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Showing posts with label Evolutionary Theory. Show all posts
Showing posts with label Evolutionary Theory. Show all posts

Sunday, March 10, 2024

The neutralist-selectionist debate in 2024

The neutral theory was first proposed by Mootoo Kimura in 1968 (Kimura, 1968). The following year, a similar idea was published in a seminal paper by Jack King and Thomas Jukes (King and Jukes, 1969). King and Jukes emphasized the importance of non-Darwinian mechanisms of evolution in order to explain protein based phylogenetic trees and the molecular clock. They made it clear that neutral alleles fixed by random genetic drift play an important part in evolution.

There appears to be considerable latitude at the molecular level for random genetic changes that have no effect upon the fitness of the organism. Selectively neutral mutations, if they occur, become passively fixed as evolutionary changes through the action of random genetic drift.

The idea of selectively neutral changes at the molecular level has not been readily accepted by many classical evolutionists, perhaps because of the pervasiveness of Darwinian thought (King and Jukes, 1969).

Friday, August 11, 2023

What is the Modern Synthesis?

Serious criticisms of evolutionary theory have been floating around for half a century. The main focus is over the Modern Synthesis and whether it's the best explanation of evolution. That requires a throrough understanding of what the Modern Synthesis actually means and how it's understood by most evolutionary biologists.

One view is that the Modern Synthesis is almost exclusively about natural selection. If that's true, then Stephen Jay Gould makes a good case when he argues that the Modern Synthesis is effectively dead—it was killed off by the neutral theory and the recognition that random genetic drift is a major player in evolution [Is the Modern Synthesis effectively dead?].

Thursday, October 13, 2022

Macroevolution

(This is a copy of an essay that I published in 2006. I made some minor revisions to remove outdated context.)

Overheard at breakfast on the final day of a recent scientific meeting: "Do you believe in macroevolution?" Came the rely: "Well, it depends on how you define it."
                                                                         Roger Lewin (1980)

There is no difference between micro- and macroevolution except that genes between species usually diverge, while genes within species usually combine. The same processes that cause within-species evolution are responsible for above-species evolution.
                                                                         John Wilkins

The minimalist definition of evolution is a change in the hereditary characteristics of a population over the course of many generations. This is a definition that helps us distinguish between changes that are not evolution and changes that meet the minimum criteria. The definition comes from the field of population genetics developed in the early part of the last century. The modern theory of evolution owes much to population genetics and our understanding of how genes work. But is that all there is to evolution?

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 (1980)

No. There's also common descent—the idea that all life has evolved from primitive species over billions of years. Common descent is about the history of life. In this essay I'll describe the main features of how life evolved but keep in mind that this history is a unique event that is accidental, contingent, quirky, and unpredictable. I'll try and point out the most important controversies about common descent.

The complete modern theory of evolution encompasses much more than changes in the genetics of a population. It includes ideas about the causes of speciation, long-term trends, and mass extinctions. This is the domain of macroevolution—loosely defined as evolution above the species level. The kind of evolution that focuses on genes in a population is usually called microevolution.

As a biochemist and a molecular biologist, I tend to view evolution from a molecular perspective. My main interest is molecular evolution and the analysis of sequences of proteins and nucleic acids. One of the goals in writing this essay is to explain this aspect of evolution to the best of my limited ability. However, another important goal is to show how molecular evolution integrates into the bigger picture of evolution as described by all other evolutionary biologists, including paleontologists. When dealing with macroevolution this is very much a learning experience for me since I'm not an expert. Please bear with me while we explore these ideas.

It's difficult to define macroevolution because it's a field of study and not a process. Mark Ridley has one of the best definitions I've seen ...

Macroevolution means evolution on the grand scale, and it is mainly studied in the fossil record. It is contrasted with microevolution, the study of evolution over short time periods., such as that of a human lifetime or less. Microevolution therefore refers to changes in gene frequency within a population .... Macroevolutionary events are more likely to take millions, probably tens of millions of years. Macroevolution refers to things like the trends in horse evolution described by Simpson, and occurring over tens of millions of years, or the origin of major groups, or mass extinctions, or the Cambrian explosion described by Conway Morris. Speciation is the traditional dividing line between micro- and macroevolution.
                                                                         Mark Ridley (1997) p. 227

When we talk about macroevolution we're talking about studies of the history of life on Earth. This takes in all the events that affect the actual historical lineages leading up to today's species. Jeffrey S. Levinton makes this point in his description of the field of macroevolution and it's worth quoting what he says in his book Genetics, Paleontology, and Macroevolution.

Macroevolution must be a field that embraces the ecological theater, including the range of time scales of the ecologist, to the sweeping historical changes available only to paleontological study. It must include the peculiarities of history, which must have had singular effects on the directions that the composition of the world's biota took (e.g., the splitting of continents, the establishment of land and oceanic isthmuses). It must take the entire network of phylogenetic relationships and impose a framework of genetic relationships and appearances of character changes. Then the nature of evolutionary directions and the qualitative transformation of ancestor to descendant over major taxonomic distances must be explained.
                                                                     Jeffrey S. Levinton (2001) p.6

Levinton then goes on to draw a parallel between microevolution and macroevolution on the one hand, and physics and astronomy on the other. He points out that the structure and history of the known universe has to be consistent with modern physics, but that's not sufficient. He gives the big bang as an example of a cosmological hypothesis that doesn't derive directly from fundamental physics. I think this analogy is insightful. Astronomers study the life and death of stars and the interactions of galaxies. Some of them are interested in the formation of planetary systems, especially the unique origin of our own solar system. Explanations of these "macro" phenomena depend on the correctness of the underlying "micro" physics phenomena (e.g., gravity, relativity) but there's more to the field of astronomy than that.

Levinton continues ....

Does the evolutionary biologist differ very much from this scheme of inference? A set of organisms exists today in a partially measurable state of spatial, morphological, and chemical relationships. We have a set of physical and biological laws that might be used to construct predictions about the outcome of the evolutionary process. But, as we all know, we are not very successful, except at solving problems at small scales. We have plausible explanations for the reason why moths living in industrialized areas are rich in dark pigment, but we don't know whether or why life arose more than once or why some groups became extinct (e.g., the dinosaurs) whereas others managed to survive (e.g., horseshoe crabs). Either our laws are inadequate and we have not described the available evidence properly or no such laws can be devised to predict uniquely what should have happened in the history of life. For better or worse, macroevolutionary biology is as much historical as is astronomy, perhaps with looser laws and more diverse objectives....

Indeed, the most profound problem in the study of evolution is to understand how poorly repeatable historical events (e.g., the trapping of an endemic radiation in a lake that dries up) can be distinguished from lawlike repeatable processes. A law that states 'an endemic radiation will become extinct if its structural habitat disappears' has no force because it maps to the singularity of a historical event.
                                                                 Jeffrey S. Levinton (2001) p.6-7

In conclusion, then, macroevolutionary processes are underlain by microevolutionary phenomena and are compatible with microevolutionary theories, but macroevolutionary studies require the formulation of autonomous hypotheses and models (which must be tested using macroevolutionary evidence). In this (epistemologically) very important sense, macroevolution is decoupled from microevolution: macroevolution is an autonomous field of evolutionary study.
     Francisco J. Ayala (1983)

I think it's important to appreciate what macroevolutionary biologists are saying. Most of these scientists are paleontologists and they think of their area of study as an interdisciplinary field that combines geology and biology. According to them, there's an important difference between evolutionary theory and the real history of life. The actual history has to be consistent with modern evolutionary theory (it is) but the unique sequence of historical events doesn't follow directly from application of evolutionary theory. Biological mechanisms such as natural selection and random genetic drift are part of a much larger picture that includes moving continents, asteroid impacts, ice ages, contingency, etc. The field of macroevolution addresses these big picture issues.

Clearly, there are some evolutionary biologists who are only interested in macroevolution. They don't care about microevolution. This is perfectly understandable since they are usually looking at events that take place on a scale of millions of years. They want to understand why some species survive while others perish and why there are some long-term trends in the history of life. (Examples of such trends are the loss of toes during the evolution of horses, the development of elaborate flowers during the evolution of vascular plants, and the tendency of diverse species, such as the marsupial Tasmanian wolf and the common placental wolf, to converge on a similar body plan.)

Nobody denies that macroevolutionary processes involve the fundamental mechanisms of natural selection and random genetic drift, but these microevolutionary processes are not sufficient, by themselves, to explain the history of life. That's why, in the domain of macroevolution, we encounter theories about species sorting and tracking, species selection, and punctuated equilibria.

Micro- and macroevolution are thus different levels of analysis of the same phenomenon: evolution. Macroevolution cannot solely be reduced to microevolution because it encompasses so many other phenomena: adaptive radiation, for example, cannot be reduced only to natural selection, though natural selection helps bring it about.
     Eugenie C. Scott (2004)

As I mentioned earlier, most of macroevolutionary theory is intimately connected with the observed fossil record and, in this sense, it is much more historical than population genetics and evolution within a species. Macroevolution, as a field of study, is the turf of paleontologists and much of the debate about a higher level of evolution (above species and populations) is motivated by the desire of paleontologists to be accepted at the high table of evolutionary theory. It's worth recalling that during the last part of the twentieth century evolutionary theorizing was dominated by population geneticists. Their perspective was described by John Maynard Smith, "... the attitude of population geneticists to any paleontologist rash enough to offer a contribution to evolutionary theory has been to tell him to go away and find another fossil, and not to bother the grownups." (Maynard Smith, 1984)

The distinction between microevolution and macroevolution is often exaggerated, especially by the anti-science crowd. Creationists have gleefully exploited the distinction in order to legitimate their position in the light of clear and obvious examples of evolution that they can't ignore. They claim they can accept microevolution, but they reject macroevolution.

In the real world—the one inhabited by rational human beings—the difference between macroevolution and microevolution is basically a difference in emphasis and level. Some evolutionary biologists are interested in species, trends, and the big picture of evolution, while others are more interested in the mechanics of the underlying mechanisms.

Speciation is critical to conserving the results of both natural selection and genetic drift. Speciation is obviously central to the fate of genetic variation, and a major shaper of patterns of evolutionary change through evolutionary time. It is as if Darwinians—neo- and ulra- most certainly included—care only for the process generating change, and not about its ultimate fate in geological time.
     Niles Eldredge (1995)

The Creationists would have us believe there is some magical barrier separating selection and drift within a species from the evolution of new species and new characteristics. Not only is this imagined barrier invisible to most scientists but, in addition, there is abundant evidence that no such barrier exists. We have numerous examples that show how diverse species are connected by a long series of genetic changes. This is why many scientists claim that macroevoluton is just lots of microevolution over a long period of time.

But wait a minute. I just said that many scientists think of macroevolution as simply a scaled-up version of microevolution, but a few paragraphs ago I said there's more to the theory of evolution than just changes in the frequency of alleles within a population. Don't these statements conflict? Yes, they do ... and therein lies a problem.

When the principle tenets of the Modern Synthesis were being worked out in the 1940's, one of the fundamental conclusions was that macroevolution could be explained by changes in the frequency of alleles within a population due, mostly, to natural selection. This gave rise to the commonly accepted notion that macroevolution is just a lot of microevolution. Let's refer to this as the sufficiency of microevolution argument.

At the time of the synthesis, there were several other explanations that attempted to decouple macroevolution from microevolution. One of these was saltation, or the idea that macroevolution was driven by large-scale mutations (macromutations) leading to the formation of new species. This is the famous "hopeful monster" theory of Goldschmidt. Another decoupling hypothesis was called orthogenesis, or the idea that there is some intrinsic driving force that directs evolution along certain pathways. Some macroevolutionary trends, such as the increase in the size of horses, were thought to be the result of this intrinsic force.

Both of these ideas about macroevolutionary change (saltation and orthogensis) had support from a number of evolutionary biologists. Both were strongly opposed by the group of scientists that produced the Modern Synthesis. One of the key players was the paleontologist George Gaylord Simpson whose books Tempo and Mode in Evolution (1944) and The Major Features of Evolution (1953) attempted to combine paleontology and population genetics. "Tempo" is often praised by evolutionary biologists and many of our classic examples of evolution, such as the bushiness of the horse tree, come from that book. It's influence on paleontologists was profound because it upset the traditional view that macroevolution and the newfangled genetics had nothing in common.

Just as mutation and drift introduce a strong random component into the process of adaptation, mass extinctions introduce chance into the process of diversification. This is because mass extinctions are a sampling process analogous to genetic drift. Instead of sampling allele frequencies, mass extinctions samples species and lineages. ... The punchline? Chance plays a large role in the processes responsible for adaptation and diversity.
        Freeman and Herron (1998)

We see, in context, that the blurring of the distinction between macroevolution and microevolution was part of a counter-attack on the now discredited ideas of saltation and orthogenesis. As usual, when pressing the attack against objectionable ideas, there's a tendency to overrun the objective and inflict collateral damage. In this case, the attack on orthogenesis and the old version of saltation was justified since neither of these ideas offer viable alternatives to natural selection and drift as mechanisms of evolution. Unfortunately, Simpson's attack was so successful that a generation of scientists grew up thinking that macroevolution could be entirely explained by microevolutionary processes. That's why we still see this position being advocated today and that's why many biology textbooks promote the sufficiency of microevolution argument. Gould argues—successfully, in my opinion—that the sufficiency of microevolution became dogma during the hardening of the synthesis in the 1950-'s and 1960's. It was part of an emphasis on the individual as the only real unit of selection.

However, from the beginning of the Modern Synthesis there were other evolutionary biologists who wanted to decouple macroevolution and microevolution—not because they believed in the false doctrines of saltation and orthogenesis, but because they knew of higher level processes that went beyond microevolution. One of these was Ernst Mayr. In his essay "Does Microevolution Explain Macroevolution," Mayr says ...

Among all the claims made during the evolutionary synthesis, perhaps the one that found least acceptance was the assertion that all phenomena of macroevolution can be ‘reduced to,' that is, explained by, microevolutionary genetic processes. Not surprisingly, this claim was usually supported by geneticists but was widely rejected by the very biologists who dealt with macroevolution, the morphologists and paleontologists. Many of them insisted that there is more or less complete discontinuity between the processes at the two levels—that what happens at the species level is entirely different from what happens at the level of the higher categories. Now, 50 years later the controversy remains undecided.
                                                                         Ernst Mayr (1988) p.402

Mayr goes on to make several points about the difference between macroevolution and microevolution. In particular, he emphasizes that macroevolution is concerned with phenotypes and not genotypes, "In this respect, indeed, macroevolution as a field of study is completely decoupled from microevolution." (ibid p. 403). This statement reiterates an important point, namely that macroevolution is a "field of study" and, as such, its focus differs from that of other fields of study such as molecular evolution.

If you think of macroevolution as a field of study rather than a process, then it doesn't make much sense to say that macroevolution can be explained by the process of changing alleles within a population. This would be like saying the entire field of paleontology can be explained by microevolution. This is the point about the meaning of the term "macroevolution" that is so often missed by those who dismiss it as just a bunch of microevolution.

The orthodox believers in the hardened synthesis feel threatened by macroevolution since it implies a kind of evolution that goes beyond the natural selection of individuals within a population. The extreme version of this view is called adaptationism and the believers are called Ultra-Darwinians by their critics. This isn't the place to debate adaptationism: for now, let's just assume that the sufficiency of microevolution argument is related to the pluralist-adaptationist controversy and see how our concept of macroevolution as a field of study relates to the issue. Niles Eldredge describes it like this ...

The very term macroevolution is enough to make an ultra-Darwinian snarl. Macroevolution is counterpoised with microevolution—generation by generation selection- mediated change in gene frequencies within populations. The debate is over the question, Are conventional Darwinian microevolutionary processes sufficient to explain the entire history of life? To ultra-Darwinians, the very term macroevolution suggests that the answer is automatically no. To them, macroevolution implies the action of processes—even genetic processes—that are as yet unknown but must be imagined to yield a satisfactory explanation of the history of life.

But macroevolution need not carry such heavy conceptual baggage. In its most basic usage, it simply means evolution on a large-scale. In particular, to some biologists, it suggests the origin of major groups - such as the origin and radiation of mammals, or the derivation of whales and bats from terrestrial mammalian ancestors. Such sorts of events may or may not demand additional theory for their explanation. Traditional Darwinian explanation, of course, insists not.
                                                              Niles Eldredge (1995) p. 126-127

Eldredge sees macroevolution as a field of study that's mostly concerned with evolution on a large scale. Since he's a paleontologist, it's likely that, for him, macroevolution is the study of evolution based on the fossil record. Eldredge is quite comfortable with the idea that one of the underlying causes of evolution can be natural selection—this includes many changes seen over the course of millions of years. In other words, there is no conflict between microevolution and macroevolution in the sense that microevolution stops and is replaced by macroevolution above the level of species. But there is a conflict in the sense that Eldredge, and many other evolutionary biologists, do not buy the sufficiency of microevolution argument. They believe there are additional theories, and mechanisms, needed to explain macroevolution. Gould says it best ....

We do not advance some special theory for long times and large transitions, fundamentally opposed to the processes of microevolution. Rather, we maintain that nature is organized hierarchically and that no smooth continuum leads across levels. We may attain a unified theory of process, but the processes work differently at different levels and we cannot extrapolate from one level to encompass all events at the next. I believe, in fact, that ... speciation by splitting guarantees that macroevolution must be studied at its own level. ... [S]election among species—not an extrapolation of changes in gene frequencies within populations—may be the motor of macroevolutionary trends. If macroevolution is, as I believe, mainly a story of the differential success of certain kinds of species and, if most species change little in the phyletic mode during the course of their existence, then microevolutionary change within populations is not the stuff (by extrapolation) of major transformations.
                                                         Stephen Jay Gould (1980b) p. 170

Naturalists such as Ernst Mayr and paleontologists such as Gould and Eldredge have all argued convincingly that speciation is an important part of evolution. Since speciation is not a direct consequence of changes in the frequencies of alleles in a population, it follows that microevolution is not sufficient to explain all of evolution. Gould and Eldredge (and others) go even further to argue that there are processes such as species sorting that can only take place above the species level. This means there are evolutionary theories that only apply in the domain of macroevolution.

The idea that there's much more to evolution than genes and population genetics was a favorite theme of Stephen Jay Gould. He advocated a pluralist, hierarchical approach to evolution and his last book The Structure of Evolutionary Theory emphasized macroevolutionary theory—although he often avoided using this term. The Structure of Evolutionary Theory is a huge book that has become required reading for anyone interested in evolution. Remarkably, there's hardly anything in the book about population genetics, molecular evolution, and microevolution as popularly defined. What better way of illustrating that macroevolution must be taken seriously!

Macroevolutionary theory tries to identify patterns and trends that help us understand the big picture. In some cases, the macroevolution biologists have recognized generalities (theories & hypotheses) that only apply to higher level processes. Punctuated equilibria and species sorting are examples of such higher level phenomena. The possible repeatedness of mass extinctions might be another.

Remember that macroevolution should not be contrasted with microevolution because macroevolution deals with history. Microevolution and macroevolution are not competing explanations of the history of life any more than astronomy and physics compete for the correct explanation of the history of the known universe. Both types of explanation are required.

I think species sorting is the easiest higher level phenomena to describe. It illustrates a mechanism that is clearly distinct from changes in the frequencies of alleles within a population. In this sense, it will help explain why microevolution isn't a sufficient explanation for the evolution of life. Of course, one needs to emphasize that macroevolution must be consistent with microevolution.

I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
        Stephen Jay Gould (2002)

If we could track a single lineage through time, say from a single-cell protist to Homo sapiens, then we would see a long series of mutations and fixations as each ancestral population evolved. It might look as though the entire history could be accounted for by microevolutionary processes. This is an illusion because the track of the single lineage ignores all of the branching and all of the other species that lived and died along the way. That track would not explain why Neanderthals became extinct and Cro-Magnon survived. It would not explain why modern humans arose in Africa. It would not tell us why placental mammals became more successful than the dinosaurs. It would not explain why humans don't have wings and can't breathe underwater. It doesn't tell us whether replaying the tape of life will automatically lead to humans. All of those things are part of the domain of macroevolution and microevolution isn't sufficient to help us understand them.


Monday, October 03, 2022

Evolution by chance

Can natural selection occur by chance or accident? No, with qualifications. Can evolution occur by chance or accident? Yes, definitely.

While tidying up my office I came across an anthology of articles by Richard Dawkins. It included a 2009 review of Jerry Coyne's book Why Evolution Is True (2009) and one of Richard's comments caught my eye because it illustrates the difference between the Dawkins' view of evolution and the current mainstream view that was described by Jerry in his book.

I can illustrate this difference by first quoting from Jerry Coyne's book.

This brings up the most widespread misunderstanding about Darwinism: the idea that, in evolution, "everything happens by chance" (also stated as "everything happens by accident"). This common claim is flatly wrong. No evolutionist—and certainly not Darwin—ever argued that natural selection is based on chance ....

True, the raw materials for evolution—the variations between individuals—are indeed produced by chance mutations. These mutations occur willy-nilly, regardless of whether they are good or bad for the individual. But it is the filitering of that variation by natural selection that produces natural selection, and natural selection is manifestly not random. (p. 119)

It's extremely important to notice that Coyne is referring to NATURAL SELECTION (or Dawinism) in this passage. Natural selection is not random or accidental, according to Coyne. This passage is followed just a few pages later by a section titled "Evolution Without Selection."

Let's take a brief digression here, because it's important to appreciate that natural selection isn't the only process of evolutionary change. Most biologists define evolution as a change in the proportion of alleles (different forms of a gene) in the population.

[Coyne then describes an example of random genetic drift and continues ...] Both drift and selection produce the genetic change that we recognize as evolution. But there's an important difference. Drift is a random process, while selection is the antithesis of randomness. Genetic drift can change the frequencies of alleles regardless of how useful they are to their carrier. Selection, on the other hand, always gets rid of harmful alleles and raises the frequencies of beneficial ones. (pp. 122-123)

Now let's look at Richard Dawkins' review of Coyne's book as published in the Times Literary Supplement in 2009 and reprinted in Books Do Furnish a Life (2021). I picked out an interesting passage from that review in order to illustrate a point.

Coyne is right to identify the most widespread misunderstanding about Darwinism as 'the idea that, in evolution, 'everything happens by chance' ... This common claim is flatly wrong.' Not only is it flatly wrong, it is obviously wrong, transparently wrong, even to the meanest intelligence (a phrase that has me actively restraining myself). If evolution worked by chance, it obviously couldn't work at all. (p. 427)

That last sentence is jarring to many scientists, including me. I think that the Dawkins' statement is 'obviously wrong' and 'transparently wrong' because, as Coyne pointed out, evolution by random genetic drift can occur by chance. [Let's not quibble about the meanings of 'random' and 'chance." That's a red herring in this context.] Clearly, evolution can work by chance so why does Dawkins say it can't?

It's not because Dawkins is unaware of random genetic drift and Neutral Theory. The explanation (I think) is that Dawkins restricts his definition of evolution to evolution by natural selection. From his perspective, the fixation of alleles by random genetic drift doesn't count as real evolution because it doesn't produce adaptations. That's the view that he described in The Extended Phenotype back in 1982 and the view that he has implicitly supported over the past few decades [Richard Dawkins' View of Random Genetic Drift].

This is one of the reasons why we refer to Dawkins as an adaptationist and it's one of the reasons why so many of today's evolutionary biologists—especially those who study evolution at the molecular level—reject the Dawkins' view of evolution in favor of a more pluralistic approach.

Note: I wrote an earlier version of this post in 2009 [Dawkins on Chance] and I wrote a long essay on Evolution by Accident where I describe many other examples of evolution by chance.


Wednesday, June 30, 2021

Richard Dawkins talks about the genetic code and information

This is a video published a few weeks ago where Jon Perry interviews Richard Dawkins. Jon Perry is the author of animations posted on his website Stated Clearly. He (Perry) has a very adaptaionist view of evolution—a view that he got from Richard Dawkins.

The main topic of the interview concerns DNA as information and the genetic code. Both Dawkins and Perry give the impression that the only kind of information in the genome is the genetic code (sensu stricto); in other words, the code that specifies a sequence of amino acids using the sequence of nucleotides in a coding region [The Real Genetic Code]. Dawkins makes the same point he has often made; namely, that this is a real code just like any other code.

Perry points out that most people don't understand this, including many atheists who argue that the "code" is merely an analogy and not to be taken literally. Atheists, and others, also argue that the information content of DNA includes lots of other things such as genes that specify functional RNAs and sites that bind proteins. It's hard to argue that a gene for tRNA functions as any kind of a code and it's hard to argue that the DNA binding sites in origins of replication are codes even though you could argue that they carry information.

I don't get excited about arguments over whether DNA carries "information" because there's not much to be gained by such arguments. Who cares whether the genetic code falls under the definition of "information theory"? However, I do get annoyed when people say that the ONLY information in DNA is in the form of the genetic code.

Watch the video and let me know what you think. Jerry Coyne watched it and he wasn't the least bit bothered by the things that bothered me [A discussion on genetics, evolution, and information with Richard Dawkins].


Wednesday, June 16, 2021

Is the Modern Synthesis effectively dead?

The Modern Synthesis is the version of evolutionary theory popularized by Julian Huxley and supported by the leading evolutionary biologists of the 1930s, 40s, and 50s.

The general idea was to merge Dawrin's view of natural selection with the relatively new field of population genetics. Evolution was now defined as a change in allele frequencies in a population and the emphasis was on natural selection as the most important mechanism although, in the original version by Huxley, the fixation of alleles by random genetic drift can occur in small populations. By the early 1960s the most popular vesion of the Modern Synthesis focused almost exclusively on natural selection—an emphasis that's referred to as the hardening of the synthesis. It was this excessively adaptationist view of evolution that led to Gould and Lewontin's paper on "The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme" (Gould and Lewontin, 1979).

Wednesday, April 21, 2021

The illusions of James Shapiro

James A. Shapiro is a professor in the Department of Biochemistry and Molecular Biology at the University of Chicago (Chicago, USA). He made signficant contributions to our understanding if the function and structure of transposons but in later years he has become a vocal opponent of evolution culminating in his 2011 book Evolution: A View from the 21st Century. He is one of the founding members of The Third Way of Evolution.

I wrote a critical review of Evolution: A View from the 21st Century for the National Center for Science Education (NCSE) Reports but the issue is no longer visible on the web. Shapiro didn't like my review so NCSE published his rebutal and that's also unavailable. You can see my response at: James Shapiro Responds to My Review of His Book.

Monday, April 19, 2021

The illusions of Denis Noble

Denis Noble was a Professor of Physiology at Oxford University in the United Kingdom until he retired. He had a distinguished career as a physiologist making significant contributions to our undestanding of the heart and its relationship to the whole organism.

In recent years, Noble has dabbled in philosophy and evolution. He has become a vocal opponent modern evolution (sensu Noble) and the way science is currently conducted. Some of his criticisms have made it onto two popular books: The Music of Life and Dance to the Tune of Life. He is one of the leading proponents of the "Extended Evolutionary Synthesis" (EES) and he is one of the founders of The Third Way of Evolution, a wishy-washy and scientifically inaccurate way of attacking a strawman version of evolution and providing a safe haven for religious scientists.

Friday, April 09, 2021

Should we teach genomics and evolution to medical students?

Rama Singh,1 a biology professor at McMaster Universtiy in Hamilton (Ontario, Canada) has just published an interesting article on The Conversation website. It's about Medical schools need to prepare doctors for revolutionary advances in genetics. You can read the full article yourself but let me highlight the last few paragraphs to start the discussion.

Future physicians will be part of health networks involving medical lab technicians, data analysts, disease specialists and the patients and their family members. The physician would need to be knowledgeable about the basic principles of genetics, genomics and evolution to be able to take part in the chain of communication, information sharing and decision-making process.

This would require a more in-depth knowledge of genomics than generally provided in basic genetics courses.

Much has changed in genetics since the discovery of DNA, but much less has changed how genetics and evolution are taught in medical schools.

In 2013-14 a survey of course curriculums in American and Canadian medical schools showed that while most medical schools taught genetics, most respondents felt the amount of time spent was insufficient preparation for clinical practice as it did not provide them with sufficient knowledge base. The survey showed that only 15 per cent of schools covered evolutionary genetics in their programs.

A simple viable solution may require that all medical applicants entering medical schools have completed rigorous courses in genetics and genomics.

Here's the problem. I've just finished research on a book about modern evolution and genomics so I think I know a little bit about the subject. I'm also on the editorial board of a journal that publishes research on biochemistry and molecular biology education. I've written a biochemistry textbook and I have far too many years of experience trying to teach this material to graduate students and undergraduates at the University of Toronto. I can safely say that we (university teachers) have done a horrible job of teaching evolution and genomics to our students. We have turned out an entire generation of students who don't understand modern molecular evolution and don't understand what's in your genome.

What this means is that there's an extremely small pool of students who have completed "rigorous courses in genetics and genomics." Nobody will be able to apply to medical school. I doubt that we could teach this material to medical students with or without the appropriate background.

But you don't have to take my word for it. Some people have tried to teach this material to health science workers so we can see how it's working at that level. Take a look at the The Genomics Education Programme supported by the NHS in the United Kingdom. They have a series of short videos and longer lessons that are designed to educate health care specialists. Here's the blurb that defines their objective.

Rapid advances in technology and understanding mean that genomics is now more relevant than ever before. As genomics increasingly becomes a part of mainstream NHS care, all healthcare professionals, and not just genomics specialists, need to have a good understanding of its relevance and potential to impact the diagnosis, treatment and management of people in our care.

In 2014, Health Education England (HEE) launched a four-year £20 million Genomics Education Programme (GEP) to ensure that our 1.2 million-strong NHS workforce has the knowledge, skills and experience to keep the UK at the heart of the genomics revolution in healthcare.

Funding for the programme has since been extended to enable us to continue our work in providing co-ordinated national direction of education and training in genomics and developing resources for a wide range of professionals.

They describe genes as 'coding' genes that build proteins. There's no mention of noncoding genes. The define a genome as "both genes (coding) and non-coding DNA." They also say that your genome is all of the DNA in our cells (46 chromosomes, 23 pairs). I don't see anything in their education packages that covers modern molecular evolution. In one of the packages they say,

The term ‘junk DNA’ has been used since the 1970s to describe non-coding regions of the genome, but today it is considered inaccurate and misleading. The term ‘junk’ suggests that 98% of the genome has no use, but in recent years, studies and projects have used advances in technology to shed light on these regions and have come to different conclusions about how much of the genome has a biological function.

Here's a link to a short video called What is a genome?. I recommend that you watch it to see the level that these experts think is suitable for health care professionals in the UK and to see the level of expertise of those who made the video. This is what seven years of work by experts and £20 million will get you.

All of this tells me that teaching genomics and evolution to medical students is going to be a lot more difficult than Rama Singh imagines. Not only would we have to counter several years of misinformation but we would have to rely on teachers who probably don't understand either topic.

Let's start by teaching these things correctly to biology and biochemistry majors. That's going to be hard enough for now.


1. Full displosure: Rama and I shared an NSERC grant in 1981 on genetic variation in Drosophila.

Wednesday, March 17, 2021

I think I'll skip this meeting

I just received an invitation to a meeting ...

On behalf of the international organizing committee, we would like to invite you to a conference to be held in Neve Ilan, near Jerusalem, from 4-8 October 2021, entitled ‘Potential and Limitations of Evolutionary Processes’. The main goal of this interdisciplinary, international conference is to bring together scientists and scholars who hold a range of viewpoints on the potential and possible limitations of various undirected chemical and biological processes.

The conference will include presentations from a broad spectrum of disciplines, including chemistry, biochemistry, biology, origin of life, evolution, mathematics, cosmology and philosophy. Open-floor discussion will be geared towards delineating mechanistic details, with a view to discussing in such a way that speakers and participants feel comfortable expressing different opinions and different interpretations of the data, in the spirit of genuine academic inquiry.

I'm pretty sure I got this invite because I attended the Royal Society Meeting on New trends in evolutionary biology: biological, philosophical and social science perspectives back in 2016. That meeting was a big disappointment because the proponents of extending the modern synthesis didn't have much of a case [Kevin Laland's new view of evolution].

I was curious to see what kind of followup the organizers of this new meeting were planning so I checked out the website at: Potential and Limitations of Evolutionary Processes. Warning bells went off immediately when I saw the list of topics.

  • Fine-Tuning of the Universe
  • The Origin of Life
  • Origin & Fine-Tuning of the Genetic Code
  • Origin of Novel Genes
  • Origin of Functional Islands in Protein Sequence Space
  • Origin of Multi-Component Molecular Machines
  • Fine-Tuning of Molecular Systems
  • Fine-Tuning in Complex Biological Systems
  • Evolutionary Waiting Times
  • History of Life & Comparative Genomics

This is a creationist meeting. A little checking shows that three of the four organizers, Russ Carlson, Anthony Futerman, and Siegfried Scherer, are creationists. (I don't know about the other organizer, Joel Sussman, but in this case guilt by association seems appropriate.)

I don't think I'll book a flight to Israel.


Saturday, October 03, 2020

On the importance of random genetic drift in modern evolutionary theory

The latest issue of New Scientist has a number of articles on evolution. All of them are focused on extending and improving the current theory of evolution, which is described as Darwin's version of natural selection [New Scientist doesn't understand modern evolutionary theory].

Most of the criticisms come from a group who want to extend the evolutionary synthesis (EES proponents). Their main goal is to advertise mechanisms that are presumed to enhance adaptation but that weren't explicitly included in the Modern Synthesis that was put together in the late 1940s.

One of the articles addresses random genetic drift [see Survival of the ... luckiest]. The emphasis in this short article is on the effects of drift in small populations and it gives examples of reduced genetic diversity in small populations.

Wednesday, September 30, 2020

New Scientist doesn't understand modern evolutionary theory

New Scientist has devoted much of their September 26th issue to evolution, but not in a good way. Their emphasis is on 13 ways that we must rethink evolution. Readers of this blog are familiar with this theme because New Scientist is talking about the Extended Evolutionary Synthesis (EES)—a series of critiques of the Modern Synthesis in an attempt to overthrow or extend it [The Extended Evolutionary Synthesis - papers from the Royal Society meeting].

My main criticsm of EES is that its proponents demonstrate a remarkable lack of understanding of modern evolutionary theory and they direct most of their attacks against the old adaptationist version of the Modern Synthesis that was popular in the 1950s. For the most part, EES proponents missed the revolution in evolutionary theory that occrred in the late 1960s with the development of Neutral Theory, Nearly-Neutral Theory, and the importance of random genetic drift. EES proponents have shown time and time again that they have not bothered to read a modern textbook on population genetics.

Wednesday, February 12, 2020

Happy Darwin Day! 2020

Charles Darwin, the greatest scientist who ever lived, was born on this day in 1809 [Darwin still spurs tributes, debates] [Happy Darwin Day!] [Darwin Day 2017]. Darwin is mostly famous for two things: (1) he described and documented the evidence for evolution and common descent and (2) he provided a plausible scientific explanation of evolution—the theory of natural selection. He put all this in a book, The Origin of Species by Means of Natural Selection published in 1859—a book that spurred a revolution in our understanding of the natural world. (You can still buy a first edition copy of the book but it will cost you several hundred thousand dollars.)

Monday, October 21, 2019

The evolution of de novo genes

De novo genes are new genes that arise spontaneously from junk DNA [De novo gene birth]. The frequency of de novo gene creation is important for an understanding of evolution. If it's a frequent event, then species with a large amount of junk DNA might have a selective advantage over species with less junk DNA, especially in a changing environment.

Last week I read a short Nature article on de novo genes [Levy, 2019] and I think the subject deserves more attention. Most new genes in a species appear to arise by gene duplication and subsequent divergence but de novo genes are genes that are unrelated to genes in any other clade so we can assume that they are created from junk DNA that accidentally becomes associated with a promoter causing the DNA to be transcribed. A new gene is formed if the RNA acquires a function. If the transcript contains an open reading frame then it may be translated to produce a polypeptide and if the polypeptide performs a new function then the resulting de novo gene is a new protein-coding gene.

The important question is whether the evolution of de novo genes is a common event or a rare event.

Sunday, September 08, 2019

Contingency, selection, and the long-term evolution experiment

I'm a big fan of Richard Lenski's long-term evolution experiment (LTEE) and of Zachary Blount's work in particular. [Strolling around slopes and valleys in the adaptive landscape] [On the unpredictability of evolution and potentiation in Lenski's long-term evolution experiment] [Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source]

The results of the LTEE raise some interesting questions about evolution. The Lenski experiment began with 12 (almost) identical cultures and these have now "evolved" for 31 years and more than 65,000 generations. All of the cultures have diverged to some extent and one of them (and only one) has developed the ability to use citrate as a carbon source. Many of the cultures exhibit identical, or very similar, mutations that have reached significant frequencies, or even fixation, in the cultures.

Several other laboratory evolution experiments have been completed or are underway in various labs around the world. The overall results are relevant to a discussion about the role of contingency and accident in the history of life [see Evolution by Accident]. Is it true that if you replay the tape of life the results will be quite different? [Replaying life's tape].

Friday, August 30, 2019

Evolution by Accident

Evolution by Accident
v1.43 ©2006 Laurence A. Moran

This essay has been transferred here from an old server that has been decommissioned.Modern concepts of evolutionary change are frequently attacked by those who find the notions of randomness, chance, and accident to be highly distasteful. Some of these critics are intelligent design creationists and their objections have been refuted elsewhere. In this essay I'm more concerned about my fellow evolutionists who go to great lengths to eliminate chance and accident from all discussions about the fundamental causes of evolution. This is my attempt to convince them that evolution is not as predictable as they claim. I was originally stimulated to put my ideas down on paper when I read essays by John Wilkins [Evolution and Chance] and Loren Haarsma [Chance from a Theistic Perspective] on the TalkOrigins Archive.

The privilege of living beings is the possession of a structure and of a mechanism which ensures two things: (i) reproduction true to type of the structure itself, and (ii) reproduction equally true to type, of any accident that occurs in the structure. Once you have that, you have evolution, because you have conservation of accidents. Accidents can then be recombined and offered to natural selection to find out if they are of any meaning or not.
Jacques Monod (1974) p.394
The main conclusion of this essay is that a large part of ongoing evolution is determined by stochastic events that might as well be called "chance" or "random." Furthermore, a good deal of the past history of life on Earth was the product of chance events, or accidents, that could not have been predicted. When I say "evolution by accident" I'm referring to all these events. This phrase is intended solely to distinguish "accidental" evolution from that which is determined by non-random natural selection. I will argue that evolution is fundamentally a random process, although this should not be interpreted to mean that all of evolution is entirely due to chance or accident. The end result of evolution by accident is modern species that do not look designed.

Thursday, August 22, 2019

Reactionary fringe meets mutation-biased adaptation.
7. Going forward

This the last of a series of posts by Arlin Stoltzfus on the role of mutation as a dispositional factor in evolution. Arlin has established that the role of mutation in evolution is much more important than most people realize. He has also built a strong case for the influence of mutation bias. How should we incorporate these concepts into modern evolutionary theory?

Click on the links in the box (below) to see the other posts in the series.



Reactionary fringe meets mutation-biased adaptation.
7. Going forward

by Arlin Stoltzfus

Haldane (1922) argued that, because mutation is a weak pressure easily overcome by selection, the potential for biases in variation to influence evolution depends on neutral evolution or high mutation rates. This theory, like the Modern Synthesis of 1959, depends on the assumption that evolution begins with pre-existing variation. By contrast, when evolution depends on the introduction of new variants, mutational and developmental biases in variation may impose biases on evolution, without requiring neutral evolution or high mutation rates.

Thursday, August 15, 2019

Reactionary fringe meets mutation-biased adaptation.
5.5 Synthesis apologetics

This is part of a continuing series of posts by Arlin Stoltzfus on the role of mutation as a dispositional factor in evolution. In this post, Arlin explains how defenders of the Modern Synthesis react in the face of serious challenges to the theory that was formulated in the 1940s and 50s. Rather than reject the theory, they engage in various forms of "synthesis apologetics."

Click on the links in the box (below) to see the other posts in the series.




Reactionary fringe meets mutation-biased adaptation. 5.6 Synthesis apologetics
by Arlin Stoltzfus

Tuesday, August 06, 2019

Reactionary fringe meets mutation-biased adaptation.
5.4. Taking neo-Darwinism seriously

This is part of a continuing series of posts by Arlin Stoltzfus on the role of mutation as a dispositional factor in evolution. In this post Arlin discusses his view of neo-Darwinism and why it is inconsistent with macromutations and lateral gene transfer. He equates neo-Darwinism with the Modern Synthesis (1959 version), a comparison that might be challenged. Click on the links in the box (below) to see the other posts in the series.




Reactionary fringe meets mutation-biased adaptation. 5.4. Taking neo-Darwinism seriously
by Arlin Stoltzfus

The Modern Synthesis is often described as the result of combining Darwinism and genetics. This description, in my opinion, is concise and historically accurate: the Modern Synthesis of 1959 is a sophisticated attempt to arrange the pieces of population genetics to justify a neo-Darwinian dichotomy in which variation merely supplies raw materials, and selection is the source of initiative, creativity and direction.

Friday, August 02, 2019

Reactionary fringe meets mutation-biased adaptation.
6. What "limits" adaptation?

This is part of a continuing series of posts by Arlin Stoltzfus on the role of mutation as a dispositional factor in evolution. In this post Arlin discusses the role of adaptation and what determines the pathway that it will take over time. Is it true that populations will always adapt quickly to any change in the environment? (Hint: no it isn't!) Click on the links in the box (below) to see the other posts in the series.




Reactionary fringe meets mutation-biased adaptation.
6. What "limits" adaptation?

by Arlin Stoltzfus
According to the hatchet piece at TREE, theoretical considerations dictate that biases in variation are unlikely to influence adaptation, because this requires small population sizes and reciprocal sign epistasis.

Yet, we have established that mutation-biased adaptation is real (see The empirical case and Some objections addressed). If theoretical population genetics tells us that mutation-biased adaptation is impossible or unlikely, what is wrong with theoretical population genetics?

Adaptation, before Equilibrium Day