring selection in experimental populations and show how changes in the frequencies of the alleles at a single locus can be used to estimate the selection acting on each genotype.”

The work of R. Britten, and E. Davidson, (Gene regulation for higher cells: A theory. Science 165, 349–357, (1969) Britten, R., and Davidson, E. (1971). Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Quart. Rev. Biol. 46, 111–133) indicated that regulatory genes directed producing genes. Work such as this challenged the early idea that most of the genome consisted of junk DNA.

1970

Observing that the fossil record is not consistent with the modern synthesis, Eldredge, Niles and S. J. Gould published Punctuated equilibria: an alternative to phyletic gradualism in 1972.  The fossil record does not contain a series of gradually changing lifeforms as assumed by the MS.  Rather, many lifeforms, such as the shark, have not changed at all.  However, at times (ex: Cambrian explosion) many new lifeforms appear very suddenly.  Niles and Gould postulated that something caused mutations and natural selection to alter lifeforms in spurts of activity separated by long periods of stasis.

King, Jack Lester. The role of mutation in evolution. Proceedings of the Sixth Berkeley Symposium on Mathematical Statistics and Probability, Volume 5: Darwinian, Neo-Darwinian, and non-Darwinian Evolution, 69--100, University of California Press, Berkeley, Calif., 1972. The paper discusses the conflict between the modern synthesis and new discoveries, particularly those related to the role of mutation.  Excerpt: “Eleven decades of thought and work by Darwinian and neo-Darwinian scientists have produced a sophisticated and detailed structure of evolutionary theory and observations. In recent years, new techniques in molecular biology have led to new observations that appear to challenge some of the basic theorems of classical evolutionary theory, precipitating the current crisis in evolutionary thought. Building on morphological and paleontological observations, genetic experimentation, logical arguments, and upon mathematical models requiring simplifying assumptions, neo-Darwinian theorists have been able to make some remarkable predictions, some of which, unfortunately, have proven to be inaccurate.”

Darwinian and non-Darwinian evolution,James F. Crow, Proc. Sixth Berkeley Symp. on Math. Statist. and Prob., Vol. 5 (Univ. of Calif. Press, 1972), 1-22. Excerpts from conclusion: “I have tried to present the main arguments for and against the hypothesis of evolution by random drift of neutral mutations, or non-Darwinian evolution.- - - I suggest that the great majority of DNA is noninformational in that it does not code for proteins or for unique sequence RNA, and that this DNA changes for the most part by mutation and random drift. The possibility that amino acid substitutions observed in evolutionary lineages have this explanation seems promising enough to deserve the exploration that it is clearly getting.”

Problems of Macroevolution (Molecular Evolution, Phenotype Definition, and Canalization) as Seen from a Hierarchical Viewpoint, S. N. Salthe, Amer. Zool., 15:295-314 (1975). Synopsis: “As seen from a hierarchical viewpoint, macroevolution is neither a functional process nor a series of events in the past. It is a record only. For this reason macro evolutionary laws are all statistical laws. Natural selection is a process that operates from one generation to the next at the population level in the hierarchy. Yet structures at the organism level are found to "evolve." It is possible to formulate only a tautological form of the concept of natural selection at the population level alone; the bridge between levels in this case is the phenotype. The phenotype (i) exists at the boundary between the organismic and population levels of the hierarchy; (ii) is a functional manifestation of the interaction between the genotype and the local environment only during the period of a single generation; (iii) should ideally be defined so as to exclude traits not reviewed by natural selection; (iv) is factorable into many individual functional traits if one views viability selection as being instituted by a sequence of environmental catastrophes, each of which emphasizes a particular set of traits as being temporarily important to survival. It is reemphasized that the action of natural selection on continuously distributed, non- polymorphic traits curtails variability in proportion to the intensity of selection. The necessity for coadaptation within the organism imposes a bell-shaped curve upon surviving variability. Canalizing selection is proposed as the process that modifies these bell-shaped curves into lognormal parametric distributions. It is also proposed that the per cent variability of the sample populations can serve as a measure of the intensity of natural selection (normalizing and directional together) that has most recently been acting upon the traits in question in the populations used to establish the parametric distributions.”

Population Genetics: The Synthesis of Mendelism, Darwinism, and Biometry, Chapter 5 in the Origin of Theoretical population Genetics by William B. Provine, U of Chicago Press, 1971, Explains how Darwin’s erroneous concept of pangenesis and blending inheritance were resolved.

The modern syntheses has considerable support, but was never supported by consensus.  One issue that has been continually disputed is the relationship between micro and macro evolution.  The synthesis holds that they are driven by the very same processes, but there are frequent claims that they are not.  Steven M. Stanley (John Hopkins U.) published A Theory of Evolution Above the Species Level in 1975 (Proc. Nat. Acad. Sci. USA).  The paper claims that Darwin was wrong about slow gradual change, and that macroevolution does not occur gradually due to natural selection.  Rather, it occurs abruptly due to other processes as shown by the fossil record.  The paper cites examples and a number of other papers that support the hypothesis.

Richard Dawkins 1976 book The Selfish Gene proposed that the species is not the basic unit that evolution operated on.  He thought evolution selected for the chemical code in the gene, and that that living creatures were just vehicles for the genes. Natural selection operates on the gene, and not on the chromosome, the population, or the species.  Biology and evolution is not concerned with organisms, but only with genes that survive unaltered through the eons by jumping from body to body. In a subsequent book (The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design, 1986) Dawkins explains his views of how evolution changes simple organisms into creatures with extreme complexity and diversity.  He emphasizes that the complex process of Darwinian natural selection is unconscious and automatic, that any apparent design is an illusion.

Ontogeny and Phylogeny (1977) by Stephen J. Gould documented the history of the theory of recapitulation. It held that an embryo repeats all stages of evolution during development.

While recapitulation may not be correct, he envisioned that the rate at which an organism grows and the rate at which it changes shape over time could be independently controlled.  Random mutations might then change each rate, thereby altering individual organs or the entire body of an organism These kinds of adjustments could then alter the entire body of an organism, or individual organs. Some credit the book with supporting the establishment of evo-devo.

In Evolution of Living Organisms (1977), micro biologist Pierre-Paul Grassé, argues that neo Darwinian evolution is impossible.  He claims that mutations only create disorder in complex living systems, and cannot cause evolution to a more complex form.  He further states that "The role assigned to natural selection in establishing adaptation, while speciously probable, is based on not one single sure datum. Paleontology does not support it …”.  Without speculating on the source, Grasse believed that information, along with material and energy, is required to produce life.  The introduction to the book states: “Any living thing possesses an enormous amount of ‘intelligence’… Today, this 'intelligence' is called 'information,' but it is still the same thing ... This ‘intelligence’ is the sine qua non of life. If absent, no living being is imaginable. Where does it come from? This is a problem which concerns both biologists and philosophers, and, at present, science seems incapable of solving it."  Grasse believed that the fossil record does prove evolution, but that Darwinism does not explain it.

1980

The University of Chicago hosted a conference entitled “Macroevolution” at the Field Museum of Natural History in October of 1980. There was a lot of discussion about the concept of punctuated equilibria that conflicts with the gradualism of Darwinian evolution.  After the conference, Dr. Roger Lewin offered the following comment: “The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. … At the risk of doing violence to the positions of some of the people at the meeting, the answer can be given as a clear, No.” (Roger Lewin, “Evolutionary Theory Under Fire,” Science, Vol. 210:883-887, Nov. 1980.)

In his 1982 paper Genetic Variation, Limitless or Limited?, biology professor Frank L. Marsh  succinctly argued that Darwin’s fundamental error was assuming variation is unlimited.  Citing numerous published examples of macroevolution, he claimed they are just microevolution because they display no change in basic form.  Specifically, some evolutionists claim P. G. Williamson’s study of speciation in snails and mollusks through 400 meters of sediments demonstrates macroevolution.  Marsh observed that; “Williamson’s study began with snails and clams and ended with snails and clams.”  He argued that since there was no change in basic form, claims of macroevolution are not valid.

Sewall Wright’s 1982 paper The Shifting Balance Theory and Macroevolution   (Annual Reviews Inc.) detailed the thinking of how the modern synthesis could produce macroevolution.  Stated briefly, if a new environmental niche appeared, mutations would eventually accumulate that allowed a species to better exploit that niche, and the population would eventually become a new species or even a new genus or family.  An environmental anomaly creates and opportunity and mutation allows a population to exploit the opportunity.  Advantageous mutations change the morphology. The process is complex because multiple genes control each morphological feature.

Darwin and His Finches: The Evolution of a Legend, Frank J. Sulloway, Journal of the History of Biology, vol. 15, no. 1 (Spring 1982), pp. 1-53.  The lengthy paper offers a historical review of the study of Darwin’s finches and an explanation of how they became overemphasized in biology textbooks.

The Growth of Biological Thought Diversity, Evolution, and Inheritance, Ernst Mayr, The Belknap Press. 1982. This book is a lengthy review (nearly 1000 pages) of the history of biology and evolution from ancient times through 1982.  It details the thinking of many contributors, exploring not only what thought they contributed by how and why they developed those thought. It is Darwin centered, organized by pre Darwin, Darwin, and post Darwin time periods.

Exaptation-a missing term in the science of form, Stephen Jay Gould and Elisabeth S. Vrba, Paleobiology, 8(1), 1982, pp. 4-15. The authors proposed the term “exaptation” to eliminate confusion caused by the following problem; “Adaptation has been defined and recognized by two different criteria: historical genesis (features built by natural selection for their present role) and current utility (features now enhancing fitness no matter how they arose). Biologists have often failed to recognize the potential confusion between these different definitions because we have tended to view natural selection as so dominant among evolutionary mechanisms that historical process and current product become one.”

Macroevolution and the Fossil Record, Steven M. Stanley (Society for the Study of Evolution, 1982):  The fossil record is not consistent with the modern synthesis.  Macroevolution often occurs rapidly and “is largely decoupled from microevolution”.  Excerpts: “Species have survived for long intervals of geological time relative to the intervals during which major adaptive transitions have occurred. A large sample of well documented Early Eocene lineages of mammals reveals no example of significant phyletic evolution over spans of 2-3 Myr.” - -  - “The implication of the stability of established species is that most evolutionary change occurs rapidly, in local populations. Because the direction taken by rapidly divergent speciation is variable and only weakly predictable for large segments of phylogeny, macroevolution is largely decoupled from microevolution.,”

The Intelligent Universe, Fred Hoyle, Michael Joseph Limited, 1983. Amazon: “Examines the origins of life on earth, analyzes the Darwinian theory of evolution, and argues that life is the result of a deliberate plan.”

Evaluation of Current Population Genetics Theory,  Oscar Kempthorne , Amer. Zool., 23:111-121 (1983) : Synopsis: “ My aim is to give a partial evaluation or critique of the state of population genetics theory. A decent theory must include the following components: the development of concepts of fitness that have demonstrated epistemic correlations, life tables, mating, fecundity, finite (even if large) niche size, and, of course, Mendelism and mutation. It must in the end also include varying environment and competition between species. The extent to which the desiderata are met is discussed. The big lacunae in the whole theory appear to be the inadequate treatment of fitness and the ignoring of niche capacity. Some theorems that are given as fundamental must be questioned and even discarded. Integration of ideas of simple Mendelism, quantitative genetic variation, and ecology is the big task ahead. It is critical that more complete theory be developed.”

Ho M.W., and Saunders, P. T., (editors). Beyond neo-Darwinism: an introduction to the New evolutionary paradigm, Academic Press, 1984. This book is a compilation of essays by fourteen different authors, offering a variety of criticisms of neo Darwinism. 

The Evolution of Darwinism: Recent developments in molecular biology and new interpretations of the fossil record are gradually altering and adding to the synthetic theory, for 40 years the standard view of the process of evolution, G Ledyard Stebbins and Francisco J Ayala, Scientific American Magazine, July 1985, pg. 72-82.  The paper briefly reviews how the modern synthesis modified Darwinism and claims that new discoveries require further modification. Excerpt: “In the 1970's and 1980's new developments confronted the synthetic theory. An explosion of investigation into the structure of DNA, the carrier of genetic information, has enabled biologists to study the mechanisms of evolution at the molecular level. The new work has thereby amplified the synthetic theory much as the discovery of genes amplified Darwinism.”

The Death Of Darwin?, Ernst Mayr, Revue de Synthese : IV' S. N° 3, September, 1986.  Excerpt: “One hundred and twenty-five years of unsuccessful refutations have resulted in an immense strengthening of Darwinism. Whatever attacks on Darwinism are made in our age are made by outsiders, jurists, journalists, etc.”

The Genus: A Macroevolutionary Problem, Cliff A. Lemen and Patricia W. Freeman, Papers in Natural Resources. 22., University of Nebraska – Lincoln, May 1984. Excerpt: “This paper centers on the macro evolutionary problem surrounding the vertebrate genus. We have been fascinated by the apparent tendency of members of a genus to have the same shape in contrast to the great differences in shape among genera at the family level.  If this is true, genera would be considered shape conservative groups. Our initial view of this contrast in shape variation within and among genera leads us question whether the same evolutionary processes that produce genera can simply be extended to produce families.”

Voipio, P.. What did Mendel say about evolution? - Hereditm 107: 103-105. 1987, Lund, Sweden: Based on a review of historic literature, the author claims Mendel accepted natural selection and thought  hybrids produced new species.

Population Genetics History: A Personal View, James F. Crow, Ann. Rev. Genet. 1987. 21 :1-22: “This review is dedicated to the proposition that the three pioneers constructed a remarkable foundation, but that the edifice itself is still under construction and the foundation, for all its strength, needs some shoring up.”

The Evolution of Complexity by means of Natural Selection, John T. Bonner, Princeton University Press, 1988. Dust jacket summary: “John Tyler Bonner makes a new attack on an old problem: the question of how progressive increase in the size and complexity of animals and plants has occurred. “How is it,” he inquires, “that an egg turns into an elaborate adult? How is it that a bacterium, given many millions of years, could have evolved into an elephant?” The author argues that we can understand this progression in terms of natural selection, but that in order to do so we must consider the role of development — or more precisely the role of life cycles — in evolutionary change. In a lively writing style that will be familiar to readers of his work The Evolution of Culture in Animals (Princeton, 1980), Bonner addresses a general audience interested in biology, as well as specialists in all areas of evolutionary biology. What is novel in the approach used here is the comparison of complexity inside the organism (especially cell differentiation) with the complexity outside (that is, within an ecological community). Matters of size at both these levels are closely related to complexity. The book shows how an understanding of the grand course of evolution can come from combining our knowledge of genetics, development, ecology, and even behavior.”

 

Morphogenesis and Evolution, Keith Stewart Thomson, 1988, Oxford University Press, Amazon synopsis: “Today developmental and evolutionary biologists are focusing renewed attention on the developmental process--those genetic and cellular factors that influence variation in individual body shape or metabolism--in an attempt to better understand how evolutionary trends and patterns within individuals might be limited and controlled. In this important work, the author reviews the classical literature on embryology, morphogenesis, and paleontology, and presents recent genetic and molecular studies on development. The result is a unique perspective on a set of problems of fundamental importance to developmental and evolutionary biologists.”

 

Genetics, Paleontology, and Macroevolution, Jeffery Levinton, 1988 Cambridge U Press, Reviewed by George Lauder in Journal of Vertebrate Paleontology, 9 (1): 122-123, March 1989:  Excerpt: “Species have survived for long intervals of geological time relative to the intervals during which major adaptive transitions have occurred. A large sample of well documented Early Eocene lineages of mammals reveals no example of significant phyletic evolution over spans of 2-3 Myr. Despite this great stability of established species, at least 20 families and hundreds of genera evolved during this interval, which lasted only about 5 Myr. For many groups of marine invertebrates, median species diversity approaches or exceeds 10 Myr. Once established, a typical lineage of eukaryotic animals or plants that has survived for 10⁵- 10⁷ generations has undergone little change in form. This characteristic stability has not been predicted by population genetic theory”

The Evolution of Darwinism, G. Ledyard Stebbins and Francisco J. Ayala, Scientific American

Vol. 253, No. 1 (July 1985), pp. 72-85. Conclusion: “Whatever new consensus emerges from ongoing research and controversy, it is not likely to require rejection of the basic tenets of Darwinism and the mid-century theory. The synthetic theory of the 21st century will differ considerably from the one developed a few decades ago, but the process by which it emerges will be one of evolution rather than upheaval.”

 

The origin and evolution of animal appendages, Grace Panganiban et al, Proc. Natl. Acad. Sci. USA Vol. 94, pp. 5162–5166, May 1997. Excerpts:  “Animals have evolved diverse appendages adapted for locomotion, feeding and other functions. The genetics underlying appendage formation are best understood in insects and vertebrates. - - - These similarities are puzzling because arthropod and vertebrate appendages have such vastly different anatomies and evolutionary histories,”

 

Form and Function of Lungs: The Evolution of Air Breathing Mechanisms, Karel F. Liem,  Amer. Zool., 28:739-759 (1988) , Excerpt: “Structural evolution of the vertebrate lung illustrates the principle that the emergence of seemingly new structures such as the mammalian lung is due to intensification of one of the functions of the original piscine lung.”

Testing Macroevolutionary Hypotheses With Cladistic Adistic Analysis: Evidence Against Rectangular Evolution,  Cliff A. Lemen and Patricia W. Freeman, Evolution, 43(7), 1989, pp. 1538-1554, abstract excerpt: “The properties of cladistic data sets from small monophyletic groups (6-1 2 species) are investigated using computer simulations of macroevolution. Two evolutionary models are simulated: gradualism and the punctuated-equilibrium hypothesis. Under the conditions of our simulations these two models of evolution make consistently different predictions about the distribution of autapomorphies among species.”

1990

'Generic' physical mechanisms of morphogenesis and pattern formation, Stuart A. Newman1 And Wayne D. Comper, Development 110, 1-18 (1990) The Company of Biologists Limited 1990, Summary: “The role of 'generic' physical mechanisms in morphogenesis and pattern formation of tissues is considered. Generic mechanisms are defined as those physical processes that are broadly applicable to living and nonliving systems, such as adhesion, surface tension and gravitational effects, viscosity, phase separation, convection and reaction-diffusion coupling. They are contrasted with 'genetic' mechanisms, a term reserved for highly evolved, machine-like, biomolecular processes. Generic mechanisms acting upon living tissues are capable of giving rise to morphogenetic rearrangements of cytoplasmic, tissue and extracellular matrix components, sometimes leading to 'microfingers', and to chemical waves or stripes. We suggest that many morphogenetic and patterning effects are the inevitable outcome of recognized physical properties of tissues, and that generic physical mechanisms that act on these properties are complementary to, and interdependent with genetic mechanisms. We also suggest that major morphological reorganizations in phylogenetic lineages may arise by the action of generic physical mechanisms on developing embryos. Subsequent evolution of genetic mechanisms could stabilize and refine developmental outcomes originally guided by generic effects.”

To Shape a Cell: an Inquiry into the Causes of Morphogenesis of Microorganisms, Franklin M. Harold, Microbiological Reviews, Dec. 1990, p. 381-431 Vol. 54, No. 4 0146-0749/90/040381-51,  1990, American Society for Microbiology, Excerpt from Introduction: “ Of cellular morphogenesis is can justly be said that we know much but understand little. Thanks to the labors of now much but understand little. Thanks to the labors of biologists over many generations, a huge body of literature now records the form, anatomy, and life cycle of innumerable single-celled creatures, procaryotes as well as eucaryotes. However, the student of morphology will be hard put  to discover in this literature more than a very few explanatory principles; we have facts in abundance, but few general relationships with which to weave the particulars into a comprehensible pattern. … How do these shapes arise as each organism grows, divides, and traverses its life cycle? How is form so faithfully transmitted from one generation to the next that a glance is often sufficient to distinguish one species from another? How is the original form regenerated after injury? And what do these forms mean: are they products of natural selection, frozen accidents of biological history, or expressions of higher-order morphogenetic laws? These riddles define the scope of the field; we have no satisfactory solution to any one of them, and to find the answers we shall plainly require much experimental information that is not now available.”

Daniel W. Mcshea (Committee on Evolutionary Biology, University of Chicago) conducted a comprehensive literature review on the development of biological complexity, from what were perceived to be the first multi-celled organisms to macroevolution.  He concluded that scientific evidence both for and against spontaneous generation of complexity is weak.  He continued with a discussion of the reason that so many in the scientific community support the concept of spontaneous complexity, and concluded that the reasons are more social rather than scientific. (Complexity and Evolution: What Everybody Knows, Biology and Philosophy 6: 303-324, 1991)

James W. Atkinson wrote Development and Macroevolution: Introduction to the Symposium in 1992 (Amer. Zool., 32:103-105).  The symposium was sponsored by the Division of the History and Philosophy of Biology of the American Society of Zoologists.  The symposium sought to join developmental biology (embryology) and evolutionary biology in the hope that developmental processes might be identified as mechanisms of evolutionary change.  Atkinson called special attention to a paper contributed by Keith Thompson that “explores the roots of the "problem of morphology" in the evolutionary synthesis of the 1940s and considers its possible solution in the role of epigenetic processes in evolutionary change.”

On the Evolution of Complexity, W. Brian Arthur, Santa Fe Institute Integrative Themes Workshop, July, 1992. The author hypothesized that there are at least three mechanisms that cause evolution to favor the development of complexity; by successive evolution of more and more new species, by increasing structural sophistication within a species, or by one system capturing and incorporating information from another\.

Hubert Yockey’s Information theory and molecular biology was published in 1992.  Looking at the information contained in DNA, he concluded that the probability of it developing by a succession of random events is extremely low.  He claimed that the difference between life and matter is information.

Beneficial Mutations?  Jay L. Wile, CEN Tech J. vol 6(1), 1992, pp 6-9, Excerpt: “In conclusion, the results of the simulation are not surprising to anyone who has studied information theory and the second law of thermodynamics. Information theory states that any highly-developed system of information will be harmed by the random mutation of any of its components. The purpose of the simulation was essentially to show that this theory is, indeed, reasonable when related to genetic evolution. In addition, the effect of eons of time (30,000 human generations correspond to approximately 600,000 years) and natural selection do nothing to damage the conclusions of the theory.”

Keith Stewart Thomson published Macroevolution: The Morphological Problem in Volume 32 of American Zoology in 1992.  Thompson observed that the problem with Darwinism and with the modern synthesis is that “no one has satisfactorily demonstrated a mechanism at the population genetic level by which innumerable, very small phenotypic changes could accumulate rapidly to produce large changes: a process for the origin of the magnificently improbable from the ineffably trivial”.   Thompson argued that many small steps of microevolution cannot produce macroevolution (as many evolutionists still claim), and cited doubts previously expressed by T. Dobzhansky, G.G. Simpson. R.B. Goldschmidt, and J. Gould.

Thompson went on to discuss examples of major phenotypic conditions that can only exist in one of two alternate states with no chance of gradual intermediates.  He cites the ankles joints of some reptiles, where the astragalus and calcaneum bones can only be on one side of the joint or the other.  He added “the shift is not a simple one because it is accompanied by matching changes in ligaments and muscle insertions to maintain a functioning joint.”

Thompson concluded that the “obvious flaw” of the modern synthesis is that it does not recognize that morphologies have their origins in embryonical development pathways as well as evolutionary family trees.  He stated that “while minor changes in phenotype might be caused at any stages in development, major changes must be caused at early stages.”

In Thompson’s view, the coming together of disciplines at the 1948 conference Committee on Common Problems of Genetics, Paleontology and Systematics of the National Research Council of the USA at Princeton University solidified a foundation based on microevolution for the modern synthesis.  (Jepsen, G. L., E. Mayr, and G. G. Simpson. 1949. Genetics, paleontology, and evolution, Princeton University Press, Princeton, New Jersey).  He also credited G.G. Simpson’s 1944 Tempo and Mode In Evolution as critical to establishing this new unity.

Molecular Basis For Genetic Recombination, Rollin D. Hotchkiss, Genetics 78: 247-257 September, 1974. Excerpt: “the past few decades have witnessed the successive description in biochemical-or “molecular”-terms of the great formal entities of classical genetics. The linkage group was early identified with the objectively seen chromosome, then the gene itself, in its wild and mutant forms, more and more closely related to the linear DNA regions thereof. We have seen the identification of the gene product or “physiological gene” with proteins and polypeptide units, and then the exciting unraveling of the widespread protein biosynthetic mechanisms and their control by the broadly applicable genetic code. A last great genetic formalism-the interaction of homologous DNA regions with each other, or genetic recombination-is now coming under detailed analysis as to its biochemical mechanism.”

Stuart Kauffman’s book Origins of Order was published in 1993.  Kauffmann presumed that that the complexity of living organisms might be due to inherent properties of self-organization as much as it is due to Darwinian evolution.  Self-organization is believed to occur due to random fluctuations in combination with positive feedback.  Kauffman’s work was preceded by William R. Ashby’s Principles of the Self-Organizing Dynamic System in 1947.  The Greek philosopher Democritus  and the Roman philosopher Lucretius also believed that, given enough time and space and matter, order can appear in nature by itself.  The thinking is somewhat consistent with the spontaneous generation of life forms promoted by Lamarck.

The Arrival Of The Fittest": Toward A Theory Of Biological Organization, Walter Fontana and Leo W. Buss, Bulletin of Mathematical Biology Vol 56, No. 1, pp. 1 64, 1994. Excerpt from conclusion: “Existing evolutionary theory is a formulation of the process of natural selection, but is incomplete in that it assumes the prior existence of selectable units and is formalized without a theory of the origin of variation. The Darwinian Theory, thus, requires augmentation with a theory of the organism. A complete theory of biological organization would explicate what organizations can emerge, combine and vary.”

Reinventing Darwin; The Great Debate at the High Table of Evolutionary Theory, Niles Eldridge, John Wiley and Sons, 1995. Amazon preview: “An insider's provocative account of one of the most contentious debates in science today. When Niles Eldredge and Stephen Jay Gould, two of the world's leading evolutionary theorists, proposed a bold new theory of evolution―the theory of "punctuated equilibria"―they stood the standard interpretation of Darwin on its head. They also ignited a furious debate about the true nature of evolution. On the one side are the geneticists. They contend that evolution proceeds slowly but surely, driven by competition among organisms to transmit their genes from generation to generation. On the other are the paleontologists, like Eldredge and Gould, who show in the fossil record that in fact evolution proceeds only sporadically. Long periods of no change―equilibria―are "punctuated" by episodes of rapid evolutionary activity. According to the paleontologists, this pattern shows that evolution is driven far more by environmental forces than by genetic competition. How can the prevailing views on evolution be so different? In Reinventing Darwin, Niles Eldredge offers a spirited account of the dispute and an impressive case for the paleontologists' side of the story. With the mastery that only a leading contributor to the debate can provide, he charts the course of theory from Darwin's day to the present and explores the fundamental mysteries and crucial questions that underlie the current quarrels. Is evolution fired by a gentle and persistent motor and fueled by the survival instincts of "selfish genes"? Or does it proceed in fits and starts, as the fossil record seems to show? What is the role of environmental changes such as habitat destruction and of cataclysmic events like meteor impacts? Are most species inherently stable, changing only very little until they succumb to extinction? Or are species highly adaptable, changing all the time? Eldredge sorts through the major findings and interpretations and presents a lively introduction to the leading edge of evolutionary theory today. Reinventing Darwin offers a rare insider's view of the sometimes contentious, but always stimulating work of scientific inquiry.”

The Modern Evolutionary Theory, Ernst Mayr, Journal of Mammalogy. 77(1):1-7, 1996, Intro: “Of all of Darwin's evolutionary theories, the one that encountered the greatest resistance, and was therefore the last one to be accepted, was the theory of natural selection. It was only about 1940 that it was adopted by the majority of biologists. In order to understand why it encountered this resistance, it is necessary to survey the history of evolutionary biology. …”

Reinventing Darwin: The Great Evolutionary Debate (1995) by Niles Eldredge envisions a debate between the “Ultra-Darwinians” and the “naturalists”.  Ultra-Darwinists take a gene and natural selection approach and think that Darwinism explains everything.  Naturalists think that is a ‘distortedly oversimplified view of the natural world'.  Naturalists think that extrapolating neo Darwinism from generation-by-generation change to change on a geological time-scale is not justified.  They think it transforms natural selection from a filter to a creative force reshaping organic form.  Naturalists do not think everything is explained by gene frequency.  Naturalists ask why living fossils, like Limulus, stay unchanged for many millions of years.  They suggest alternate processes such as 'habitat tracking', in which species move to a suitable environment rather than change their anatomy.  Reinventing Darwin begins with a history of twentieth century evolutionary theory and then develops the alternate concepts to neo (ultra) Darwinism.

Tempo and Mode in Evolution - Genetics and Paleontology 50 Years after Simpson (1995), 

Walter M. Fitch and Francisco J. Ayala, Editors, Excerpt: “Since George Gaylord Simpson published Tempo and Mode in Evolution in 1944, discoveries in paleontology and genetics have abounded. This volume brings together the findings and insights of today's leading experts in the study of evolution, including Ayala, W. Ford Doolittle, and Stephen Jay Gould.”

 

Mendel's Opposition to Evolution and to Darwin, B. E. Bishop, Journal of Heredity 1996, 87: 205-213;   The authors challenged the common belief that the work of Mendel compliments the work of Darwin as assumed by the modern synthesis, Abstract: “Although the past decade or so has seen a resurgence of interest in Mendel's role in the origin of genetic theory, only one writer, L. A. Callender (1988), has concluded that Mendel was opposed to evolution. Yet careful scrutiny of Mendel's Pisum paper, published in 1866, and of the time and circumstances in which it appeared suggests not only that it is antievolutionary In content, but also that it was specifically written in contradiction of Darwin's book The Origin of Species, published in 1859, and that Mendel's and Darwin's theories, the two theories which were united in the 1940s to form the modern synthesis, are completely antithetical.”

Microbiologist Michael Behe studied the details of living cells, and formed the concept of irreducible complexity.  In 1996, Behe published his ideas on irreducible complexity in his book Darwin's Black Box.  He argued that some biological structure is so complex that it could not evolve incrementally over time simply due to an accumulation of random errors.  All of the components have to be present for the organism to function; therefore they could not have evolved independently, because natural selection could not preserve a mutation that had no immediate survival benefit.  He developed his though further in subsequent publications, arguing that life requires information as well as matter and energy to develop.  Some other scientists support Behe’s conclusions.  Among them are Stephen Meyers who published Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design in 2013, Michael Denton  who wrote the book Evolution: A Theory in Crisis, in 1985, and computer scientist David Gelernter who wrote the 2019 essay Giving Up Darwin; A fond farewell to a brilliant and beautiful theory. An essay entitled “The Deniable Darwin” by David Berlinsky appeared in the June 1996 issue of Commentary.  He also challenged the Darwinian fundamentalist belief that chance and random mutation, modified natural selection, could account for the biochemical complexity things such as the eye and the immune system. More than three decades after Evolution: A Theory in Crisis, Denton published Evolution, still a theory in crisis (2015).

When Does Morphology Matter?, M. A. R. Koehl, Annu. Rev. Ecol. Syst. 1996. 27:501–42. Conclusion: “Quantitative mechanistic analyses of how function depends on biological form, and on the ecological context in which an organism operates, should complement descriptive statistical and phylogenetic studies to provide insights about ecological and evolutionary questions. Such quantitative studies have shown that the relationship between morphology and performance is often nonlinear and sometimes surprising. These mechanistic studies not only reveal potential misconceptions that can arise from the descriptive statistical analyses often used in ecological and evolutionary research, but they also show how new functions, and novel consequences of changes in morphology, can arise simply as the result of changes in size or habitat.”

Dobzhansky, Bateson, and the Genetics of Speciation , H. Allen Orr, Perspectives: Anecdotal, Historical And Critical Commentaries on Genetics, Edited by Jams F. Crow and William F. Dove,  Genetics 144: 1331-1335 (December, 1996).  The paper reviews the curious fact that Darwin’s Origin of Species did not explain the origin of species.  The paper goes on to explain how, many decades later, T. Dobzhansky, determined how speciation could occur, in spite of many sterile hybrids, by variation in a combination of two Medallion genes.

Michael Denton wrote that there is still “an irresistible consilience (convergence) of evidence for rejecting Darwinian cumulative selection as the major driving force of evolution.”  Denton claims the fossil record has still not produced a series of adaptive transition forms predicted by Darwin.  He also argues that biology displays pervasive non-adaptive order that cannot be explained by the mechanism of neo Darwinism.  In Evolution, still a theory in crisis he cites many examples of life forms that cannot have developed through an accumulation of incremental changes.

Macroevolution in the 21st Century, David Jablonski et al, paleo 21, Frankfurt, 1997,  http://paleonet.org/paleo21/mevolution.html  Excerpts: “With its unique time perspective, paleontology has a central role to play in this area: the fossil record provides a direct, empirical window onto large-scale evolutionary patterns, and thus is invaluable both as a document of macro evolutionary phenomena, and as a natural laboratory for the framing and testing of macro evolutionary hypotheses. - - - One striking macro evolutionary pattern that has emerged from the fossil record is that major groups and evolutionary novelties have not originated randomly in time and space. The Cambrian Explosion at the beginning of the Paleozoic Era established virtually all of the major body plans seen in present-day oceans - - - . The mechanisms underlying the origins of novelties remain poorly understood. - - - Much macro evolutionary research was triggered by the realization that many species appeared to be almost static morphologically after their first appearance in the fossil record rather than evolving continuously. This led to the hypothesis of punctuated equilibrium - - -. The relative roles of physical and biotic factors in shaping macro evolutionary patterns also remain hotly debated, and surely vary among taxa, times, and places. - - - .”

Evolution: Setting the mutation rate, Paul Sniegowski, Current Biology, 1997, 7:R487–R488: The rate of mutation is continually discussed in the literature, especially since some challenges to Darwinism claim the mutation rate is too low for evolution to have produced complex lifeforms during the time he earth has been inexistence. Excerpt:  “ A recent study of X-chromosome and autosome genes in mammals suggests that selective trade-offs are important in the long-term evolution of mutation rates; but recent studies with bacteria show that high mutation rates can nonetheless evolve in the short term in clonal populations.”

In her PhD dissertation  The Chances of Evolution: An Analysis of the Roles of Chance in Microevolution and Macroevolution (U of Minnesota, 1997), Roberta Lynn Millstein reviewed a considerable amount of literature related to the cause (if any) of mutations.  Her lengthy summary shows that, after over a century, the issue of Lamarckian or Darwinian mutation is still unresolved.  Some evolutionists firmly believe that all mutations are random, while others, citing experiments with bacteria, believe that some beneficial mutations are directed (result from environmental influences to enhance survival).

Transposable elements, gene silencing and macroevolution,. John F. McDonald, TREE vol 13, no. 3 March 1998, Excerpt: “Two major macro evolutionary events in the history of life were the origin of eukaryotes and the origin of vertebrates. Quantum increases in gene number are correlated with these landmark evolutionary events and presumably provided the coding potential to evolve the many novel structures and functions which distinguish prokaryotes from eukaryotes and invertebrates from vertebrates. Adrian Bird has persuasively argued that the evolution of two major epigenetic silencing mechanisms (chromatin formation for the prokaryotic/eukaryotic transition and methylation for the invertebrate/vertebrate transition) were prerequisite to the quantum expansions in gene number that accompanied the emergence of eukaryotes and vertebrates. Without the evolution of these and perhaps other global repression mechanisms, the aggregate of spurious transcription from inappropriate genes would have greatly reduced the probability that new lineages would survive.”

Macro-evolution, Pattern and Process, Steven M. Stanley, John Hopkins Paperbacks, 1998. Amazon summary: “In Macroevolution, Steven Stanley addresses, from a paleo biologist’s perspective, the question of whether punctuated equilibria or gradualism offers the best account of the history of life. Punctuated equilibria, a view popularized by Stephen Jay Gould among others, holds that species remain evolutionarily static for long periods of time and undergo substantial genetic changes and develop new, primarily adaptive, strategies during speciation. In contrast, gradualism views large-scale changes as the result of continual and successive small-scale changes. Coming down on the side of those who favor the model of punctuated equilibria, Stanley argues that only "quantum speciation" (speciation that is rapid and radically divergent) can explain the story of life revealed in the fossil record; macro evolutionary trends, he contends, can be explained by selection among species and, to a lesser extent, by phylogenetic drift and directed speciation.”

Preservation of Duplicate Genes by Complementary, Degenerative , Mutations, Allan Force,  et al, Genetics 151: 1531–1545 (April 1999), Excerpt from abstract: “The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum.”

Origin of Genes (intron/exon/module/evolution), Walter Gilbert, Sandro J. De Souza, and Manyuan Long,  Proc. Natl. Acad. Sci. USA Vol. 94, pp. 7698–7703, July 1997, Abstract:  ‘We discuss two tests of the hypothesis that the first genes were assembled from exons. The hypothesis of exon shuffling in the progenote predicts that intron phases will be correlated so that exons will be an integer number of codons and predicts that the exons will be correlated with compact regions of polypeptide chain. These predictions have been tested on ancient conserved proteins (proteins without introns in prokaryotes but with introns in eukaryotes) and hold with high statistical significance. We conclude that introns are correlated with compact features of proteins 15-, 22-, or 30-amino acid residues long, as was predicted by ‘‘The Exon Theory of Genes.””

Transcriptional Regulators and the Evolution of Plant Form,  John Doebley  and Lewis Lukens, The Plant Cell, Vol. 10, 1075–1082, July 1998.  The authors reviewed the history of hypothesis concerning the connection between genetic information and life forms, and explain how plant forms are believed to be governed by changes in the cis-regulatory regions of the DNA.

DNA By Design: An Inference To The Best Explanation For The Origin Of Biological Information, Stephen C. Meyer, Rhetoric & Public Affairs Vol. 1, No. 4, 1998, pp. 519-556.  The paper reviews origin of life hypothesis, and discusses the problems with each.  It concludes that the origin of information by design is the least improbable.

Not By Chance! -Shattering The Modern Theory of Evolution, Dr Lee Spetner.1997,
The Judaica Press, New York.  Dr. Spetner, a physicist, applied statistical analysis to argue that the addition of complexity by mutation and natural selection is most improbable.  He also claims that the typical mutation will result in a loss, rather than a gain, of information in the genome.

2000

In 2000, paleo-biologist Douglas H. Erwin published “Macroevolution is more than repeated rounds of microevolution” in the journal Evolution and Development.  He cited many examples of significant evolutionary change that cannot be satisfactorily explained by iterations of microevolution.  The paper discusses a number of processes that might cause macroevolution, but not indicate that any of them were gaining appreciable support.

A Mathematician's View of Evolution, Granville Sewell, The Mathematical Intelligencer 22, no. 4 (2000): Sewell, a professor of mathematics at the U of Texas El Paso, wrote this article after reading Dr. Michael Behe’s book entitled "Darwin's Black Box" and discussing it with him when Behe was a guest speaker at the U of Texas.  Behe’s book and presentation introduced the concept of irreducible complexity in micro biology, which Behe claims could not be the result of a long series of errors (mutations).  Sewell stated that the laws of probability indicate Behe is correct, and discussed why he believes that is more obvious to mathematicians than biologists.

Limits to natural selection, Nick Barton and Linda Partridge, BioEssays 22:1075±1084, 2000. Summary: “We review the various factors that limit adaptation by natural selection. Recent discussion of constraints on selection and, conversely, of the factors that enhance ``evolvability'', have concentrated on the kinds of variation that can be produced. Here, we emphasize that adaptation depends on how the various evolutionary processes shape variation in populations. We survey the limits that population genetics places on adaptive evolution, and discuss the relationship between disparate literatures.”

Robert L. Carroll, Towards a new evolutionary synthesis, Trends in Ecology and Evolution, 15 (January, 2000): 27. Abstract: “New concepts and information from molecular developmental biology, systematics, geology and the fossil record of all groups of organisms, need to be integrated into an expanded evolutionary synthesis. These fields of study show that large-scale evolutionary phenomena cannot be understood solely on the basis of extrapolation from processes observed at the level of modern populations and species. Patterns and rates of evolution are much more varied than had been conceived by Darwin or the evolutionary synthesis, and physical factors of the earth’s history have had a significant, but extremely varied, impact on the evolution of life.”

David L. Stern, Perspective: Evolutionary Developmental Biology and the Problem of Variation, Evolution 54 (2000): 1079-1091. Abstract: “One of the oldest problems in evolutionary biology remains largely unsolved. Which mutations generate evolutionarily relevant phenotypic variation? What kinds of molecular changes do they entail? What are the phenotypic magnitudes, frequencies of origin, and pleiotropic effects of such mutations? How is the genome constructed to allow the observed abundance of phenotypic diversity? Historically, the neo‐Darwinian synthesizers stressed the predominance of micro mutations in evolution, whereas others noted the similarities between some dramatic mutations and evolutionary transitions to argue for macromutationism. Arguments on both sides have been biased by misconceptions of the developmental effects of mutations. For example, the traditional view that mutations of important developmental genes always have large pleiotropic effects can now be seen to be a conclusion drawn from observations of a small class of mutations with dramatic effects. It is possible that some mutations, for example, those in cis‐regulatory DNA, have few or no pleiotropic effects and may be the predominant source of morphological evolution. In contrast, mutations causing dramatic phenotypic effects, although superficially similar to hypothesized evolutionary transitions, are unlikely to fairly represent the true path of evolution. Recent developmental studies of gene function provide a new way of conceptualizing and studying variation that contrasts with the traditional genetic view that was incorporated into neo‐Darwinian theory and population genetics. This new approach in developmental biology is as important for micro‐evolutionary studies as the actual results from recent evolutionary developmental studies. In particular, this approach will assist in the task of identifying the specific mutations generating phenotypic variation and elucidating how they alter gene function. These data will provide the current missing link between molecular and phenotypic variation in natural populations.”

Silva, E. P. DA.: ëUma breve histÛria da teoria evolutivaí. (A short history of evolutionary theory). HistÛria, CiÍncias, Sa˙de ó Manguinhos, vol. VIII(3): 671-87, set.-dez. 2001. Abstract: “The history of the Theory of Evolution has been told a number of times by historians, philosophers, professors, writers, scientists and so on. However, many of these versions differ from or even contradict one another. In this article, the history of the Theory of Evolution is retold according to a dialectical-materialistic perspective. It analyzes the historical contradictions between Darwinian evolution theory and Mendel’s model, the background that led to the synthetic theory of evolution, the debate carried out by classic schools and the result of synthesis, as well as the still current debate between Neutralism and Selectionism.” Introduction: “The history of evolutionary theory has been told and retold. However, no general agreement can be found among the different accounts of the facts. Disagreements are abundant about the relative importance of different fields (e.g. population genetics, experimental genetics, natural history, developmental biology) for the synthetic theory, as well as about the correct epistemological framework in which the history should be interpreted (e.g. falsificationism, relativism, dialectical materialism). Therefore, any attempt to tell again such history will need to make choices at all steps. The brief overview on evolutionary theory given here will try to make these choices as explicit as possible. The final aim is not that of reaching a specific solution, which seems a lost cause, but of reading through the published material to analyze the way in which science operates.”

The Membrane Code: A Carrier of Essential Biological Information That Is Not Specified by DNA and Is Inherited Apart from It, Jonathan Wells. “https://www.worldscientific.com/doi/epdf/10.1142/9789814508728_0021  Abstract: “According to the most widely held modern version of Darwin’s theory, DNA mutations can supply raw materials for morphological  evolution because they alter a genetic program that controls embryo development. Yet a genetic program is not sufficient for  embryogenesis: biological information  outside of DNA is needed to specify the body plan of the embryo and much of its subsequent development. Some of that information is in cell membrane patterns, which contain a two-dimensional code mediated by proteins and carbohydrates. These molecules specify targets for morphogenetic determinants in the cytoplasm, generate  endogenous electric fields that provide spatial coordinates for embryo development, regulate intracellular signaling, and participate in cell–cell interactions. Although the individual membrane molecules are at least partly specified by DNA sequences, their two-dimensional patterns are not. Furthermore, membrane patterns can be inherited independently of the DNA. I review some of the evidence for the membrane code and argue that it has important implications for modern evolutionary theory.”

Pigliucci, Massimo. "Impossible Evolution? Another Physicist Challenges Darwin." Skeptic [Altadena, CA], vol. 8, no. 4, 2001, p. 54.   (Piglucci reviews Hoyles book) Excerpt; “The underlying premise of Hoyle’s "demonstration" of the ineffectiveness of natural selection is that there are more mutations with negative or even lethal effects than there are mutations with positive effects. This, coupled with another of Hoyle's fundamental assumptions, that living organisms are so complex and finely tuned that any change in their machinery is overwhelmingly more likely to cause damage than benefit, leads to his conclusion that evolution by natural selection cannot possibly work. There are two problems with this reasoning. First, biologists have known now for decades that most mutations are neither positive nor negative, but neutral or quasi-neutral. This leaves much more room for natural selection to maneuver than in the tight scenario adopted by Hoyle. The reason for such a surprising amount of neutrality of mutational effects is related to the second problem embedded in Hoyle's argument: organisms are not designed according to stringent engineering principles where every part has to work exactly in a particular manner and interact with precision with all other parts. Rather, living beings are put together in a rather loose way, with a lot of redundancy and suboptimal design, exactly as one would expect if they were the result of a natural process instead of an intelligent designer.”

Hugo De Vries: From the theory of intracellular pangenesis to the rediscovery of Mendel, Charles Lenay, Comptes Rendus de l Académie des Sciences - Series III - Sciences de la Vie 323(12):1053-60, January 2001. The paper reviews the contributions of De Vries and traces the eventual blending of Darwinism and Mendelism.

 

What Evolution Is, Ernst Mayr, A Phoenix Paperback, 2001. A popular paperback book explaining evolution by an author who believes there is absolute proof for evolution.

 

Evolution of biological complexity, Christoph Adami, Charles Ofria, and Travis C. Collier, PNAS u April 25, 2000 u vol. 97 u no. 9 u 4463–4468, Abstract; “To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural ‘‘Maxwell Demon,’’ within a fixed environment, genomic complexity is forced to increase.”

Jeffry S. Levinton (Genetics, Paleontology, and Macroevolution, 2001) attempted to establish a more specific definition of macroevolution; “Macroevolution is the sum of a range of processes that explain evolutionary changes that resulted in the diversity of major body plans of living organisms through geological time and at present.”  The requirement for “diversity of major body plan” excludes example such as the commonly cited peppered moth and Galapagos finch.  A key concept presented in the book is that; “Form variation among major groups has to be understood in terms of evolutionary history, major adaptive constraints on form and to some extent by constraints on form that arise from limited variation of developmental mechanisms. The power of natural selection has been verified even with this larger‐scale approach.”

Darwin on Variation and Heredity, Rasmus G. Winther, Journal of the History of Biology 33: 425–455, 2000. Abstract: “Darwin’s ideas on variation, heredity, and development differ significantly from twentieth-century views. First, Darwin held that environmental changes, acting either on the reproductive organs or the body, were necessary to generate variation. Second, heredity was a developmental, not a transmissional, process; variation was a change in the developmental process of change. An analysis of Darwin’s elaboration and modification of these two positions from his early notebooks (1836–1844) to the last edition of the Variation of Animals and Plants Under Domestication (1875) complements previous Darwin scholarship on these issues. Included in this analysis is a description of the way Darwin employed the distinction between transmission and development, as well as the conceptual relationship he saw between heredity and variation.”

Darwin assumed the life began spontaneously, but only once.  The modern synthesis adopted that assumption, and much of biology is currently built on the idea of a common ancestor.  Microbiologist Christian Schwabe determined that some of life’s chemistry is not consistent with the assumption of a single common ancestor.  Rather, life originated many different times, and that, rather than macroevolution, explains the diversity of life.  Schwabe published The Genomic Potential Hypothesis: A Chemist's View of the Origins, Evolution and Unfolding of Life in 2001.

Schwabe was not the first microbiologist to challenge the common ancestor assumption.  Previously, Carl Woese proposed several different origins of life on earth. Another Schwabe publication is Evolution And Chaos The Genomic Potential Hypothesis And Phase-State Mathematics, Applic. Vol. 20, No. 4--6, pp. 287-301, 1990. Excerpt: “Darwinism existed before molecular data were available and before genes had been discovered. It was based upon perhaps less than 10% of the fossil record available today and therefore all of the molecular data, and about 90% of the fossil data, had to be retrofitted into the existing hypothesis and in that process the hypothesis took precedence. In contrast, the genomic potential hypothesis is a "post-data" model that was innocently built upon the new information and the results do not point to a random chance-oriented model but rather to a deterministic, yet unpredictable one. It is the ultimate purpose of this paper to examine how well the evolutionary process might be represented by a general chaotic attractor model and to provide a few parameters that might stimulate the mathematician among the readers to formulate a proper model in terms of phase-space mathematics.” Later, Schwabe published Genomic Potential Hypothesis of Evolution: A Concept of Biogenesis in Habitable Spaces of the Universe, The Anatomical Record 268:171–179 (2002). “The new hypothesis of evolution establishes a contiguity of life sciences with cosmology, physics, and chemistry, and provides a basis for the search for life on other planets. Chemistry is the sole driving force of the assembly of life, under the subtle guidance exerted by bonding orbital geometry. That phenomenon leads to multiple origins that function on the same principles but are different to the extent that their nucleic acid core varies. Thus, thoughts about the origins of life and the development of complexity have been transferred from the chance orientation of the past to the realm of atomic structures, which are subject to the laws of thermodynamics and kinetics. Evolution is a legitimate subject of basic science, and the complexity of life will submit to the laws of chemistry and physics as the problem is viewed from a new perspective. The paradigm connects life to the big events that formed every sphere of our living space and that keeps conditions fine-tuned for life to persist, perhaps a billion years or more. The “genomic potential” hypothesis leads to the prediction that life like ours is likely to exist in galaxies that are as distant from the origin of the universe as the Milky Way, and that the habitable zone of our galaxy harbors other living planets as well.”

 

Wallace Arthur, The Origin of Animal Body Plans, 2002 , Observing that neo-Darwinism has no satisfactory explanation for the origin of variation, the author explains the approach of evolutionary development biology to explore the deficiency.

Icons of Evolution: Science or Myth? Why Much of What We Teach About Evolution Is Wrong, Johnathan Wells, January 1, 2002 (there were prior editions). The author is a unique participant in the evolutionary literature, having received two Ph.D.’s, one in Molecular and Cell Biology from the University of California at Berkeley, and one in Religious Studies from Yale University. He has worked as a postdoctoral research biologist at the University of California at Berkeley and the supervisor of a medical laboratory in Fairfield, California. He also taught biology at California State University in Hayward. Icons of Evolution argues that ten classic evidences of evolution included in text books are not accurate. The book received very critical reviews published by various scientists. Wells subsequently published a sarcastically titled rebuttal to seven of the major reviews: Critics Rave Over Icons of Evolution: A Response to Published Reviews Jonathan Wells May 25, 2001.

Hox protein mutation and macroevolution of the insect body plan, Nature · March 2002, Matthew Ronshaugen, Nadine McGinnis & William McGinnis; Excerpt. “A fascinating question in biology is how molecular changes in developmental pathways lead to macroevolutionary changes in morphology. Mutations in homeotic (Hox) genes have long been suggested as potential causes of morphological evolution, and there is abundant evidence that some changes in Hox expression patterns correlate with transitions in animal axial pattern. A major morphological transition in metazoans occurred about 400 million years ago, when six-legged insects diverged from crustacean-like arthropod ancestors with multiple limbs.”

First Genetic Evidence Uncovered of How Major Changes in Body Shapes Occurred During Early Animal Evolution, Kim McDonald, February 6, 2002 UC SanDiego https://biology.ucsd.edu/about/news/article_020602.html ; Excerpt; “Using laboratory fruit flies and a crustacean known as Artemia, or brine shrimp, the scientists showed how modifications in the Hox gene Ubx—which suppresses 100 percent of the limb development in the thoracic region of fruit flies, but only 15 percent in Artemia—would have allowed the crustacean-like ancestors of Artemia, with limbs on every segment, to lose their hind legs and diverge 400 million years ago into the six-legged insects.”

Irreducible Complexity And Darwinian Gradualism: A Reply To Michael J. Behe, Paul Draper, Faith And Philosophy Vol. 19 No.1 January 2002. Draper presents a detailed, scientific rebuttal to the claims made in “Darwin's Black Box”. Abstract excerpt: “I conclude that, while Behe successfully rules out some Darwinian paths to the biochemical systems he discusses, others remain open. Thus, his argument against Darwinian gradualism (and ipso facto his argument for intelligent design) is at best incomplete.” (Behe wrote rebuttal years later: https://evolutionnews.org/2020/02/philosophical-ish-objections-to-intelligent-design-a-response-to-paul-draper/)

In The Structure of Evolutionary Theory (2002), Stephen Jay Gould described the history and origin of three basic tenets of classical Darwinism: 1) natural selection works on organisms, not genes or species, 2) it is almost exclusively the mechanism of adaptive evolutionary change, and 3) these changes are incremental, not drastic.  He credited Theodosius Dobzhansky’s 1937 Genetics and the Origin of Species for helping to formalize the MS by the late 1950s.  Next, he examined three challenges to these three tenets of the MS: 1) selection operates on multiple levels, from the gene to the group, and 2) evolution proceeds by a variety of mechanisms, not just natural selection, and 3) causes operating at broader scales, including catastrophes, have been very significant.  Gould proposed a new structure for evolutionary thought, or, in his words a “revised and expanded evolutionary theory”.  It includes punctuated equilibria, constraints, and adaptations, and hierarchical levels of selection (selection acting at all possible levels of life, not just the individual organism). Gould, a paleontologist, encountered problems with Darwinism and also the MS when he looked for gradual change from one species to another in the fossil record.  Instead, he found species remaining unchanged for long periods of time.  In between were brief episodes of step-wise change.  Gould determined that many species accumulated virtually no change at all between their initial appearance in the fossil record and extinction millions of years later.  Therefore, Gould supported Goldschmidt’s claim that changes in gene frequency in a population (standing variation), what some call microevolution, did not produce new species.  Gould suspected that a more likely cause of species change is explained by evolutionary developmental biology (evo devo).  This thinking essentially abandoned Darwinian functionalism, the idea that evolution is caused by competition (natural selection).

Michael Dietrich published Microevolution and Macroevolution Are Governed by the Same Processes in 2002 (Dartmouth Faculty Open Access Articles. 12). He reviewed the historical distinction between the two, and well as the ongoing debate about the difference (if any) that had been going on since the modern synthesis was established.  His paper shows that the problem is due to the fact that microevolution and macroevolution are defined in terms of the effect they have species, rather than in terms of how they change the genome.  That is because their chemical function is not understood.  Thus, some evolutions think they are the very some process operation over different time scales, and some think they represent a fundamentally different process. --- Like many disputes in biology over the past 100 years, the dispute over the existence of distinct processes for micro and macro evolution is a matter of relative significance.--- As more cases of species selection accumulate, unique macro evolutionary processes will be acknowledged. How long it will take evolutionary biologists to reach agreement regarding their relative significance will depend on an array of factors from the scientific to the sociological. If the track record of other relative significance controversies in biology is any indication, however, we will have a long time to wait to see this form of the dispute over macro evolutionary processes resolved.”

First Genetic Evidence Uncovered of How Major Changes in Body Shapes Occurred During Early Animal Evolution, Kim McDonald, February 6, 2002, an advance online publication of a paper scheduled to appear in Nature, https://biology.ucsd.edu/about/news/article_020602.html ----- the scientists show how mutations in regulatory genes that guide the embryonic development of crustaceans and fruit flies allowed aquatic crustacean-like arthropods, with limbs on every segment of their bodies, to evolve 400 million years ago into a radically different body plan: the terrestrial six-legged insects. --- The achievement is a landmark in evolutionary biology, not only because it shows how new animal body plans could arise from a simple genetic mutation, but because it effectively answers a major criticism creationists had long leveled against evolution—the absence of a genetic mechanism that could permit animals to introduce radical new body designs.

100 Years Ago: Walter Sutton and the Chromosome Theory of Heredity, Ernest W. Crow and James F. Crow, Genetics 160: 1–4 (January 2002):  The paper review Sutton’s discovery that chromosomes explain Mendelian genetics.

Andrew M. Simons proposed a somewhat unique argument for micro and macro evolution being governed by the same processes.  In The continuity of microevolution and macroevolution Ca ( J. EVOL. BIOL., 2002) he argued that “The predominant view of discontinuity of microevolution and macroevolution is based on observations of trend reversals that effectively negate the effects of selection that have accumulated over short time scales.”  In other words, he thinks random extinctions erase slight, recent morphological changes created by microevolution; there is not enough time to preserve them.  He further argues that “there should be no expectation of optimality for traits of extant organisms under present conditions or over short time scales.”  In effect, non-optimized organisms have a “memory”.  Their gnome includes old adaptations acquired during a prior, more extreme environmental challenge.  So, micro and macro evolution blend together, with ancient adaptations developed by microevolution long before the current environmental challenge preserved in the genome.

Generating and filtering major phenotypic novelties: neoGoldschmidtian saltation revisited Richard N\. Bateman and William A. DiMichele. In Developmental Genetics and Plant Evolution (2002) (eds Q. C. B. Cronk, R. M. Bateman and J. A. Hawkins), Taylor & Francis, London, pp. 109-159.  “Further developing a controversial neoGoldschmidtian paradigm that we first published in 1994, we here narrowly define saltational evolution as a genetic modification that is expressed as a profound phenotypic change across a single generation and results in a potentially independent evolutionary lineage ---.”

Modeling the Emergence of Complexity: Complex Systems, the Origin of Life and Interactive On-Line Art, Christa Simmerer and Laurent Mignonneau, Leonardo, Vol. 35, No. 2, pp. 161–169, 2002, Excerpt: “The aim of the research presented here is to construct an Internet-based interactive artwork that applies and tests principles of complex-system and origin-of-life theories to the creation of a computer-generated and audience-participatory networked system on the Internet.”  The paper includes a historical review of origin of life theories.

The evolution of plants: a major problem for Darwinism, Jerry Bergman, TJ 16(2) 2002, Abstract: “A major problem for Neo-Darwinism is the complete lack of evidence for plant evolution in the fossil record. As a whole, the fossil evidence of prehistoric plants is actually very good, yet no convincing transitional forms have been discovered in the abundant plant fossil record. This fact has been recognized by both creationists and evolutionists as providing strong evidence for abrupt appearance theory. If macroevolution were true, some evidence of plant evolution should exist in the abundant plant fossil record. Instead, what is found are many examples of modern plants, variations of modern plants, or extinct plants that require still more transitional forms.”

Evo-Devo: the Long and Winding Road, Jaume Baguñà and Jordi Garcia-Fernàndez, Int. J. Dev. Biol. 47: 705-713 (2003), Abstract excerpt: “Evolutionary developmental biology (Evo-Devo) aims to unveil how developmental processes and mechanisms become modified during evolution and how from these changes the past and present biodiversity arose. The first wave of Evo-Devo identified a conserved set of toolkits common to most metazoans. The present second wave has changed gear and aims to identify how genes and modules were used differently through evolution to build the past and present morphological diversity. The burgeoning third wave is introducing experimental testing of predictions drawn from the first and second waves.”

Evolutionary Morphology, Innovation, and the Synthesis of Evolutionary and Developmental Biology, Alan C. Love, Biology and Philosophy 18: 309–345, 2003. Abstract: “One foundational question in contemporary biology is how to ‘rejoin’ evolution and development. The emerging research program (evolutionary developmental biology or ‘evodevo’) requires a meshing of disciplines, concepts, and explanations that have been developed largely in independence over the past century. In the attempt to comprehend the present separation between evolution and development much attention has been paid to the split between genetics and embryology in the early part of the 20th century with its codification in the exclusion of embryology from the Modern Synthesis. This encourages a characterization of evolutionary developmental biology as the marriage of evolutionary theory and embryology via developmental genetics. But there remains a largely untold story about the significance of morphology and comparative anatomy (also minimized in the Modern Synthesis). Functional and evolutionary morphology are critical for understanding the development of a concept central to evolutionary developmental biology, evolutionary innovation. Highlighting the discipline of morphology and the concepts of innovation and novelty provides an alternative way of conceptualizing the ‘evo’ and the ‘devo’ to be synthesized.”

Evolution: The Erratic Path Towards Complexity, Nick Barton and Willem Zuidema, Current Biology, Vol. 13, R649–R651, August 19, 2003,  “Artificial Life models may shed new light on the long-standing challenge for evolutionary biology of explaining the origins of complex organs. Real progress on this issue, however, requires Artificial Life researchers to take seriously the tools and insights of population genetics.”

Evolution, Douglas J. Futuyma, 2003. A 600 page undergraduate text book that is now available online.

Origination of Organismal Form, Beyond the Gene in Developmental and Evolutionary Biology, Gerd B. Müller and Stuart A. Newman, January, 2003, MIT Press,  Summary: “A more comprehensive version of evolutionary theory that focuses as much on the origin of biological form as on its diversification. --- Drawing on work from developmental biology, paleontology, developmental and population genetics, cancer research, physics, and theoretical biology, this book explores the multiple factors responsible for the origination of biological form. It examines the essential problems of morphological evolution—why, for example, the basic body plans of nearly all metazoans arose within a relatively short time span, why similar morphological design motifs appear in phylogenetically independent lineages, and how new structural elements are added to the body plan of a given phylogenetic lineage. --- By placing epigenetic processes, rather than gene sequence and gene expression changes, at the center of morphological origination, this book points the way to a more comprehensive theory of evolution.”  Excerpt from chapter 1: Although the forces driving morphological evolution certainly include natural selection, the appearance of specific, phenotypic elements of construction must not be taken as being caused by natural selection; selection can only work on what already exists. Darwin acknowledges this point in the first edition of The Origin of Species, where he states that certain characters may have “originated from quite secondary causes, independently from natural selection”.”

The Species Problem, Biological Species, Ontology, and the Metaphysics of Biology, David N. Stamos, Lexington Books, 2003. Excerpt from introduction:” In a sense, the species problem is really quite simple. Are biological species real, and, if real, what is the nature of their reality? Are species words merely operational conveniences made for the purpose of conveying various information and theories, or do species words refer to entities in the objective world with a real existence independent of science? My purpose in writing the present work was basically fourfold and closely interconnected: (i) to fill a large void by weaving together the bulk of the more important (and much of the less important) of the vast literature on the modern species problem into one comprehensive, cohesive, and informative whole, useful for an interdisciplinary audience of professional scholars and students alike; ---“.

Milton H. Gallardo published Genome dynamics, genetic complexity and macroevolution in 2003 ( Revista Chilena de Historia Natural).  He cited evidence that complex lifeforms developed complexity through gene duplication.   Once duplicated, the extra genes could mutate and take on new functions.  He also expressed support for Wrights (1982) idea that environmental opportunities allow new mutations that exploit the environmental opportunity.

Stephen C. Meyer, The Origin of Biological Information and the Higher Taxonomic Categories, Proceedings of the Biological Society of Washington, August 4, 2004. Meyer presents an argument for intelligent design as source of biological information. He examines many other hypotheses for the origin of the information, and concludes that all other hypotheses are less probable. Many peer reviewed papers are cited. The primary argument is that neither the genome nor the epigenome are capable of providing specific information on beneficial mutations that natural selection can act on. Critical  information determining biologic form is contained in other components of the cell.

Evolutionary Theory in the 1920s: The Nature of the “Synthesis”, Sahotra Sarkar, Philosophy of Science, 71 (December 2004) pp. 1215–1226: Abstract: “This paper analyzes the development of evolutionary theory in the period from 1918 to 1932. It argues that: (i) Fisher’s work in 1918 constituted a not fully satisfactory reduction of biometry to Mendelism; (ii) there was a synthesis in the 1920s but that this synthesis was mainly one of classical genetics with population genetics, with Haldane’s The Causes of Evolution being its founding document; (iii) the most important achievement of the models of theoretical population genetics was to show that natural selection sufficed as a mechanism for evolution; and (iv) Haldane formulated a prospective evolutionary theory in the 1920s whereas Fisher and Wright formulated retrospective theories of evolutionary history.”

The modern theory of biological evolution: an expanded synthesis, Ulrich Kutschera and Karl J. Niklas, Naturwissenschaften (2004) 91:255–276, Abstract excerpts: “In this article we first summarize the history of life on Earth and provide recent evidence demonstrating that Darwin’s dilemma (the apparent missing Precambrian record of life) has been resolved. --- In addition, we discuss the expansion of the modern synthesis, embracing all branches of scientific disciplines. It is concluded that the basic tenets of the synthetic theory have survived, but in modified form. These sub-theories require continued elaboration, particularly in light of molecular biology, to answer open-ended questions concerning the mechanisms of evolution in all five kingdoms of life.”

Evolution, Third Edition, Mark Ridley, Blackwell Publishing, 2004. A 700 page introductory textbook on evolution.  It assumes and abiotic origin of life and presents numerous hypothesis without favoring any.  It states that micro or macro evolution may or not be driven by the same process It presumes that macroevolution did happen, by whatever means, and presents many examples of macroevolution from the fossil record.  The progression from first cell to higher life forms, drive by natural selection, is presented without discussion of the sources of the variations that made it possible.

2005

Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, Sean B. Carroll, 2005:  This book, by a  molecular biologist, claimed that animal evolution proceeds mostly by modifying the way that regulatory genes control embryonic development. Those genes are based on a very old and highly conserved set of genes the author called the “toolkit”.  Nearly identical sequences can be found across the animal kingdom.  The author believes the genes are reused with little or no change to new function during development to form different body plans.  The gene signals may be given at different times during embryo development to form widely different effects on the adult form.  Carroll believed that this can explain how so many different body forms can be produced by relatively few structural genes.

Fisher’s Microscope and Haldane’s Ellipse, D. Waxman and J. J. Welch, vol. 166, no. 4 The American Naturalist October 2005: Abstract: “Fisher’s geometrical model was introduced to study the phenotypic size of mutations contributing to adaptation. However, as pointed out by Haldane, the model involves a simplified picture of the action of natural selection, and this calls into question its generality. In particular, Fisher’s model assumes that each trait contributes independently to fitness. Here, we show that Haldane’s concerns may be incorporated into Fisher’s model solely by allowing the intensity of selection to vary between traits. We further show that this generalization may be achieved by introducing a single, intuitively defined quantity that describes the phenotype prior to adaptation. Comparing the process of adaptation under the original and generalized models, we show that the generalization may bias results toward either larger or smaller mutations. The applicability of Fisher’s model is then discussed.”

The Plausibility of Life, Resolving Darwin’s Dilemma, Marc W. Kirchner and John C. Gerhart. Yale university Press, 2005. Amazon: “Offering daring new ideas about evolution, two highly respected biologists here tackle the central, unresolved question in the field―how have living organisms on Earth developed with such astounding variety and complexity? Marc Kirschner and John Gerhart draw on cutting-edge biological and medical research to provide an original solution to this longstanding puzzle.”

Soft Sweeps: Molecular Population Genetics of Adaptation From Standing Genetic Variation , Joachim Hermisson and Pleuni S. Pennings, Genetics 169: 2335–2352 (April 2005), Abstract: “A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario—standing variation vs. new mutations—is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of “soft sweeps,” where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.”

Darwinism versus Evo-Devo, Jeffrey H. Schultz, A Cultural History of Heredity III: 19th and Early 20th Centuries, . 2005, Max Planck Institute for the History of Science, pp 67-84. A review of the difference in the inheritance theories of Darwin and St. George Mivart (gradualism versus sudden change).

Genetic Variation: Polymorphisms and Mutations, Alan F Wright, Encyclopedia Of Life Sciences & 2005, John Wiley & Sons, Ltd, Abstract: “The amount of sequence variation in different regions of the human genome varies by an order of magnitude. Mutations give rise to all variation, but their survival in the genome is influenced by many factors including effects on reproductive fitness, human population history, chromosomal location and recombination rates.”

Gene regulatory networks for development, Michael Levine, and Eric H. Davidson, 4936–4942 PNAS April 5, 2005 vol. 102 no. 14.  The paper provides very detailed information about what was understood about the development of animal body plans in 2005.  Gene regulatory networks provide sequential instructions that direct tissue growth.

The Origin of Animal Body Plans, Douglas H. Erwin, From Evolving Form and Function: Fossils and Development: Proceedings of a symposium honoring Adolf Seilacher for his contributions to paleontology, in celebration of his 80th birthday. D.E.G. Briggs, ed., 2005. Abstract: “Economic historians make a useful distinction between inventions and innovations (inventions that succeed within an economy). Applying this distinction to the evolutionary novelties of the Cambrian metazoan radiation suggests many developmental inventions were necessary but insufficient as causes for the breadth of the diversification. Comparative developmental studies of modern animals are providing a detailed window into these developmental inventions, with the protostome–deuterostome ancestor, or urbilaterian, occupying a critical node at the origin of the bilaterian clades. Highly conserved developmental elements between vertebrates and arthropods indicate that there was considerable developmental complexity at this node, but the level of morphological complexity remains disputed. Such inventions do not, however, seem sufficient to generate the morphological breadth of the radiation of body plans. Here the primary factor was likely the construction of new ecospace through positive ecological feedback.”

Bushes in the Tree of Life,  Antonis Rokas , Sean B. Carroll, Rokas A, Carroll SB (2006) Bushes in the tree of life. PLoS Biol 4(11): e352. DOI: 10.1371/journal. pbio.0040352,  Excerpt: “Genome analyses are delivering unprecedented amounts of data from an abundance of organisms, raising expectations that in the near future, resolving the tree of life (TOL) will simply be a matter of data collection. However, recent analyses of some key clades in life’s history have produced bushes and not resolved trees. The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted. Here we examine how the combination of the spacing of cladogenetic events and the high frequency of independently evolved characters (homoplasy) limit the resolution of ancient divergences.”

Genomes, phylogeny, and evolutionary systems biology, Monica Medina,   6630–6635  PNAS May 3, 2005  vol. 102,  suppl. 1, Abstract; “With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics, and computer science are now known as systems biology. Here, I present an overview, with an emphasis on eukaryotes, of how the postgenomic era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.”

 

Sean B. Carroll, Evolution at Two Levels: On Genes and Form, PLoS Biology |www.plosbiology.org  July 2005 | Volume 3 | Issue 7 | e245, Excerpt: “Changes in the expression of an individual gene may evolve through alterations in cis-regulatory sequences or in the deployment and activity of the transcription factors that control gene expression, or both. --- These studies—highlighted below—have firmly eliminated coding sequences as a possible cause and thereby implicated regulatory sequence evolution at loci encoding pleiotropic transcription factors.--- The examples I have described demonstrate that both regulatory sequences and coding regions of the genome can and do contribute to the evolution of form. -- I argue that there is adequate basis to conclude that the evolution of anatomy occurs primarily through changes in regulatory sequences ---.”

Explanatory Unification and the Early Synthesis, Anya Plutynski , Brit. J. Phil. Sci. 56 (2005), 595–609, Abstract. “The object of this paper is to reply to Morrison’s ([2000]) claim that while ‘structural unity’ was achieved at the level of the mathematical models of population genetics in the early synthesis, there was explanatory disunity. I argue to the contrary, that the early synthesis effected by the founders of theoretical population genetics was unifying and explanatory both. Defending this requires a reconsideration of Morrison’s notion of explanation. In Morrison’s view, all and only answers to ‘why’ questions which include the cause or mechanism’ for some phenomenon count as explanatory. In my view, mathematical demonstrations that answer ‘how possibly’ and ‘why necessarily’ questions may also count as explanatory. The authors of the synthesis explained how evolution was possible on a Mendelian system of inheritance, answered skepticism about the sufficiency of selection, and thus explained why and how a Darwinian research program was warranted. While today we take many of these claims as obvious, they required argument, and part of the explanatory work of the formal sciences is providing such arguments. Surely, Fisher and Wright had competing views as to the optimal means of generating adaptation. Nevertheless, they had common opponents and a common unifying and explanatory goal that their mathematical demonstrations served.

The Plausibility of Life: Resolving Darwin's Dilemma, Marc W. Kirschner and John C. Gerhart, xvi + 314 pp. Yale University Press, 2005,  The book claims that the modern synthesis does not adequately explain the source of variation and requires revision. Abstract: “In the 150 years since Darwin, the field of evolutionary biology has left a glaring gap in understanding how animals developed their astounding variety and complexity. The standard answer has been that small genetic mutations accumulate over time to produce wondrous innovations such as eyes and wings. Drawing on cutting-edge research across the spectrum of modern biology, Marc Kirschner and John Gerhart demonstrate how this stock answer is woefully inadequate. Rather they offer an original solution to the longstanding puzzle of how small random genetic change can be converted into complex, useful innovations. In a new theory they call "facilitated variation," Kirschner and Gerhart elevate the individual organism from a passive target of natural selection to a central player in the 3-billion-year history of evolution. In clear, accessible language, the authors invite every reader to contemplate daring new ideas about evolution. By closing the major gap in Darwin's theory Kirschner and Gerhart also provide a timely scientific rebuttal to modern critics of evolution who champion "intelligent design."

The definition of life in the context of its origin. Y. N. Zhuravlev and V. A. Avetisov, Biogeosciences, 3, 281–291, 2006 www.biogeosciences.net/3/281/2006/  The paper observes that there are over 80 proposed scientific definitions of life, but none are generally accepted. It proposes yet another which is admittedly only a partial definition because the available information is limited.

Pattern pluralism and the Tree of Life hypothesis, W. Ford Doolittle* and Eric Bapteste, PNAS  February 13, 2007  vol. 104  no. 7  2043–2049, Abstract; “Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.”

Ventegodt, Soren, et al, “Human Development V: Biochemistry Unable to Explain the Emergence of Biological Form (Morphogenesis) and Therefore a New Principle as Source of Biological Information is Needed”, The Scientific World Journal (2006) 6, 1359–1367.  Briefly stated, the paper argues that there is no existing, plausible explanation for the detailed development of biological form. For example, existing chemistry based models cannot explain how each leg of a mammal grows to approximately the same length.

The proper place of hopeful monsters in evolutionary biology, Gunter Theißen, Theory in Biosciences 124 (2006):  This paper begins with a discussion of the inadequacies of the modern synthesis, including statements such as: “ maintaining that evolution must be gradual and that macroevolutionary patterns can be fully explained by the action of natural selection and adaptation to the environment alone, the Synthetic Theory made over-extended claims, and hence left the realm of science and developed into an ideology. … That all forms of life originated in a gradual way, therefore, might be considered an extremely interesting hypothesis, but in the natural sciences there is no such thing as a proven fact.”  There is also: “But given the problems the Synthetic Theory faces in explaining the modes and mechanisms of macroevolution biology should also consider alternative mechanisms, as long as they are accessible by scientific methods.” (Synthetic Theory same as MS)

Given the inability of the modern synthesis to adequately support evolution with a series of small, incremental changes, Theißen’s paper proposes revisiting the concepts of larger increments of change. It reviews the concepts of Goldschmidt and Gould, and suggests that descendants of “hopeful monsters” may be present on earth.  The subsequent discussion of various abrupt changes in plants and animals includes the turtle.  Theißen claims that a turtle shell could not evolve from a rib cage by micro evolutionary processes.

Macroevolution, Minimalism, and The Radiation of the Animals, Kim Sterelny: Essay for   David Hull and Michael Ruse (editors) Cambridge Companion to the Philosophy of Biology May 2006.  The essay considers the transition to multicellularity, the evolution of complexity, and sudden pulses of innovation, and concludes that the fundamentals of the modern synthesis are not adequate for explaining macroevolution.

Mutationism and the dual causation of evolutionary change, Arlin Stoltzfus, Evol Dev May-Jun 2006;8(3):304-17.  A review of the development of evolutionary theory after Darwin, the paper discusses the changing role of mutation in the modern synthesis, Abstract: “The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis view was a prevailing orthodoxy: under its influence, "evolution" was redefined as "shifting gene frequencies," that is, the sorting out of pre-existing variation without new mutations; and the notion that mutation-and-altered-development can exert a predictable influence on the course of evolutionary change was seen as heretical. Nevertheless, mutationist ideas re-surfaced: the notion of mutational determinants of directionality emerged in molecular evolution by 1962, followed in the 1980s by an interest among evolutionary developmental biologists in a shaping or creative role of developmental propensities of variation, and more recently, a recognition by theoretical evolutionary geneticists of the importance of discontinuity and of new mutations in adaptive dynamics. The synthetic challenge presented by these innovations is to integrate mutation-and-altered-development into a new understanding of the dual causation of evolutionary change--a broader and more predictive understanding that already can lay claim to important empirical and theoretical results--and to develop a research program appropriately emphasizing the emergence of variation as a cause of propensities of evolutionary change.”

Mutation Rate and the Cost of Complexity, Ralph Haygood Biology Department, Duke University,  Mol. Biol. Evol. 23(5):957–963. 2006, Abstract: “Two recent theoretical studies of adaptation suggest that more complex organisms tend to adapt more slowly. Specifically, in Fisher’s ‘‘geometric’’ model of a finite population where multiple traits are under optimizing selection, the average progress ensuing from a single mutation decreases as the number of traits increases—the ‘‘cost of complexity.’’ Here, I draw on molecular and histological data to assess the extent to which on a large phylogenetic scale, this predicted decrease in the rate of adaptation per mutation is mitigated by an increase in the number of mutations per generation as complexity increases. As an index of complexity for multicellular organisms, I use the number of visibly distinct types of cell in the body. Mutation rate is the product of mutational target size and population mutation rate per unit target. Despite much scatter, genome size appears to be positively correlated with complexity (as indexed by cell-type number), which along with other considerations suggests that mutational target size tends to increase with complexity. In contrast, effective population mutation rate per unit target appears to be negatively correlated with complexity. The net result is that mutation rate probably does tend to increase with complexity, although probably not fast enough to eliminate the cost of complexity.”

Evolution on rails: Mechanisms and levels of orthogenesis, Georgy S Levit  and L. Olsso, Nov 2006, Researchgate.  The authors reviewed the history of orthogenesis and explained how it was distinguished from Lamarckism.  They showed that it, in some countries, it was preferred over the modern synthesis throughout the first half of the twentieth century.  They then state that “the idea of evolutionary and developmental constraints, this crucial orthogenetic concept, was rediscovered and is now used in evolutionary development biology and paleobiology”, and “

At present there are a variety of concepts employing the idea of constraints: The "canalization" or "hardening"; "spontaneous order" or "crystallization of life"; "developmental biases"; "evolutionary channeling", "non-random production of variants" and many others.  Considering our definition of orthogenesis, many of these concepts can be classified as weak or strong versions of orthogenesis.”  The obvious implication is that evolution is not entirely random as held by the modern synthesis.

Sudden Origins: A General Mechanism of Evolution Based on Stress Protein Concentration and Rapid Environmental Change, Bruno Maresca and Jeffrey H. Schwartz, The Anatomical Record (Part B: New Anat.) 289b:38 – 46, 2006   Excerpt: “If severe stress disrupts DNA homeostasis during meiosis (gametogenesis), this could allow for the appearance of significant mutational events that would otherwise be corrected or suppressed.”

As scientific doubts about Darwinism increased during the second half of the twenties century, a proliferation of books defending Darwinism appeared.  An example is Michael Ruse’s Darwinism and Its Discontents (2006).  Ruse is a historian and philosopher with many publications about science.  Ruse reviewed the historical thinking related to origins of life, the fossil record, the mechanism of natural selection, and human evolution.  He also reviewed some material inconsistent with the modern synthesis, such as punctuated equilibrium.  Intending to present a robust defense of the modern synthesis, the only evidence he presented for macroevolution was the spotted moth and Darwin’s finches.  Roth may not be aware that both have been discredited within the scientific community.   There are only evidence of reversible variation within the respective gnomes, and do not prove macroevolution.  In the introduction to the book, Ruse claimed that “well-qualified and articulate evolutionary biologists . . . have been showing so visceral a hatred of Darwinian thinking that one suspects that their objections cannot be grounded purely in theory or evidence."  Ruse thereby implied that there cannot be legitimate, purely scientific doubts about Darwinism.  Apparently, he was unaware of the growing body of scientific evidence (as of 2006) that is not consistent with the modern synthesis

Theodosius Dobzhansky And The Synthetic Theory Of Evolution - 30 Years After The Death Of The “20th Century’s Darwin”, D. Marinković, Arch. Biol. Sci., Belgrade, 58 (3), 141-143, 2006. Excerpt: “Accepting as a basic theory of organic evolution Darwin’s theory of natural selection, D o b z h a n s k y (1937) emphasized that: (1) populations are the basic units of evolution; (2) fitness of specific genotypes determines the chance of increasing or decreasing their frequency in future generations; (3) differential reproduction rates, rather than survival rates, are of more importance for determination of the genetic constitution of a population; (4) balancing selections are the basic forces maintaining the genetic variability of a population. In the light of only these four postulates, it was now possible to explain the paradoxical effects of natural selection and other evolutionary factors, which result in a systematic increase of biological variation during processes of evolution, as well as in maintenance of genetic loads in natural populations. With his populational thinking Dobzhansky proved that Darwin’s evolutionary theory and Mendelian genetics are mutually supportive, and demonstrated that various other discoveries in paleontology, zoological systematics, and in botany are compatible with this approach.

Pictures of Evolution and Charges of Fraud Ernst Haeckel’s Embryological Illustrations, Nick Hopwood, Isis, 2006, 97:260–301, The History of Science Society.  Excerpt from abstract; “Comparative illustrations of vertebrate embryos by the leading nineteenth-century Darwinist Ernst Haeckel have been both highly contested and canonical. Though the target of repeated fraud charges since 1868, the pictures were widely reproduced in textbooks through the twentieth century.”

Molecular Clock: An Anti-neo-Darwinian Legacy,  Naoyuki Takahata, Genetics 176: 1–6 (May 2007), Excerpt: “It seems, however, that the most important implication of the molecular clock is concerned with the link between molecular and phenotypic evolution. This question has persisted since originally raised by Zuckerkandl and Pauling (1965). Published in the era of neoDarwinism when the importance of natural selection in evolution was overvalued, the article raised the contrasting view: ‘‘Many phenotypic differences may be the result of changes in the patterns of timing and rate of activity of structural genes rather than of changes in functional properties of the polypeptides as a result of changes in amino acid sequence’’

Thompson, B,. Neo-Darwinism: A Look At The Alleged Genetic Mechanism Of Evolution

 (2007). semanticscholar.org/: A microbiologist reviews the complex, simultaneous mutations required for a reptile to evolve into a mammal.

 

The rise and fall of Hox gene clusters,Denis Duboule, Development 134, 2549-2560 (2007) doi:10.1242/dev.001065.  The paper describes an anomaly in the organization of vertebrate genes. Abstract: “Although all bilaterian animals have a related set of Hox genes, the genomic organization of this gene complement comes in different flavors. In some unrelated species, Hox genes are clustered; in others, they are not. This indicates that the bilaterian ancestor had a clustered Hox gene family and that, subsequently, this genomic organization was either maintained or lost. Remarkably, the tightest organization is found in vertebrates, raising the embarrassingly finalistic possibility that vertebrates have maintained best this ancestral configuration. Alternatively, could they have co-evolved with an increased ‘organization’ of the Hox clusters, possibly linked to their genomic amplification, which would be at odds with our current perception of evolutionary mechanisms? When discussing the why’s and how’s of Hox gene clustering, we need to account for three points: the mechanisms of cluster evolution; the underlying biological constraints; and the developmental modes of the animals under consideration. By integrating these parameters, general conclusions emerge that can help solve the aforementioned dilemma.”

 

Innovation and robustness in complex regulatory gene networks,  S. Ciliberti, O. C. Martin, and A. Wagner, PNAS  August 21, 2007  vol. 104  no. 34  13591–13596. Discusses how gene networks can preserve a phenotype even when there are minor mutations.  Excerpt: “In summary, we have shown that networks with vastly different organizations can have the same phenotype. In contrast, two networks with completely unrelated phenotypes can be found very close to each other in genotype space, even though changing a genotype at random will often lead to highly similar phenotypes. This latter property, a genotype’s long ‘‘memory’’ of past phenotypes, is not self-evident.”

The Evolution of Organ Systems, A. Schmidt-Rhaesa, Published to Oxford Scholarship Online: September 2007. Abstract: “The field of systematics has developed remarkably over the last few decades. A multitude of new methods and contributions from diverse biological fields — including molecular genetics and developmental biology — have provided a wealth of phylogenetic hypotheses, some confirming traditional views and others contradicting them. There is now sufficient evidence to draw up a ‘tree of life’ based on fairly robust phylogenetic relationships. This book aims to apply these new phylogenies to an evolutionary interpretation of animal organ systems and body architecture. Organs do not appear suddenly during evolution: instead they are composed of far simpler structures. In some cases, it is even possible to trace particular molecules or physiological pathways as far back as pre-animal history. What emerges is a fascinating picture, showing how animals have combined ancestral and new elements in novel ways to form constantly changing responses to environmental requirements. The book starts with a general overview of animal systematics to set the framework for the discussion of organ system evolution. The chapters deal with the general organization, integument, musculature, nervous system, sensory structures, body cavities, excretory, respiratory and circulatory organs, the intestinal and reproductive system, and spermatozoa. Each organ system is presented with its function, the diversity of forms that are realized among metazoan animals, and the reconstruction of its evolution.”

McCarthy, E. M. 2008. On the Origins of New Forms of Life. macroevolution.net. McCarthy claims that Darwin was fundamentally wrong.  New lifeforms are not produced by gradual change, and they are not shaped by the environment.  He produced an alternate hypothesis called stabilization theory which he claims better explains physical observation of life, and especially the fossil record.  According to him, species appear suddenly by processes such as hybridization and then remain relatively unchanged until they become extinct.  He states that stabilization theory is consistent with the fossil record as is.  Darwinian evolution is not.  Darwinian evolution assumes the many presumably missing transition fossils cannot be observed because of imperfect preservation. According to McCarthy, they were never there.

Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution, Rick Durrett and Deena Schmidt, Genetics 180: 1501–1509 (November 2008). Abstract: “Results of Nowak and collaborators concerning the onset of cancer due to the inactivation of tumor suppressor genes give the distribution of the time until some individual in a population has experienced two prespecified mutations and the time until this mutant phenotype becomes fixed in the population. In this article we apply these results to obtain insights into regulatory sequence evolution in Drosophila and humans. In particular, we examine the waiting time for a pair of mutations, the first of which inactivates an existing transcription factor binding site and the second of which creates a new one. Consistent with recent experimental observations for Drosophila, we find that a few million years is sufficient, but for humans with a much smaller effective population size, this type of change would take .100 million years. In addition, we use these results to expose flaws in some of Michael Behe’s arguments concerning mathematical limits to Darwinian evolution.”

 

Evolution and Complexity: The Double-Edged Sword, Thomas Miconi, University of Birmingham, Artificial Life 14: 325 –344 (2008).  Abstract: “We attempt to provide a comprehensive answer to the question of whether, and when, an arrow of complexity emerges in Darwinian evolution. We note that this expression can be interpreted in different ways, including a passive, incidental growth, or a pervasive bias towards complexification. We argue at length that an arrow of complexity does indeed occur in evolution, which can be most reasonably interpreted as the result of a passive trend rather than a driven one. What, then, is the role of evolution in the creation of this trend, and under which conditions will it emerge? In the later sections of this article we point out that when certain proper conditions (which we attempt to formulate in a concise form) are met, Darwinian evolution predictably creates a sustained trend of increase in maximum complexity (that is, an arrow of complexity) that would not be possible without it; but if they are not, evolution will not only fail to produce an arrow of complexity, but may actually prevent any increase in complexity altogether. We conclude that, with regard to the growth of complexity, evolution is very much a double-edged sword.”

 

Network Evolution of Body Plans,  Koichi Fujimoto, Shuji Ishihara, and Kunihiko Kaneko, PLoS ONE,  1 July 2008 | Volume 3 | Issue 7 | e2772. Excerpt: “Evolutionary diversification of multi-cellular organisms largely depends on body plans, in which complex morphologies develop under the integrated control of multiple genes. The interaction among genes and gene products forms a regulatory network that orchestrates gene expression pattern to specify the morphologies. Mutational modification in gene regulation networks alters gene expression dynamics that provide a basis for morphogenetic diversity. A fundamental key to understanding evolutionary developmental biology is to elucidate how a gene network determines body plan, its diversity, and its potential to evolve.”

Speciation and Macroevolution Anya Plutynski, 2007: The essay claims that though much has been learned in the many decades since the modern synthesis was established, it is not in need of revision or replacement.  Macroevolution is nothing more that accumulated microevolution. The author is a professor of philosophy.

Scale And Hierarchy In Macroevolution, David Jablonski, Paleontology, Vol. 50, Part 1, 2007, pp. 87–109, Excerpt from abstract: “Scale and hierarchy must be incorporated into any conceptual framework for the study of macroevolution, i.e. evolution above the species level. Expansion of temporal and spatial scales reveals evolutionary patterns and processes that are virtually inaccessible to, and unpredictable from, short-term, localized observations. These larger-scale phenomena range from evolutionary stasis at the species level and the mosaic assembly of complex morphologies in ancestral forms to the non-random distribution in time and space of the origin of major evolutionary novelties, as exemplified by the Cambrian explosion and post-extinction recoveries of metazoans, and the preferential origin of major marine groups in onshore environments and tropical waters. Virtually all of these phenomena probably involve both ecological and developmental factors, but the integration of these components with macro evolutionary theory has only just begun.”

Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape Artem S Novozhilov, Yuri I Wolf and Eugene V Koonin, Biology Direct 2007, 2:24, Abstract excerpt: “The standard genetic code table has a distinctly non-random structure, with similar amino acids often encoded by codons series that differ by a single nucleotide substitution, typically, in the third or the first position of the codon. It has been repeatedly argued that this structure of the code results from selective optimization for robustness to translation errors such that translational misreading has the minimal adverse effect. Indeed, it has been shown in several studies that the standard code is more robust than a substantial majority of random codes. However, it remains unclear how much evolution the standard code underwent, what is the level of optimization, and what is the likely starting point.”

The national roots of evo– devo, S. F. Gilbert and G. S. Levit, Theory Biosci. (2007) 126:115–116, “The present Special Issue was conceived as a venue to publish the papers delivered to the first and founding meeting of the European Society for Evolutionary Developmental Biology in the frames of the Symposium devoted to the national traditions in the history and pre-history of evo–devo. This symposium attempted to return to see what it was that these earlier scientists had been studying and how their ideas might be put into dialogue with our own. New disciplines demand a re-connection to the old, and, evolutionary developmental biology, a science deeply involved in questions of origin, needs to establish the conditions of its own ancestry. It cannot let other disciplines decide for it who its progenitors are.”

The new mutation theory of phenotypic evolution, Masatoshi Nei, PNAS,  July 24, 2007 vol. 104 no. 30. The paper identifies which parts of the genome tend to be altered by mutations to provide variation. Excerpt from abstract: “Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments.”

The new biology: beyond the Modern Synthesis, Michael R Rose and Todd H Oakley, Biology Direct 2007, 2:30, Excerpt from abstract: “The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research during that century. The foundations of that "Modernist" biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century.”

Todd Grantham published Is Macroevolution More Than Successive Rounds Of Microevolution?  Vol. 50 of Paleontology (2007).  Based on a logical analysis of  reproduction, extinction, and the range living organisms occupy, he concluded that the processes of microevolution are not sufficient to explain macroevolution.  Grantham is a professor of philosophy at the College of Charleston.

Functional Versus Morphological Diversity in Macroevolution, Peter C. Wainwright, Annual Rev. Ecol. Evol. Syst. 2007. 38:381–401, Abstract: “Studies of the evolution of phenotypic diversity have gained momentum among neontologists interested in the uneven distribution of diversity across the tree of life. Potential morphological diversity in a lineage is a function of the number of independent parameters required to describe the form, and innovations such as structural duplication and functional decoupling can enhance the potential for diversity in a given clade. The functional properties of organisms are determined by underlying parts, but any property that is determined by three or more parts expresses many-to-one mapping of form to function, in which many morphologies will have the same functional property. This ubiquitous feature of organismal design results in surfaces of morphological variation that are neutral with respect to the functional property, and enhances the potential for simultaneously optimizing two or more functions of the system.”

Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach, Bor-Sen Chen and Wei-Sheng Wu, Evolutionary Bioinformatics 2007:3 245–262: “Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations.  … In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology.”

Origin of phenotypes: Genes and transcripts, Thomas R. Gingeras, 2007,  by Cold Spring Harbor Laboratory Press,  Excerpt: “---, the recent emergence of a large collection of unannotated transcripts with apparently little protein coding capacity, collectively called transcripts of unknown function (TUFs), has begun to blur the physical boundaries and genomic organization of genic regions with noncoding transcripts often overlapping protein-coding genes.”

Beneficial Mutation–Selection Balance and the Effect of Linkage on Positive Selection, Michael M. Desai and Daniel S. Fisher, Genetics 176: 1759–1798 ( July 2007), Excerpt: “To summarize our work, we have explored evolutionary dynamics when beneficial mutations are common and there are many present concurrently. We have laid out an analytical and conceptual framework for understanding how asexual populations accumulate beneficial mutations—the dynamics of adaptation in this extremely basic situation. Using this framework, we have demonstrated that the rate at which a population accumulates beneficial mutations does increase only slowly with population size or mutation rate beyond a certain point.”

Estimating the size of the human interactome, Michael P. H. Stumpf, et al, PNAS May 13, 2008 vol. 105 no. 19, 6959–6964, Excerpt: “After the completion of the human and other genome projects it emerged that the number of genes in organisms as diverse as fruit flies, nematodes, and humans does not reflect our perception of their relative complexity. Here, we provide reliable evidence that the size of protein interaction networks in different organisms appears to correlate much better with their apparent biological complexity.”

What, if Anything, Is an Evolutionary Novelty? Massimo Pigliucci, Philosophy of Science, 75 (December 2008) pp. 887–898, Excerpt: “while the modern synthesis has given us an account of genetic variation and of how it changes in populations over time, it has reached an impasse on the question of the origin and evolution of phenotypic novelties and organismal body plans. Since the MS has had several decades to try, it seems sensible to seriously explore some of the potential additions and see where they might lead us.”

Network Evolution of Body Plans, Koichi Fujimoto, Shuji Ishihara, Kunihiko Kaneko, PLoS ONE | 1 July 2008 | Volume 3 | Issue 7.  Excerpt: “The interaction among genes and gene products forms a regulatory network that orchestrates gene expression pattern to specify the morphologies. Mutational modification in gene regulation networks alters gene expression dynamics that provide a basis for morphogenetic diversity. A fundamental key to understanding evolutionary developmental biology is to elucidate how a gene network determines body plan, its diversity, and its potential to evolve.”

Duret, L. (2008) Neutral theory: The null hypothesis of molecular evolution. Nature Education 1(1):218, Excerpt; “In the decades since its introduction, the neutral theory of evolution has become central to the study of evolution at the molecular level, in part because it provides a way to make strong predictions that can be tested against actual data. The neutral theory holds that most variation at the molecular level does not affect fitness and, therefore, the evolutionary fate of genetic variation is best explained by stochastic processes. This theory also presents a framework for ongoing exploration of two areas of research: biased gene conversion, and the impact of effective population size on the effective neutrality of genetic variants. ---The evolution of living organisms is the consequence of two processes. First, evolution depends on the genetic variability generated by mutations, which continuously arise within populations. Second, it also relies on changes in the frequency of alleles within populations over time. --- The fate of those mutations that affect the fitness of their carrier is partly determined by natural selection. On one hand, new alleles that confer a higher fitness tend to increase in frequency over time until they reach fixation, thus replacing the ancestral allele in the population. This evolutionary process is called positive or directional selection. Conversely, new mutations that decrease the carrier's fitness tend to disappear from populations through a process known as negative or purifying selection. ---“

The Molecular Clock and Estimating Species Divergence, Simon Ho,  Nature Education 1(1):168 (2008), Excerpt: “The molecular clock hypothesis states that DNA and protein sequences evolve at a rate that is relatively constant over time and among different organisms. A direct consequence of this constancy is that the genetic difference between any two species is proportional to the time since these species last shared a common ancestor. Therefore, if the molecular clock hypothesis holds true, this hypothesis serves as an extremely useful method for estimating evolutionary timescales.”

A Scientific History and Philosophical Defense of the Theory of Intelligent Design, Journal for the Study of Beliefs and Worldviews, vol. 7 , Stephen C. Meyer, October 7, 2008, Excerpt: “Since 2005, the theory of intelligent design has been the focus of a frenzy of international media coverage, with prominent stories appearing in The New York Times, Nature, The London Times, The Independent (London), Sekai Nippo (Tokyo), The Times of India, Der Spiegel, The Jerusalem Post and Time magazine, to name just a few. And recently, a major conference about intelligent design was held in Prague (attended by some 700 scientists, students and scholars from Europe, Africa and the United States), further signaling that the theory of intelligent design has generated worldwide interest. But what is this theory of intelligent design, and where did it come from? And why does it arouse such passion and inspire such apparently determined efforts to suppress it?”

From Bad to Good: Fitness Reversals and the Ascent of Deleterious Mutations, Matthew C. Cowperthwaite, J. J. Bull1, Lauren Ancel Meyers, PLoS Computational Biology | www.ploscompbiol.org October 2006 | Volume 2 | Issue 10 | e141, Concluding paragraph: “In our study, deleterious mutations accumulated rapidly without impeding adaptation—a result counter to most theoretical predictions. We attribute our results, at least in part, to the fact that the fitness effect of a mutation can change dramatically and rapidly upon additional mutations. It remains unclear whether these reversions are sufficient not only to ensure fixation of the original mutation, but also to constitute major adaptive steps.”

Functional Versus Morphological Diversity in Macroevolution , Peter C. Wainwrigh, Annu. Rev. Ecol. Evol. Syst. 2007. 38:381-4. Abstract: “Studies of the evolution of phenotypic diversity have gained momentum among neontologists interested in the uneven distribution of diversity across the tree of life. Potential morphological diversity in a lineage is a function of the number of independent parameters required to describe the form, and innovations such as structural duplication and functional decoupling can enhance the potential for diversity in a given clade. The functional properties of organisms are determined by underlying parts, but any property that is determined by three or more parts expresses many-to-one mapping of form to function, in which many morphologies will have the same functional property. This ubiquitous feature of organismal design results in surfaces of morphological variation that are neutral with respect to the functional property, and enhances the potential for simultaneously optimizing two or more functions of the system.”

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution, Sean B. Carroll, Cell 134, July 11, 2008: Abstract: “Biologists have long sought to understand which genes and what kinds of changes in their sequences are responsible for the evolution of morphological diversity. Here, I outline eight principles derived from molecular and evolutionary developmental biology and review recent studies of species divergence that have led to a genetic theory of morphological evolution, which states that (1) form evolves largely by altering the expression of functionally conserved proteins, and (2) such changes largely occur through mutations in the cis-regulatory sequences of pleiotropic developmental regulatory loci and of the target genes within the vast networks they control.”

Darwin’s Ancestors: The Evolution of Evolution, Michael Rectenwald, 2008, Publisher

VictorianWeb. The author provides a detailed; twenty page review of the historical background of evolution.  Introduction: “Despite his unique contribution to evolutionary theory—the mechanism of natural selection—Charles Darwin can hardly be considered the first evolutionary theorist in history. It is generally acknowledged that organic evolution, or “transmutation” as it was called during his lifetime, was hardly a new idea when Darwin published On the Origin of Species in 1859. If ancient Indian and Greek thought is included, evolutionary ideas were thousands of years old by the time Darwin wrote. But even considering his own times, Darwin was not the evolutionary lone wolf that he is often made out to be. In fact, Darwin not only followed closely behind other transmutation theorists, but his own views met with a degree of skepticism not altogether unlike that which greeted his predecessors. As James Secord notes, the scientific consensus regarding natural selection “is a twentieth-century creation” and the “centrality given to Darwin” is also a recent phenomenon (Intro. to Vestiges x). As historians of science have begun to dismantle the “all-roads-lead-to-Darwin” consensus (Secord, Intro. to Vestiges x) by exploring its social, cultural and even ideological contingencies, an exploration of the evolutionary roads not taken promises to be an important and illuminating venture.’

The Distribution of Beneficial and Fixed Mutation Fitness Effects Close to an Optimum, Guillaume Martin and Thomas Lenormand, Excerpt from abstract: “In this article, we derive the distribution of beneficial mutation effects under a general model of stabilizing selection, with arbitrary selective and mutational covariance between a finite set of traits. We assume a well-adapted wild type, thus taking advantage of the robustness of tail behaviors, as in extreme value theory. We show that, under these general conditions, both beneficial mutation effects and fixed effects (mutations escaping drift loss) are beta distributed.”  --date?

The fixation probability of beneficial mutations , Z. Patwa and L. M. Wahl, J. R. Soc. Interface (2008) 5, 1279–1289.  Abstract excerpt: “The fixation probability, the probability that the frequency of a particular allele in a population will ultimately reach unity, is one of the cornerstones of population genetics. In this review, we give a brief historical overview of mathematical approaches used to estimate the fixation probability of beneficial alleles. We then focus on more recent work that has relaxed some of the key assumptions in these early papers, providing estimates that have wider applicability to both natural and laboratory settings.”

On the origins of novelty in development and evolution, Armin P. Moczek, BioEssays 30:432–447,  2008 Wiley Periodicals, Inc., Excerpt:  “The origin of novel traits is what draws many to evolutionary biology, yet our understanding of the mechanisms that underlie the genesis of novelty remains limited”.

Complexity in biology Exceeding the limits of reductionism and determinism using complexity theory, Fulvio Mazzocchi, EMBO reports VOL 9 | NO 1 | 2008, Current scientific methods are inadequate for systems as complex as living organisms.

The Origins of Form, Sean B. Carrol, Natural History Magazine, 2008 (https://www.naturalhistorymag.com).  When the modern synthesis was developed, biologists thought every life form had a unique set of genes.  The study of evolutionary development has shown that similar Hox genes are found in many different animals. For example, all vertebrates have very similar Hox genres.  The many different forms of vertebrates are not determined by unique genes, but by different expressions of  similar genes as the cells process the genetic information.

The Evolution of Complex Organs, T. Ryan Gregory, Evo Edu Outreach (2008) 1:358–389 DOI 10.1007/s12052-008-0076. The paper reviews the various possible forms of direct and indirect evolution, and then hypothesis that, while direct evolution of the eye is improbable, there are various ways in which indirect evolution might produce such a complex organ. A large variety of intermediate stages are proposed.

The Timetree of Life, S. Blair Hedges and Sudhir Kumar, editors, New York: Oxford University Press, 2009. The 550 page book attempts to synthesize an absolute timescale for all life on earth. Most chapters, by various authors, present timetrees for many different taxonomic groups using available molecular data.

Signature in the Cell: DNA and the Evidence for Intelligent Design, Stephen C. Meyer, June 23, 2009:  “Signature in the Cell is a defining work in the discussion of life’s origins and the question of whether life is a product of unthinking matter or of an intelligent mind. For those who disagree with ID, the powerful case Meyer presents cannot be ignored in any honest debate. For those who may be sympathetic to ID, on the fence, or merely curious, this book is an engaging, eye-opening, and often eye-popping read” — American Spectator and “Named one of the top books of 2009 by the Times Literary Supplement (London), this controversial and compelling book from Dr. Stephen C. Meyer presents a convincing new case for intelligent design (ID), based on revolutionary discoveries in science and DNA. Along the way, Meyer argues that Charles Darwin’s theory of evolution as expounded in The Origin of Species did not, in fact, refute ID. If you enjoyed Francis Collins’s The Language of God, you’ll find much to ponder—about evolution, DNA, and intelligent design—in Signature in the Cell. --- Amazon  promotion

Darwin’s warm little pond revisited: from molecules to the origin of life, Hartmut Follmann & Carol Brownson, Naturwissenschaften (2009) 96:1265–1292.  The paper assumes the spontaneous origin of life is possible and reviews two decades of related research.

Revisiting the Central Dogma in the 21st Century, James A. Shapiro, Natural Genetic Engineering and Natural Genome Editing: Ann. N.Y. Acad. Sci. 1178: 6–28 (2009). Abstract: “             Since the elaboration of the central dogma of molecular biology, our understanding of cell function and genome action has benefited from many radical discoveries. The discoveries relate to interactive multimolecular execution of cell processes, the modular organization of macromolecules and genomes, the hierarchical operation of cellular control regimes, and the realization that genetic change fundamentally results from DNA biochemistry. These discoveries contradict atomistic pre-DNA ideas of genome organization and violate the central dogma at multiple points. In place of the earlier mechanistic understanding of genomics, molecular biology has led us to an informatic perspective on the role of the genome. The informatic viewpoint points towards the development of novel concepts about cellular cognition, molecular representations of physiological states, genome system architecture, and the algorithmic nature of genome expression and genome restructuring in evolution.

Revolutions in Evolutionary Thought: Darwin and After. Renee Borges, Resonance , February 2009, Excerpt: “A progression of great thinkers led to Darwin. Who were these revolutionaries and what are the frontiers of modern evolutionary thought? Some of these questions are addressed in this article.”  

J. David Logan, A Primer on Population Genetics, August 11, 2009, Department of Mathematics, University of Nebraska Lincoln, “Population genetics forms the mathematical basis for the key ideas in the evolution of species: random variation and natural selection.”

The Darwinian revolution: Rethinking its meaning and significance, Michael Ruse, PNAS June 16, 2009 vol. 106 suppl. 1, 10040 –10047, Abstract; “The Darwinian revolution is generally taken to be one of the key events in the history of Western science. In recent years, however, the very notion of a scientific revolution has come under attack, and in the specific case of Charles Darwin and his Origin of Species there are serious questions about the nature of the change (if there was such) and the specifically Darwinian input. This article considers these issues by addressing these questions: Was there a Darwinian revolution? That is, was there a revolution at all? Was there a Darwinian revolution? That is, what was the specific contribution of Charles Darwin? Was there a Darwinian revolution? That is, what was the conceptual nature of what occurred on and around the publication of the Origin?”

Anya Plutynski , The Modern Synthesis, 2009, Encyclopedia of Philosophy, Taylor and Francis,-Abstract:  “Huxley coined the phrase, the “evolutionary synthesis” to refer to the acceptance by a vast majority of biologists in the mid-20th Century of a “synthetic” view of evolution. According to this view, natural selection acting on minor hereditary variation was the primary cause of both adaptive change within populations and major changes, such as speciation and the evolution of higher taxa, such as families and genera. This was, roughly, a synthesis of Mendelian genetics and Darwinian evolutionary theory; it was a demonstration that prior barriers to understanding between various subdisciplines in the life sciences could be removed. The relevance of different domains in biology to one another was established under a common research program. The evolutionary synthesis may be broken down into two periods, the “early” synthesis from 1918 through 1932, and what is more often called the “modern synthesis” from 1936-1947. The authors most commonly associated with the early synthesis are J.B.S. Haldane, R.A. Fisher, and S. Wright. These three figures authored a number of important synthetic advances; first, they demonstrated the compatibility of a Mendelian, particulate theory of inheritance with the results of Biometry, a study of the correlations of measures of traits between relatives. Second, they developed the theoretical framework for evolutionary biology, classical population genetics. This is a family of mathematical models representing evolution as change in genotype frequencies, from one generation to the next, as a product of selection, mutation, migration, and drift, or chance. Third, there was a broader synthesis of population genetics with cytology (cell biology), genetics, and biochemistry, as well as both empirical and mathematical demonstrations to the effect that very small selective forces acting over a relatively long time were able to generate substantial evolutionary change, a novel and surprising result to many skeptics of Darwinian gradualist views. The later “modern” synthesis is most often identified with the work of Mayr, Dobzhansky and Simpson. There was a major institutional change in biology at this stage, insofar as different subdisciplines formerly housed in different departments, and with different methodologies were united under the same institutional umbrella of “evolutionary biology.” Mayr played an important role as a community architect, in founding the Society for the Study of Evolution, and the journal Evolution, which drew together work in systematics, biogeography, paleontology, and theoretical population genetics.”

Darwin’s Other Mistake, Michael R. Rose and Theodore Garland, Jr., in Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments, edited by Theodore Garland, Jr., and Michael R. Rose, 2009.  The paper argues that, besides being wrong about inheritance, Darwin was also wrong about the very slow rate of evolution.  It claims that it can, at times, move quickly, and promotes laboratory experiments as proof.  Excerpts: “Darwin’s mistake about inheritance probably cost the field of evolutionary biology some decades of delay. --- Darwin’s other mistake also came from his gradualist preconceptions. He repeatedly emphasized that natural selection acts only by slow accretion. Darwin expected the action of selection within each generation to be almost imperceptible, even if thousands of generations of selection could evidently produce large differences between species: “natural selection will always act very slowly, often only at long intervals of time, and generally on only a very few of the inhabitants of the same region at the same time. ” (Darwin, Origin of Species, first ed., chap. 4).”

Peter J. Bowler, Evolution: The History of an Idea (Berkley: University of California, 3^rd edtn., revised, 2009).  The book is a length, historic review of how Darwinism changed the world view of life and geology.

How evolution guides complexity, Larry S. Yaeger, HFSP Journal Vol. 3, No. 5, October 2009, 328–339. The paper claims computer simulations can provide and understanding of natural selection that cannot be obtained from the fossil record. Abstract: “Long-standing debates about the role of natural selection in the growth of biological complexity over geological time scales are difficult to resolve from the paleobiological record. Using an evolutionary model—a computational ecosystem subjected to natural selection - - - we investigate evolutionary trends - - -. Our results suggest that evolution always guides complexity change, just not in a single direction. We also demonstrate that neural complexity correlates well with behavioral adaptation but only when complexity increases are achieved through natural selection, as opposed to increases generated randomly or optimized via a genetic algorithm."

The Evolution of Evolutionary Theory, by Massimo Pigliucci (philosophynow.org, 2009) begins by stating that “Unbeknownst to the majority of the public, evolutionary theory has already passed through three major modifications since Darwin, and is in the midst of a fourth stage of its evolution.”  Evolution 1.0 was Darwinism, 1.1 was neo-Darwinism which eliminated Lamarckism, 2.0 was a synthesis of Mendelism and neo Darwinism supported by statistical analysis, and 2.1 (the modern synthesis) “showed how mutation and natural selection can account for long-term changes in the fossil record;  how speciation, the origin of new species, naturally takes place in populations; and how selection can be demonstrated (i.e. observed) to take place in contemporary natural populations of plants and animals.”  Pigliucci identified recent discoveries that will eventually be included in 3.0, and claimed that all revisions and future revisions are merely refinements that are consistent with the fundamental assumptions in 1.0 as established by Darwin.

Genetic Redundancy: New Tricks for Old Genes, Ran Kafri, Michael Springer, and Yitzhak Pilpel, Cell 136, February 6, 2009 ©2009 Elsevier Inc. Contrary to the commonly held belief that duplicate genes are errors and available to facilitate mutation driven evolution, the paper claims that at least some duplicate genes perform a critical function in the cell as is. Abstract: “Many crucial components of signal transduction, developmental, and metabolic pathways have functionally redundant copies. Further, these redundancies show surprising evolutionary stability over prolonged time scales. We propose that redundancies are not just archeological leftovers of ancient gene duplications, but rather that synergy arising from feedback between redundant copies may serve as an information processing element that facilitates signal transduction and the control of gene expression.”

What is epigenesis? or Gene’s place in development,  A n d r e a s W e s s e l, Human  Ontogenetics, 2009. The paper claims that DNA does not contain all the information necessary to support life.  Excerpt: “Returning finally to the problem of information transmission during inheritance, we have so far considered the importance of the zygote in addition to that of the genome, but neglected another, third factor. Our epigenetic concept requires, if consistently applied to organisms whose early development takes place within a womb, a transmission of information via the specific maternal environment created. From a biological point of view this information is equal to genetic and cytoplasmic information.”

Survey And Summary : Darwinian evolution in the light of genomics, Eugene V. Koonin, Nucleic Acids Research, 2009, Vol. 37, No. 4 1011–1034. The paper claims that natural selection is not the sole guiding force for evolution as assumed by Darwin. Excerpt from conclusion: “The emerging landscape of genome evolution includes the classic, Darwinian natural selection as an important component but is by far more pluralistic and complex than entailed by Darwin’s straightforward vision that was solidified in the Modern Synthesis (16,184). The majority of the sequences in all genomes evolve under the pressure of purifying selection or, in organisms with the largest genomes, neutrally, with only a small fraction of mutations actually being beneficial and fixed by natural selection as envisioned by Darwin. Furthermore, the relative contributions of different evolutionarily forces greatly vary between organismal lineages, primarily, owing to differences in population structure.”

Darwin and Genetics. Brian Charlesworth and Deborah Charlesworth, Genetics 183: 757–766 (November 2009). The paper explores Darwin’s failure to understand the basics of inherited variations. Abstract; “Darwin’s theory of natural selection lacked an adequate account of inheritance, making it logically incomplete. We review the interaction between evolution and genetics, showing how, unlike Mendel, Darwin’s lack of a model of the mechanism of inheritance left him unable to interpret his own data that showed Mendelian ratios, even though he shared with Mendel a more mathematical and probabilistic outlook than most biologists of his time. Darwin’s own ‘‘pangenesis’’ model provided a mechanism for generating ample variability on which selection could act. It involved, however, the inheritance of characters acquired during an organism’s life, which Darwin himself knew could not explain some evolutionary situations. Once the particulate basis of genetics was understood, it was seen to allow variation to be passed intact to new generations, and evolution could then be understood as a process of changes in the frequencies of stable variants. Evolutionary genetics subsequently developed as a central part of biology. Darwinian principles now play a greater role in biology than ever before, which we illustrate with some examples of studies of natural selection that use DNA sequence data and with some recent advances in answering questions first asked by Darwin.”

In A framework for evolutionary systems biology (BMC Systems Biology 2009), Laurence Loewe envisioned the future of using computer simulations to examine the effect of small mutations on biological systems.  He stated that wet laboratory tests, which can detect the effects of large mutations, are not sensitive enough to determine the effects of small mutations.  He predicted that the large genome data base that is being developed will allow simulations to be more accurate than laboratory tests.

An Extended Synthesis for Evolutionary Biology,  Massimo Pigliucci, Acad. Sci. 1168: 218–228 (2009),  Excerpt from abstract: “In this essay I briefly trace the conceptual history of evolutionary theory from Darwinism to neo-Darwinism, and from the Modern Synthesis to what I refer to as the Extended Synthesis, a more inclusive conceptual framework containing among others evo–devo, an expanded theory of heredity, elements of complexity theory, ideas about evolvability, and a reevaluation of levels of selection.”

Darwin’s warm little pond revisited: from molecules to the origin of life, Hartmut Follmann & Carol Brownson, Naturwissenschaften (2009) 96:1265–1292, Excerpt from abstract: “All known cosmic and geological conditions and laws of chemistry and thermodynamics allow that complex organic matter could have formed spontaneously on pristine planet Earth about 4,000 mya. Simple gasses and minerals on the surface and in oceans of the early Earth reacted and were eventually organized in supramolecular aggregates and enveloped cells that evolved into primitive forms of life. Chemical evolution, which preceded all species of extant organisms, is a fact. In this review, we have concentrated on experimental and theoretical research published over the last two decades, which has added a wealth of new details and helped to close gaps in our previous understanding of this multifaceted field.”

Genetic Redundancy: New Tricks for Old Genes , Ran Kafri, Michael Springer  and Yitzhak Pilpel, Cell 136, February 6, 2009 ©2009 Elsevier Inc., Abstract: “Many crucial components of signal transduction, developmental, and metabolic pathways have functionally redundant copies. Further, these redundancies show surprising evolutionary stability over prolonged time scales. We propose that redundancies are not just archeological leftovers of ancient gene duplications, but rather that synergy arising from feedback between redundant copies may serve as an information processing element that facilitates signal transduction and the control of gene expression.”

The Problem Of Constraints On Variation, From Darwin To The Present, Igor Popov and  Ludus Vitalis, vol. XVII, num. 32, 2009, pp. 201-220.   Abstract. “The real number of variations is lesser than expected. There are no blue-eyed Drosophila, no viviparous birds or turtles, no hexapod mammals, etc. Such observations provoke non-Darwinian evolutionary concepts. Darwin tried rather unsuccessfully to solve the problem of the contradictions between his model of random variability and the existence of constraints. He tried to hide this complication citing abundant facts on other phenomena. The authors of the modern versions of Darwinism followed this strategy, allowing the question to persist.  Conclusion:  “The problem of the constraints on variation was not solved neither within the framework of the proper Darwin’s theory, nor within the framework of modern Darwinism. Both Darwin and the authors of the modern version of natural selection theory were sharply opposed to include concepts based on constraints, and tried to conceal or discredit any data on this subject. To ignore the problem, they refer to an abundance of facts from other fields of biology. This move has turn (caused?)  the constraint phenomenon to be considered a “special case”, insignificant to the general theory. In the works of the modern followers of Darwin, the contradiction of selection and constraints seem to be less sharp. Constraints are examined and in some special cases considered as the effective factor of evolution. This means an allowance into Darwinism through the back entrance. However, such “compromises” were limited to isolated instances within empirical studies. Otherwise, if recognized, the limitation to variation will always and everywhere affect evolution, and this means that evolution is a movement on rails, instead of wandering through the vast space of adaptation. If that is the case, selection should be considered a destructive force. Moreover, such a standpoint is not Darwinism anymore, it is orthogenesis, and it cannot be included into the Darwinian paradigm. Any compromise between both positions is hardly possible now, because the tendency to favor at any price selectionistic explanations for evolutionary phenomena dominates biology.”

Darwin and Mendel: Evolution and genetics Nelio Bizzo and Charbel El-Hani, June 2009, Journal of biological education 43(3):108-114: Abstract excerpt: “We intend to review some research on the history of biology, attempting to show that, even if Darwin had had notice of Mendel’s works – which we think he did – he would not have changed his views on heredity.” The paper goes on to say that, although Darwin maintained an incorrect model of heredity, “To build a model of natural selection, it does not really matter what are the origins of variation.”

 

As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates, Thomas Wilke, Roland Schultheiß, and Christian Albrecht , Amer. Malac. Bull. 27: 25-45 (2009), Abstract excerpt: “Biologists have used a wide range of organisms to study the origin of taxa and their subsequent evolutionary change in space and time. One commonly used tool is the molecular clock approach, relating substitution rates of nucleotide or amino acid sequences to divergence times. The accuracy of the molecular clock, however, has long been subject to controversy, and numerous papers have addressed problems associated with estimating divergence times. Some workers pointed out a striking imbalance between sophisticated software algorithms used for molecular clock analyses on the one hand, and the poor data on the other hand”

Darwin’s bridge between microevolution and macroevolution, David N. Reznick & Robert E. Ricklefs,  Nature|Vol 457|12 February 2009, Excerpt: “Darwin’s proposal carries a more general message for contemporary discussions of macroevolution, namely that microevolution alone cannot explain macroevolution. Understanding macroevolution requires the integration of ecology, evolution and the role of history in shaping the diversification or decline of lineages.”

Evolutionary preservation of redundant duplicated genes, David C. Krakauer and Martin A. Nowak, Cell & Developmental Biology, Vol 10, 1999: pp. 555]559, Abstract, “Gene duplication events produce both perfect and imperfect copies of genes. Perfect copies are said to be functionally redundant when knockout of one gene produces no ‘scoreable’, phenotypic effects. Preserving identical, duplicate copies of genes is problematic as all copies are prone to accumulate neutral mutations as pseudogenes, or more rarely, evolve into new genes with novel functions. We summarize theoretical treatments for the invasion and subsequent evolutionary modification of functionally redundant genes. We then consider the preservation of functionally identical copies of a gene over evolutionary time. We present several models for conserving redundancy: asymmetric mutation, asymmetric efficacy, pleiotropy, developmental buffering, allelic competition and regulatory asymmetries. In all cases, some form of symmetry breaking is required to maintain functional redundancy indefinitely.”

The population genetics of beneficial mutations, H. Allen Orr, Phil. Trans. R. Soc. B (2010) 365, 1195–1201, Abstract: “The population genetic study of advantageous mutations has lagged behind that of deleterious and neutral mutations. But over the past two decades, a number of significant developments, both theoretical and empirical, have occurred. Here, I review two of these developments: the attempt to determine the distribution of fitness effects among beneficial mutations and the attempt to determine their average dominance. Considering both theory and data, I conclude that, while considerable theoretical progress has been made, we still lack sufficient data to draw confident conclusions about the distribution of effects or the dominance of beneficial mutations.”

Mapping the Tree of Life: Progress and Prospects, Norman R. Pace, Microbiology and Molecular Biology Reviews, Dec. 2009, p. 565–576 Vol. 73, No. 4 1092-2172/09, American Society for Microbiology. Introduction: “Gene sequence variation between different organisms provides a metric for biological diversification. Sequence variation can also serve as the basis for inference of the patterns of evolution from precellular life until now. The intent of this article is to assess critically our current understanding of life’s phylogenetic diversity on a large scale. My view is from the molecular standpoint, mainly from the perspective of rRNA phylogeny. A molecular perspective on life’s diversity and evolution is only now unfolding, and there is much controversy and paradox, only some of which I can address here. All molecular phylogenetic trees have systematic limitations that cloud our view of the deeper branches in the tree of life (ToL). Consequently, I discuss the building of phylogenetic trees and emphasize the intrinsic limitations of any results. Progress toward assembly of a universal phylogenetic tree of life also relies on how comprehensive is our knowledge of the extent and the richness of life’s diversity. Therefore, I show how the recent explosion of environmental sequences has heavily influenced the patterns seen in the trees. I conclude that we have in place the outlines of a universal tree of life, but the details of the patterns of deep evolution in all the phylogenetic domains remain obscure.”

2010

Evolutionary Chance Mutation: A Defense of the Modern Synthesis’ Consensus View, Francesca Merlin, Philos Theor Biol (2010) 2:e103, Abstract:  “One central tenet of the Modern Evolutionary Synthesis (1930s-1950s), and the consensus view among biologists until now, is that all genetic mutations occur by “chance” or at “random” with respect to adaptation. However, the discovery of some molecular mechanisms enhancing mutation rate in response to environmental conditions has given rise to discussions among biologists, historians and philosophers of biology about the “chance” vs “directed” character of mutations (1980s-2000s). In fact, some argue that mutations due to a particular kind of mutator mechanisms challenge the Modern Synthesis because they are produced when and where needed by the organisms concerned. This paper provides a defense of the Modern Synthesis’ consensus view about the chance nature of all genetic mutations by reacting to Jablonka and Lamb’s analysis of genetic mutations (2005) and the explicit Lamarckian flavor of their arguments. I argue that biologists can continue to talk about chance mutations according to what I call and define as the notion of “evolutionary chance,” which I claim is the Modern Synthesis’ consensus view and a reformulation of Darwin’s most influential idea of “chance” variation. Advances in molecular genetics are therefore significant but not revolutionary with respect to the Modern Synthesis’ paradigm.”

Controversies on the origin of life, Juli Peretó, International Microbiology (2005) 8:23-31 www.im.microbios.org:  This paper summarizes the many possibilities that have been pursued to explain the spontaneous origin of life.  It shows that there is considerable, ongoing debate over what the exact form of the first life was and how it functioned.  It does not appear that all the research conducted to date has brought science any closer to the answer for the deeper question over how it may have begun.

Scientists recreated a key step for the origin of life at hydrothermal vents, Cassie Freund, January 26, 2010, Wakfield University, https://massivesci.com/articles/origin-of-life-deep-sea-vents-hydrothermal-chemistry/. The article supports the hypothesis that life may have begun in hydrothermal ocean vents.

Evolutionary Novelty and the Evo-Devo Synthesis: Field Notes , Ingo Brigandt and Alan C. Love. Evol Biol (2010) 37:93–99,     Abstract: “Accounting for the evolutionary origins of morphological novelty is one of the core challenges of contemporary evolutionary biology. A successful explanatory framework requires the integration of different biological disciplines, but the relationships between developmental biology and standard evolutionary biology remain contested. There is also disagreement about how to define the concept of evolutionary novelty. These issues were the subjects of a workshop held in November 2009 at the University of Alberta. We report on the discussion and results of this workshop, addressing questions about (i) how to define evolutionary novelty and understand its significance, (ii) how to interpret evolutionary developmental biology as a synthesis and its relation to neo Darwinian evolutionary theory, and (iii) how to integrate disparate biological approaches in general.”

Pocheville, A. (2010) ‘What Niche Construction is (not)’, in Pocheville, A., La Niche Ecologique: Concepts, Modèles, Applications. (Thèse de Doctorat). Paris: Ecole Normale Supérieure Paris, pp. 39–124. doi: 10.13140/RG.2.1.3160.7848. http://hal.upmc. fr/tel-00715471/. Excerpt from abstract: For the past three decades, evolutionary theory has delivered a growing movement “that has sought a re-conceptualization of adaptation by placing emphasis on niche construction” (Laland 2004, 316). Niche construction is the process whereby organisms, through their metabolism, activities, choices etc, modify the selection pressures to which their or other’s populations are exposed (Odling-Smee et al. 2003, 419). Thus to the proponents of this movement, “there are in fact two logically distinct routes to the evolving match between organisms and their environments: either the organism changes to suit the environment, or the environment is changed to suit the organism.” (ibid., 18). Taking niche construction into account should lead to a new, extended, evolutionary theory.  In this chapter, I investigate the organism-environment symmetry introduced by niche construction, in particular as regards adaptation, and how niche construction theory introduces novelty in evolutionary biology. I argue that niche construction reduces to classical natural selection except in a new, special case: when construction and natural selection processes interact on commensurate time-scales. This case represents a new field for empirical and theoretical investigations. I call this ‘niche interaction’.”

A formal test of the theory of universal common ancestry, Douglas L. Theobald, Nature Vol 465|13 May 2010| doi:10.1038/nature09014, Abstract excerpt: “I test UCA by applying model selection theory to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.”

An Outline of the Fodor & Piattelli-Palmarini Argument against Natural Selection, Norbert Hornstein,  Biolinguistics 4.4: 382–384, 2010     Jerry Fodor and Massimo Piattelli-Palmarini have recently argued that the theory of natural selection (NS) fails to explain how evolution occurs (Fodor & PiattelliPalmarini 2010; F&PP). Their argument is not with the fact of evolution but with the common claim that NS provides a causal mechanism for this fact. Their claim has been greeted with considerable skepticism, if not outright hostility.1 Despite the rhetorical heat of much of the discussion, I do not believe that critics have generally engaged the argument that F&PP have actually presented. It is clear that the validity of F&PP’s argument is of interest to biolinguists. Indeed, there has been much discussion of late concerning the evolution of the faculty of language and what this implies for the structure of Universal Grammar. To facilitate evaluation of F&PP’s proposal, the following attempts to sketch a reconstruction of their argument that, to my knowledge, has not been considered.

Contemporary Debates in Philosophy of Biology, Edited by Francisco J. Ayala and Robert Arp, Wiley Blackwell, 2010. The 360 page book is a collection of essays various topics on biology and evolution written by a variety of authors.

Darwin's error? Patrick Matthew and the catastrophic nature of the geologic record, Michael R. Rampino , Historical Biology 23:2-3 , Pages 227-230, 2010, A challenge to Darwin’s concept of gradualism. Abstract: “In 1831, the Scottish horticulturalist Patrick Matthew (1790–1874) published a clear statement of the law of natural selection in an Appendix to his book Naval Timber and Arboriculture, which both Darwin and Wallace later acknowledged. Matthew, however, was a catastrophist, and he presented natural selection within the contemporary view that relatively long intervals of environmental stability were episodically punctuated by catastrophic mass extinctions of life. Modern studies support a similar picture of the division of geologic time into long periods of relative evolutionary stability ended by sudden extinction events. Mass extinctions are followed by recovery intervals during which surviving taxa radiate into vacated niches. This modern punctuated view of evolution and speciation is much more in line with Matthew's episodic catastrophism than the classical Lyellian–Darwinian gradualist view.”

Why was Darwin’s view of species rejected by twentieth century biologists?, James Mallet, Biol Philos (2010) 25:497–527, Abstract excerpts: “Why then, in the 1930s and 1940s, did Dobzhansky, Mayr and others argue that Darwin failed to understand species and speciation? Mayr and Dobzhansky argued that reproductively isolated species were more distinct and ‘real’ than Darwin had proposed. Believing species to be inherently cohesive, Mayr inferred that speciation normally required geographic isolation, an argument that he believed, incorrectly, Darwin had failed to appreciate. … Today, abundant genetic markers are available and widely used to delimit species, for example using assignment tests: genetics has replaced a Darwinian reliance on morphology for detecting gaps between species.”

Evolution, the Extended Synthesis was edited by Massimo Pigliucci and Gerd B. Müller in 2010. Citing numerous discoveries made during the three quarters of a century after the Modern Synthesis was established, they argue that evolutionary theory must be updated, just as the Moderns Synthesis updated the theories of Mendel and Darwin.  They argue that, because the science of evolution has changed very slowly, and has become incredibly more complex, many biologists are not aware of the deficiencies in the Modern Synthesis. (chapter downloads available at https://muse.jhu.edu/book/22140)

Origins, evolution, and phenotypic impact of new genes, Henrik Kaessmann, 20:1313–1326 2010 by Cold Spring Harbor Laboratory Press, Excerpt: “ Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. “

 

Hox genes and regional patterning of the vertebrate body plan, Moises Mallo, Deneen M. Wellik and Jacqueline Deschamps, Developmental Biology 344 (2010) 7–15. Excerpts:  “The present overview of recent progress on the role of Hox genes in vertebrate embryonic morphogenesis (mostly the mouse) has focused on three major recent discoveries that shed new light on Hox function. First, the recently uncovered concept that some Hox genes confer properties to a collection of structures within a given anatomical region has gained wider and wider support by both loss- and gain-of function studies.--- A second important area of recent progress in the Hox field that we have covered in this review is an insight into the mechanism of action of regional patterning by Hox genes. --- The third recent advance in the molecular genetics of Hox gene function during vertebrate development that we review here concerns the involvement of these genes in controlling body axis length. Hox genes thus appear as regulators of both body length body shape.”

 

Jerry Fodor and Massimo Piattelli-Palmarini published What Darwin Got Wrong in 2010.  They claimed that Darwin’s theory overestimates the contribution of the environment to natural selection while ignoring the effect of variables within the living organisms.  The book received mixed reviews, with Jerry Coyne attacking it as "a profoundly misguided critique of natural selection” and Mary Midgley supporting it as "an overdue and valuable onslaught on neo-Darwinist simplicities". William Dembski also provided a favorable review.

Biology’s First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems, Daniel W. McShea and Robert N. Brandon, U. of Chicago Press, 2010.  The book introduces and attempts to support a concept named Biology’s first Law” which states:  “In any evolutionary system in which there is variation and heredity, there is a tendency for diversity and complexity to increase, one that is always present but may be augmented or opposed by natural selection, other forces, or constraints working on diversity and complexity’.  The authors carefully establish a specific definition of “complexity” as pure complexity which depends on  “number of part types” or “degree of differentiation among parts”. It is not to be confused with the common definition of complexity.

Hierarchical evolution of animal body plans, Jiankui He, Michael W. Deem, Developmental Biology 337 (2010) 157–161.  Excerpt: “We found that the genes which determine the phylum and superphylum characters evolve slowly, while those genes which determine the classes, families, and speciation evolve more rapidly. This result furnishes genetic support to the hypothesis that the hierarchical structure of developmental regulatory networks provides an organizing structure which guides the evolution of aspects of the body plan.”

Chapter 13 Genetic Redundancies and Their Evolutionary Maintenance, Jianzhi Zhang, in Evolutionary Systems Biology, Advances in Experimental Medicine and Biology 751, O.S. Soyer (ed), 2012, Excerpt: “I show that genetic redundancies are highly abundant. While some of them may be evolutionarily transient, many are stable. The majority of the stable redundancies are likely to have been selectively kept, not because of their potential benefits in regard to future deleterious mutations, but because of their actual benefits at present or in the recent past. The rest are probably preserved by selection on no redundant pleiotropic functions.”

Evolutionary Developmental Biology (Evo-Devo): Past, Present, and Future, Brian K. Hall, Evo Edu Outreach (2012) 5:184–193, Published online: 8 June 2012 # Springer Science+Business Media, LLC 201. The paper provides a historical review of the literature on evo devo. It points out that Darwin believed development has a role in evolution, but it was not included in the modern synthesis.  Since recent research shows Darwin’s assumption was correct, the modern synthesis is incomplete and in need of revision.

The population genetics of mutations: good, bad and indifferent, Laurence Loewe and William G. Hill, Phil. Trans. R. Soc. B (2010) 365, 1153–1167, Extract from abstract: “We review current knowledge on mutation rates and their harmful and beneficial effects on fitness and then consider theories that predict the fate of individual mutations or the consequences of mutation accumulation for quantitative traits. Many advances in the past built on models that treat the evolution of mutations at each DNA site independently, neglecting linkage of sites on chromosomes and interactions of effects between sites (epistasis). We review work that addresses these limitations, to predict how mutations interfere with each other”

How Did Insect Metamorphosis Evolve?, Ferris Jabr, Scientific American, August 10, 2012.  Addressing a challenging topic for evolutionary theory, the paper suggests that natural selection favored metamorphosis because the young do not compete with the adults for food.  Because it is therefore so very advantageous, about half the animals on earth are insects that go through metamorphosis. The author proposed that metamorphism began when immature embryos hatched and survived.

Self-organization, Natural Selection, and Evolution: Cellular Hardware and Genetic Software, Brian R. Johnson and Sheung Kwan Lam, BioScience , December 2010 / Vol. 60 No. 11:  All of the information for life is not contained in the DNA.  The genes do not code for the construction of cells, and the cell must be inherited.  The cell is completely independent of the DNA, is incredibly complex, and must be inherited.  Self-organizing processes within the cell, not currently understood, may introduce spontaneous formation of variations that natural selection can act on.  Selection determines the direction of evolution, but self-organizing processes within the sell (independent of DNA mutations) contribute to the variations offered for selection.

Mutation and the evolution of recombination, N. H. Barton, Phil. Trans. R. Soc. B (2010), Abstract: “Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fueled by new favorable mutations. Recombination is favored if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill–Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favorable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.”

Laws of biology: why so few? Pawan K. Dhar and Alessandro Giuliani, Syst Synth Biol (2010) 4:7–13, Excerpt: “Here, we present an approach as old as Mendel that could help uncover fundamental organizing principles in biology. Our approach essentially consists of identifying constants at various levels and weaving them into a hierarchical chassis. As we identify and organize constants, from pair-wise interactions to networks, our understanding of the fundamental principles in biology will improve, leading to a theory in biology.”

Evolution and the Origin of Biological Information, Dennis Venema, March 10, 2011, online at biologos:  The paper refutes publications by Stephen Meyer claiming that the modern synthesis cannot explain the origin of complex lifeforms. It claims that a long term experiment with bacteria has shown that random mutation and natural selection can produced complex, specified, information.  --- Meyer refutes this at https://evolutionnews.org/2011/10/of_molecules_and_straw_men_a_r/    and again at https://evolutionnews.org/2011/10/responding_to_venemas_response/

Reinventing Richard Goldschmidt: Reputation, Memory, and Biography, Michael Dietrich, Journal of the History of Biology, Feb. 2011.  Abstract; “Richard Goldschmidt was one of the most controversial biologists of the mid-twentieth century. Rather than fade from view, Goldschmidt’s work and reputation has persisted in the biological community long after he has. Goldschmidt’s longevity is due in large part to how he was represented by Stephen J. Gould. When viewed from the perspective of the biographer, Gould’s revival of Goldschmidt as an evolutionary heretic in the 1970s and 1980s represents a selective reinvention of Goldschmidt that provides a contrast to other kinds of biographical commemorations by scientists.”

Biological Information—Definitions from a Biological Perspective, Jan Charles Biro, Information 2011, 2, 117-139; doi:10.3390/info2010117. Conclusion: “The science concerning biological information is very young. DNA was discovered in 1953 (Wilkins, Crick and Watson), the genetic code in 1961 (Nirenberg and Matthaei), protein sequencing in 1951 (Sanger), effective nucleic acid sequencing in 1977 (Sanger); the first sequence database was published in 1965 (Dayhoff), and human genome sequencing was completed in 2003 (led by Collins and Venter). Bioinformatics, a new interdisciplinary science field, probably emerged in 1981 when Smith & Waterman described their fundamental equation for sequence similarity searches [18]. This field has become fruitful during the past 10 years or so. The first generation of bio-informatitians—mostly young scientists from a biological or computational background—will have to face the hard reality that bioinformatics, if it is carried out properly, is not the ‘wet variant’ of the well-developed field of physical informatics and communication sciences. This is an entirely new way of thinking about information. Bioinformatics is somewhat disadvantaged compared with physical or mathematical informatics. Scientists working with the latter categories usually have an idea of what are they working with and often know that the message in question (even if coded) is meaningful, i.e., it is information. Bioinformatitians do not have this luxury. The human genome contains 3 × 109 bases (letters of a four letters alphabet) which are approximately 60 gigabits of ‘information’ (uncompressed). We have reason to suppose that this is important biological information as it has allowed the species to exist for at least 35,000 years and it is carefully preserved from generation to generation. However, we have to learn the language of life (Francis Collins calls it the “Language of God” [19]) and the biological meaning of DNA and protein sequences to understand biological communication. Understanding produces information from data and knowledge from information.”

Levit, Georgy S. and Hoßfeld, Uwe, Darwin without borders? Looking at ‘generalised Darwinism’ through the prism of the ‘hourglass model’,Theory Biosci. DOI 10.1007/s12064-011-0138-8, Nov., 2011. The paper summarizes the history of Darwinism, from the initial introduction, through the many years of challenges, the eventual formation of the modern synthesis, and lingering uncertainties.

Darwin's error? Patrick Matthew and the catastrophic nature of the geologic record, Michael R. Rampino , Historical Biology An International Journal of Paleobiology, Volume 23, 2011 - Issue 2-3, Pages 227-230. Abstract: In 1831, the Scottish horticulturalist Patrick Matthew (1790–1874) published a clear statement of the law of natural selection in an Appendix to his book Naval Timber and Arboriculture, which both Darwin and Wallace later acknowledged. Matthew, however, was a catastrophist, and he presented natural selection within the contemporary view that relatively long intervals of environmental stability were episodically punctuated by catastrophic mass extinctions of life. Modern studies support a similar picture of the division of geologic time into long periods of relative evolutionary stability ended by sudden extinction events. Mass extinctions are followed by recovery intervals during which surviving taxa radiate into vacated niches. This modern punctuated view of evolution and speciation is much more in line with Matthew's episodic catastrophism than the classical Lyellian–Darwinian gradualist view.

Chance and Necessity in Eye Evolution, Walter J. Gehring, Genome Biol. Evol. 3:1053–1066. Excerpt: “The relatively simple prototypic eye postulated by Darwin has been found in flat worms and in many trochophora larvae. The discovery of Pax6 as a master control gene for eye development strongly supports the idea that the various eye types originated monophyletically from such a prototype. What is still surprising is the rapidity of eye evolution, because compound eyes with over 3,000 ommatidia were discovered in the early Cambrium, some 515 Ma, in early arthropods.”

Biological Information, Molecular Structure, and the Origins Debate Jonathan K. Watts, Perspectives on Science and Christian Faith, Volume 63, Number 4, December 2011. Abstract: “Biomolecules contain tremendous amounts of information; this information is “written” and “read” through their chemical structures and functions. A change in the information of a biomolecule is a change in the physical properties of that molecule—a change in the molecule itself. It is impossible to separate the information contained in biomolecules from their structure and function. For molecules such as DNA and RNA, new information can be incorporated into the sequence of the molecules when that new sequence has favorable structural and functional properties. New biological information can arise by natural processes, mediated by the interactions between biomolecules and their environment, using the inherent relationship between structure and information. This fact has important implications for the generation of new biological information and thus the question of origins.” Excerpt from conclusion: “We must be careful when comparing biological information to familiar forms of information such as text or computer code. Biological information is not abstract; it is intimately tied to the structure and function of biomolecules. As such, the biological information in cells can increase through natural processes. Perhaps the first cell was created out of nothing—but the high information content of modern cells does not prove this “special creation” of the first life. Another option is that processes closely or distantly analogous to SELEX (Systematic Evolution of Ligands by Exponential enrichment) could have been used to increase the amount of information in a primitive replicating system, although science has not yet identified such a system.”

The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations. Etienne Joly Toulouse, Academia.com, December 2011. Excerpt: “Among the myriad of reviews and articles that have been written about “The Origin of Species” by Charles Darwin, a very large proportion underlines the fact that, despite the title of his book, what Darwin established 150 years ago was the mechanism of adaptive evolution by the process of natural selection, but that he failed to provide answers to the many questions that surround the origin of species. One of the important reasons for this failure was related to an issue to which he alluded to repeatedly in his book, which is that species are basically impossible to define.”

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability,  Kirsten H. ten Tusscher and Paulien Hogeweg, PLoS Computational Biology , 1 October 2011 | Volume 7 | Issue 10.  Authors Summary: “An important question in evolutionary developmental biology is how the complex organisms we see around us have evolved, and how this complexity is encoded in their DNA. An often heard statement is that the gene regulatory networks underlying developmental processes are modular; that is, different functions are carried out by largely independent network parts. It is argued that this network modularity allows both for robust functioning and evolutionary tinkering, and that selection thus produces modular networks. Here we use a simulation model for the evolution of animal body plan patterning to investigate these ideas.

Natural Genetic Engineering: Intelligence & Design in Evolution? David W Ussery, Ussery Microbial Informatics and Experimentation 2011, 1:11. Abstract: “There are many things that I like about James Shapiro’s new book “Evolution: A View from the 21st Century” (FT Press Science, 2011). He begins the book by saying that it is the creation of novelty, and not selection, that is important in the history of life. In the presence of heritable traits that vary, selection results in the evolution of a population towards an optimal composition of those traits. But selection can only act on changes - and where does this variation come from? Historically, the creation of novelty has been assumed to be the result of random chance or accident. And yet, organisms seem ‘designed’. When one examines the data from sequenced genomes, the changes appear NOT to be random or accidental, but one observes that whole chunks of the genome come and go. These ‘chunks’ often contain functional units, encoding sets of genes that together can perform some specific function. Shapiro argues that what we see in genomes is ‘Natural Genetic Engineering’, or designed evolution: “Thinking about genomes from an informatics perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a select-biased random walk through limitless space of possible DNA configurations””.

The Myth of the Natural Origin of Life, Lee M Spetner,  http://www.sciencevsevolution.org 2010 (approximate); The author presents arguments  claiming the peppered moth and antibiotic resistance bacteria are not legitimate examples of macroevolution because no new information was created. Various color patterns already existed in the standing variation of the peppered moth, and the bacterium actually lost information to become antibiotic resistant.

Diminishing Returns From Beneficial Mutations and Pervasive Epistasis Shape the Fitness Landscape for Rifampicin Resistance in Pseudomonas ,  R. C. MacLean, G. G. Perron,  and A. Gardner, Genetics 186: 1345–1354 (December 2010), Excerpt from abstract: “Because adaptation depends upon the fixation of novel beneficial mutations, the fitness effects of beneficial mutations that are substituted by selection are key to our understanding of the process of adaptation. In this study, we experimentally investigated the fitness effects of beneficial mutations that are substituted when populations of the pathogenic bacterium Pseudomonas aeruginosa adapt to the antibiotic rifampicin.”

Puzzles for ZFEL, McShea and Brandon’s zero force evolutionary ,  Martin Barrett, et al, Biol Philos DOI 10.1007/s10539-012-9321-7, 2012, Abstract: “In their 2010 book, Biology’s First Law, D. McShea and R. Brandon present a principle that they call ‘‘ZFEL,’’ the zero force evolutionary law. ZFEL says (roughly) that when there are no evolutionary forces acting on a population, the population’s complexity (i.e., how diverse its member organisms are) will increase. Here we develop criticisms of ZFEL and describe a different law of evolution; it says that diversity and complexity do not change when there are no evolutionary causes.”

Fundamental relationship between operon organization and gene expression, Han N. Lim, Yeong Lee, and Razika Hussein, 10626–10631 | PNAS | June 28, 2011 | vol. 108 | no. 26, Excerpt: “Here we show using synthetic operons in Escherichia coli that the expression of a given gene increases with the length of the operon and as its position moves farther from the end of the operon. These findings can be explained by a common mechanism; increasing the distance from the start of a gene to the end of the operon (termed the “transcription distance”) provides more time for translation to occur during transcription, resulting in increased expression.”

How stands the Tree of Life a century and a half after The Origin?, Maureen A O'Malley & Eugene V Koonin,  Biology Direct , volume 6, Article number: 32 (2011),  Abstract: “We examine the Tree of Life (TOL) as an evolutionary hypothesis and a heuristic. The original TOL hypothesis has failed but a new "statistical TOL hypothesis" is promising. The TOL heuristic usefully organizes data without positing fundamental evolutionary truth.”

Evolution of molecular error rates and the consequences for evolvability, Etienne Rajon and Joanna Masel, 1082–1087 | PNAS | January 18, 2011 | vol. 108 | no. 3, Excerpt from abstract: “Making genes into gene products is subject to predictable errors, each with a phenotypic effect that depends on a normally cryptic sequence. Many cryptic sequences have strongly deleterious effects, for example when they cause protein misfolding. Strongly deleterious effects can be avoided globally by avoiding making errors (e.g., via proofreading machinery) or locally by ensuring that each error has a relatively benign effect.”

Wandering drunks and general lawlessness in biology: does diversity and complexity tend to increase in evolutionary systems? Daniel W. McShea and Robert N. Brandon: Biology’s first law: the tendency for diversity and complexity to increase in evolutionary systems, The University of Chicago Press, Chicago, London, ,  Lindell Bromham,  Biol Philos (2011) 26:915–933 D, Abstract: “Does biology have general laws that apply to all levels of biological organization, across all evolutionary time? In their book ‘‘Biology’s first law: the tendency for diversity and complexity to increase in evolutionary systems’’ (2010), Daniel McShea and Robert Brandon propose that the most fundamental law of biology is that all levels of biological organization have an underlying tendency to become more complex and diverse over time. A range of processes, most notably selection, can prevent the expression of this tendency, but they predict that, on average, we should see that lineages tend toward greater diversity and complexity, driven by fundamentally neutral processes. Their hypothesis can be summarized as ‘‘diversity is easy, stasis is hard’’. Here, I consider evidence for this ‘‘zero force evolutionary law’’. It provides a fair description of evolutionary change at the genomic level, but the predictions of the proposed law are not met for broad scale patterns in the evolution of the animal kingdom.”

Robust Design of Biological Circuits: Evolutionary Systems Biology Approach, Bor-Sen Chen, Chih-Yuan Hsu, and Jing-Jia Liou, Journal of Biomedicine and Biotechnology, Volume 2011: Recognizing that biological functions depend on interacting cell networks, the authors attempted to explore their function by designing and studying synthetic circuits.

The Fate of Darwinism: Evolution after the Modern Synthesis, David J. Depew and Bruce H. Weber, December 2011, Biological Theory 6(1). The authors believe the modern synthesis is obsolete. Abstract: “We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetic Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes. We go on to discuss two conceptual issues: whether natural selection can be the “creative factor” in a new, more general framework for evolutionary theorizing; and whether in such a framework organisms must be conceived as self-organizing systems embedded in self-organizing ecological systems.”

Macroevolution: Dynamics of Diversity, Douglas H. Erwin, Current Biology Vol 21 No 24, 2011, Abstract: “The fossil record typically exhibits very dynamic patterns of innovation, diversification and extinction. In contrast, molecular phylogenies suggest smoother patterns of evolutionary change. Several new studies reconcile this difference and reveal more about the mechanisms behind macro evolutionary change.” --- -Excerpt: “Do the evolutionary mechanisms available to manipulation, such as laboratory or field studies of adaptation and population genetics, reveal the full scope of evolutionary processes, or are there processes that operate over longer timescales and that are responsible for the diversity of life, both today and in the fossil record? This question encompasses the tension between micro evolutionists and macro evolutionists (originally mainly paleontologists, but recently including evolutionary developmental biologists and others).”

Origins of cellular geometry, Wallace F Marshall, BMC Biology 2011, 9:57. An observation of the unexplained complexity of cells. Excerpt from abstract: “Cells are highly complex and orderly machines, with defined shapes and a startling variety of internal organizations. Complex geometry is a feature of both free-living unicellular organisms and cells inside multicellular animals. Where does the geometry of a cell come from? Many of the same questions that arise in developmental biology can also be asked of cells, but in most cases we do not know the answers.

Molecular Darwinism: The Contingency of Spontaneous Genetic Variation, Werner Arber, Genome Biol. Evol. 3:1090–1092. 2011. The sources of genetic variation are more complex than observed in laboratory experiments. Abstract: “The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions.”

Roles of Mutation and Selection in Speciation: From Hugo de Vries to the Modern Genomic Era, Masatoshi Nei and Masafumi Nozawa, Genome Biol. Evol. 3:812–829, 2011.  New techniques are providing new information on speciation, but the results are hard to explain. Excerpt from abstract: “One of the most important problems in evolutionary biology is to understand how new species are generated in nature. In the past, it was difficult to study this problem because our lifetime is too short to observe the entire process of speciation. In recent years, however, molecular and genomic techniques have been developed for identifying and studying the genes involved in speciation. Using these techniques, many investigators have already obtained new findings. At present, however, the results obtained are complex and quite confusing. We have therefore attempted to understand these findings coherently with a historical perspective and clarify the roles of mutation and natural selection in speciation.”

Evolutionary Developmental Biology (Evo-Devo): Past, Present, and Future, Brian K. Hall, Evo Edu Outreach (2012) 5:184–193, Excerpt from abstract; “. After the discovery in 1900 of Mendel’s research on genetics, however, any relationship between development and evolution was either regarded as unimportant for understanding the process(es) of evolution or as a black box into which it was hard to see. Research over the past two decades has opened that black box, revealing how studies in evo–devo highlight the mechanisms that link genes (the genotype) with structures (the phenotype). This is vitally important because genes do not make structures. Developmental processes make structures using road maps provided by genes, but using many other signals as well—physical forces such as mechanical stimulation, temperature of the environment, and interaction with chemical products produced by other species—often species in entirely different kingdoms as in interactions between bacteria and squid or between leaves and larvae.”

From Darwinian Metaphysics towards Understanding the Evolution of Evolutionary Mechanisms: A Historical and Philosophical Analysis of Gene-Darwinism and Universal Darwinism, Momme von Sydow, 2012, Universitätsverlag Göttingen. A 470 page book reviewing the thought supporting Darwinism.  Excerpt from preface: “My present work begins with a historical investigation of the background to biological Darwinian paradigms. This background is no irrelevant ornament to the main theme of systematically discussing Darwinism; rather, it provides the basis from which to establish differences between Darwinian paradigms and detect the conceptual core of universal Darwinism. The definition of this core in turn has an incontrovertible impact on the systematic critique of gene-Darwinism, process Darwinism and Darwinian metaphysics in general.”

 Code Biology – A New Science of Life, Marcello Barbier, Biosemiotics DOI 10.1007/s12304-012-9147-3, Mar 2012, Biosemiotics DOI 10.1007/s12304-012-9147-3. Abstract: “Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely internal processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life.”

In 2012, Guillermo Folguera and Olimpia Lombardi reviewed the historical relationship between microevolution and macroevolution (The relationship between microevolution and macroevolution, and the structure of the extended synthesis).  They described how the founders of the modern synthesis reluctantly assumed macroevolution is just extended microevolution.  Like Darwin, they did not know the cause(s) of variation, because the DNA molecule had still not been discovered.  The founders understood Mendelian genetics, but genetics does not explain macroevolution.  Guillermo and Folguera also described how the shortcomings of the modern synthesis became very apparent in the 1970s, and how biologists and paleontologists struggled to define an extended evolutionary synthesis.  They were unable to achieve a consensus on the cause of macroevolution.

Origins of Variation, Laura M. Zahn, Science 02 Nov 2012: Vol. 338, Issue 6107, pp. 582. Abstract: “It is not clear whether the majority of selection on human genetic variation originates from de novo mutations or from selection on previously neutral, or nearly neutral, standing genetic variation.  --- Examining genes previously identified to be under selection, but not yet fixed within humans, revealed that both models were applicable - - - .  Furthermore, when regions currently not under selection were examined, it was not possible to discriminate between selected and neutral variants. These results support the notion that the origin of human genetic variation that is subject to selection is complex and that an understanding of both standing variation and the de novo mutation rate is important to trace our evolution.”

“The Geometry of Morphogenesis and the Morphogenetic Field Concept”, Nadya Morozova and Mikhail Shubin, 2012, online. Much of the information determine complex biological form is not in the DNA. It is coded on the surface of the cell  in a not yet understood form.

Physico-Genetic Determinants in the Evolution of Development, Stuart A. Newman, October 2012, Science 338(6104):217-9.  Abstract: “Animal bodies and the embryos that generate them exhibit an assortment of stereotypic morphological motifs that first appeared more than half a billion years ago. During development, cells arrange themselves into tissues with interior cavities and multiple layers with immiscible boundaries, containing patterned arrangements of cell types. These tissues go on to elongate, fold, segment, and form appendages. Their motifs are similar to the outcomes of physical processes generic to condensed, chemically excitable, viscoelastic materials, although the embryonic mechanisms that generate them are typically much more complex. I propose that the origins of animal development lay in the mobilization of physical organizational effects that resulted when certain gene products of single-celled ancestors came to operate on the spatial scale of multicellular aggregates.”

 

Positional information, in bits. Julien O. Dubuisa, et al, PNAS | October 8, 2013 | vol. 110 | no. 41 | 16301–16308. Abstract: “Cells in a developing embryo have no direct way of “measuring” their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for “positional information.” We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as would be expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell’s location with an error bar of ∼ 1% along the anterior/posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.”

Darwin's principles of divergence and natural selection: Why Fodor was almost right, Robert J. Richards, Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):256-268 (2012), Excerpt:” In a series of articles and in a recent book, What Darwin Got Wrong, Jerry Fodor has objected to Darwin’s principle of natural selection on the grounds that it assumes nature has intentions. Despite the near universal rejection of Fodor’s argument by biologists and philosophers of biology (myself included), I now believe he was almost right. I will show this through a historical examination of a principle that Darwin thought as important as natural selection, his principle of divergence. The principle was designed to explain a phenomenon obvious to any observer of nature, namely, that animals and plants form a hierarchy of clusters.”

Adaptive Radiations in the Context of Macroevolutionary Theory: A Paleontological Perspective, Bruce S. Lieberman, Evolutionary Biology (39):181-191, Abstract; “Adaptive radiations are often invoked anytime clades show significant bursts of diversification, but it is important to not simply assume that any radiating clade constitutes an adaptive radiation. ---different types of evolutionary radiations are identified, including geographic radiations. Special emphasis is placed on considering the role that abiotic as opposed to biotic factors may play in motivating diversification during evolutionary radiations. Further, recent paleontological data suggesting that rather than organismal adaptation it may be principally abiotic factors, such as climate change and a taxon’s presence in a geographically complex region, that cause clades to diversify. - - -”

Current hypotheses for the evolution of sex and recombination, Matthew Hartfield And Peter D. Keightley, Integrative Zoology 2012; 7: 192–209. Review of the inability to explain the evolution of sex. Extract from abstract: "The evolution of sex is one of the most important and controversial problems in evolutionary biology. Although sex is almost universal in higher animals and plants, its inherent costs have made its maintenance difficult to explain. The most famous of these is the twofold cost of males, which can greatly reduce the fecundity of a sexual population, compared to a population of asexual females. Over the past century, multiple hypotheses, along with experimental evidence to support these, have been put forward to explain widespread costly sex. In this review, we outline some of the most prominent theories, along with the experimental and observational evidence supporting these.”

Darwinism, not mutationism, explains the design of organisms (Andy Gardner, 2012) expresses concern over 2011 and 2012 publications by J.A. Shapiro.  Gardner’s concern is that Shapiro wrote that recent discoveries in molecular biology require that Darwinism be replaced with mutationism.  Gardner strongly disagreed, claiming that Shapiro misinterpreted the new information.

Epigenetic Inheritance: A Contributor to Species Differentiation? Dario Boffelli and David I.K. Martin, DNA And Cell Biology Volume 31, Supplement 1, 2012, Mary Ann Liebert, Inc. Pp. S-11–S-16 ,2012. The author claims that environmentally caused changes in epigenome may be inherited. If so, this means that Lamarck (discredited during the preparation of the modern synthesis) was at least partially correct.

The Origin and Evolution of New Genes, Margarida Cardoso Moreira and Manyuan Long, January 2012, Methods in molecular biology (Clifton, N.J.) . Excerpt:  “This chapter explores how genomic data can and is being used to study both the origin and evolution of new genes and the surprising discoveries made thus far.”

Electromagnetic Resonance in Biological Form: A Role for Fields in Morphogenesis , Alexis M Pietak, 2011 J. Phys.: Conf. Ser. 329 012012: Excerpt from abstract: “This work explores the hypothesis of developing biological structures as dielectric microwave resonators, using plant leaves as a working example.”

The Role of Standing Genetic Variation in Adaptation of Digital Organisms to a New Environment, Carlos J. R. Anderson, Artificial Life 13: 3–10, 2012, Excerpt from summary: “In summary, this study has shown the importance of standing genetic variation in populations of digital organisms adapting to a new environment. That is, (1) most beneficial alleles came from standing genetic variation rather than from new mutations, (2) populations that started with standing genetic variation adapted faster than populations that started with identical genotypes, and (3) the fitness effects of alleles from standing genetic variation were less harmful than new mutations.”  (based on simulation)

Dissecting Darwinism, Joseph A. Kuhn, MD, Proc (Bayl Univ Med Cent) 2012;25(1):41–47: Observing that  Darwinism does not appear to be consistent with the present understand of life’s complexity, Kuhn stated; “Based on an awareness of the inexplicable coded information in DNA, the inconceivable self-formation of DNA, and the inability to account for the billions of specified organized nucleotides in every single cell, it is reasonable to conclude that there are severe weaknesses in the theory of gradual improvement through natural selection (Darwinism) to explain the chemical origin of life. Furthermore, Darwinian evolution and natural selection could not have been causes of the origin of life, because they require replication to operate, and there was no replication prior to the origin of life.”

Kuhn also claims that “biochemists have shown that even a simple light-sensitive spot requires a complex array of enzyme systems, and that “Geoffrey Simmons, MD, has presented 17 examples within the human body of irreducibly complex systems that could not have formed by sequential or simultaneous mutation, since all components must be present to work correctly.” 

Citing work done by paleoanthropologists J. Valentine and D. H. Erwin, Kuhn asserts that the absence of transitional species for any of the Cambrian phyla is not consistent with the modern synthesis.  He further states that “the modern evolution data do not convincingly support a transition from a fish to an amphibian.”

Finally Kuhn quotes Darwin as follows: “If it could be shown that complex systems could not arise by small sequential steps, then my theory would completely break down.”   Kunh then states that “Irreducibly complex systems involving thousands of interrelated specifically coded enzymes do exist in every organ of the human body. At an absolute minimum, the inconceivable self-formation of DNA and the inability to explain the incredible information contained in DNA represent fatal defects in the concept of mutation and natural selection to account for the origin of life and the origin of DNA.”

J. A. Shapiro (Physiology and Evolution: has physiology become relevant again to evolutionary biology? 37th Congress of IUPS, Birmingham, UK, 2013) suggested another major level of complexity for biological information.  He observed that; “the genome is traditionally treated as a Turing tape or Read-Only Memory (ROM) subject to change by copying errors. This default assumption of accidental mutation arose from the inevitable ignorance of the mechanisms of genome change in the 19th and early 20th Centuries.”  Schapiro then claims “In contrast to early assumptions about genomic accidents, research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply damage to the DNA.”  As he developed his thoughts further, he proposed that biologic information is actually stored in a read-write (RW) memory.  Both the organism and the environment can change it.

Evolution in Fossil Lineages: Paleontology and The Origin of Species, Gene Hunt, vol. 176, supplement the American Naturalist, December, 2010: The author believes the fossil record supports Darwin. Excerpt: “Darwin concluded that whereas the broad outline of the fossil history of life was consistent with descent with modification and natural selection, the geological record was too incomplete and too poorly known to document in detail the transformation of species. One hundred and fifty years later, we are in a different position. The fossil record is much better known, and its strengths and weaknesses are much better understood. Under the most promising circumstances, it is possible to document in fossil strata the transformation of a lineage by natural selection as Darwin envisioned, although he underestimated the speed at which such changes occur.”

The Evolutionary Origins of Genetic Information,  Stephen Freeland, Perspectives on Science and Christian Faith, Volume 63, Number 4, December 2011,  “Current science does not have a detailed, widely accepted description for how a genetic information system evolved in the first place. Intelligent design (ID) proponents suggest that this is a key weakness of existing evolutionary theory, consistent with the need for an intelligent designer. I describe the progress that mainstream science has made toward understanding the origin of genetic information ever since the molecular basis of genetic information was first understood, encouraging readers to reach their own conclusions.”

Interacting Gears Synchronize Propulsive Leg Movements in a Jumping Insect, Malcom Burrows and Gregory Sutton, Article in Science · September 2013, Source: PubMed: The paper describes a very unique  insect nymph that has spur gears to synchronize rear leg motion during jumping. No other application of a functional gear mechanism in a life form is currently known.  The authors do not speculate on the origin of the gears by natural selection.

Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, Stephen C. Meyer, Harper, 2013, excerpt from publishers introduction; “When Charles Darwin finished The Origin of Species, he thought that he had explained every clue, but one. Though his theory could explain many facts, Darwin knew that there was a significant event in the history of life that his theory did not explain. During this event, the “Cambrian explosion,” many animals suddenly appeared in the fossil record without apparent ancestors in earlier layers of rock.  In Darwin’s Doubt, Stephen C. Meyer tells the story of the mystery surrounding this explosion of animal life—a mystery that has intensified, not only because the expected ancestors of these animals have not been found, but because scientists have learned more about what it takes to construct an animal. …”

The problem of morphogenesis: unscripted biophysical control systems in plants, Philip M. Lintilhac, Protoplasma DOI 10.1007/s00709-013-0522-y, 2013. This article is published with open access at Springerlink.com. Excerpt from Conclusion: “So, what is the role of the genome itself, and how do we understand the governing roles of the many cellular and subcellular control circuits that are embedded in the living system that we call the organism? When it comes to interpreting the flow of morphological forms that constitute development, do we look for scripted instructions in the genome when the most relevant control circuitry seems to be inherent in the architecture of the developing organ and the biophysical properties of the cell wall itself?”

Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution, Jaroslav Flegr, Biology Direct 2013, 8:1:  Extract from abstract: “Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III), genetic revolution model of Mayr (class IV) or the frozen plasticity theory of Flegr (class V), suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation – while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III) or elastic (class IV and V) on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation.”

Mechanisms and constraints shaping the evolution of body plan segmentation, K.H.W.J. ten Tusschera, Eur. Phys. J. E (2013) 36: 54. Excerpt: “Segmentation of the major body axis into repeating units is arguably one of the major inventions in the evolution of animal body plan pattering. It is found in current day vertebrates, annelids and arthropods.”

Richard A. Richards, The Species Problem: A Conceptual Problem?, 2013, http://dx.doi.org/10.5772/54134. Whenever science encounters a persistent, unsolved problem, it attracts the attention of philosophers. This publication is a detailed discussion of exactly a species is. Since the time of Darwin, science has not produced a precise, logical definition of a species.  Different disciplines use different definitions to suit their needs. Richards claims the literature currently contains over twenty distinctly different definition of a species.

Finkelman, Leonard, Systematics and the Selection of Species, PhD dissertation, The City University of New York, 2013. Excerpt from abstract: “Resolution of the species problem is complicated by the fact that species are considered “fundamental units” of biological theories in at least two senses. Species are units of taxonomy: they are the smallest “real” groups into which organisms can be classified. Species are also units of evolution: they are the entities that change over time due to Natural Selection. Following Darwin, philosophers of biology traditionally argue that these units can only be identified if species are nominal entities. More recently, paleontologists suggest that species may be “fundamental units” in a third sense: as units of selection in a higher-order process of differential speciation and extinction. Species selection would therefore have a place in a hierarchy of selection processes.”

Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution, Jaroslav Flegr, Biology Direct 2013, 8:1.  This is a unique paper with a unique hypothesis.  It expands the concept of punctuated evolution which holds that species appear suddenly and then remain unchanged until extinction as suggested by the fossil record.  According to Flegr, there are potentially five different classes of punctuated evolution. Four appeared previously in the literature (eg: Punctuated Equilibrium by Eldridge and Gould) and one was developed by him. Flegr calls his hypothesis frozen plasticity and claims that natural selection can shape a species for only a short time after it appears.  After that, it cannot change form (other than slightly by standing variation). The reason is that a mutation can become fixed in a sexually reproducing species only when the gene pool is uniform and that happens only after a mass extinction or a geographical separation.  Table 1 in Flegr’s paper summarizes the differences in the five classes of punctuational evolution and Figure 1 summarizes the argument supporting Flegr’s version.  Flegr has been promoting his hypothesis  for some time with at least five other papers and a book. One of his later papers was published in 2017.

Explore Evolution: The Arguments for and Against Neo-Darwinism by Stephen C. Meyer et al, July 1, 2013. Introduction: The purpose of Explore Evolution is to examine the scientific controversy about Darwin's theory, and in particular, the contemporary version of the theory known as neo-Darwinism. Whether you are a teacher, a student, or a parent, this book will help you understand what Darwin's theory of evolution is, why many scientists find it persuasive, and why other scientists question the theory or some key aspects of it. Sometimes, scientists find that the same evidence can be explained in more than one way. When there are competing theories, reasonable people can (and do) disagree about which theory best explains the evidence. Furthermore, in the historical sciences, neither side can directly verify its claims about past events. Fortunately, even though we can't directly verify these claims, we can test them. How? First, we gather as much evidence as possible and look at it carefully. Then, we compare the competing theories in light of how well they explain the evidence. Looking at the evidence and comparing the competing explanations will provide the most reliable path to discovering which theory, if any, gives the best account of the evidence at hand. In science, it is ultimately the evidence-and all of the evidence-that should tell us which theory offers the best explanation. This book will help you explore that evidence, and we hope it will stimulate your interest in these questions as you weigh the competing arguments.

Where’d Hugo Go?,   Ronald Ladouceur, Textbook History, 2013, https://textbookhistory.com/whered-hugo-go/. Excerpt: “Rather than suggesting that speciation resulted from an accumulation of small variations over long periods of time, like Darwin’s theory implied, De Vries posited that new species could actually pop into existence in a single generation. In fact, according to De Vries, multiple representatives of the same new species could pop simultaneously, creating a pool that would breed true. Many biologists felt De Vries had solved the most vexing problem in evolution – how variations could avoid being swamped or blended back to average through interbreeding.”

The Surprising Origins of Evolutionary Complexity, Carl Zimmer, Scientific American, August 1, 2013. Zimmer explores the puzzling origins of biological complexity. Excerpts: “Scientists are exploring how organisms can evolve elaborate structures without Darwinian selection ---Conventional wisdom holds that complex structures evolve from simpler ones, step-by-step, through a gradual evolutionary process, with Darwinian selection favoring intermediate forms along the way. --- But recently some scholars have proposed that complexity can arise by other means—as a side effect, for instance—even without natural selection to promote it. --- Studies suggest that random mutations that individually have no effect on an organism can fuel the emergence of complexity in a process known as constructive neutral evolution.”

How life changes itself: The Read–Write (RW) genome, James A. Shapiro, Physics of Life Reviews, Volume 10, Issue 3, September 2013, Pages 287-323, Abstract: “The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read–Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.”

Circular RNA Is Expressed across the Eukaryotic Tree of Life, Peter L. Wang et al, PLOS ONE | www.plosone.org 1 March 2014 | Volume 9 | Issue 3.  Abstract: “An unexpectedly large fraction of genes in metazoans (human, mouse, zebrafish, worm, fruit fly) express high levels of circularized RNAs containing canonical exons. Here we report that circular RNA isoforms are found in diverse species whose most recent common ancestor existed more than one billion years ago: fungi (Schizosaccharomyces pombe and Saccharomyces cerevisiae), a plant (Arabidopsis thaliana), and protists (Plasmodium falciparum and Dictyostelium discoideum). For all species studied to date, including those in this report, only a small fraction of the theoretically possible circular RNA isoforms from a given gene are actually observed.  - - - Circular RNA may be an ancient, conserved feature of eukaryotic gene expression programs.”

The Princeton Guide to Evolution, Jonathan B. Losos, 2014. An 830 page, 107 chapter reference book with each chapter written by and expert on the specific topic. The guide is now on line as an open source reference.

Philippe Huneman, Evolutionary Theory in Philosophical Focus, 14 Aug 2014, http://www.springerreference.com/index/chapterdbid/135037 14 Aug 2014 04:21,  A 30 page discussion of the unsolved problems surrounding evolution.  Conclusion: “However interpreted, evolutionary theory is beset with theoretical problems concerning its major concepts (selection, fitness, adaptation). Those problems, while never dissociated from empirical biological issues, are at the same time philosophical, since they involve conceptual matters that imply epistemological and metaphysical choices. Although the problems of evolutionary theory cannot be solved independently of biological results, and above all could not have been formulated without reference to known facts of evolutionary biology, they are not likely to be solved purely within biological science itself. Reciprocally, their insightful articulation and attempts at solutions are of vital interest to the field of philosophy of science in general, as well as to metaphysics. Surely the most tangible effect of evolutionary theory on philosophy is the opportunity it provides for elaboration of a new framework of inquiry about many philosophical topics - first of all, about the nature of man. This chapter intended to survey the objectives of current research programs in this realm, their variedness, and the difficulties they are facing. No integrative, synthetic knowledge of man, and no methodological framework for philosophical problems, has yet been established within the evolutionary perspective that parallels and is compatible with (and could ultimately be integrated into) the Modern Synthesis. For the moment, we have local results, new challenges, and insightful ways of approaching long-standing puzzles. But in the end, the broad rise of the evolutionary perspective will have profound consequences for the way we conceive of philosophical problems generally and, most of all, for our image of man - who is uniquely able to concern himself with those problems.”

Charles Darwin's Theory of Pangenesis, Yawen Zou, The Embryo Project Encyclopedia, 2014, Reviews the history of Darwin’s theory of pangenesis from 1864 to 1900.

Does evolutionary theory need a rethink? Researchers are divided over what processes should be considered fundamental, Kevin Laland and Gregory A. Wray, October 2014 | VOL 514 | Nature | 161:  Point and counterpoint discussion on whether the modern synthesis requires revision. Both authors are professors of biology, but have opposite views.

Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration, Michael Levin, J Physiol 592.11 (2014) pp 2295–2305 2295 The Journal of Physiology. Excerpt: “Here, I briefly review exciting new data in developmental bioelectricity, and argue three main points. First, that bioelectric networks among all cells are an autonomous layer of instructive information that regulates complex pattern formation. Second, that the current gene-centric paradigm needs to be expanded with conceptual tools and new physiomic data, to fully understand the control of anatomy by bioelectricity and the evolutionary implications of its top-down causal efficacy. Third, that transformative changes in biomedicine and synthetic bioengineering will result from the functional taming of the unique properties of bioelectrical signaling.”

Evolution: Rooting the Eukaryotic Tree of Life, Tom A. Williams, Current Biology Vol 24 No 4, Dec., 1914. Abstract: “The root of the eukaryotic tree is a major unresolved question in evolutionary biology. A recent study marshals mitochondrial genes to place that root between the enigmatic Excavates and all other eukaryotes, providing an interesting new perspective on early eukaryotic evolution.”

Evolutionary Cell Biology: Two Origins, One Objective, Michael Lynch, et al, PNAS | December 2, 2014 | vol. 111 | no. 48. Excerpt: “Because all evolutionary change ultimately requires modifications at the cellular level, questioning and understanding how cellular features arise and diversify should be a central research venue in evolutionary biology. However, if there is one glaring gap in this field, it is the absence of widespread cell-biological thinking. Despite the surge of interest at the molecular, genomic, and developmental levels, much of today’s study of evolution is only moderately concerned with cellular features, perhaps due to lack of appreciation for their wide variation among taxa. However, a full mechanistic understanding of evolutionary processes will never be achieved without an elucidation of how cellular features become established and modified.”

The Top Ten Scientific Problems with Biological and Chemical Evolution, Casey Luskin, February 20, 2015, Intelligent Design. The paper includes the rational for numerous claims that Darwinian evolution is not able to explain the origin of life or the development of complexity.

Huneman, Philippe, Macroevolution and microevolution: issues of time scale in evolutionary biology, SHPSSB 2015 meeting in Montréal. Excerpt from abstract: “According to the Modern Synthesis (MS), population genetics, as the science of the dynamics of changing allele frequencies in a population, is the core of evolutionary biology since it explains the arising of adaptations by cumulative selection. Its scale is microevolution, namely, evolution of the population of one species within a timescale not too large, defined by a small window of variations and environmental changes. Microevolution contrasts with macroevolution, that is, evolution above the level of speciation, such as the extinction or emergence of species and clades, which involves a longer timescale and therefore may assume large environmental changes. MS claimed that macroevolution is not different from macroevolution. This “extrapolationist” thesis formulated by Simpson has been challenged for three decades: by the “punctuated equilibrium” thesis, and recently by Evo-Devo. Here I question the reasons why the extrapolationist thesis is threatened by advances in paleobiology and evolutionary developmental theory. The paper essentially distinguishes between biological and mathematical reasons why there could be principled differences between microevolution and macroevolution. --- I conclude by showing that the mathematical differences between micro and macroevolution are more general, and therefore may challenge the extrapolation thesis even if empirical facts do not support the biological differences.” The body of the paper reviews challenges to the modern synthesis assumption that microevolution and macroevolution are based on the very same process.”

Arrival of the Fittest: Solving Evolution’s Greatest Puzzle, Andreas Wagner, Penguin Books, New York, 2014. From publishers summary : “ Can random mutations over a mere 3.8 billion years really be responsible for wings, eyeballs, knees, camouflage, lactose digestion, photosynthesis, and the rest of nature’s creative marvels? And if the answer is no, what is the mechanism that explains evolution’s speed and efficiency? -- In Arrival of the Fittest, renowned evolutionary biologist Andreas Wagner draws on over fifteen years of research to present the missing piece in Darwin’s theory. Using experimental and computational technologies that were heretofore unimagined, he has found that adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.”

Molecular insights into the origin of the Hox-TALE patterning system, Bruno Hundry, eLife 2014;3:e01939”. The paper describes how the development of body plans depends on the interaction of gene networks, using ancient and highly conserved genes commonly used in a wide variety of lifeforms. Abstract: “Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families.- - - ”

Brasier M., 2015, Deep questions about the nature of early-life signals: a commentary on Lister (1673) ‘A description of certain stones figured like plants’.Phil. Trans. R. Soc. A 373: 20140254. Excerpt from conclusion: In 1673, the biological nature of fossils was a highly controversial matter. Kircher [13] had argued that they formed by means of abiogenic ‘plastic forces’ within the rock. Hooke [20] and Steno [17] suggested that they were the remains of living organisms. Martin Lister [1] was seemingly the first to explore the ways in which direct observation could help to show whether fossil remains (in this case, Carboniferous crinoids) had grown abiogenically within the limestone or whether they had once formed part of a formerly living biological population. Prophetically, he achieved this by using the earliest known example of taphonomic reasoning in a scientific paper: that fossils of biological origin should show various lines of evidence, including those for life posture, growth, death, transport, breakage, burial, decomposition and subsequent mineral replacement and infilling.

Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework, Gasper Tkacik, Genetics, Vol. 199, 39–59 January 2015. Excerpt from Discussion: “To generate a differentiated body plan during the development of a multicellular organism, cells with identical genetic material need to reproducibly acquire distinct cell fates, depending on their position in the embryo. The mechanisms of establishment and acquisition of such positional information have been widely studied, but the concept of positional information itself has, surprisingly, eluded formal definition. Here we have provided a mathematical framework for positional information and positional error based on information theory. These are principled measures for quantifying how much knowledge cells can gain about their absolute location in the embryo—and thus how precisely they can commit to correct cell fates—by locally reading out noisy gene expression profiles of (possibly multiple) morphogen gradients.

A Temporary Convenience* A Critical Review of the Species Concept, William S. Abruzzi Academia.edu (2015).  Abstract: “Although species are widely understood as genetic units defined by the ability of individual organisms to exchange hereditary material (DNA), this view of species does not accurately reflect the species concept as it is understood and applied in contemporary biological and ecological research. This paper critically examines the species concept and suggests that, given the arbitrariness of the definition of species and the inability to apply the concept consistently and universally to all species, the species concept should be recognized not as a natural entity, but rather as a human construct with only limited validity and utility ---“.

Gontier, Nathalie, Uniting Micro- with Macroevolution into an Extended Synthesis: Reintegrating Life’s Natural History into Evolution Studies, © Springer International Publishing Switzerland 2015 E. Serrelli and N. Gontier (eds.), Macroevolution, Interdisciplinary Evolution Research 2, DOI 10.1007/978-3-319-15045-1_7. Abstract: “The Modern Synthesis explains the evolution of life at a mesolevel by identifying phenotype–environmental interactions as the locus of evolution and by identifying natural selection as the means by which evolution occurs. Both micro and macroevolutionary schools of thought are post-synthetic attempts to evolutionize phenomena above and below organisms that have traditionally been conceived as non-living. Microevolutionary thought associates with the study of how genetic selection explains higher-order phenomena such as speciation and extinction, while macroevolutionary research fields understand species and higher taxa as biological individuals and they attribute evolutionary causation to biotic and abiotic factors that transcend genetic selection. The microreductionist and macroholistic research schools are characterized as two distinct epistemic cultures where the former favor mechanical explanations, while the latter favor historical explanations of the evolutionary process by identifying recurring patterns and trends in the evolution of life. I demonstrate that both cultures endorse radically different notions on time and explain how both perspectives can be unified by endorsing epistemic pluralism

Landscape Approach to Evolutionary Systems Biology Bridging the Genotype and the Phenotype: Towards An Epigenetic Landscape Approach to Evolutionary Systems Biology, Jose Davila-Velderrain and Elena R Alvarez-Buylla, bioRxiv posted online April 14, 2014.  Acknowledging that the sequenced genome does not define complex lifeforms as once expected, the paper explores the function of gene regulatory networks.  Abstract: “Understanding the mapping of genotypes into phenotypes is a central challenge of current biological research. Such mapping, conceptually represents a developmental mechanism through which phenotypic variation can be generated. Given the nongenetic character of developmental dynamics, phenotypic variation to a great extent has been neglected in the study of evolution. What is the relevance of considering this generative process in the study of evolution? How can we study its evolutionary consequences? Despite an historical systematic bias towards linear causation schemes in biology; in the post-genomic era, a systems-view to biology based on nonlinear (network) thinking is increasingly being adopted. - - - “

The Cell’s View of Animal Body-Plan Evolution,  Deirdre C. Lyons, Mark Q. Martindale,  and Mansi Srivastava, Integrative and Comparative Biology, volume 54, number 4, pp. 658–666, 2014. Excerpt: “Understanding how diverse body-plans evolved remains one of the most exciting and challenging goals for evolutionary and developmental biologists alike. Over the past few decades, genomic and molecular genetic approaches have uncovered gene networks that regulate tissue patterning during development. However, we are currently lacking in the understanding of how specification of cell types generates specific cells’ biological properties, such as polarity, migration, and adhesion from a highly conserved set of effector proteins. Yet, cells are the fundamental unit of all biological structures and phenomena—evolution shapes phenotypes by ultimately changing cellular characteristics.

Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods, Paul G. Harnik, Paul C. Fitzgerald, Jonathan L. Payne, and Sandra J. Carlson   Paleobiology, 40(4), 2014, pp. 675–692, Abstract: “Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular phylogenies. --- These results provide evidence for the phylogenetic conservatism of organismal and emergent traits.”

Darwin Was Right: Information and the Collapse of Macroevolutionary Theory, Dean H. Kenyon, January 7, 2014, Excerpt: “The all-embracing grip of macroevolution on modern scientific thought, and especially on the thinking of academic biologists, has had an unfortunate dampening effect on open and frank discussion of problems in evolutionary theory, especially in the primary literature.” The paper is posted on a creationist website, but it was written by a biology professor at a state university and the arguments against Darwinism are based on science, not theology. It tells of the unsuccessful scientific literature search by the professor and his students for solid support for macroevolution.”

Complexity, Natural Selection and the Evolution of Life and Humans,  Börje Ekstig Published online: 3 May 2014,  Springerlink.com. The paper claims natural selection produces complexity. Abstract:” In this paper, I discuss the concept of complexity. I show that the principle of natural selection as acting on complexity gives a solution to the problem of reconciling the seemingly contradictory notion of generally increasing complexity and the observation that most species don’t follow such a trend. I suggest the process of evolution to be illustrated by means of a schematic diagram of complexity versus time, interpreted as a form of the Tree of Life. The suggested model implies that complexity is cumulatively increasing, giving evolution a direction, an arrow of time, thus also implying that the latest emerging species will be the one with the highest level of complexity. Since the human species is the last species evolved in the evolutionary process seen at large, this means that we are the species with the highest complexity. The model implies that the human species constitutes an integral part of organic evolution, yet rendering us the exclusive status as the species of the highest complexity.”

Mendelian-Mutationism: The Forgotten Evolutionary Synthesis, Arlin Stoltzfus and Kele Cable, Journal of the History of Biology (2014) 47:501–546. This extraordinary paper is a lengthy historic review of the formation of the modern synthesis.  It argues that much of the recent literature presents and inaccurate interpretation of how the synthesis developed and claims that it would have been established decades earlier if it were not for miscommunication and misunderstanding.  The paper also very clearly states that the modern synthesis is not simply a blend of Darwinism and Mendelism as is so often claimed. Rather mutationism was also an essential element. As the paper explains; “Mendelism is not a theory of growth-like change, but a theory of chemical constancy with conservative reconfigurations. Such a view begs for a theory of mutation …” It goes on to quote a 1906 reference by Pearson to further explain: “… there must be a manifest want in Mendelian theories of inheritance. Reproduction from this standpoint can only shake the kaleidoscope of existing alternatives; it can bring nothing new into the field. To complete a Mendelian theory we must apparently associate it for the purposes of evolution with some hypothesis of ‘‘mutations.’’ The chief upholder of such a hypothesis has been de Vries…”  Abstract: “According to a classical narrative, early geneticists, failing to see how Mendelism provides the missing pieces of Darwin’s theory, rejected gradual changes and advocated an implausible yet briefly popular view of evolution-by-mutation; after decades of delay (in which synthesis was prevented by personal conflicts, disciplinary rivalries, and anti-Darwinian animus), Darwinism emerged on a new Mendelian basis. Based on the works of four influential early geneticists – Bateson, de Vries, Morgan and Punnett –, and drawing on recent scholarship, we offer an alternative that turns the classical view on its head. For early geneticists, embracing discrete inheritance and the mutation theory (for the origin of hereditary variation) did not entail rejection of selection, but rejection of Darwin’s non-Mendelian views of heredity and variation, his doctrine of natura non facit saltum, and his conception of ‘‘natural selection’’ as a creative force that shapes features out of masses of infinitesimal differences. We find no evidence of a delay in synthesizing mutation, rules of discrete inheritance, and selection in a Mendelian-Mutationist Synthesis. Instead, before 1918, early geneticists had conceptualized allelic selection, the Hardy–Weinberg equilibrium, the evolution of a quantitative trait under selection, the probability of fixation of a new mutation, and other key innovations. Contemporary evolutionary thinking seems closer to their more ecumenical view than to the restrictive mid-twentieth-century consensus known as the Modern Synthesis.”

As it became apparent that biology was far more complex than ever imagined by the authors of the modern synthesis, many scientific disciplines besides biology and paleontology became interested.  Writing for Human Events (August 19, 2014) electrical engineer Robert J. Marks II stated: “A diverse group of scientists gathered at Cornell University in 2011 to discuss their research into the nature and origins of biological information. The symposium brought together experts in computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics. … Most of these researchers, with Ph.D.’s from places like Cal Tech, UC Berkeley, Yale and Cornell, do not believe the traditional Darwinist explanation of natural selection of random mutations is adequate to explain the origin of biological information (in the DNA, for example), and many consider intelligent design as a possible source for this information.  The Cornell symposium proceedings were published in the book Biological Information: New Perspectives (https://www.biologicalinformationnewperspectives.org/) 

Biological Information – New Perspectives: A Synopsis and Limited Commentary,  J.C. Sanford, Published by FMS Publications Waterloo, NY, 2011. In 2011, a symposium was held at Cornell University, entitled Biological Information - New Perspectives. The proceedings of that symposium (by the same title), have now been published by World Scientific. That volume was edited by Drs. Marks, Behe, Dembski, Gordon, and Sanford. Dr. Sanford, organizer of the symposium and a co-editor of the proceedings, wrote this booklet to make the information within the proceedings more generally accessible. This booklet greatly condenses the information within the 563 pages of the much larger volume, and uses much less technical language. In addition, this booklet contains limited commentary on the significance of each of the 24 scientific papers. Lastly, the booklet includes credentials and a short bio for the first author of each

Zou, Yawen, Charles Darwin's Theory of Pangenesis, Embryo Project Encyclopedia (2014-07-20). ISSN: 1940-5030 http://embryo.asu.edu/handle/10776/8041.  Excerpt: “Darwin's theory of pangenesis gradually lost popularity in the 1890s when biologists increasingly abandoned the theory of inheritance of acquired characteristics, on which the pangenesis theory partially relied. Around the turn of the twentieth century, biologists replaced the theory of pangenesis with germ plasm theory and then with chromosomal theories of inheritance, and they replaced the concept of gemmules with that of genes.”

 

Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology. Christy A. Hipsley and Johannes Müller ^, Front. Genet., 26 May 2014. The molecular clock produces a historical sequence, but no absolute times.  The paper discusses various ways of calibrating the clock to obtain absolute times. Conclusions: “The confounding nature of evolutionary rates and time in divergence dating analyses requires that the molecular clock be calibrated independently using information from the evolutionary timescale. Here we show that this evidence can come from multiple sources, ranging from mutation rates measured in pedigree and laboratory lines, to fossil material and geological events millions of years in the past. Although paleontological calibration is not always possible, age constraints based on other types of data provide alternative means that, when well justified, can contribute critical information on the evolutionary history of life. ---“

Masatoshi Nei questioned the usefulness of Fisher’s population genetics (used to establish the modern synthesis) and challenged the assumption that natural selection drives the development of novelty and complexity.  Nei believes that a variety of mutational processes are the primary driver. (Mutation Driven Evolution, Oxford U. Press, 2014)

The work of Keith Baverstock and Mauno Ronkko, (The evolutionary origin of form and function, J Physiol 592.11 (2014) pp 2261–2265) presented many challenges to the modern synthesis. A chemist and computer scientist, they found that DNA alone does not determine form and function. Rather genes are merely recipes for producing proteins; they do not define structure. Furthermore, that energy conversion processes with the cell produce new information for variations.

Is the following material in Baverstock?

  “However, Noble (2013)has systematically rejected the tenets of the Modern Synthesis.”- Noble D (2013). Physiology is rocking the foundations of evolutionary biology. Exp Physiol 98, 1235–1243.- These interactions upon which phenotype is contingent, are symmetry breaking and lead to cellular phenotype being an emergent property of the system (Anderson, 1972). --- Anderson PW (1972). More is different. Science 177, 393–396.------bacteria have more variation than mammals ---- mutation not necessary ---- peptide folding produces information ----protien interaction produces infinite variety for form that natural selection can act upon .

Effect of Duplicate Genes on Mouse Genetic Robustness: An Update, Zhixi Su,  Junqiang Wang, and Xun Gu, BioMed Research International Volume 2014, Excerpt from introduction: “Functional compensation of duplicate (paralogous) genes has been thought to play an important role in genetic robustness. Indeed, existence of a close paralog in the same genome could result in null mutations of the gene with little effect on the organismal fitness (nonessential gene), as observed in both yeast and nematode. However, the role and magnitude of the duplicate genes contributing to genetic robustness in mammals remain controversial.”

The Evolution Revolution—Why Thinking People are Rethinking the Theory of Evolution, Lee Spetner Judaica Press, Brooklyn, NY, 2014:  The author claims that much of adaption is not due to random mutations that are selected by natural selection. Rather, it is a result of complex inbuilt systems that responds to the environment.  Inbuilt mechanisms such as epigenetics are influenced by the environment and activate or deactivate appropriate genes to implement a beneficial response. Spetner states that most changes thought to be microevolution occur much too rapidly to be explained by random mutation and selection, and cites supporting literature.  Dr. Spentner, a physicist with professional experience in biology, also published Not by chance! Shattering the Modern Theory of Evolution in 1997.  In that book, he attempted to demonstrate by analysis that the probability of complex genetic information accruing from random errors is essentially zero.  He also demonstrated that commonly cited examples of macroevolution (resistance of bacteria to antibiotics, resistance of insects to pesticides, breeding of “quantitative traits,” and adaptation of soil bacteria to new nutrients) are unique cases that are not the result of added information.  Rather, they are anomalies resulting from the destruction of existing information.

Macroevolution of Animal Body Plans: Is There Science after the Tree? Ronald A. Jenner, August 2014 / Vol. 64 No. 8 • BioScience, Abstract: “A renewed emphasis on the gaps in organization that exist between the crown-group body plans of higher-level animal taxa is a hallmark of the emerging consensus in metazoan phylogenetics. Bridging these gaps is the greatest hurdle that stands in the way of translating our knowledge of phylogeny into a renewed understanding of the macroevolution of animal body plans. Unless a good fossil record is available, there is little hope that we will be able to bridge many of these gaps empirically. We have, therefore, little choice but to resort to our more-or-less informed imagination to produce the historical narratives that are the ultimate goal of our studies of animal evolution. Only by fully engaging with the challenges of devising testable scenarios will we be able to tell where along the spectrum of science and fiction our understanding of animal body plan evolution will finally come to rest.”

2015

Sorry, Darwin: Chemistry never made the transition to Biology, Bhakti Niskama Shanta, Research · November 2015, excerpt:  “Abiogenesis was popular for years as an explanatory theory of self-assembly as the starting point for chemical evolution. Recently however, the abiogenesis hypothesis has been experiencing critical shortcomings, and rapid advancements in cellular biology have led biologists to seriously doubt the veracity of this hypothesis. The present article aims at summarizing a few crucial scientific facts, which are leading us towards a paradigm shift in our understanding of the ontogenesis of life.”

Limits in the evolution of biological form: a theoretical morphologic perspective, George R. McGhee Jr., 2015, published by the Royal Society. Excerpt: “Limits in the evolution of biological form can be empirically demonstrated by using theoretical morphospace analyses, and actual analytic examples are given for univalved ammonoid shell form,”

A Surprise Source of Life’s Code, Quanta Magazine, Emily Singer, August 31, 2015: Emerging data suggests the seemingly impossible; that mysterious new genes arise from “junk” DNA.

Huneman, Philippe, Chapter 4 Selection, Springer Science+Business Media Dordrecht 2015 37 T. Heams et al. (eds.), Handbook of Evolutionary Thinking in the Sciences, DOI 10.1007/978-94-017-9014-7_4. Excerpt from abstract: “One of Darwin’s major contributions to our understanding of evolution, namely natural selection, seems a very simple idea. However natural selection is a very subtle concept and biologists and philosophers have been struggling for decades to make sense of it and justify its explanatory power. In this chapter, first I present the most general formulations of natural selection in terms of necessary conditions, and I argue that none of them capture all the aspects of the concept. Second, I question the explanatory status of selection, asking what exactly it is supposed to explain, and considering its relationship with stochastic factors (i.e. genetic drift). Second, I investigate its metaphysical status, asking whether it can be seen as a law, and to what extent it would deprive evolution of any contingency. The last section presents controversies about the units and levels of selection, and, after exposing the philosophical assumptions proper to various positions, sketches a pluralist conception.”

 Voje KL, Holen ØH, Liow LH, Stenseth NC. The role of biotic forces in driving macroevolution: beyond the Red Queen,  2015, Proc. R. Soc. B 282: 20150186. Abstract extract: “A multitude of hypotheses claim that abiotic factors are the main drivers of macro evolutionary change. By contrast, Van Valen’s Red Queen hypothesis is often put forward as the sole representative of the view that biotic forcing is the main evolutionary driver. This imbalance of hypotheses does not reflect our current knowledge: theoretical work demonstrates the plausibility of biotically driven long-term evolution, whereas empirical work suggests a central role for biotic forcing in macroevolution.”

Impossible of Macroevolution of New Species via Changing of Chromosome Number Mutation and Structural Mutation (Invalid chromosomal speciation Theory): Darwin’s Theory and Neo- Darwinian Theory Oppose it, Muhmmad Abdul Ahad and A.S.M. Anas Ferdous, Martinia,  Vol.6 No.2 Page: 68-84, May, 2015. A literature review demonstrating that hybridization cannon cause macroevolution.

Benton MJ. 2015 Exploring macroevolution using modern and fossil data. Proc. R. Soc. B 282: 20150569, Abstract: “Macroevolution, encompassing the deep-time patterns of the origins of modern biodiversity, has been discussed in many contexts. Non-Darwinian models such as macromutations have been proposed as a means of bridging seemingly large gaps in knowledge, or as a means to explain the origin of exquisitely adapted body plans. However, such gaps can be spanned by new fossil finds, and complex, integrated organisms can be shown to have evolved piecemeal. For example, the fossil record between dinosaurs and Archaeopteryx has now filled up with astonishing fossil intermediates that show how the unique plexus of avian adaptations emerged step by step over 60 Myr. - - - “

Koonin EV. 2016 The meaning of biological information. Phil. Trans. R. Soc. A 374: 20150065. Abstract: “Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. - - - Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.”

 

Lindholm, Markus, DNA Dispose, but Subjects Decide. Learning and the Extended Synthesis, Biosemiotics (2015) 8:443–461.  Abstract: “Adaptation by means of natural selection depends on the ability of populations to maintain variation in heritable traits. According to the Modern Synthesis this variation is sustained by mutations and genetic drift. Epigenetics, evodevo, niche construction and cultural factors have more recently been shown to contribute to heritable variation, however, leading an increasing number of biologists to call for an extended view of speciation and evolution. An additional common feature across the animal kingdom is learning, defined as the ability to change behavior according to novel experiences or skills. Learning constitutes an additional source for phenotypic variation, and change in behavior may induce long lasting shifts in fitness, and hence favor evolutionary novelties. Based on published studies, I demonstrate how learning about food, mate choice and habitats has contributed substantially to speciation in the canonical story of Darwin’s finches on the Galapagos Islands. Learning cannot be reduced to genetics, because it demands decisions, which requires a subject. Evolutionary novelties may hence emerge both from shifts in allelic frequencies and from shifts in learned, subject driven behavior. The existence of two principally different sources of variation also prevents the Modern Synthesis from self-referring explanations.”

Tree of Life Reveals Clock-Like Speciation and Diversification, S. Blair Hedges et al, Mol. Biol. Evol. 32(4):835–845, March 3, 2015.  Abstract:  “Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding --- . Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.

Updating Darwin: Information and entropy drive the evolution of life, Irun R. Cohen, https://f1000research.com/articles/5-2808/v1,  2016. A claim that the basis of life is information. Abstract excerpt: “The evolution of species, according to Darwin, is driven by struggle – by competition between variant autonomous individuals for survival of the fittest and reproductive advantage; the outcome of this struggle for survival is natural selection. The Neo-Darwinians reframed natural selection in terms of DNA: inherited genotypes directly encode expressed phenotypes; a fit phenotype means a fit genotype – thus the evolution of species is the evolution of selfish, reproducing individual genotypes. --- Four general characteristics of advanced forms of life are not easily explained by this Neo-Darwinian paradigm: 1) Dependence on cooperation rather than on struggle, manifested by the microbiome, ecosystems and altruism; 2) The pursuit of diversity rather than optimal fitness, manifested by sexual reproduction; 3) Life’s investment in programmed death, rather than in open-ended survival; and 4) The acceleration of complexity, despite its intrinsic fragility. ---Here I discuss two mechanisms that can resolve these paradoxical features; both mechanisms arise from viewing life as the evolution of information. - - - ”

 

Mutation—The Engine of Evolution: Studying Mutation and Its Role in the Evolution of Bacteria, Ruth Hershber, Rachel & Menachem Mendelovitch, Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a018077, Abstract: ”Mutation is the engine of evolution in that it generates the genetic variation on which the evolutionary process depends. To understand the evolutionary process we must therefore characterize the rates and patterns of mutation. Starting with the seminal Luria and Delbruck fluctuation experiments in 1943, studies utilizing a variety of approaches have revealed much about mutation rates and patterns and about how these may vary between different bacterial strains and species along the chromosome and between different growth conditions. This work provides a critical overview of the results and conclusions drawn from these studies, of the debate surrounding some of these conclusions, and of the challenges faced when studying mutation and its role in bacterial evolution."

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution, Dawn Thompson, Aviv Regev, and Sushmita Roy, www.annualreviews.org, From Network Reconstruction to Evolution, 2015, Abstract: “Regulation of gene expression is central to many biological processes. Although reconstruction of regulatory circuits from genomic data alone is therefore desirable, this remains a major computational challenge. Comparative approaches that examine the conservation and divergence of circuits and their components across strains and species can help reconstruct circuits as well as provide insights into the evolution of gene regulatory processes and their adaptive contribution. In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level. Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequences to functional data. We highlight how these methods use evolutionary conservation and divergence to reliably detect regulatory components as well as estimate the extent and rate of divergence. Finally, we discuss the promise and open challenges in linking regulatory divergence to phenotypic divergence and adaptation.”

Forterre P., The universal tree of life: an update, Front. Microbiol. 6:717 (2015).  Excerpt: “I propose here an updated version of Woese’s universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented.”

Is there a unique process which governs macroevolution?, by Tonći Kokic, (Nova prisutnost 13 (2015) 3, 319-336) illustrates a continuing problem for evolutionists.  There is no consensus on the definitions of microevolution and macroevolution.  Some think they are essentially the same thing, with macroevolution resulting from a lengthy series of microevolution.  Others think they are different, with macroevolution depending upon unique processes which do not occur in microevolution.  Without conclusively convincing examples of macroevolution (major change in morphology) the debate may continue for some time.

Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum,  Sebastian Matuszewski, Joachim Hermisson,  and Michael Kopp, Genetics, Vol. 200, 1255–1274 August 2015, Abstract excerpt: “Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so called adaptive-walk models consider adaptation from the successive fixation of de novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from preexisting standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles.”

Novelty and Innovation in the History of Life by Douglas H. Erwin (Current Biology, October 5, 2015) reviews the relationship between the appearance of morphological novelty and environmental change in the fossil record , and suggests that the modern synthesis assumption of novelty first and adaptation second  may have to be reconsidered.

A Philosophical Perspective on Evolutionary Systems Biology, Maureen A. O’Malley, Orkun S. Soyer, and Mark L. Siegal, Biol Theory (2015) 10:6–17:  “Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis.”

Evolution 2.0: Breaking the Deadlock Between Darwin and Design, Perry Marshall, Benbella Books, Inc., September 1, 2015:  The book records the experience of a computer engineer as he spent years reviewing the history of evolution and the current status of microbiology. He concluded that life is far more complex than assumed by the modern synthesis, and that DNA includes a very sophisticated code that controls and sustains the evolution and preservation of life.

Laland, K., N,, et al, 2015, The extended evolutionary synthesis: its structure, assumptions and predictions. Proc. R. Soc. B, 282: 20151019. The authors claim the modern synthesis does need upgrading but that the changes will be complementary rather than revolutionary. Abstract extract: “The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework.” Excerpt from conclusion: “Evolutionary biology has never been more vibrant, and it would be a distortion to characterize it as in a (Kuhnian) state of crises. In the EES, all processes central to contemporary evolutionary theory (e.g. natural selection, genetic drift, Mendelian inheritance), and its empirical findings, remain important; in this respect, the EES requires no ‘revolution’. In fact, modern thinking in philosophy of science challenges the hypothesis that scientific change occurs through a single kind of revolution. Nevertheless, our analysis suggests that the EES is more than simply an extension of ‘business as usual’ science: it requires conceptual change . The additional evolutionary processes that the EES highlights are more than just nonessential ‘add-ons’ and may be as important in shaping evolution as those recognized within the field over the past century. Consequently, the requisite changes are non-trivial. Irrespective of how this debate unfolds, researchers will continue to make use of the existing quantitative machinery of evolutionary theory; indeed, formal models that incorporate aspects of developmental plasticity, inclusive inheritance and niche construction are already being developed.”

How complexity originates: The evolution of animal eyes, Todd H. Oakley1 and Daniel I. Speiser, bioRxiv preprint doi: https://doi.org/10.1101/017129,  March 26, 2015, Excerpt: “Here, we first sketch historical perspectives on trait origins and argue that new technologies offer key new insights. Next, we articulate four open questions about trait origins. To address them, we define a research program to break complex traits into components and study the individual evolutionary histories of those parts.”

A Surprise for Evolution in Giant Tree of Life, Emily Singer, Quanta Magazine, May 5, 2015. The subtitle is: “Researchers build the world’s largest evolutionary tree and conclude that species arise because of chance mutations — not natural selection”.

Evolution beyond neo-Darwinism: a new conceptual framework, Denis Noble, The Journal of Experimental Biology, 2015.  According to Noble, “Experimental results in epigenetics and related fields of biological research show that the Modern Synthesis (neo-Darwinist) theory of evolution requires either extension or replacement.”  He then argues that replacement is appropriate because “In retrospect, neo-Darwinism can be seen to have oversimplified biology and over-reached itself in its rhetoric. By so conclusively excluding anything that might be interpreted as Lamarckism, it assumed what couldn’t be proved.”  He supported these statements with detailed discussion about the differences in the understanding of cellular structure between 1930 and today.  In summary, noble states that all of the biological information transmitted to the next generation is not contained in the DNA. Rather, there is a network of information contained in various cellular components.  Both the cell and the DNA have to be replicated to provide complete transfer of all hereditary information.  In other words, the “gene”, envisioned as a sequence of code in the DNA, does not contain all of the information necessary for reproduction and evolution.

Evolution beyond neo-Darwinism: a new conceptual framework, Denis Noble, The Journal of Experimental Biology (2015) doi:10.1242/jeb.106310: Abstract: “Experimental results in epigenetics and related fields of biological research show that the Modern Synthesis (neo-Darwinist) theory of evolution requires either extension or replacement. This article examines the conceptual framework of neo-Darwinism, including the concepts of ‘gene’, ‘selfish’, ‘code’, ‘program’, ‘blueprint’, ‘book of life’, ‘replicator’ and ‘vehicle’. This form of representation is a barrier to extending or replacing existing theory as it confuses conceptual and empirical matters. These need to be clearly distinguished. In the case of the central concept of ‘gene’, the definition has moved all the way from describing a necessary cause (defined in terms of the inheritable phenotype itself) to an empirically testable hypothesis (in terms of causation by DNA sequences). Neo-Darwinism also privileges ‘genes’ in causation, whereas in multi-way networks of interactions there can be no privileged cause. An alternative conceptual framework is proposed that avoids these problems, and which is more favorable to an integrated systems view of evolution”.

McLysaght A, and  Guerzoni D., New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Phil. Trans. R. Soc. B 370: 20140332 (2015).  Excerpt; “The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages.”

Our ideas about vertebrate evolution challenged by a new tree of life, Phys.ord, 6 December 2016, by Benedict King, John Long And Mike Lee, Excerpt: “Several studies have strongly argued that placoderms are the direct ancestors of all other jawed vertebrates, a huge branch of the tree of life that includes mammals, birds, reptiles, amphibians and most fish.”

Spontaneous mutations and the origin and maintenance of quantitative genetic variation, Wen Huang et al, 2016.  eLife.14625, 1-23.  Abstract:  Mutation and natural selection shape the genetic variation in natural populations. Here, we directly estimated the spontaneous mutation rate by sequencing new Drosophila mutation accumulation lines maintained with minimal natural selection. We inferred strong stabilizing natural selection on quantitative traits because genetic variation among wild-derived inbred lines was much lower than predicted from a neutral model and the mutational effects were much larger than allelic effects of standing polymorphisms. Stabilizing selection could act directly on the traits, or indirectly from pleiotropic effects on fitness. However, our data are not consistent with simple models of mutation-stabilizing selection balance; therefore, further empirical work is needed to assess the balance of evolutionary forces responsible for quantitative genetic variation.

Scott F. Gilbert and R. Rice. (2016). 3rd. Principles of Differentiation and Morphogenesis. Epstein's Inborn Errors of Development: The Molecular Basis of Clinical Disorders on Morphogenesis. 9-21. https://works.swarthmore.edu/fac-biology/436. Excerpts: “Developmental biology is the science connecting genetics with anatomy, making sense out of both. The body builds itself from the instructions of the inherited DNA and the cytoplasmic system that interprets the DNA into genes and creates intracellular and cellular networks to generate the observable phenotype. Even ecological factors such as diet and stress may modify the DNA such that different phenotypes can be constructed from the same DNA. … With few exceptions (e.g., lymphocytes and blood cells), every cell nucleus in the body contains the complete genome established in the fertilized egg. In molecular terms, the DNAs of all differentiated cells within an organism are identical. … How, then, is the inherited repertoire of genes differentially expressed during development? It appears that this can be accomplished at the 4 major steps of protein synthesis. Some genes are regulated at different steps in different cells, and certain genes can be regulated at multiple steps in the same cell.”

Rethinking Evolution, J. Joseph, 2016. This online book presents unique concepts of speciation supported by considerable technical detail.  It argues that the modern synthesis is not compatible with the fossil record because the Darwinian concept of very gradual change over very long periods of time is not consistent with the way speciation really occurs.

DNA as information, Wills, Peter R., Phil. Trans. R. Soc. A.37420150417, 2016; the paper addresses the difficulty of understanding how the cell interprets the information in DNA. Excerpt; “To understand DNA's biological action, one must go to the detailed molecular level. And then one also fails to find any simple answer in the DNA itself, because single molecules can have vastly different biological effects, covering the entire range of possibilities depending on the molecular biological context, even though they are identical except for the exchange of a particular one of the 10⁹ nucleotide moieties of a genome, most such exchanges having very little effect. This drives us immediately to the conclusion that the DNA in organisms functions as information  and that the internal DNA-dependent dynamics of cells embody functional information processing, that is, computation. DNA-based molecular biological computation can be said to control, perhaps even ‘direct’, the entire panoply of biochemical events occurring in cells.”

Barbieri M. 2016 A new theory of development: the generation of complexity in ontogenesis. Phil. Trans. R. Soc. A 374: 20150148. http://dx.doi.org/10.1098/rsta.2015.0148. Abstract: “Today there is a very wide consensus on the idea that embryonic development is the result of a genetic program and of epigenetic processes. Many models have been proposed in this theoretical framework to account for the various aspects of development, and virtually all of them have one thing in common: they do not acknowledge the presence of organic codes (codes between organic molecules) in ontogenesis. Here it is argued instead that embryonic development is a convergent increase in complexity that necessarily requires organic codes and organic memories, and a few examples of such codes are described. This is the code theory of development, a theory that was originally inspired by an algorithm that is capable of reconstructing structures from incomplete information, an algorithm that here is briefly summarized because it makes it intuitively appealing how a convergent increase in complexity can be achieved. The main thesis of the new theory is that the presence of organic codes in ontogenesis is not only a theoretical necessity but, first and foremost, an idea that can be tested and that has already been found to be in agreement with the evidence.”

Doolittle WF, Brunet TDP (2016) What Is the Tree of Life? PLoS Genet 12(4): e1005912. https://doi.org/10.1371/journal.pgen.1005912, 2016, Abstract; “A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.”

A new view of the tree of life, Laura A. Hug, et al., Nature Microbiology | Vol 1 | May 2016.  The paper describes how new microbiological technique are greatly expanding and altering the tree of life. Excerpt: “Early approaches to describe the tree of life distinguished organisms based on their physical characteristics and metabolic features. Molecular methods dramatically broadened the diversity that could be included in the tree because they circumvented the need for direct observation and experimentation by relying on sequenced genes as markers for lineages. Gene surveys, typically using the small subunit ribosomal RNA (SSU rRNA) gene, provided a remarkable and novel view of the biological world, but questions about the structure and extent of diversity remain. Organisms from novel lineages have eluded surveys, because many are invisible to these methods due to sequence divergence relative to the primers commonly used for gene amplification. Furthermore, unusual sequences, including those with unexpected insertions, may be discarded as artefacts.”

Understanding macroevolution through the origin of higher taxa, Simpson, C. 2016. Ecology, 97: 3246–3248. doi:10.1002/ecy.1550 as reviewed by T.S. Kemp in The origin of higher taxa: palaeobiological, developmental, and ecological perspectives. The University of Chicago Press, Chicago, Illinois, Excerpt from review: “I suspect that this is the path that will lead to a new evolutionary synthesis because it focuses our attention onto the mechanisms that produce phenotypic and ecological discontinuities. Those higher taxa that show a macroevolutionary lag between the developmental novelties at their origin and ecological innovations that proliferate when they become successful are the most promising cases for teasing apart how it all works. If ecological interactions between higher taxa are important factors in the duration of macroevolutionary lags, as Van Valen (1976) suggests, then we might have to embrace the reality and evolutionary significance of higher taxa.”

Undeniable: How Biology Confirms Our Intuition That Life Is Designed, Douglas Axe, Harperone, 2017. Excerpt: “Throughout his distinguished and unconventional career, engineer-turned-molecular-biologist Douglas Axe has been asking the questions that much of the scientific community would rather silence. - - - Starting with the hallowed halls of academic science, Axe dismantles the widespread belief that Darwin’s theory of evolution is indisputably true, showing instead that a gaping hole has been at its center from the beginning. He then explains in plain English the science that proves our design intuition scientifically valid.”

Genetic drift, selection and the evolution of the mutation rate ,  Michael Lynch,  October 2016, Nature Reviews Genetics, 17(11):704-714,  Abstract : “ As one of the few cellular traits that can be quantified across the tree of life, DNA-replication fidelity provides an excellent platform for understanding fundamental evolutionary processes. Furthermore, because mutation is the ultimate source of all genetic variation, clarifying why mutation rates vary is crucial for understanding all areas of biology. A potentially revealing hypothesis for mutation-rate evolution is that natural selection primarily operates to improve replication fidelity, with the ultimate limits to what can be achieved set by the power of random genetic drift. This drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.”

 

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process , James A. Shapiro , Biology 2016, 5, 27; doi:10.3390/biology5020027, Abstract: “Abstract: The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. …  Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.”

Editorial Overview: Development, regulation and evolution of organ systems. Cassandra G Extavour, and Leslie Pick, Curr Opin Insect Sci. 2016 February ; 13: vii–ix,  Excerpt; “The collected articles in this issue share a comparative focus and address the development and regulation of different organ systems, with particular emphases on key evolutionary innovations.”

High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays, Emily A. Ellis, Todd H. Oakley, 2016, Current Biology 26, 1916–1921: Excerpt from abstract: “These results document an association between the origin of bioluminescent courtship and increased accumulation of species, supporting theory predicting sexual selection increases rates of speciation at macroevolutionary scales to influence global patterns of biodiversity.”

Tickle C, Urrutia AO. 2016 Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era. Phil. Trans. R. Soc. B 372: 20150473, Abstract excerpt: “A fundamental question in biology is how the extraordinary range of living organisms arose. In this theme issue, we celebrate how evolutionary studies on the origins of morphological diversity have changed over the past 350 years since the first publication of the Philosophical Transactions of The Royal Society. Current understanding of this topic is enriched by many disciplines, including anatomy, palaeontology, developmental biology, genetics and genomics. Development is central because it is the means by which genetic information of an organism is translated into morphology. The discovery of the genetic basis of development has revealed how changes in form can be inherited, leading to the emergence of the field known as evolutionary developmental biology (evo-devo).”

Darwin and Mendel today: a comment on “Limits of imagination: the 150th Anniversary of Mendel’s Laws, and why Mendel failed to see the importance of his discovery for Darwin’s theory of evolution, Yongsheng Liu and Xiuju Li, Genome 59: 75–77 (2016): “We comment on a recent paper by Rama Singh, who concludes that Mendel deserved to be called the father of genetics, and Darwin would not have understood the significance of Mendel’s paper had he read it. We argue that Darwin should have been regarded as the father of genetics not only because he was the first to formulate a unifying theory of heredity, variation, and development — Pangenesis, but also because he clearly described almost all genetical phenomena of fundamental importance, including what he called “prepotency” and what we now call “dominance” or “Mendelian inheritance”. The word “gene” evolved from Darwin’s imagined “gemmules”, instead of Mendel’s so-called “factors”. “(abstract)

In 2016, the Royal Society hosted New trends in evolutionary biology: biological, philosophical and social science perspectives.  The meeting addressed the claim that developments in evolutionary biology and adjacent fields call for revision of the standard theory of evolution (Darwinism).  Evolutionists calling for change are promoting an Extended Evolutionary Synthesis which they think might better explain recent discoveries in microbiology and genetics.  This represents continuing effort as indicated by The extended evolutionary synthesis: its structure, assumptions and predictions which the Society published in August of 2015.  Kevin N. Laland, https://doi.org/10.1098/rspb.2015.1019  EES  https://royalsocietypublishing.org

Phenotypic Novelty in EvoDevo: The Distinction Between Continuous and Discontinuous Variation and Its Importance in Evolutionary Theory, Tim Peterson and Gerd B. Muller, Evol Biol (2016) 43:314–335.  Excerpt: “It is argued that an EvoDevo-based approach to novelty is inherently mechanistic, treats the phenotype as an agent with generative potential, and prompts a distinction between continuous and discontinuous variation in evolutionary theory.”

Ball P. 2016 The problems of biological information. Phil. Trans. R. Soc. A 374: 20150072.  The author presents the opinion, supported by numerous references, that all of the information needed to sustain life is not included in the DNA.  The cell must be a system with a hierarchy of information levels that is far more complex than our most advanced computer systems.  He considers “the profound difficulty of understanding how the property of information encoding could have arisen from scratch in the prebiotic world”.  He further observes that “… there is no linear genotype-to-phenotype correspondence. There are more rules to learn, more systems to navigate.”

Quantitative Genetics and Macroevolution, PD Polly, Encyclopedia of Evolutionary Biology, Volume 2, 2016:  The article proposes that resolution of the macro micro dispute is hindered by lack of adequate tools for analyzing the fossil record.  Several recommendations are made for new techniques that might be able to analyze macro evolutionary processes.

Evolution of vertebrates: a view from the crest,  Stephen A. Green, Marcos Simoes-Costa, and Marianne E. Bronner, Nature. 2015 April 23; 520(7548): 474–482, Excerpt: “The origin of vertebrates was accompanied by the advent of a novel cell type: the neural crest,”

Novelty by Furcation and Fusion: How tree-like is evolution?, Todd H. Oakley, Department of Ecology Evolution and Marine Biology University of California, Santa Barbara, 2017, preprint, Abstract : “Novelty and innovation are fundamental yet relatively understudied concepts in evolution. We may study novelty phylogenetically, with a key question of whether evolution occurs by tree-like branching, or through exchange of distantly related parts in processes akin to horizontal transfer. Here, I argue that except at the lowest levels of biological organization, evolution is not usually tree-like. --- evolution often involves events that incorporate or fuse more distantly related parts into new units during evolution, which herein I call 'fusion'. Exon shuffling, horizontal gene transfer, introgression and co-option are such fusion processes at different levels of organization. - - - The ubiquity of processes that fuse distantly related parts has wide ranging implications for the study of macroevolution. For one, the central metaphor of a tree of life will often be violated, to the point where we may need a different metaphor, such as a ‘web of life’.

60 years ago, Francis Crick changed the logic of biology, Matthew Cobb, PLOS Biology, September 18, 2017.  Abstract:  “In September 1957, Francis Crick gave a lecture in which he outlined key ideas about gene function, in particular what he called the central dogma. These ideas still frame how we understand life. This essay explores the concepts he developed in this influential lecture, including his prediction that we would study evolution by comparing sequences."

The origin of animal multicellularity and cell differentiation, Thibaut Brunet and Nicole King, Dev Cell. 2017 October 23; 43(2): 124–140. doi:10.1016/j.devcel.2017.09.016. Excerpt from Introduction: “Every aspect of animal life – from morphology to physiology and behavior – requires the cooperation of thousands to billions of cells. In nearly all animals, the multicellular state is established in each generation through serial divisions of a single founding cell, the zygote. Under joint control by the genome and the environment, daughter cells produced by these divisions change shape, migrate, and selectively attach or detach to give rise to the adult body form through a process known as morphogenesis. In parallel, a process of cell differentiation under fine spatiotemporal control delineates the division of labor between the final cell types. The correct execution of this cellular choreography, repeated anew in every generation, is fundamental to the life of every animal on the planet. Yet, this type of complex development did not always exist. The discontinuous phylogenetic distribution of multicellularity and differences in cellular mechanisms argue that multicellularity evolved independently in at least 16 different eukaryotic lineages, including animals, plants, and fungi. Thus, the mechanisms underpinning animal multicellularity and spatially controlled cell differentiation were likely elaborated in the stem lineage of animals, building upon pathways present in their single-celled ancestors. Despite the centrality of multicellularity and cell differentiation to animal biology, their origins are little understood. What did the single-celled ancestors of animals look like? How and when did multicellularity and cell differentiation evolve, and what were the underlying molecular mechanisms? Did features of the single-celled progenitors of animals facilitate the early evolution of multicellularity? Conversely, did this single-celled ancestry exert constraints upon the form and function assumed by early animal ancestors?

Austin L. Hughes; The Neutral Theory of Evolution, by Chase Nelson, https://inference-review.com/article/the-neutral-theory-of-evolution/. This essay reviews the neutral theory of evolution and goes on to cite numerous examples of changes in lifeforms that are not driven by natural selection. Most surprisingly, it cites examples of species diverging by a loss of existing information rather than by a gain of new information by mutations.

Darwinism for the Genomic Age: Connecting Mutation to Diversification, Xia Hua and Lindell Bromham, 07 February 2017 | https://doi.org/10.3389/fgene.2017.00012, Excerpt from abstract: “A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness. Here we draw together empirical studies and theoretical concepts that may help to build links in the explanatory chain that connects mutation to diversification.”

Erwin DH. 2017 The topology of evolutionary novelty and innovation in macroevolution. Phil. Trans. R. Soc. B 372: 20160422. Abstract: “Sewall Wright’s fitness landscape introduced the concept of evolutionary spaces in 1932. George Gaylord Simpson modified this to an adaptive, phenotypic landscape in 1944 and since then evolutionary spaces have played an important role in evolutionary theory through fitness and adaptive landscapes, phenotypic and functional trait spaces, morphospaces and related concepts. Although the topology of such spaces is highly variable, from locally Euclidean to pre-topological, evolutionary change has often been interpreted as a search through a pre-existing space of possibilities, with novelty arising by accessing previously inaccessible or difficult to reach regions of a space. Here I discuss the nature of evolutionary novelty and innovation within the context of evolutionary spaces, and argue that the primacy of search as a conceptual metaphor ignores the generation of new spaces as well as other changes that have played important evolutionary roles. This article is part of the themed issue ‘Process and pattern in innovations from cells to societies.”

 Haldane’s The causes of evolution and the Modern Synthesis in evolutionary biology, Sahotra Sarkar, Journal of Genetics, Vol. 96, No. 5, November 2017, pp. 753–763, Abstract: This paper argues that Haldane’s The causes of evolution was the most important founding document in the emergence of the received view of evolutionary theory which is typically referred to as the Modern Synthesis. Whether or not this historical development is characterized as a synthesis (which remains controversial), this paper argues the most important component of the emergence of the received view consisted of showing how the formal rules of Mendelian inheritance are based on (or emerge from) the material basis of heredity established by classical genetics primarily through the experimental work on Drosophila genetics of the Morgan school in the 1910s and 1920s. This is one of the most important achievements of Haldane’s book. Thus this paper rejects both (i) the view that the synthesis was a unification of biometry and Mendelism and (ii) the claim that it arose from work primarily done in the late 1930s and 1940s by naturalists rather than theoretical population and classical experimental geneticists.”

A major, but not often discussed, problem with the modern synthesis is pointed out in “Seeing Emergent Physics Behind Evolution” (Jordana Cepelwicz, Quanta Magazine, August 31, 2017). The article documents an interview with Nigel Goldenfield, a physicist researching biology.  He observes that the last common ancestor assumed by the modern synthesis was a relatively sophisticated and complex lifeform.  It had genes and cellular structure that could not have appeared spontaneously.  If the origin of life was spontaneous, it had to evolve by different processes prior to the appearance of the last common ancestor.

 

Developmental push or environmental pull? The causes of macroevolutionary dynamics, Douglas H. Erwin, HPLS (2017) 39:36, Excerpt: “Comparative studies of developmental evolution, however, have implicated the origin of variants as a driving macroevolution force. In particular, the repatterning of gene regulatory networks provides new insights into the origins of developmental novelties. This raises the question of whether macroevolution has been pulled by the generation of environmental opportunity, or pushed by the introduction of new morphologies. The contrast between distributional and origination scenarios has implications for understanding evolutionary novelty and innovation and how macro evolutionary process may have evolved over time.”

On the origin of biological construction, with a focus on multicellularity. Jordi van Gestela and Corina E. Tarnitae, 11018–11026 | PNAS | October 17, 2017 | vol. 114 | no. 42. While Darwinism assumes very small increments of change continuing over very long periods of time, the authors observe that there had to be a series of major transitions along the way. “From a primordial soup of elements to the emergence of protocells, from single cells to multicellular organisms, and from multicellular organisms to animal groups, evolution has been punctuated by hierarchical evolutionary transitions (HET), whereby simple units assembled into groups that themselves became new units of biological organization”.  They proposed mythologies for organized studies of these HET, and concluded that: “we proposed an integrative, bottom-up approach to study the dynamics underlying HET in biological organization. Starting from the solitary ancestor and its life cycle, we discussed how the first life cycles with a group life stage could originate ; what properties characterize the first groups ; how selection could act on those properties and subsequently alter the organization of the groups ; and, finally, how new organizing principles could evolve and influence future organizational complexity . We argue that only by starting with the solitary ancestor and its life cycle, and studying these six questions, can we derive an understanding of the causal factors underlying HET.”

Approaches to Macroevolution: 1. General Concepts and Origin of Variation, David Jablonski, Evol Biol, 03 June 2017: The author claims there are many sources of variation and they are complex.  Abstract: “Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks.”

Approaches to Macroevolution: 2. Sorting of Variation, Some Overarching Issues, and General Conclusions David Jablonski,  Evol Biol (2017) 44:451–475,    “Approaches to macroevolution require integration of its two fundamental components, within a hierarchical framework. Following a companion paper on the origin of variation, I here discuss sorting within an evolutionary hierarchy.”

The old and new faces of morphology: the legacy of D’Arcy Thompson’s ‘theory of transformations’ and ‘laws of growth’, Arhat Abzhanov, Published by The Company of Biologists Ltd | Development (2017) 144, 4284-4297, Excerpt from abstract: “Thompson’s work was based on the ideas of Galileo and Goethe on morphology and of Russell on functionalism, but he was first to postulate that physical forces and internal growth parameters regulate biological forms and could be revealed via geometric transformations in morphological space. Such precise mathematical structure suggested a unifying generative process, as reflected in the title of the book. To Thompson it was growth that could explain the generation of any particular biological form, and changes in ontogeny, rather than natural selection, could then explain the diversity of biological shapes.”

Philippe Huneman and Denis M. Walsh (eds.), Challenging the Modern Synthesis: Adaptation, Development, and Inheritance, Oxford University Press, 2017, 368 pp. This book is a collection of papers by thirteen different contributors that discuss the many, continuing philosophical challenges to the modern synthesis.

Amitabh Joshi (Search for a Direct Proof of Natural Selection and the Tortuous Path to the Neo-Darwinian Synthesis , Resonance | June 2017, 525-548)  prepared a detailed review of the reaction of the scientific community to Darwin’s work during the half century following the publication of Origins.  Almost immediately recognizing the obvious flaws in Origins, various scientist proposed numerous imaginative hypothesis to hopefully rectify the errors.

Muller GB. 2017 Why an extended evolutionary synthesis is necessary. Interface Focus 7: 20170015. The author claims the modern synthesis requires significant change because it cannot account for recent discoveries as is. Abstract: “Since the last major theoretical integration in evolutionary biology—the modern synthesis (MS) of the 1940s—the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the ‘-omics’ revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology.”

The Evolution of Lactose Tolerance in Dairying Populations, Pascale Gerbault, Catherine Walker, Katherine Brown, Ekaterina YonovaDoing, and Mark G. Thomas The Oxford Handbook of the Archaeology of Diet Edited by Julia Lee-Thorp and M. Anne Katzenberg, 2017

The fundamental theorem of natural selection with mutations, William F. Basener and John C. Sanford, J. Math. Biol. (2018) 76:1589–1622, Excerpt from abstract: “Fisher did not include mutations in his model, but believed that mutations would provide a continual supply of variance resulting in perpetual increase in mean fitness, thus providing a foundation for neo-Darwinian theory. In this paper we re-examine Fisher’s Theorem, showing that because it disregards mutations, and because it is invalid beyond one instant in time, it has limited biological relevance. We build a differential equations model from Fisher’s first principles with mutations added, and prove a revised theorem showing the rate of change in mean fitness is equal to genetic variance plus a mutational effects term."

Physical foundations of biological complexity, Yuri I. Wolf et al,  September 11, 2018, 115 (37) | PNAS; the paper discusses the possibility that biological complexity can be explained by laws of physics and chemistry.

On the evolution of extreme structures: static scaling and the function of sexually selected signals, Devin M. O'Brien  et al, Behavior Volume 144, October 2018, Pages 95-108

Volume 144, October 2018, Pages 95-108. The paper explores the nature of extreme animal structures, such as the peacock’s tail and elephant tusks. Abstract: “The ‘positive allometry hypothesis’ predicts that ornaments and weapons of sexual selection will scale steeply when among-individual variation in trait size is compared with variation in overall body size. Intuitive and striking, this idea has been explored in hundreds of contemporary animal species and sparked controversy in paleobiologic over the function of exaggerated structures in dinosaurs and other extinct lineages. Recently, however, challenges to this idea have raised questions regarding the validity of the hypothesis. We address this controversy in two ways. First, we suggest the positive allometry hypothesis be applied only to morphological traits that function as visual signals of individual body size. Second, because steep scaling slopes make traits better signals than other body parts, we propose that tests of the positive allometry hypothesis compare the steepness of the scaling relationships of focal, putative signal traits to those of other body parts in the same organism (rather than to an arbitrary slope of 1). We provide data for a suite of 29 extreme structures and show that steep scaling relationships are common when structures function as signals of relative body size, but not for comparably extreme structures that function in other contexts. We discuss these results in the context of animal signaling and sexual selection, and conclude that patterns of static scaling offer powerful insight into the evolution and function of disproportionately large, or extreme, animal structures. Finally, using data from a ceratopsid dinosaur and a pterosaur, we show that our revised test can be applied to fossil assemblages, making this an exciting and powerful method for gleaning insight into the function of structures in extinct taxa.

Physical foundations of biological complexity, Yuri . Wolf , Mikhail . Katsnelsonb , and Eugene V. Koonina, PNAS | vol. 115 | no. 37, 2018, Abstract: “Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today’s physics provide an explanatory framework for understanding the evolution of biological complexity? We argue that the physical foundation for understanding the origin and evolution of complexity can be gleaned at the interface between the theory of frustrated states resulting in pattern formation in glass-like media and the theory of selforganized criticality (SOC). On the one hand, SOC has been shown to emerge in spin-glass systems of high dimensionality. On the other hand, SOC is often viewed as the most appropriate physical description of evolutionary transitions in biology. We unify these two faces of SOC by showing that emergence of complex features in biological evolution typically, if not always, is triggered by frustration that is caused by competing interactions at different organizational levels. Such competing interactions lead to SOC, which represents the optimal conditions for the emergence of complexity. Competing interactions and frustrated states permeate biology at all organizational levels and are tightly linked to the ubiquitous competition for limiting resources. This perspective extends from the comparatively simple phenomena occurring in glasses to large-scale events of biological evolution, such as major evolutionary transitions. Frustration caused by competing interactions in multidimensional systems could be the general driving force behind the emergence of complexity, within and beyond the domain of biology.”

Stoeckle M.Y. and Thaler D.S., Why should mitochondria define species?  Human Evolution Vol. 33 - n. 1-2 (1-30) – 2018, Abstract:  “More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes—drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years.”

Influence of Gene Expression Gradients on Positional Information Content in Fly Embryos,  Alasdair Hastewell,  Massachusetts Institute Of Technology, June 2018. The first chapter of this thesis is a literature review of cell positioning information, beginning with the work of D'Arcy Thomson in 1917.

Modern Synthesis, Vertiga Singh and Kiran Singh, Springer International Publishing AG 2018 J. Vonk, T.K. Shackelford (eds.), Encyclopedia of Animal Cognition and Behavior, https://doi.org/10.1007/978-3-319-47829-6_203-1.  The article explains why and extended synthesis is required.  Epigenetics, and some other factors, which were unknown when the modern synthesis was formulated are required to explain macroevolution.

The Rate of Molecular Evolution When Mutation May Not Be Weak, A.P. Jason de Koning, and Bianca D. De  Sanctis, bioRxiv preprint doi: https://doi.org/10.1101/259507. August 28, 2018 Abstract: One of the most fundamental rules of molecular evolution is that the rate of neutral evolution equals the mutation rate and is independent of effective population size. This result lies at the heart of the Neutral Theory, and is the basis for numerous analytic approaches that are widely applied to infer the action of natural selection across the genome and through time, and for dating divergence events using the molecular clock. However, this result was derived under the assumption that evolution is strongly mutation-limited, and it has not been known whether it generalizes across the range of mutation pressures or the spectrum of mutation types observed in natural populations. Validated by both simulations and exact computational analyses, we present a direct and transparent theoretical analysis of the Wright-Fisher model of population genetics, which shows that some of the most important rules of molecular evolution are fundamentally changed by considering recurrent mutation’s full effect. Surprisingly, the rate of the neutral molecular clock is found to have population-size dependence and to not equal the mutation rate in general. This is because, for increasing values of the population mutation rate parameter (θ), the time spent waiting for mutations quickly becomes smaller than the cumulative time mutants spend segregating before a substitution, resulting in a net deceleration compared to classical theory that depends on the population mutation rate. Furthermore, selection exacerbates this effect such that more adaptive alleles experience a greater deceleration than less adaptive alleles, introducing systematic bias in a wide variety of methods for inferring the strength and direction of natural selection from across-species sequence comparisons. Critically, the classical weak mutation approximation performs well only when θ <0. 1,a threshold that many biological populations seem to exceed.

Amphioxus functional genomics and the origins of vertebrate gene regulation.  Ferdinand Marlétaz, et al, Nature| Vol 564 | 6 Dec., 2018, Excerpt: “Taken together, these observations indicate that the two rounds of WGD (whole genome duplication) not only caused an expansion and diversification of gene repertoires in vertebrates, but also allowed functional and expression specialization of the extra copies by increasing the complexity of their gene regulatory landscapes. We suggest that these changes to the gene regulatory landscapes underpinned the evolution of morphological specializations in vertebrates.”

Tanghe, K.B., De Tiège, A., Pauwels, L. et al. What’s wrong with the modern evolutionary synthesis? A critical reply to Welch (2017). Biol Philos 33, 23 (2018). https://doi.org/10.1007/s10539-018-9633-3,  Excerpt: “It is probably no coincidence that the question of how the modern synthesis emerged, remains “one of the most vexing problems in the history of biology”), despite the existence of a veritable ‘Synthesis Industry’. So vexing in fact, that scholars tend to avoid the subject of its historical origin altogether. This suggests that its true nature is still poorly understood, which, in turn, may help explain why it is a quite contentious paradigm.” The paper concludes that the modern synthesis requires revision to account for discoveries made in the last half century. It further opines that revision will be difficult because there is not a common understanding of what the modern synthesis is.”

Dynamic pattern generation in cell membranes: Current insights into membrane organization, Krishnan Raghunathana and Anne K. Kenworthy, Biochimica et Biophysica Acta (BBA) - Biomembranes, Volume 1860, Issue 10, October 2018, Pages 2018-203, Abstract: “It has been two decades since the lipid raft hypothesis was first presented. Even today, whether these nanoscale cholesterol-rich domains are present in cell membranes is not completely resolved. However, especially in the last few years, a rich body of literature has demonstrated both the presence and the importance of non-random distribution of biomolecules on the membrane, which is the focus of this review. These new developments have pushed the experimental limits of detection and have brought us closer to observing lipid domains in the plasma membrane of live cells. Characterization of biomolecules associated with lipid rafts has revealed a deep connection between biological regulation and function and membrane compositional heterogeneities. Finally, tantalizing new developments in the field have demonstrated that lipid domains might not just be associated with the plasma membrane of eukaryotes but could potentially be a ubiquitous membrane-organizing principle in several other biological systems. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.”

Cellular Control of Time, Size, and Shape in Development and Evolution, Richard A. Schneider, 2018, Chapter 7 in Cells in Evolutionary Biology, Excerpt: “…the theory that changes to the rate of growth and/or timing of events during ontogeny could alter the course of phylogeny continued as a subplot to the main story of evolution until becoming more generally accepted during the rebirth of evo-devo in the 1970s. Even Darwin in his Origin of Species was vexed and tantalized by the correlations of growth observed in embryos, which he acknowledged were a potential source of evolutionary variation”,

Origins of building blocks of life: A review, Norio Kitadai and Shigenori Maruyama,  Geoscience Frontiers, Volume 9, Issue 4, July 2018, Pages 1117-1153, thirty five page review of life origin research.  Excerpt: “How and where did life on Earth originate? To date, various environments have been proposed as plausible sites for the origin of life. However, discussions have focused on a limited stage of chemical evolution, or emergence of a specific chemical function of proto-biological systems. It remains unclear what geochemical situations could drive all the stages of chemical evolution, ranging from condensation of simple inorganic compounds to the emergence of self-sustaining systems that were evolvable into modern biological ones. In this review, we summarize reported experimental and theoretical findings for prebiotic chemistry relevant to this topic, including availability of biologically essential elements (N and P) on the Hadean Earth, abiotic synthesis of life’s building blocks (amino acids, peptides, ribose, nucleobases, fatty acids, nucleotides, and oligonucleotides), their polymerizations to bio-macromolecules (peptides and oligonucleotides), and emergence of biological functions of replication and compartmentalization.”

Standing genetic variation as the predominant source for adaptation of a songbird, Yu-Ting Laia et al, 2152–2157 | PNAS | February 5, 2019 | vol. 116 | no. 6. Abstract excerpt: “What kind of genetic variation contributes the most to adaptation is a fundamental question in evolutionary biology. By resequencing genomes of 80 individuals, we inferred the origin of genomic variants associated with a complex adaptive syndrome involving multiple quantitative traits, namely, adaptation between high and low altitudes, in the vinous-throated parrotbill in Taiwan. By comparing these variants with those in the Asian mainland population, we revealed standing variation in 24 noncoding genomic regions to be the predominant genetic source of adaptation”. Additional Excerpt: “It is a tenet of modern biology that species adapt through natural selection to cope with the ever-changing environment. By comparing genetic variants between the island and mainland populations of a passerine, we inferred the related age of genetic variants across its entire genome and suggest that preexisting standing variants played the predominant role in local adaptation. Our findings not only resolve a long-standing fundamental problem in biology regarding the genetic sources of adaptation, but imply that the evolutionary potential of a population is highly associated with its preexisting genetic variation.”

Competition-driven evolution of organismal complexity, Iaroslav Ispolatov, Evgeniia Alekseeva, Michael Doebeli3, PLOS Computational Biology,  October 3, 2019,  Abstract: “Non-uniform rates of morphological evolution and evolutionary increases in organismal complexity, captured in metaphors like “adaptive zones”, “punctuated equilibrium” and “blunderbuss patterns”, require more elaborate explanations than a simple gradual accumulation of mutations. Here we argue that non-uniform evolutionary increases in phenotypic complexity can be caused by a threshold-like response to growing ecological pressures resulting from evolutionary diversification at a given level of complexity. Acquisition of a new phenotypic feature allows an evolving species to escape this pressure but can typically be expected to carry significant physiological costs. Therefore, the ecological pressure should exceed a certain level to make such an acquisition evolutionarily successful. We present a detailed quantitative description of this process using a microevolutionary competition model as an example. The model exhibits sequential increases in phenotypic complexity driven by diversification at existing levels of complexity and a resulting increase in competitive pressure, which can push an evolving species over the barrier of physiological costs of new phenotypic features.”

How Does the Regulatory Genome Work?,  Sorin Istrail and Isabelle S. Peter, Journal Of Computational Biology , Volume 26, Number 7, 2019 Mary Ann Liebert, Inc. Pp. 685–695, Abstract excerpt: “The regulatory genome controls genome activity throughout the life of an organism. This requires that complex information processing functions are encoded in, and operated by, the regulatory genome. Although much remains to be learned about how the regulatory genome works, we here discuss two cases where regulatory functions have been experimentally dissected in great detail and at the systems level, and formalized by computational logic models. Both examples derive from the sea urchin embryo, but assess two distinct organizational levels of genomic information processing. The first example shows how the regulatory system of a single gene, endo16, executes logic operations through individual transcription factor binding sites and cis-regulatory modules that control the expression of this gene. The second example shows information processing at the gene regulatory network (GRN) level.”

Genetic control of cellular morphogenesis in Müller glia, Mark Charlton-Perkins, et al, Glia. 2019;67:1401–1411. Excerpt from introduction: “The genetic control of postmitotic cell shapes is very poorly understood, especially for the cells making up the central nervous system (CNS), that is, the neurons and glia. These cells assume an immense variety of cell type-specific morphologies necessary for building their precise connections during development. Glial cells have elaborate morphologies that facilitate their ability to make precise contacts with specific partner neurons, blood vessels, and other glia.”

Mike Levin on electrifying insights into how bodies form; Using bioelectricity to study how cells make collective decisions about growth and shape, Lindsay Brownell, July 26, 2019, https://wyss.harvard.edu/news/mike-levin-on-electrifying-insights-into-how-bodies-form/ The article describes how bioelectric information within the cell influences morphology.

 Manicka S, and Levin M., The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis. Phil. Trans. R. Soc. B 374: 20180369, 2019. Excerpt from Introduction: “Anatomical pattern control is one of the most remarkable processes in biology. Large-scale spatial order, involving numerous tissues and organs in exquisitely complex yet invariant topological relationships, must be established by embryogenesis—a process in which genetic clones of a single gamete cooperate to construct a functional body. This is often modelled as a feed-forward process with complex anatomy as an emergent result. However, a key part of robustness across many levels of organization is the remarkable plasticity revealed by regulative development and regeneration which can achieve a specific patterning outcome despite a diverse range of starting configurations and perturbations. For example, mammalian embryos can be split in half or fused; resulting in normal animals Salamanders can regenerate perfect copies of amputated legs, eyes, jaws, spinal cords and ovaries. Remarkably, scrambled organs move to correct positions to implement normal craniofacial pattern despite radically displaced configurations at early developmental stages. Cells can work together to maintain a body plan over decades, but occasional defections in this process result in a return to unicellular behaviors such as cancer. Yet, this process is not necessarily unidirectional, as tumor reprogramming allows cells to functionally rejoin a metazoan collective. Such dynamic plasticity and anatomical homeostasis represent clear examples of pattern memory and flexible decision making by cells, tissues and organs: systems-level functions such as recognizing damage, building exactly what is needed in the right location, and ceasing activity when the correct target morphology is achieved. One of the key aspects of a homeostatic process is a stored set point, to which the system regulates. Classic data in deer antler regeneration and recent work showing permanent reprogramming of planarian target morphology without genomic editing reveal the ability to alter the anatomical set point in vivo. It is crucial to understand how living systems encode and regulate toward specific patterning outcomes, and where on Wiener’s cognitive scale the decision-making processes of patterning systems lie.

Early animal evolution: a morphologist’s view, Claus Nielsen, R. Soc. open sci. 6: 190638., 2019. Abstract excerpt: “Two hypotheses for the early radiation of the metazoans [animals with specialized cells and organs] are vividly discussed in recent phylogenomic studies, the ‘Poriferafirst’ hypothesis, which places the poriferans as the sister group of all other metazoans, and the ‘Ctenophora-first’ hypothesis, which places the ctenophores as the sister group to all other metazoans. It has been suggested that an analysis of morphological characters (including specific molecules) could throw additional light on the controversy, and this is the aim of this paper.”

Nathan H. Lents et al, A biochemist’s crusade to overturn evolution misrepresents theory and ignores evidence, 7 February, 2019,  https://blogs.sciencemag.org/books/2019/02/07/darwin-devolves/: This online article cites numerous examples which purportedly prove errors in Michel Behe’s book Darwin Devolves: The New Science About DNA That Challenges Evolution.

Evolution: Remodeling Animal Body Plans, Gene Benjamin Prud’homme  and Nicolas Gompel, Current Biology 29, R623–R646, July 8, 2019.  Abstract: “Changes in Homeotic (Hox) gene regulation have long been thought to drive the evolution of animal body plans. Direct genetic evidence of their evolutionary role has, however, remained limited. A new study reveals how several mutations distributed across a gene network mask the phenotypic effects of a Hox gene’s evolution.”

Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution, Yang Liu, et al, Current Biology 29, 2157–2166 July 8, 2019, Excerpt: A major challenge for evolutionary biology is to understand how phenotypic evolution results from genomic divergence. Hox genes, a family of Homeobox-containing transcription factors that regulate differential development along the anterior-posterior animal axis, have been singled out as particularly important for body plan evolution. - - - Unbiased approaches, such as genetic linkage studies, often find that morphological traits are polygenic, and these studies have rarely implicated Hox genes as likely contributors to morphological variation. It is thus unclear precisely how Hox gene evolution contributes to differences in animal body plans.”

Connecting micro and macroevolution using genetic incompatibilities and natural selection on  additive genetic variance,  Greg M. Walter et al, University of Queensland, School of Biological Sciences, St. Lucia QLD 4072, Australia, bioRxiv preprint doi: https://doi.org/10.1101/520809,  January 16, 2019, excerpt: “Evolutionary biologists have long sought to identify the links between micro and macroevolution to better  understand how biodiversity is created. Despite the pursuit, it remains a challenge to understand how allele frequency changes correlate with the evolution of morphological diversity, and the build-up of reproductive isolation. To connect micro and macroevolution, we tested the adaptive importance of alleles underlying genetic incompatibilities, and the consequences for predicting evolutionary trajectories.”

Indirect genetic effects clarify how traits can evolve even when fitness does not, David N. Fisher and Andrew G. McAdam, Evolution Letters February 2019.  The paper discusses how social interaction within a population may cause traits to evolve without an increase in overall fitness.

Multiple macroevolutionary routes to becoming a biodiversity hotspot , J. Igea and A. J. Tanentzap, Sci. Adv. 2019; 5 : eaau8067 6 February 2019 , Abstract: “Why is species diversity so unevenly distributed across different regions on Earth? Regional differences in biodiversity may stem from differences in rates of speciation and dispersal and colonization times, but these hypotheses have rarely been tested simultaneously at a global scale. Our study reveals the macroevolutionary routes that have generated hotspots of mammal and bird biodiversity by analyzing the tempo and mode of diversification and dispersal within major biogeographic realms. Hotspots in tropical realms had higher rates of speciation, whereas those in temperate realms received more immigrant species from their surrounding regions. We also found that hotspots had higher spatial complexity and energy availability, providing a link between the environment and macroevolutionary history. Our study highlights how assessing differences in macroevolutionary history can help to explain why biodiversity varies so much worldwide.”

Danchin E´, Pocheville A, Huneman P., Early in life effects and heredity: reconciling neo-Darwinism with neo-Lamarckism under the banner of the inclusive evolutionary synthesis. Phil. Trans. R. Soc. B 374: 20180113 (2019) . Abstract excerpt; “Recent discoveries show that early in life effects often have long-lasting influences, sometimes even spanning several generations. Such intergenerational effects of early life events appear not easily reconcilable with strict genetic inheritance. However, an integrative evolutionary medicine of early life effects needs a sound view of inheritance in development and evolution. Here, we show how to articulate the gene-centered and non-gene-centered visions of inheritance. --- One surprising consequence of this integrative vision of inheritance is that early in life effects start much earlier than fertilization.”

Origin and Evolution of Deleterious Mutations in Horses,  Ludovic Orlando and Pablo Librado,  Genes 2019, 10, 649; doi:10.3390/genes10090649    Abstract: Domestication has changed the natural evolutionary trajectory of horses by favoring the reproduction of a limited number of animals showing traits of interest. Reduced breeding stocks hampered the elimination of deleterious variants by means of negative selection, ultimately inflating mutational loads. However, ancient genomics revealed that mutational loads remained steady during most of the domestication history until a sudden burst took place some 250 years ago. … . Our work illustrates the paradoxical effect of some conservation and improvement programs, which reduced the overall genomic fitness and viability.”

Modeling somatic computation with non-neural bioelectric networks, Santosh Manicka & Michael Levin, Scientific Reports | (2019) 9:18612 | https://doi.org/10.1038/s41598-019-54859-8, Excerpt from abstract: “The field of basal cognition seeks to understand how adaptive, context-specific behavior occurs in non-neural biological systems. Embryogenesis and regeneration require plasticity in many tissue types to achieve structural and functional goals in diverse circumstances. Thus, advances in both evolutionary cell biology and regenerative medicine require an understanding of how non-neural tissues could process information. Neurons evolved from ancient cell types that used bioelectric signaling to perform computation. However, it has not been shown whether or how non-neural bioelectric cell networks can support computation.”

From Darwin to DNA - redrawing the tree of life, Kat Arney, The Genetics Society Podcast, Nov 2119, https://geneticsunzipped.com/news/2019/11/21/redrawing-the-tree-of-life; explains how DNA sequencing is invalidating Darwin’s simplistic tree of life.

Unifying macro ecology and macroevolution to answer fundamental questions about biodiversity, Brian J. McGill, Global Ecology and Biogeography, 28(12), 1925-1936 - December 2019.  Abstract: “The study of biodiversity started as a single unified field that spanned both ecology and evolution and both macro and micro phenomena. But over the 20th century major trends drove  ecology and evolution apart and pushed an emphasis towards the micro perspective in both disciplines. Macroecology and macroevolution reemerged as self-consciously distinct fields in the 1970s and 1980s, but they remain largely separated from each other. Here we argue that despite the challenges it is worth working to combine macroecology and macroevolution. We present  fundamental questions about biodiversity that are really only answerable with a mixture of the views and tools of both macroecology and macroevolution.”

A quantitative formulation of biology’s first law,  Daniel W. McShea, Steve C. Wang,  and Robert N. Brandon, Evolution 73-6: 1101–1115 (2019),  Abstract: ”The zero-force evolutionary law (ZFEL) states that in evolutionary systems, in the absence of forces or constraints, diversity and complexity tend to increase. The reason is that diversity and complexity are both variance measures, and variances tend to increase spontaneously as random events accumulate. Here, we use random-walk models to quantify the ZFEL expectation, producing equations that give the probabilities of diversity or complexity increasing as a function of time, and that give the expected magnitude of the increase. We produce two sets of equations, one for the case in which variation occurs in discrete steps, the other for the case in which variation is continuous. The equations provide a way to decompose actual trajectories of diversity or complexity into two components, the portion due to the ZFEL and a remainder due to selection and constraint. Application of the equations is demonstrated using real and hypothetical data.”

Beyond Reproductive Isolation: Demographic Controls on the Speciation Process Michael G. Harvey, Sonal Singhal, and Daniel L. Rabosky,  Annu. Rev. Ecol. Evol. Syst. 2019. 50:75–95. Excerpt from Introduction: “What processes might explain the spectacular diversity of organisms on Earth—from birds and insects to flowering plants and fungi, microscopic bacteria and protozoans? To explore this question, scientists have assumed one of two largely distinct research paradigms. In what might be termed a microevolutionary approach, many researchers focus on the origin of species through the lens of reproductive and geographic isolation between contemporary populations. This research program frequently includes assessments of hybrid sterility and fitness, reciprocal transplant experiments, mate choice trials, and dissection of the genetic architecture underpinning key species-specific traits. Other researchers take a macroevolutionary approach, studying ecological, organismal, and historical factors associated with the dynamics of speciation as measured using phylogenetic or paleontological data. Unfortunately, these micro- and macroevolutionary research programs rarely meet in dialogue, and this gap is consequential. We might even question whether the two are studying the same phenomena.”

Cartwright JHE, Russell MJ. 2019 The origin of life: the submarine alkaline vent theory at 30. Interface Focus 9: 20190104. --- Excerpt from abstract: “The submarine alkaline vent theory (SAVT) for the emergence of life, now 30 years old, has reached the stage where it provides a clear path forward in experimentally testable hypotheses that involve a transdisciplinary approach to the issue. These papers record a meeting from the 11th to 15th March 2019 in Granada, Spain, to celebrate the 30th anniversary of the alkaline vent theory of the origin of life.”

Introns as Gene Regulators: A Brick on the Accelerator, Alan B. Rose, Front. Genet., 07 February 2019,  Abstract excerpt: “A picture is beginning to emerge from a variety of organisms that for a subset of genes, the most important sequences that regulate expression are situated not in the promoter but rather are located within introns in the first kilobase of transcribed sequences. The actual sequences involved are difficult to identify either by sequence comparisons or by deletion analysis because they are dispersed, additive, and poorly conserved. However, expression-controlling introns can be identified computationally in species with relatively small introns, based on genome-wide differences in oligomer composition between promoter-proximal and distal introns. The genes regulated by introns are often expressed in most tissues and are among the most highly expressed in the genome.”

Comments On Igor Popov’s Book Orthogenesis versus Darwinism, Springer International Publishing AG, part of Springer Nature, Switzerland, 2018 Georges Chapouthier, ---Biocosmology – Neo-Aristotelism, Vol. 9, Nos. 1&2, Winter/Spring 2019. Introduction:” For a long time now, arguments opposing blind evolutionary processes to predispositions in the evolution of living organisms have been a subject of conflict in theories propounded by biologists. Darwinism, as described by Popov, is based on the idea that “evolution occurs due to selection from a large or an almost unlimited source of variability and that its direction is determined by adaptation to a constantly changing environment. Arguing against this Darwinian stance, “an alternative viewpoint implies that organisms are predisposed to vary in certain directions and that this predisposition is the determinant of evolution” . This is orthogenesis. “The ideas of directed evolution date back to antiquity but orthogenesis as an articulated evolutionary concept emerged in the second half of the nineteenth century”.

Special Issue Editor’s Introduction: “Revisiting the Modern Synthesis, Philippe Huneman, Journal of the History of Biology (2019) 52:509–518, the paper assumes there is not, and never was, a common understanding of the modern synthesis. The closing statement is “In any case, we hope that the present issue contributes to the question of deciding whether the Synthesis is still alive and , or just belongs to the past.”

Evolutionary biology today and the call for an extended synthesis by Douglas J. Futuyma appeared in a Royal Society publication in 2017.  Futuyma began with a summary of the modern synthesis as he understands it and claimed that the basic assumptions are still valid.  In particular, he pointed out that it holds that “The frequencies of hereditary variants are altered by mutation (very slightly), gene flow, genetic drift, and natural selection. Directional or positive natural selection is the only known cause of adaptive change.”  He then goes on to define mutation as “any new alteration of the hereditary material that is stably transmitted across generations. The discovery of the molecular basis of heredity after the ES led to a greatly amplified understanding of evolutionary process and history, but the core theory of population genetics remained intact. For example, the core theory does not specify whether a mutation is a single base pair substitution, an insertion of a transposable element in a regulatory sequence, a gene duplication or a doubling of the entire genome. The framework of population genetics has incorporated new kinds of mutations, such as transposable elements, as they have been discovered.”  He then added “Thus, the broad concepts of mutation and natural selection lack material content, in the sense that empirical data are needed to describe real instances of evolution, by identifying the agents of selection and the molecular and developmental basis of phenotypic variants. The conception of causes of evolution embodied in the synthetic theory, i.e. allele frequency change, differs from the ‘structuralist’ view of the causes of differences in morphology, physiology or behavior that are commonly envisioned by mechanistic developmental biologists, physiologists or neurobiologists.”  In other words, the modern synthesis works even if no one understands exactly how it advances complexity.

The sources of adaptive variation, Deborah Charlesworth, Nicholas H. Barton and Brian Charlesworth, rspb.royalsocietypublishing.org, May 2017;  The authors argue that there is no need to revise the modern synthesis because  evidence for epigenetic change is limited, and there is no evidence that it causes significant phenotype change, especially after a few generations.  Phynotype change is constrained by the organisms’ development systems.  They cited many references on epigenetic variations that they claim support their position.

Recombination Alters the Dynamics of Adaptation on Standing Variation in Laboratory Yeast Populations, Katya Kosheleva1 and Michael M. Desai, Mol. Biol. Evol. 35(1):180–201, 2017, Excerpt from abstract: “The rates and selective effects of beneficial mutations, together with population genetic factors such as population size and recombination rate, determine the outcomes of adaptation and the signatures this process leaves in patterns of genetic diversity. Previous experimental studies of microbial evolution have focused primarily on initially clonal populations, finding that adaptation is characterized by new strongly selected beneficial mutations that sweep rapidly to fixation. Here, we study evolution in diverse outcrossed yeast populations, tracking the rate and genetic basis of adaptation over time.”

Evolution of genetic variance during adaptive radiation, Greg M. Walter, et al, bioRxiv preprint doi: https://doi.org/10.1101/097642; January 2, 2017. Conclusion: “If genetic correlations between traits bias evolution then it is difficult to see how rapid adaptive divergence leads to adaptive radiation. Our results suggest that alleles present in standing genetic variation (possibly rare) may become beneficial when new environments are colonized, increasing their frequency in the population and aligning the distribution of genetic variation with the direction of natural selection. Adaptation from standing genetic variation can be rapid, suggesting that natural selection shaping the distribution of genetic variation can provide the mechanism for understanding how adaptive radiation proceeds. Ascension of adaptive peaks on the adaptive landscape can then occur when different alleles are favored in different environments, aligning the direction of greatest genetic variation with the direction of selection in each environment. The presence of repeated adaptation to similar environments further suggests that natural selection has favored the same alleles in similar environments, driving the adaptive radiation of ecotypes into multiple contrasting environments.”

Why we don’t want another “Synthesis”, Arlin Stoltzfus, Biology Direct (2017):  The author poses the thought that recent discoveries have shown that the modern synthesis is not correct, and the current state of knowledge does not permit establishing one that is.  The goal of a general law of biology and evolution may not be achievable, and an imperfect one is worse than none.  The paper presents detailed evidence that scientists never reached a common understanding of the existing modern synthesis, and various fields of research simply twisted it to fit their individual interpretations.

In What’s wrong with evolutionary biology? (Biol Philos 2017), John J. Welch expressed frustration with the many papers being published about many perceived problems with evolutionary biology.  He suggests, at length, that the fundamental problem is the complexity of biology, the many specialties included under the umbrella of evolutionary biology, and the difficulty of effective communication.  He believes that that is nothing wrong with the theory, and all that is needed is more respect and better communication.  Koen B Tanghe and four others quickly rebutted Welch’s argument in What’s Wrong with the Modern Evolutionary Synthesis? A Critical Reply to Welch (2017) (http://philsci-archive.pitt.edu/14703/).  They argued that there is definitely a problem and it is centered around the modern synthesis.  They claimed that the modern synthesis was never supported by a consensus, has four major weakness (which they describe in detail), and is definitely in need of revision.

Developmental push or environmental pull? The causes of macroevolutionary dynamics by Douglas H. Erwin (2017) reviewed the never ending debate over microevolution and macroevolution, citing many related publication’s as he did so. He recognized that the modern synthesis was forged around the concept of macroevolution being nothing more than an accumulation of microevolution, but that the assumption has been repeatedly challenged.  The modern synthesis was founded on a model of variation by genetic recombination and mutation, and recent discoveries have indicated some variation may also come from reconfiguration of gene regulation networks during development.  Such regulatory networks were unknown when the modern synthesis was established.  Therefore, there may be some processes driving macroevolution that are not connected to the micro-evolutionary processes of the modern synthesis.

Evolution Driven by Organismal Behavior: A Unifying View of Life, Function, Form, Mismatches and Trends, Rui Diogo, (2017):  This book reviews the history of evolution beginning with Aristotle and then proposes a replacement for the modern synthesis.  The proposed replacement theory presumes variation is driven by the behavior of organisms.  Dr. Diogo is an Associate Professor at the Howard University College of Medicine.

Tom Bethell, Darwin’s House of Cards: A Journalist’s Odyssey Through The Creation Debates, Seattle: Discovery Press International, 2017.  Goodreads.com summary: “In this provocative history of contemporary debates over evolution, veteran journalist Tom Bethell depicts Darwin's theory as a nineteenth-century idea past its prime, propped up by logical fallacies, bogus claims, and empirical evidence that is all but disintegrating under an onslaught of new scientific discoveries. Bethell presents a concise yet wide-ranging tour of the flash points of modern evolutionary theory, investigating controversies over common descent, natural selection, the fossil record, biogeography, information theory, evolutionary psychology, artificial intelligence, and the growing intelligent design movement. Bethell's account is enriched by his own personal encounters with of some of our era's leading scientists and thinkers, including Harvard biologists Stephen Jay Gould and Richard Lewontin; British paleontologist Colin Patterson; and renowned philosopher of science Karl Popper. “

Purpose And Desire: What Makes Something "Alive" And Why Modern Darwinism Has Failed To Explain It, J. Scott Turner, 2017:  Professor Turner claims that “no Darwinian explanation exists for the origin of life or the origin of the cornerstone of modern biology, the gene.”  He further states that Darwinism ignores the “obvious ability of living organisms to maintain internal consistency in the face of environmental perturbation”.  Turner maintains he does not support either intelligent design or creationism, but believes that the founders of the modern synthesis (Lewis Henry Morgan, Ronald Fisher, Sewall Wright, J.B.S. Haldane) missed a vital property of life.

Improbable Destinies: Fate, Chance, And The Future Of Evolution, Jonathan B. Losos, 2017, Excerpt from Amazon synopsis of book: “Earth’s natural history is full of fascinating instances of convergence: phenomena like eyes and wings and tree-climbing lizards that have evolved independently, multiple times. But evolutionary biologists also point out many examples of contingency, cases where the tiniest change—a random mutation or an ancient butterfly sneeze—caused evolution to take a completely different course. What role does each force really play in the constantly changing natural world? Are the plants and animals that exist today, and we humans ourselves, inevitabilities or evolutionary flukes?  Jonathan Losos reveals what the latest breakthroughs in evolutionary biology can tell us about one of the greatest ongoing debates in science. He takes us around the globe to meet the researchers who are solving the deepest mysteries of life on Earth through their work in experimental evolutionary science. Losos himself is one of the leaders in this exciting new field, and he illustrates how experiments with guppies, fruit flies, bacteria, foxes, and field mice, along with his own work with anole lizards on Caribbean islands, are rewinding the tape of life to reveal just how rapid and predictable evolution can be. “

Ruiz-Mirazo K, Briones C, de la Escosura A. 2017 Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems. Open Biol. 7: 170050: Excerpt from abstract:  “In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analyzed in this critical review …”

Making Heredity Matter: Samuel Butler’s Idea of Unconscious Memory, Cristiano Turbil, Journal of the History of Biology, 2017 DOI 10.1007/s10739-017-9469-8, Excerpt from abstract: “Starting with a historical introduction, this paper aspires to ascertain the logic, meaning and significance of Butler’s idea of ‘unconscious memory’ in the post Darwinian physiological and psychological Pan-European discussion.”

Genetic Redundancy Eliminates the Dream of Beneficial Mutations,  Haitham Talaat, Advances in Biotechnology and Microbiology,  Volume 7 Issue 5 - December 2017:  Talaat is an engineer who introduces a new perspective to redundant genes.  Rather than just the product of duplication error (junk DNA) or material available for future beneficial mutation, he proposes that they are performing an essential function in their respective genomes.  That function is to provide reliability through redundancy.  He compares biological systems to manned space flight systems.  Because they are so complex, the probability of failure would be unacceptably high without redundancy in critical components and systems.  Manned space missions are triple redundant to prevent a single failure from causing mission failure.  Talaat argues that redundant genes provide the same function in living systems.  They prevent a mutation from causing catastrophic system failure.  Rather than providing a platform for beneficial mutations, they prevent mutations from destroying the system.

Morphogenesis one century after On Growth and Form, Thomas Lecuit and L. Mahadevan, The Company of Biologists Ltd | Development (2017) 144, 4197-4198 doi:10.1242/dev.161125. Excerpt: “The past two decades have seen an increasing influx of physicists, mathematicians, engineers and computer scientists into the field of developmental biology, who are all attempting to determine the correspondence between the parameters that describe shape and those that define its generation and transformation.”

Denis Noble, Central Dogma or Central Debate? University of Oxford, Oxford, United Kingdom Physiology 33: 246–249, 2018. Excerpt: “A central feature of evolutionary biology as it developed during the last century was that acquired characteristics could not be inherited. Physiologists now know that there are many paternal and maternal effects transmitted to subsequent generations. The implications for health are important. The way in which parents live inevitably influences their children even from birth. It is not “all in the genes.” ---Physiologists today know that Darwin was right. We characterize this kind of transmission as maternal and paternal effects. We have even identified some of Darwin’s imagined particles; they are the innumerable RNAs in sperm in the male line, and the many cytoplasmic materials in the inherited egg cell in the maternal line, including the eukaryotic cell structure and metabolism.--- Weismann did not know any of this, of course. But he did have a brilliant simplifying thought. This was that he could explain all the examples of the phenomenon given by Darwin in The Origin of Species even if one supposed that there were no such particles and/or that there was a completely tight barrier between the soma and the germline. His idea was that random variations in the inherited material would be sufficient, together with Darwin’s theory of Natural Selection, to explain evolution entirely. As the evolutionary biologist and historian Ernst Mayr showed very clearly in his magisterial book, The Growth of Biological Thought, this idea, together with Mendelian genetics, formed the cornerstone of what became called The Modern Synthesis, often also called neo-Darwinism.”

Igor Popov published Orthogenesis versus Darwinism in 2018 following years of research on variation.  He determined that variation is not truly random because all possible Mendelian combinations of variations never appear.  Sometimes, nature uses less than ¼ of the theoretically possible variations.  He concluded that variation is constrained by some yet to be identified means within the cell.

What Is Evolutionary Novelty? Process Versus Character Based Definitions Tim Peterson and Gerd B. Müller, Journal of Experimental Zoology Part B Molecular and Developmental Evolution · September 2013, excerpt: “With the rise of EvoDevo, the topic of evolutionary novelty has received renewed attention. Indeed, it has been argued that one of the major contributions of EvoDevo to evolutionary theory is the explanation of phenotypic novelty. Despite such assertions, dispute continues over what exactly a novelty is and whether the term applies to a unique type of evolutionary phenomenon or whether it merely has informal meaning.”

Genetic Alterations That Do or Do Not Occur Naturally; Consequences for Genome Edited Organisms in the Context of Regulatory Oversight, René Custers,, Frontiers in Bioengineering and Biotechnology, 16 January 2019, modern genome sequencing technology has revealed to us what type of alterations have occurred during evolution, domestication and breeding. 

Origin of spontaneous mutations in maize has been hiding in plain sight, Susan R. Wesslera, PNAS | May 28, 2019 | vol. 116 | no. 22 | 10617–10619:  Excerpt from introduction: “Spontaneous mutations are the raw material of evolutionary change. Given their importance, it is surprising that so little is known about their origin, frequency, or molecular structure. These questions have weighed on me since my laboratory published a series of papers, with the first appearing in PNAS in 1985, on the structure of spontaneous mutations at the maize waxy gene. This and subsequent studies revealed the predominance of two classes of mutations: long-terminal repeat (LTR) retrotransposons and complex deletions.”

Unraveling the tree of life: A grand challenge for Biology. Scott V. Edwards, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 .  Abstract:” Building the Tree of Life is an ongoing activity of scientists around the world, one that combines information from both the genotype and phenotype of organisms. I review recent trends in this effort and describe a number of models, including the multispecies coalescent model, as means to achieve this end.”

Evolutionary consequences of epigenetic inheritance, Martin I. Lind and Foteini Spagopoulou, Heredity (2018) 121:205–209 (The Genetic Society):  The authors address the effect of epigenetic modifiers on form. They report that organisms with an identical genome can have Ency of variation in form, and that variation can be inherited for at least several generations. Furthermore, they report that experiments show the environment can affect the epigenetic modifiers. 

Paul Davies’s recently published the book The Demon in the Machine: How Hidden Webs of Information Are Solving the Mystery of Life (2019).  He included the statement “Semantic information is a higher-level concept that is simply meaningless at the level of molecules. Chemistry alone, however complex, can never produce the genetic code or contextual instructions.  Asking chemistry to explain coded information is like expecting computer hardware to write its own software. “

A 30 page entry in the online (https://plato.stanford.edu/entries/macroevolution/) Stanford Encyclopedia of Philosophy entitled Philosophy of Macroevolution (Jun 3, 2019) reviewed nine different issues related to macroevolution the appeared after the 1970s and considered their consistency.

Prospects for a General Theory of Evolutionary Novelty, Douglas H. Erwin, Journal Of Computational Biology Volume 26, Number 7, 2019:  The author claims the modern synthesis may not properly account for the appearance of variation and novelty. Abstract; “Novelty is a topic of broad interest, with two distinct approaches within evolutionary biology. The dominant approach since Darwin has been transformationist, with novelty arising through gradual changes in morphology. The Modern Synthesis emphasized the importance of ecological opportunity rather than the source of variation, and this view has many adherents today. Yet, since well before Darwin, an alternative view has held that novelties could arise by rapid changes and many not necessarily be connected to ecological opportunity. The rise of comparative evolutionary developmental biology since 1990 has led to a resurgence of these arguments. Many case studies have documented novelties and there have been rigorous efforts to define the attributes of novelty, but there have been few attempts at a more general model. In contrast, studies of technological innovation have been replete with qualitative models since the 1930s. In this article I consider several possibilities for constructing a general model of novelty and innovation: (1) A general formal theory. (2) Commonalities between different levels, such as genes and morphology, but with sufficient differences between domains that any formal theory would be level specific. (3) Commonalities across levels but for various reasons developing a formal theory even within domains is improbable. A final alternative is that novelty and innovation may be so deeply historical that any general framework is impossible. I conclude that a common conceptual framework can be developed and serve as the foundation for simulation studies, but the importance of feedbacks and potentiating factors renders a formal model implausible.”

Genetic Novelty -How new genes are born, Urminder Singh And Eve Syrkin Wurtele, eLife 2020;9:e55136, excerpt: “ One possible mechanism is the ’de novo’ appearance of a gene from an intergenic region or a completely new reading frame within an existing gene (Tautz and Domazet-Losˇo, 2011). An alternative mechanism is that the coding sequence of the orphan gene arises by rapid divergence from the coding sequence of a preexisting gene.”

Memory in Trait Macroevolution, Emma E. Goldberg and Jasmine Foo, vol. 195, no. 2,  the American naturalist, February 2020. The authors claim the biological history of a life form limits future evolutionary opportunities. Abstract: ‘The history of a trait within a lineage may influence its future evolutionary trajectory, but macroevolutionary theory of this process is not well developed. For example, consider the simplified binary trait of living in cave versus surface habitat. The longer a species has been cave dwelling, the more accumulated loss of vision, pigmentation, and defense may restrict future adaptation if the species encounters the surface environment.--- “

Ayaka Sakata, Kunihiko Kaneko., Dimensional Reduction in Evolving Spin-Glass Model: Correlation of Phenotypic Responses to Environmental and Mutational Changes, Physical Review Letters, 2020; 124 (21).  Observing that life forms do not appear in in all possible combinations, researchers attempted to explain why using computer simulations.

The Demise of the Artifact Hypothesis, Günter Bechly, Evolution News @DiscoveryCSC, October 7, 2020, the paper claims the fossil record contradicts Darwinism.  “Darwinian gradualism predicts biological forms evolving gradually from one to another. However, it is widely acknowledged that this is not what the fossil record shows. Darwinists have long suggested that the fossil record’s pattern of major discontinuities is merely an artifact of that record being incomplete. But on a new episode of ID the Future, paleoentomologist Günter Bechly makes the case that recent findings have put the nails in the coffin of this “artifact hypothesis.” He goes on to argue that these findings are “not just a tiny problem but a fatal problem” for modern Darwinism.”

Autopolyploidy: an epigenetic macromutation, Jeff J. Doyle and Jeremy E. Coate, American Journal of Botany 107(8): 1097–1100, 2020; Excerpt: “In conclusion, whole-genome duplication causes sweeping alterations to the 4D nucleome, which likely drive phenotypic changes independent of classic genetic mutation, making autopolyploidy an epigenomic macromutation. Emerging techniques to quantify chromatin-level changes will yield key insights into the effects of “pure polyploidy” and position autopolyploids as key models for understanding epigenetic interactions and their effects on evolutionarily relevant phenotypes.”

Schneider, Thomas D., Evolution of biological Information, Nucleic Acids Research, 2000. Vol 28, No 14, 2794-2799. The paper supports punctuated equilibrium with info gain in a computer simulation of a protein.

He, C., Han, et al, On the origin of vertebrate body plan: Insights from the endoderm using the hourglass model, Gene Expression Patterns (2020). Excerpt from Introduction: “The Cambrian explosion has been an extensively debated topic in animal evolution for more than one century Biological organisms were composed of individual cells, occasionally organized into colonies, before the Cambrian explosion. Subsequent to the Cambrian explosion, evolution greatly sped up, and the major phyla appeared. For example, the bilateral, anterior– posterior organization of body plan appears in fossil records from the early Cambrian. These results are the basis for the open question in animal evolution of why the phylum- and superphylumlevel body plans have changed so little and no more new phylum- and superphylum-level body plans appeared, while the class- and family level body plans have changed so greatly with so many class, family, and species appearing since the early Cambrian. Since the development of the animal body plan is precisely controlled by gene regulatory networks, the mechanism to explain the different rates of change of the phylum- and superphylum-level body plans versus the class- and family-level body plans may lie in the structure and evolution of gene regulatory networks.”

EvoDevo: An Ongoing Revolution?, Salvatore Ivan Amato, Philosophies 2020, 5, 35. Abstract: “Since its appearance, Evolutionary Developmental Biology (EvoDevo) has been called an emerging research program, a new paradigm, a new interdisciplinary field, or even a revolution. --- In this article, an epistemological analysis of EvoDevo is presented, with particular attention paid to the relations to the Extended Evolutionary Synthesis (EES) and the Standard Evolutionary Synthesis (SET).”

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times, Sudhir Kumar et al, Mol. Biol. Evol. 34(7):1812–1819 , 2017: “Evolutionary information on species divergence times is fundamental to studies of biodiversity, development, and disease. Molecular dating has enhanced our understanding of the temporal patterns of species divergences over the last five decades, and the number of studies is increasing quickly due to an exponential growth in the available collection of molecular sequences from diverse species and large number of genes.”

Genetic, epigenetic and exogenetic information in development and evolution,  Paul E. Griffiths, 2017, Published by the Royal Society   The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology.

Genes From The Junkyard, Adam Levy, Nature | Vol 574 | 17 October 2019: Some genes appear to be made from scratch, rather than from a duplicated gene.  The unique protein preventing the blood in Arctic cod to freeze is cited as an example.

Natural reward as the fundamental macroevolutionary force, Owen M. Gilbert, Preprint · March 2019:  The author claims Darwinian evolution cannot explain advanced lifeforms. Excerpt from abstract: “Darwin’s theory of evolution by natural selection does not predict long-term progress or advancement, nor does it provide a useful way to define or understand these concepts. Nevertheless, the history of life is marked by major trends that appear progressive, and seemingly more advanced forms of life have appeared. To reconcile theory and fact, evolutionists have proposed novel theories that extend natural selection to levels and time frames not justified by the original structure of Darwin’s theory.”

Inherency of Form and Function in Animal Development and Evolution, Stuart A. Newman, Front. Physiol., 19 June 2019: Reviewed recent work on the origins of morphology and cell-type diversification in animals. Material properties of various cellular tissues “resulted from the recruitment of “generic” physical forces and mechanisms – adhesion, contraction, polarity, chemical oscillation, and diffusion”.

A way forward with eco evo devo: an extended theory of resource polymorphism with postglacial fishes as model systems, Skulason, et al. Biol. Rev. (2019). Abstract: A major goal of evolutionary science is to understand how biological diversity is generated and altered. Despite considerable advances, we still have limited insight into how phenotypic variation arises and is sorted by natural selection. Here we argue that an integrated view, which merges ecology, evolution and developmental biology (eco evo devo) on an equal footing, is needed to understand the multifaceted role of the environment in simultaneously determining the development of the phenotype and the nature of the selective environment, and how organisms in turn affect the environment through eco evo and eco devo feedbacks. To illustrate the usefulness of an integrated eco evo devo perspective, we connect it with the theory of resource polymorphism (i.e. the phenotypic and genetic diversification that occurs in response to variation in available resources). In so doing, we highlight fishes from recently glaciated freshwater systems as exceptionally well-suited model systems for testing predictions of an eco evo devo framework in studies of diversification. Studies on these fishes show that intraspecific diversity can evolve rapidly, and that this process is jointly facilitated by (i) the availability of diverse environments promoting divergent natural selection; (ii) dynamic developmental processes sensitive to environmental and genetic signals; and (iii) eco evo and eco devo”

Life History Divergence in Livebearing Fishes in Response to Predation: Is There a Microevolution to Macroevolution Barrier? Mark C. Belk, Spencer J. Ingley and Jerald B. Johnson, Diversity 2020, 12, 179, Abstract excerpt: “Abstract: A central problem in evolutionary biology is to determine whether adaptive phenotypic variation within species (microevolution) ultimately gives rise to new species (macroevolution). Predation environment can select for trait divergence among populations within species. The implied hypothesis is that the selection resulting from predation environment that creates population divergence within species would continue across the speciation boundary such that patterns of divergence after speciation would be a magnified accumulation of the trait variation observed before speciation.”

Essay by David Gelernter, Giving Up Darwin, Claremont Review of Books, Spring 2019 Page 104, Excerpt: “There’s no reason to doubt that Darwin successfully explained the small adjustments by which an organism adapts to local circumstances: changes to fur density or wing style or beak shape. Yet there are many reasons to doubt whether he can answer the hard questions and explain the big picture—not the fine-tuning of existing species but the emergence

Giving Up Darwin, David Gelernter   https://www.claremont.org/crb/article/giving-up-darwin/  Claremont Review of Books, Volume XIX, Number 2, Spring 2019, page 104.   Excerpt: “There’s no reason to doubt that Darwin successfully explained the small adjustments by which an organism adapts to local circumstances: changes to fur density or wing style or beak shape. Yet there are many reasons to doubt whether he can answer the hard questions and explain the big picture—not the fine-tuning of existing species but the emergence of new ones. The origin of species is exactly what Darwin cannot explain.”

Opinion: Interdisciplinary Approach Needed to Crack Morphogenesis: Physicists, geneticists, computer scientists, and biologists are working together to gain a full appreciation of the intricacies of organismal growth and form, Joshua Finkelstein, et al, The Scientist, Dec 1, 2019. Excerpt: “Over the past 20 years, researchers have made tremendous progress in identifying specific genes necessary for development, mostly by chronicling mutations or deletions of genes that lead to the onset of diseases and anatomical defects. But this information is just the tip of the iceberg. While the genome specifies the crucial “parts list” for individual cells, researchers have much to learn about the signaling events that coordinate the collaborative cellular processes to create and repair complex anatomies.”

2020

Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia,  Morgan Beeby et al, FEMS Microbiology Reviews , 2020, Vol. 44, No. 3. In a rebuttal to the concept of irreducible complexity, the authors claim it is disproved by the repeated convergent evolution of basic propulsion mechanisms. Abstract: “Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required evolving a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.”

Mechanical control of plant morphogenesis: concepts and progress, Fei Du and Yuling Jiao, Current Opinion in Plant Biology 2020, 57:16–23. Introduction: “Understanding how the genome encodes organismal shape is fundamental to biology. Extensive molecular genetic studies have uncovered genes regulating morphogenesis, that is, the generation of shape, however, such genes do not directly determine cell and tissue shape. Recent studies have started to elucidate how mechanical cues mediate the physical shaping of cells and tissues. In particular, the mechanical force generated during cell and tissue growth coordinates deformation at the tissue and organ scale. In this review, we summarize the recent progress of mechanical regulation of plant development. We focus our discussion on how patterns of mechanical stresses are formed, how mechanical cues are perceived, and how they guide cell and organ morphogenesis.”

Positional Information—A concept underpinning our understanding of developmental biology,  Neil Vargesson, Developmental Dynamics. 2020;249:298–312, Abstract: “It is now 50 years since Lewis Wolpert published the paper in which he set out the concept of Positional Information to explain how spatial patterns of cellular differentiation are generated. This concept has provided a universal model for pattern formation in embryonic development and regeneration and become part of the fabric of the field of developmental biology. Here I outline how Wolpert devised the concept of Positional Information and describe landmark studies from his lab investigating how Positional Information is specified in the developing chick limb.”

In Chromoanagenesis: a piece of the macroevolution scenario, (Molecular Cytogenetics,  2020 13:3)  Franck Pellestor and Vincent Gatinois report that; “Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals.”  They propose that abrupt but fortuitous rearrangements such as these could cause macroevolution in the way that Goldschmidt thought that “hopeful monsters” might cause sudden and large differences between species.

Viviane Callier wrote By Losing Genes, Life Often Evolved More Complexity, Quanta Magazine (September 1, 2020) and made the rather unique claim that a loss of information can  allow increased complexity to evolve. She reported on surprising research conducted by Cristian Cañestro, a professor of genetics, microbiology and statistics at the University of Barcelona.  He discovered that genes assumed to be essential are missing from presumed descendants to certain plants and animals.

Using statistical methods to model the fine-tuning of molecular machines and systems, Steinar Thorvaldsen and Ola Hössjer, Journal of Theoretical Biology 501 (2020) ; summarized by Discovery Institute (first serious recognition of ID in peer reviewed journal)

The origin of life as a planetary phenomenon, Dimitar D. Sasselov,  John P. Grotzinger , John D. Sutherland, Sci. Adv. 2020; 6 : 5 February 2020: Excerpt from abstract: “We advocate an integrative approach between laboratory experiments in prebiotic chemistry and geologic, geochemical, and astrophysical observations to help assemble a robust chemical pathway to life that can be reproduced in the laboratory.”

Barrandeguy ME, Sanabria DJ, García MV (2020) Fisher, Haldane and Wright would be proud owing to population genetics has become in a defiant study area in the genetics researches. Open J Biol Sci 5(1): 038-040; a complimentary review of population genetics.  Excerpt: “Along this brief summary about the protruding landmarks in the development of population genetics, we can see that Fisher, Haldane and Wright sowed their ideas in a fertile field. Nowadays an uncountable number of researchers are still sowing new questions, harvesting answers, formulating hypothesis, generating challenges and testing models because of population genetics is an alive and dynamics discipline that demands creative minds as a consequence of its defiant subject of study, i.e. past, present and future of the genetic variability in the populations.’

Emergence of life in an inflationary universe, Tomonori Totani, Scientific Reports (2020) 10:1671: Excerpt from abstract: “Abiotic emergence of ordered information stored in the form of RNA is an important unresolved problem concerning the origin of life. A polymer longer than 40–100 nucleotides is necessary to expect a self-replicating activity, but the formation of such a long polymer having a correct nucleotide sequence by random reactions seems statistically unlikely. However, …”.

The origin of animal body plans: a view from fossil evidence and the regulatory genome, Douglas H. Erwin, Development (2020) 147,.  The Company of Biologists Ltd. Excerpt: “In this Review, I assess the emerging view that the early diversification of animals involved small organisms with diverse cell types, but largely lacking complex developmental patterning, which evolved independently in different bilaterian clades during the Cambrian Explosion.”

Extended Evolutionary Synthesis: Neither Synthesis Nor Extension, Claudio Ricardo Martins dos Reis and Leonardo Augusto Luvison Araújo, Biological Theory (2020) 15:57–60: Excerpt from abstract: “The extended evolutionary synthesis (EES) intends to offer a new framework for understanding evolution based mainly on empirical and theoretical findings of current studies, including heredity and evolutionary developmental biology.”

Does the extended evolutionary synthesis entail extended explanatory power?, Jan Baedke1  · Alejandro Fábregas‑Tejeda1 and Francisco Vergara‑Silva, Biology & Philosophy (2020) 35:20, Excerpt from abstract: “Biologists and philosophers of science have recently called for an extension of evolutionary theory. This so-called ‘extended evolutionary synthesis’ (EES) seeks to integrate developmental processes, extra-genetic forms of inheritance, and niche construction into evolutionary theory in a central way.”

A 27.5-My underlying periodicity detected in extinction episodes of non-marine tetrapods Michael R. Rampino , Ken Caldeira & Yuhong Zhu, Historical Biology, 10 Dec 2020,                   https://doi.org/10.1080/08912963.2020.1849178. Abstract: “Non-marine tetrapods (amphibians, reptiles, birds and mammals) have apparently experienced at least 10 distinct episodes of intensified extinctions over the past 300 My. Eight of these ten non-marine extinction events are concurrent with known marine-extinction episodes, which previously yielded evidence for an underlying period of ~26.4 to 27.3 My. We performed circular spectral analysis and Fourier transform analysis of the ages of the ten recognized tetrapod-extinction events, and detected a statistically significant (99% confidence) underlying periodicity of ~27.5 My. We also find that the eight coeval non-marine/marine extinction pulses all occurred at the times of eruptions of Large Igneous Provinces (LIPs) (continental flood basalts and oceanic plateaus), with potentially severe environmental effects. Three of these co-extinction episodes are further correlated with the ages of the three largest (≥100-km diameter) impact craters of the last 260 My, which are also apparently capable of causing extinction events. These findings suggest that global cataclysmal events with an underlying periodicity of ~27.5 My were the cause of the coordinated periodic extinction episodes of non-marine tetrapods and marine organisms.”

Origin story: The start of life on earth is an event horizon we struggle to see beyond, Natalie Elliot, Aeon, Sep. 8, 2020,   https://aeon.co/essays/physics-and-information-theory-give-a-glimpse-of-lifes-origins  An essay reviewing originof life studies from Darwin to the present.

Rethinking Evolution, The Revolution That’s Hiding In Plain Sight, Gene Levinson, World Scientific Publishing Company, Oct 2019.  The book claims the Modern Synthesis is obsolete and should be replaced with an Updated Evolutionally Synthesis (UES). Excerpt from Eurakalert.org review: “ Years from now, the updated evolutionary synthesis will be viewed as a twenty-first century conceptual advance in evolutionary theory comparable to the "Modern Synthesis" or the discovery of the genetic code. One of the stunning conceptual advances is that natural selection actually changes the potential for higher levels of complexity to arise, in a non-random fashion. There is more to natural selection than accumulation of incremental, random mutations. Each evolutionary innovation lays the groundwork for more complex innovations to emerge, and when they prove useful in the struggle for existence, they tend to be preserved. I refer to this natural process as Emergent Evolutionary Potential (EEP).”

A simple rule drives the evolution of useless complexity, Alison Caldwell, University of Chicago Medical Center. https://www.sciencedaily.com/releases/2020/12/201209115209.htm  Biochemistry preserves complexity in biological structure even when the complexity provides no evolutionally advantage to the organism.

Linde-Medina, M. On the problem of biological form. Theory Biosci. 139, 299–308 (2020). (paywall) https://doi.org/10.1007/s12064-020-00317-3. Abstract: “Embryonic development, which inspired the first theories of biological form, was eventually excluded from the conceptual framework of the Modern Synthesis as irrelevant. A major question during the last decades has centered on understanding whether new advances in developmental biology are compatible with the standard view r whether they compel a new theory. Here, I argue that the answer to this question depends on which concept of morphogenesis is held. Morphogenesis can be conceived as (1) a chemically driven or (2) a mechanically driven process. According to the first option, genetic regulatory networks drive morphogenesis. According to the second, morphogenesis results from an invariant tendency of embryonic tissues to restore changes in mechanical stress. While chemically driven morphogenesis allows an extension of the standard view, mechanically driven morphogenesis would deeply transform it. Which of these hypotheses has wider explanatory power is unknown. At present, the problem of biological form remains unsolved.”

Coordinating cell polarization and morphogenesis through mechanical feedback, Samhita P. Banavar, et al, PLoS Comput Biol 17(1): e1007971. https://doi.org/10.1371/journal. pcbi.100797. Abstract: “Many cellular processes require cell polarization to be maintained as the cell changes shape, grows or moves. Without feedback mechanisms relaying information about cell shape to the polarity molecular machinery, the coordination between cell polarization and morphogenesis, movement or growth would not be possible. Here we theoretically and computationally study the role of a genetically-encoded mechanical feedback (in the Cell Wall Integrity pathway) as a potential coordination mechanism between cell morphogenesis and polarity during budding yeast mating projection growth. We developed a coarse-grained continuum description of the coupled dynamics of cell polarization and morphogenesis as well as 3D stochastic simulations of the molecular polarization machinery in the evolving cell shape. Both theoretical approaches show that in the absence of mechanical feedback (or in the presence of weak feedback), cell polarity cannot be maintained at the projection tip during growth, with the polarization cap wandering off the projection tip, arresting morphogenesis. In contrast, for mechanical feedback strengths above a threshold, cells can robustly maintain cell polarization at the tip and simultaneously sustain mating projection growth. These results indicate that the mechanical feedback encoded in the Cell Wall Integrity pathway can provide important positional information to the molecular machinery in the cell, thereby enabling the coordination of cell polarization and morphogenesis.”

The many bits of positional information, Gašper Tkačik and Thomas Gregor, Development (2021) 148, dev176065. doi:10.1242/dev.176065, Excerpt from abstract: “We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?”

 

NOTE: The hundreds of references represent only a small percentage of the scientific publications on evolution, and they were not selected randomly.  Except for a few books, they only include open source documents readily available on the internet.  No papers requiring fees are included. 

Wiggly red lines are courtesy of Blogger and Microsoft.  Several hours were wasted trying to eliminate them