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Tuesday, May 02, 2017

The selfish gene vs the lucky allele

The Selfish Gene was published forty-one years ago (1976) and last year there was a bit of a celebration. I think we can all appreciate the impact that the book had at the time but I'm not sure it's as profound and lasting as most people believe ["The Selfish Gene" turns 40] [The "selfish gene" is not a good metaphor to describe evolution] [Die, selfish gene, die!].

The main criticisms fall into two categories: (1) the primary unit of selection is the individual organism, not the gene, and (2) the book placed too much emphasis on adaptation (Darwinism). I think modern evolutionary theory is based on 21st century population genetics and that view puts a great deal of emphasis on the power of random genetic drift. The evolution of a population involves the survival of individuals within the population and that, in turn, depends on the variation that exists in the population. Thus, evolution is characterized by changes in the frequencies of alleles in a population.

Thursday, January 28, 2016

"The Selfish Gene" turns 40

Richard Dawkins published The Selfish Gene 40 years ago and Matt Ridley notes the anniversary in a Nature article published today (Jan. 28, 2016): In retrospect: The selfish gene.

I don't remember when I first read it—probably the following year when the paperback version came out. I found it quite interesting but I was a bit put off by the emphasis on adaptation (taken from George Williams) and the idea of inclusive fitness (from W.D. Hamilton). I also didn't much like the distinction between vehicles and replicators and the idea that it was the gene, not the individual, that was the unit of selection ("selection" not "evolution").
It is finally time to return to the problem with which we started, to the tension between individual organism and gene as rival candidates for the central role in natural selection...One way of sorting this whole matter out is to use the terms ‘replicator’ and ‘vehicle’. The fundamental units of natural selection, the basic things that survive or fail to survive, that form lineages of identical copies with occasional random mutations, are called replicators. DNA molecules are replicators. They generally, for reasons that we shall come to, gang together into large communal survival machines or ‘vehicles’.

Richard Dawkins

Thursday, December 01, 2016

Learning about modern evolutionary theory: the drift-barrier hypothesis

Many evolutionary biologists are engaged in research that focuses on large organisms that are (presumably) adapting to a local environment. These "field biologists" are mostly concerned with rapid evolutionary changes. Those kind of changes are almost always due to natural selection. Many of these biologists are not interested in molecular evolution and not interested in any process other than natural selection.

Unfortunately, this promotes an adaptationist mentality where all of evolution is viewed through the filter of natural selection. This is the view criticized by Stephen Jay Gould and Richard Lewontin back in 1978 when they presented the Spandrels paper at a Royal Society meeting in London (UK).
Gould, S. J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proc. R. Soc. Lond. B 205:581-598. [doi: 10.1098/rspb.1979.0086
I believe there was a substantive change in our view of evolution back in the late 1960s and early 1970s. That's when the results of evolution at the molecular level were first being published. It lead to the development of Neutral Theory, Nearly-Neutral Theory and a growing appreciation of the importance of random genetic drift. Modern population genetics was able to cope easily with this new view of evolution.

Friday, April 22, 2016

Don't call it "The Theory of Evolution"

By now, we all know that a "theory" in science is much more than idle speculation, a point that has been made repeatedly over the past century. With respect to evolution, the most famous essay is by Stephen Jay Gould: "Evolution as Fact and Theory" and the latest explanation is an article in the New York Times by Carl Zimmer: In Science, It’s Never ‘Just a Theory’.

Unfortunately, it's not that simple and there are many scientists who use "theory" in the sense of hypothesis or speculation [see Facts and theories of evolution according to Dawkins and Coyne]. That's not what I want to talk about today.

What do scientists really mean when they refer to "The Theory of Evolution"? There is no single theory of evolution that covers all the mechanisms of evolution. There's the Theory of Natural Selection, and Neutral Theory, and the Theory of Random Genetic Drift, and a lot of theoretical population genetics. Sometimes you can lump them all together by referring to the Modern Synthesis or Neo-Darwinism. These terms are much more accurate than simply saying "The Theory of Evolution" as long as we all understand what those theories mean.

The problem with "The Theory of Evolution" is not only that it's ambiguous but it's misleading. It implies that there's only one theory to explain evolution. Another problem is that it sounds too much like we're talking about the history of life and saying that it's a "theory" that can be explained by evolution.

Instead of using the phrase "The Theory of Evolution," I think we should be referring to "evolutionary theory," which may come in different flavors. The term "evolutionary theory" encompasses a bunch of different ideas about the mechanisms of evolution and conveys a much more accurate description of the theoretical basis behind evolution. Douglas Futuyma prefers "evolutionary theory" in his textbook Evolution and I think he's right. It allows him to devote individual chapters to "The Theory of Random Genetic Drift" and "The Theory Natural Selection."

Here's how Futuyma explains the concept of theory in his book Evolution 2nd ed. p. 613.
So is evolution a fact or a theory? In light of these definitions, evolution is a scientific fact. That is, descent of all species, with modification, from common ancestors is a hypothesis that in the past 150 years or so has been supported by so much evidence, and so successfully resisted all challenges, that it has become a fact. But this history of evolutionary change is explained by evolutionary theory, the body of statements (about mutation, selection, genetic drift, developmental constraints, and so forth) that together account for the various changes that organisms have undergone. [my emphasis ... LAM]
He makes the same point in the opening pages of his book where he uses both terms when discussing the history of evolutionary theory. (Note that when Darwin used the word "theory" to describe natural selection he was not using it in the same sense as Gould and Zimmer to describe a modern scientific theory. That's why Futuyma uses "hypothesis" in the quote below.)
We now know that Darwin's hypothesis of natural selection on hereditary variation was correct, but we also know that there are more causes of evolution than Darwin realized, and that natural selection and hereditary variation themselves are more complex than he imagined. A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitute our current theory of evolution, or "evolutionary theory." Like all theories in science, it is a work in progress, for we do not yet know the causes of all of evolution, or all the biological phenomena that evolutionary biology will have to explain. Indeed, some details may turn out to be wrong. But the main tenets of the theory, as far as it goes, are so well supported that most biologists confidently accept evolutionary theory as the foundation of the science of life. p. 14 [my emphasis ... LAM]
When you're talking about the mechanisms of evolution, please use "evolutionary theory" instead of "the theory of evolution."

I wish the proponents of the Extended Evolutionary Synthesis would agree that the version of evolutionary theory they wish to extend is the one described by Douglas Futuyma. This would make it easier for them to explain what's wrong with that version and why their proposals are an improvement [see Templeton gives $8 million to prove that there's more to evolution than natural selection].


Saturday, January 23, 2016

Richard Dawkins makes a mistake when describing why gene trees are evidence of evolution

Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."

There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.

Thursday, August 18, 2011

Evolution Is a Fact and a Theory

This year is the 30th anniversary of the publication of Stephen Jay Gould's famous essay, Evolution as Fact and Theory in Discover magazine (May 1981).1

Back in 1993, I wrote a essay for talk.origins promoting the basic concepts that Gould, and others, advocated [Evolution is a Fact and a Theory (1993)]. This essay has been modified and updated several times since then—the latest version was on my website [Evolution Is a Fact and a Theory (2007)].

You would think that the simple concept described in all those articles would be widely understood by creationists but that's not the case. Even today, there are creationists who struggle to understand the difference between fact and theory. That's why I'm posting the 2011 version of my essay.

Evolution Is a Fact and a Theory

When non-biologists talk about biological evolution they often get confused over several different meanings of the word "evolution." On the one hand, there's the question of whether or not modern organisms have evolved from older ancestral organisms or whether modern species are continuing to change over time. On the other hand, there are questions about the mechanism of the observed changes... how did evolution occur? Biologists consider the existence of biological evolution to be a fact. It can be demonstrated today and the historical evidence for its occurrence in the past is overwhelming. However, biologists readily admit that they are less certain of the exact mechanism of evolution; there are several theories of the mechanisms of evolution. Stephen J. Gould has put this as well as anyone else:

In the American vernacular, "theory" often means "imperfect fact"--part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus the power of the creationist argument: evolution is "only" a theory and intense debate now rages about many aspects of the theory. If evolution is worse than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science—that is, not believed in the scientific community to be as infallible as it once was."

Well evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts don't go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's in this century, but apples didn't suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered.



Moreover, "fact" doesn't mean "absolute certainty"; there ain't no such animal in an exciting and complex world. The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us falsely for a style of argument that they themselves favor). In science "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional consent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

Evolutionists have been very clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory—natural selection—to explain the mechanism of evolution.


Stephen J. Gould, "Evolution as Fact and Theory"; Discover, May 1981
Gould is stating the prevailing view of the scientific community. In other words, the experts on evolution consider it to be a fact. This is not an idea that originated with Gould. The same point was made by Theodosius Dobzhansky eight years earlier—and by others before him.

Let me try to make crystal clear what is established beyond reasonable doubt, and what needs further study, about evolution. Evolution as a process that has always gone on in the history of the earth can be doubted only by those who are ignorant of the evidence or are resistant to evidence, owing to emotional blocks or to plain bigotry. By contrast, the mechanisms that bring evolution about certainly need study and clarification. There are no alternatives to evolution as history that can withstand critical examination. Yet we are constantly learning new and important facts about evolutionary mechanisms.

Theodosius Dobzhansky "Nothing in Biology Makes Sense Except in the Light of Evolution" American Biology Teacher vol. 35 (March 1973) reprinted in Evolution versus Creationism, J. Peter Zetterberg ed., ORYX Press, Phoenix AZ 1983
Dobzhansky's point is that evolution is occurring and has occurred in the
past. These facts are not questioned by anyone who is familiar with the evidence for evolution. He and Gould both knew that there are people who do have doubts about evolution. The scientists' goal is not so much to convince the doubters but to stop them from claiming that evolution is "only" a theory.

It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).

Richard Dawkins
This concept isn't so hard to understand when you are talking about gravity. Gravity is a fact but scientists still have a theory of gravity to explain how gravity works. The anti-evolutionists will not concede that the same distinction applies to the facts of evolution and evolutionary theory. They continue to proclaim that evolution (the fact) is "only a theory." Dobzhansky suggests that these anti-evolutionists are either ignorant of the evidence or resistant to the evidence. I think he should have entertained the possibility that some of the knowledgeable anti-evolutionists are well aware of the distinction but choose to lie to their audience.

Note that I used the term "evolutionary theory" rather than "the theory of evolution." That's because there's no such thing as "the theory of evolution" and it's time we stopped using that phrase. In its place we talk about evolutionary theory that encompasses a wide variety of ideas ranging from the theories of population genetics to models of how speciation occurs.

What are some of the facts that demonstrate evolution? Lewontin explains,

It is time for students of the evolutionary process, especially those who have been misquoted and used by the creationists, to state clearly that evolution is a fact, not theory, and that what is at issue within biology are questions of details of the process and the relative importance of different mechanisms of evolution. It is a fact that the earth with liquid water, is more than 3.6 billion years old. It is a fact that cellular life has been around for at least half of that period and that organized multicellular life is at least 800 million years old. It is a fact that major life forms now on earth were not at all represented in the past. There were no birds or mammals 250 million years ago. It is a fact that major life forms of the past are no longer living. There used to be dinosaurs and Pithecanthropus, and there are none now. It is a fact that all living forms come from previous living forms. Therefore, all present forms of life arose from ancestral forms that were different. Birds arose from nonbirds and humans from nonhumans. No person who pretends to any understanding of the natural world can deny these facts any more than she or he can deny that the earth is round, rotates on its axis, and revolves around the sun.

The controversies about evolution lie in the realm of the relative importance of various forces in molding evolution.


R. C. Lewontin "Evolution/Creation Debate: A Time for Truth"
Bioscience 31, 559 (1981) reprinted in Evolution
versus Creationism, op cit.
The sad thing about the Gould, Dobzhansky, and Lewontin articles is that they were written so long ago but they continue to be relevant today. An entire generation has grown up since Dobzhansky's 1973 essay was published in American Biology Teacher yet we still have political leaders who question the scientific fact of evolution.

This ignorance can't be due to the lack of education since the fact/theory concept has been explained in introductory biology books that are used in colleges and universities (and in some of the better high schools). For example, in some of the best such textbooks from twenty years ago, we found:
Today, nearly all biologists acknowledge that evolution is a fact. The term theory is no longer appropriate except when referring to the various models that attempt to explain how life evolves... it is important to understand that the current questions about how life evolves in no way implies any disagreement over the fact of evolution.

Neil A. Campbell, Biology 2nd ed., 1990, Benjamin/Cummings, p. 434
Also:

Since Darwin's time, massive additional evidence has accumulated supporting the fact of evolution--that all living organisms present on earth today have arisen from earlier forms in the course of earth's long history. Indeed, all of modern biology is an affirmation of this relatedness of the many species of living things and of their gradual divergence from one another over the course of time. Since the publication of The Origin of Species, the important question, scientifically speaking, about evolution has not been whether it has taken place. That is no longer an issue among the vast majority of modern biologists. Today, the central and still fascinating questions for biologists concern the mechanisms by which evolution occurs.

Helena Curtis and N. Sue Barnes, Biology 5th ed. 1989,
Worth Publishers, p. 972
One of the best introductory books on evolution (as opposed to introductory biology) is that by Douglas J. Futuyma. In the 2nd edition back in 1986 he makes the following comment:
A few words need to be said about the "theory of evolution," which most people take to mean the proposition that organisms have evolved from common ancestors. In everyday speech, "theory" often means a hypothesis or even a mere speculation. But in science, "theory" means "a statement of what are held to be the general laws, principles, or causes of something known or observed." as the Oxford English Dictionary defines it. The theory of evolution is a body of interconnected statements about natural selection and the other processes that are thought to cause evolution, just as the atomic theory of chemistry and the Newtonian theory of mechanics are bodies of statements that describe causes of chemical and physical phenomena. In contrast, the statement that organisms have descended with modifications from common ancestors--the historical reality of evolution--is not a theory. It is a fact, as fully as the fact of the earth's revolution about the sun. Like the heliocentric solar system, evolution began as a hypothesis, and achieved "facthood" as the evidence in its favor became so strong that no knowledgeable and unbiased person could deny its reality. No biologist today would think of submitting a paper entitled "New evidence for evolution;" it simply has not been an issue for a century.

Douglas J. Futuyma, Evolutionary Biology, 2nd ed., 1986, Sinauer Associates, p. 15
This is not an argument from authority. I'm simply pointing out that the distinction between evolutionary facts and evolutionary theory has been explained over and over for the past half century and there's no excuse for not knowing what scientists think about evolution.

Evolutionary Theory

There are several possible mechanisms of evolution.
There are many people who reject evolution for religious reasons. In general these readers oppose both the fact of evolution and evolutionary theory, although some anti-evolutionists have come to realize that there is a difference between the two concepts. That is why we see some leading anti-evolutionists admitting to the fact of "microevolution"—they know that evolution can be demonstrated. These people will not be convinced of the "facthood" of (macro)evolution by any logical argument and it is a waste of time to make the attempt. The best that we can hope for is that they understand the argument that they oppose. Even this simple hope is rarely fulfilled.

There are some people who are not anti-science but still claim that evolution is "only" a theory that can't be proven. This group needs to distinguish between the fact that evolution occurs and evolutionary theories about the mechanisms of evolution. But there's an additional point that needs to be emphasized. Some of the proposed mechanisms of evolution, such as natural selection and random genetic drift, are facts, not speculations. We know for a fact that both these mechanisms occur in living populations. These are not "theoretical models" of evolution, they actually occur. They are part of evolutionary theory because, in many cases, we don't know for sure which one predominates in a particular case—or even if there might be another mechanism such as Lamarckian inheritance, molecular drive, or mutationism.

Fact of Evolution

Chimps and humans share a common ancestor.
Similarly, there are degrees of facthood. Some facts that are easy to demonstrate and others are more circumstantial. Examples of evolution that are readily apparent include the fact that modern populations are evolving and the fact that two closely related species share a common ancestor. The evidence that Homo sapiens and chimpanzees share a recent common ancestor falls into this category. There is so much evidence in support of this aspect of primate evolution that it qualifies as a fact by any common definition of the word "fact."

This is an important point. It is not, by any stretch of the imagination, a "theory" that humans and chimps share a common ancestor. We know enough about the history of life to state that this is a scientific fact.

In other cases, the available evidence is less strong. For example, the relationships of some of the major phyla are still being worked out. Also, the statement that all organisms have descended from a single common ancestor is strongly supported by the available evidence, and there is no opposing evidence. However, it is not yet appropriate to call this a "fact" since it's possible that there were several independent life forms that exchanged genes early on in evolution. This would mean that modern species have descended from more than one common ancestor. Most of us don't think this is very likely but the possibility exists. Common descent may not be a hard fact but it's not part of evolutionary theory either. Evolutionary theory is silent about most aspects of the unique history of life on this planet just as gravitational theory is silent about the unique formation of an eight-planet solar system around an average star at the edge of the Milky Way galaxy. The history of life and the formation of our solar system have to be consistent with what we know about evolution and gravity but neither evolutionary theory nor gravitational theory predict what that history should be.

Finally, there is an epistemological argument against evolution as fact. Some philosophers point out that nothing in science can ever be "proven" and this includes evolution. According to this argument, the probability that evolution is the correct explanation of the origin of chimps and humans may approach 99.9999...9% but it will never be 100%. Thus, the common ancestry of chimps and humans can never be a fact. This kind of argument might be appropriate in a philosophy class (it is essentially correct) but it won't do in the real world. A "fact," as Stephen J. Gould pointed out (see above), means something that is so highly probable that it would be silly not to accept it. This point has also been made by others who contest the nit-picking epistemologists.

The honest scientist, like the philosopher, will tell you that nothing whatever can be or has been proved with fully 100% certainty, not even that you or I exist, since we might be dreaming the whole thing. Thus there is no sharp line between speculation, hypothesis, theory, principle, and fact, but only a difference along a sliding scale, in the degree of probability of the idea. When we say a thing is a fact, then, we only mean that the probability of it being true is high—so high that we are not bothered by doubt about it and are ready to act accordingly. By this use of the term "fact"—the only proper definition—evolution is a fact. For the evidence in favor of it is as voluminous, diverse, and convincing as in the case of any other well established fact of science concerning the existence of things that cannot be directly seen, such as atoms, neutrons, or solar gravitation ....
So enormous, ramifying, and consistent has the evidence for evolution become that if anyone could now disprove it, I should have my conception of the orderliness of the universe so shaken as to lead me to doubt even my own existence. If you like, then, I will grant you that in an absolute sense evolution is not a fact, or rather, that it is no more a fact than that you are hearing or reading these words.

H. J. Muller, "One Hundred Years Without Darwin Are Enough"
School Science and Mathematics 59, 304-305. (1959)
reprinted in Evolution versus Creationism op cit.
In any meaningful sense evolution is a fact, but there are various theories concerning the mechanism of evolution.

Creationists will never accept that evolution is a fact and they will continue to lump the history of life into "the theory of evolution." They will never accept that evolutionary theory includes many models and many proven mechanisms. They insist that it's all "Darwinism." I don't expect to change their minds—I'm not that naive—but I do expect them to learn the truth about what scientists are saying, even if it's only to criticize the science. Surely that's not too much to ask?


1. Republished in Hen's Teeth and Horse's Toes, New York: W. W. Norton & Company, 1983, pp. 253-262.

Friday, December 06, 2013

Die, selfish gene, die!

"Die, selfish gene, die!" is the provocative title of an article by science writer David Dobbs [Die, selfish gene die!].

Dobbs begins with ....
The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong.
The article attracted the attention of Jerry Coyne who effectively dismantles the strange ideas promoted by Dobbs. Read all about it at: David Dobbs mucks up evolution, part I and David Dobbs mucks up evolution, part II.

As it turns out, this is just another example of a science writer who has been mesmerized by the latest effort to overthrow modern evolutionary theory by some scientist promoting their own work. In this case it's Mary Jane West-Eberhard.

But there's a more serious issue here and I'm not sure that Jerry Coyne recognizes it. The selfish gene metaphor can be interpreted in several different ways. Here's how Richard Dawkins describes it in the preface to the 1989 edition of The Selfish Gene.
The selfish gene theory is Darwin's theory, expressed in a way that Darwin did not choose but whose aptness, I should like to think, he would instantly have recognized and delighted in. It is in fact a logical outgrowth of orthodox neo-Darwinism, but expressed as a novel image. Rather than focus on the individual organism, it takes a gene's-eye view of nature.
Lot's of people misunderstand the selfish gene metaphor. They think it means that organisms behave selfishly but that's not what Dawkins meant at all.

Jerry Coyne explains this in his book Why Evolution Is True (p. 226) ....
As Dawkins shows clearly, the "selfish" gene is a metaphor for how natural selection works. Genes act as if they're selfish molecules: those that produce better adaptations act as if they're elbowing out other genes in the battle for future existence. And, to be sure, selfish genes can produce selfish behaviors. But there is also a huge scientific literature on how evolution can favor genes that lead to cooperation, altruism, and even morality.
There are two main criticisms of the selfish gene metaphor and both of them are quite valid. It's the reason why Dawkin's view hasn't caught on the the evolutionary biology textbooks. It usually merits nothing more than a footnote.

The most damning criticism comes from evolutionary biologists who point out that the primary unit of selection is the individual and not the gene. Stephen Jay Gould and Richard Lewontin are prominent opponents of what they see as an unnecessary reductionism in Dawkins' writing. Clearly, hierarchical theory (Gould) is inconsistent with the selfish gene metaphor because evolution can also operate at the level of groups and species (according to Gould and others). There are plenty of other evolutionary biologists who object to selfish genes for these reasons.

The second objection comes from the focus on natural selection and "Darwinism" (or neo-Darwinism). Many evolutionary biologists have a pluralistic view of modern evolutionary theory. That view includes random genetic drift where the appropriate metaphor might be "lucky gene" or "accidental gene." The problem with the Dawkins' metaphor, according to these critiques, is not that "selfish genes" don't exist, it's that the metaphor is not appropriate for evolution in general.

While I admire Jerry's take-down of Dobbs, I'm not sure that he (Jerry Coyne) fully appreciates these other criticisms of the selfish gene. Here's what Coyne wrote ...
Let me add one thing, though. I’m constantly puzzled these days by how often people argue that the neo-Darwinian synthesis is wrong, and that we need a new paradigm. Genetic assimilation, epigenetics, horizontal gene transfer—all of these buzzwords are evoked as reasons to jettison our “conventional” view of evolution. But always, when you look at the data, the evidence that these phenomena will overturn neo-Darwinism is nonexistent.

I’ve already written a lot on the epigenetics hype, and have shown that there’s no evidence that a single adaptation in nature involves the fixation in the DNA of an epigenetic alteration of the genome that isn’t initially inherited. Yet people keep banging on about epigenetics.

I’m not sure why the hype continues, but perhaps it has to do with the fact that the main paradigm of evolution—the neo-Darwinian synthesis—is largely consolidated, and is correct. Sure, there are surprises to come, and interesting new phenomena, but there’s no “quantum mechanics” of evolution on the horizon. Some theories don’t need to be overthrown because they’re generally right. Perhaps people don’t like working in a field where there’s no new “paradigm” to forge, and Kuhn has ruined us all!

The "neo-Darwinism is dead" trend may have to do with ambition, or perhaps with boredom. I don’t know. What I do know is that the many recent challenges to neo-Darwinism have all failed to hold water, but people keep pouring liquid into that sieve.
The problem here is that Jerry doesn't really say what he means by "neo-Darwinism." Most of his writing suggests that he's talking about natural selection, albeit updated by a knowledge of genetics. He does mention, from time to time, random genetic drift and other aspects of modern evolutionary theory but I'm not sure if he appreciates the fact that some legitimate evolutionary biologists really do think that neo-Darwinism is dead.

Here's the Wikipedia description of neo-Darwinism. It illustrates the problem.
Neo-Darwinism is the 'modern synthesis' of Darwinian evolution through natural selection with Mendelian genetics, the latter being a set of primary tenets specifying that evolution involves the transmission of characteristics from parent to child through the mechanism of genetic transfer, rather than the 'blending process' of pre-Mendelian evolutionary science. Neo-Darwinism can also designate Darwin's ideas of natural selection separated from his hypothesis of Pangenesis as a Lamarckian source of variation involving blending inheritance.
I think we should refer to modern evolutionary theory as "modern evolutionary theory" in order to make sure we're not talking about "Darwinism," "neo-Darwinism," or the hardened version of the "Modern Synthesis." Modern evolutionary theory includes an important role for random genetic drift, Neutral Theory, and population genetics.

We could clarify a lot of discussion if we stopped talking about extending "Darwinism" or extending the Modern Synthesis or proclaiming once again that the selfish gene has died. In fact, the selfish gene has died, it died almost thirty years ago but most people don't know that. RIP.


Tuesday, June 22, 2010

The Mutationism Myth, V: The response to Mendelian heterodoxies

This is the seventh in a series of postings by guest blogger, Arlin Stoltzfus. You can read the introduction to the series at: Introduction to "The Curious Disconnect". The first part is at: The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion. The second installment is: Theory vs Theory. The third part is: The Mutationism Myth, II. Revolution. The fourth installment is: The Mutationism Myth: III Foundations of Evolutionary Genetics. Part five is The Mutationism Myth, IV: Mendelian Heterodoxies.

There are many ways in which the so-called "Modern" Synthesis has to be revised and extended. One of them is to reinstate the concept of mutationism which was purged from evolutionary theory in the 1940s. If you want to understand why this is important then these articles are the place to start.




Deconstructing The Mutationism Myth erodes the conventional wisdom about the early Mendelians, and also exposes the incompatibility with genetics that led the Mendelians to reject Darwin's theory. As we will see today on the Curious Disconnect (credits), unraveling the Mutationism Myth also puts the Modern Synthesis in a new light.

The Mutationism Myth, part 5. The Restoration

In the Mutationism Myth (see part 1), the Modern Synthesis (MS) rescues evolutionary biology from the Mendelian heresy, by showing that genetics is consistent with selection. In reality, the Mendelians had already synthesized genetics and selection (part 3), but rejected Darwin's errant views of heredity (part 2) and rejected, to varying degrees, the Darwinian doctrines that subordinated the role of variation so as to render selection the ruling principle in evolution. How, then, did the Modern Synthesis restore Darwinism?

The response to Mendelian heterodoxies

As recounted previously (part 4), the Mendelians recognized mutation as a source of discontinuity, initiative, direction and creativity in evolution. In this section, we will look at the MS (Modern Synthesis) as a Darwinian response to these Mendelian heterodoxies 1.

Initiative

Darwin knew that spontaneously arising "sports" (mutants) occurred in nature, but denied them any meaningful role in evolution. Hereditary fluctuation, induced by altered "conditions of life", would produce subtle variations in bulk, providing suitable material for selection. Evolution, in this view, is a process of automatic adjustment to altered "conditions of life".

The Mendelians frequently invoked a quite different view of evolution as a causal sequence initiated by a new mutation. This made the impetus for change internal rather than external, and suggested that, to understand evolution, it would be important to understand the rates and propensities of mutations.

The architects of the MS rejected this view and asserted that evolution begins, not with a new mutation, but with the abundance of variation in the "gene pool"
"evolution is not primarily a genetic event. Mutation merely supplies the gene pool with genetic variation; it is selection that induces evolutionary change" (Mayr 1963, p. 613).
Rates and propensities of mutation are rendered irrelevant, because the "gene pool" serves as a dynamic buffer that insulates evolution from mutational effects:
"mutations are rarely if ever the direct source of variation upon which evolutionary change is based. Instead, they replenish the supply of variability in the gene pool . . . . Consequently, we should not expect to find any relationship between rate of mutation and rate of evolution. There is no evidence that such a relationship exists." (Stebbins, 1966, p. 29)
"The large number of variants arising in each generation by mutation represents only a small fraction of the total amount of genetic variability present in natural populations. ... It follows that rates of evolution are not likely to be closely correlated with rates of mutation. Besides mutation, natural selection and migration help maintain high levels of genetic variation in natural populations. Even if mutation rates would increase by a factor of 10, newly introduced mutations would represent only a very small fraction of the variation present at any one time in populations of outcrossing, sexually reproducing organisms." (Dobzhansky, et al., 1977, p. 72) 2
"Those authors who thought that mutations alone supplied the variability on which selection can act, often called natural selection a chance theory. They said that evolution had to wait for the lucky accident of a favorable mutation before natural selection could become active. This is now known to be completely wrong. Recombination provides in every generation abundant variation on which the selection of the relatively better adapted members of a population can work." (Mayr, 1994, p. 38)
Thus, Darwin's view of a process initiated by a change in conditions is restored: the source of initiative is not the occurrence of mutations, which are individually insignificant (Dobzhansky et al. 1977, p. 72) and merely "replenish the supply of variability in the gene pool" (Stebbins 1966, p. 29), but the change in conditions that brings on selection of variation already present (e.g., Dobzhansky 1955, p. 282; Dobzhansky et al. 1977, p. 6; e.g., Stebbins 1982, p. 160).

Infinitesimalism ("gradualism")

Darwin believed that evolution always proceeds by "infinitesimal" or "insensible" steps, and he stated this clear commitment in various ways, e.g., he said that "Natural selection can act only by the preservation and accumulation of infinitesimally small inherited modifications" (Origin of Species, Ch. 4) and that
If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. (Darwin, Ch. 6, Origin)
The "saltationist" alternative typically offered to this doctrine, as stated by Huxley in his 1860 review of the Origin of Species (online source), is merely that evolution takes some jumps:
Mr. Darwin's position might, we think, have been even stronger than it is if he had not embarrassed himself with the aphorism, "Natura non facit saltum," which turns up so often in his pages. We believe, as we have said above, that Nature does make jumps now and then, and a recognition of the fact is of no small importance in disposing of many minor objections to the doctrine of transmutation.
As we found out in part 4, the Mendelians sided with Huxley on this issue, and did not share Darwin's commitment to infinitesimalism.

Fisher (1930) and Dobzhansky (1937) played a significant role in restoring a "Darwinian" view, at least superficially. Fisher argued on theoretical grounds that evolution was more likely to take place by arbitrarily small modifications. He considered the evolutionary prospects of a phenotypic form represented by a point located somewhere near a point in geometric space that represents a global fitness optimum. Under this condition, the chance that a shift in location will be beneficial approaches an upper limit of 50 % as the size of the shift becomes arbitrarily small, i.e., infinitesimal. This argument was influential with MS authors in spite of the fact that the model was geometrical rather than biological (Orr and Coyne, 1992).

The architects of the MS developed a second line of argument based on the genetics of differences between species or sub-specific races, to the effect that the analysis of such differences showed a predominance of "small" or "slight" effects. Dobzhansky (1937) tied these arguments together:
"The high frequency of mutations producing small changes in the phenotype raises a strong presumption in favor of supposing that such mutations play a greater role in evolutionary processes than mutations with grosser effects. Fisher (1930) has given an interesting mathematical argument in favor of this view. These considerations agree very well with the results of the genetic analysis of the interracial and interspecific differences (Chapter III), showing these differences to be caused in a majority of cases by cooperation of numerous genes, each of which taken separately has only slight effects on the phenotype." (p. 26)
I think this aspect of the MS is familiar and uncontroversial, so I won't bore the reader with more quotations from original sources, several of which are given in the review by Orr and Coyne (1992). In general, the architects of the MS emphasized the importance of "slight" or "small" differences, and they claimed that this position was borne out by theoretical considerations, as well as by experimental studies.

Orr and Coyne took issue— rather audaciously— with the latter claim. They argue that the architects of the MS "seem to have based their support of micromutationism on almost no data at all", claiming that the studies reviewed by Dobzhansky above did not justify Dobzhansky's own stated conclusions.

Another interpretation of this apparent discrepancy is that Orr and Coyne are taking Darwin literally, while the MS architects did not.3 That is, the architects of the MS aligned themselves rhetorically with Darwin, and against the mythic saltationists-who-believe-in-evolution-by-large-jumps-without-selection. By doing so, they leveraged loyalty to the Darwin brand, but in reality, their scientific product was not the same as Darwin's. Darwin says that the fraction of saltations in evolution is zero, whereas Dobzhansky, in the passage quoted above, says merely that mutations producing "small changes" play a "greater role" than those with "grosser effects", and that evidence for this view is seen, not universally, but merely in "the majority of cases". Orr and Coyne (1992) conclude that large effects are common, which contradicts Darwin's extreme view but not the fuzzier claims made by MS advocates.

Creativity (novelty)

The Darwinian claim that natural selection is "creative" 4 was disputed initially (see Beatty, 2010) and continues to be questioned by critics (e.g., Kirschner and Gerhardt, 2005) and defended by Darwin's followers (e.g., Charlesworth, 2005).

The critics always make the same objection, namely that creativity resides somehow in the process of variation, which accounts for "the arrival of the fittest", rather than selection ("the survival of the fittest"), which merely decides what will live and what will die. The Mendelians, in particular, argued that the discovery of genetics had clarified the previously fuzzy line between selection and hereditary variation, which is not induced but arises spontaneously by mutation, making clear that, in Punnett's words, "the function of natural selection is selection and not creation" (see part 4).

The architects of the MS responded by renewing the claim for the creativity of selection. However, its also interesting to note that, early in the "Synthesis" period, some of the architects (to my knowledge, only Huxley and Dobzhansky) appeared to offer a compromise, to the effect that creativity was shared by selection and mutation, e.g., Huxley wrote that "Neither mutation nor selection alone is creative of anything important in evolution; but the two in conjunction are creative" (Huxley, 1942, p. 28).

The more prominent argument, which eventually became orthodox, was to attribute creativity to selection by depicting it as a craftsman or artist using "raw materials" supplied by variation. Gould (1977) has analyzed this pattern extensively, and I will simply repeat a passage that he offers in explanation:
"But why was natural selection compared to a composer by Dobzhansky; to a poet by Simpson; to a sculptor by Mayr; and to, of all people, Mr. Shakespeare by Julian Huxley? I won't defend the choice of metaphors, but I will uphold the intent, namely, to illustrate the essence of Darwinism— the creativity of natural selection. Natural selection has a place in all anti-Darwinian theories that I know. It is cast in a negative role as an executioner, a headsman for the unfit . . . The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies the raw material only. Natural selection directs the course of evolutionary change. It preserves favorable variants and builds fitness gradually. In fact, since artists fashion their creations from the raw material of notes, words, and stone, the metaphors do not strike me as inappropriate."
Dobzhansky also invokes the same "raw materials" metaphor, but in the context of a factory rather than an artist:
"the objection [that natural selection cannot be the guiding agent in evolution because it produces nothing new] became invalid in the light of modern biological knowledge . . .We should clearly distinguish the two basic evolutionary processes: that of the origin of the raw materials from which evolutionary changes can be constructed, and that of building and perfecting the organic form and function. Evolution can be compared to a factory: any factory needs a supply of raw materials to work with, but when the materials are available they must be transformed into a finished product by means of some manufacturing process. " (Dobzhansky, 1955, p. 131)
That is, selection is understood to be the builder or artist or manufacturing process, while mutation supplies "raw" materials. Note that Gould ultimately endorses the creativity claim precisely on the grounds that variation supplies raw material only. It might seem surprising that the metaphor of "raw materials" should play such an important role in evolutionary reasoning.

However, as we will learn later, metaphors are vital for causal reasoning, filling a gap that mathematics (which is not itself a language of causation) cannot cover. In the context of an argument about causation, to designate something as "raw material" is to reference the classic distinction 5 between material causes (stuff, material) and efficient causes (forces, agents). The architects of the MS had a theory of "forces", and they believed that population genetics had proven that mutation (variation), though it contributes stuff or material to evolution, is not an effective force. This claim is explained further below.

Directionality

Many authors have suggested that the essence of Darwin's "Natural Selection" theory is that evolution emerges by combining a random process of variation and a non-random process of selection, with selection directing the outcome, adding a previously absent component of direction:
"Darwin assumed in the Origin of Species that the evolution of living organisms depended on the origin of new forms which varied from old forms by continuous differences in no constant or predictable direction. Crossed together the new and the old showed blending inheritance. To these variations direction was given by a process of natural selection which, like artificial selection, preserved some while it destroyed others. A direction, an adaptive direction, was thus given to variations after they arose. This view was intended by Darwin to supplant the alternative view that direction was given to variations before they arose." (Darlington, 1958, p. 231)
"The idea that evolution comes about from the interaction of a stochastic and a directed process was the essence of Darwin's theory. The stochastic process that he invoked was the occurrence of small random variations which he supposed, provided the raw material for natural selection, a process directed by the requirements of the environment and one that builds up, step by step, changes that would be inconceivably improbable at a single step . . .The meaning of 'random' . . . is that the variations are, as a group, not correlated with the course subsequently taken by evolution (which is determined by selection)." (Wright, 1967, p. 117)
As noted in part 4, the Mendelians were ready to challenge this assumption, though their alternative view was not well developed. Some Mendelians noted that the repeated occurrence of a mutation improved its chance of being established in evolution (part 4), and that "in the deal out of mutations, the cards are stacked" (Shull, 1936). Vavilov (1922) applied this line of thinking at length in his explication of a possible role for parallel variations in parallel evolution.

The architects of the Modern Synthesis returned to the Darwinian view expressed in the statements of Wright and Darlington above. Frequently in MS writings, mutation is contrasted with selection and described as a "random" process. 6 In Mayr's 1980 reflection on the Modern Synthesis, he defines "Darwinism" as "the theory that selection is the only direction-giving factor in evolution." In the passage below, Dobzhansky refers to selection as "the directional force of evolution":
"Each unitary random variation is therefore of little consequence, and may be compared to random movements of molecules within a gas or liquid. Directional movements of air or water can be produced only by forces that act at a much broader level than the movements of individual molecules, e.g., differences in air pressure, which produce wind, or differences in slope, which produce stream currents. In an analogous fashion, the directional force of evolution, natural selection, acts on the basis of conditions existing at the broad level of the environment as it affects populations." (Dobzhansky, et al., 1977, p. 6)
Note that Dobzhansky uses an analogy with statistical physics to argue that selection's unique role is due to its status as a high-level "force", whereas a "random variation" is not a force, but is like the movement of a single particle.

Dobzhansky's comment suggests that the MS position on direction is tied to "gene pool" thinking. Indeed, in the passage below, Stebbins 7 makes clear that selection "directs evolution" by choosing from among the abundance of offerings in the "gene pool":
"Natural selection directs evolution not by accepting or rejecting mutations as they occur, but by sorting new adaptive combinations out of a gene pool of variability which has been built up through the combined action of mutation, gene recombination, and selection over many generations" (p. 31 Stebbins, 1966, Processes of Organic Evolution)
Finally, given this position, its not surprising that Vavilov's hypothesis about the role of parallel variation in parallel evolution was not taken seriously. Given the abundance of variation in the "gene pool", and the ability of selection to shape this gene pool to fit circumstances, it was not safe to assume that shared characters had a shared genetic basis, as Mayr (1963) argued in one of his more famous erroneous claims 8:
"In the early days of Mendelism there was much search for homologous genes that would account for such similarities. Much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives (Dobzhansky, 1955). If there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved." (p. 609)

Defining "forces" and re-defining "evolution"

The previous section suggested the central importance of the "gene pool" view, which argues that evolution begins, not with a new mutation, but with the abundance of variation "maintained" in the "gene pool". On the basis of this view, "evolution" was redefined so as to exclude the mutationist alternative:
"The theory of evolution by natural selection is a theory that relates the variation between individuals within a population to variation of populations in time and space. The theory amounts, in short, to the realization that intrapopulation variation is converted into spatial and temporal differentiation. The process of this conversion is the process of evolution." (Lewontin, 1965, p. 67)
That is, "the process of evolution" ("evolution by natural selection") literally does not include the introduction of new alleles, but instead corresponds to the sorting out of available variation.

Given that "evolution" (redefined) is all about "shifting gene frequencies", the causes of evolution may be presented as "pressures" or "forces" that shift frequencies. Lets suppose we have two alleles, A1 and A2, with frequencies f(A1) = f(A2) = 0.5. If A1 improves fitness relative to A2, then "selection" can be seen as a "force" that shifts its frequency over some period of time to f(A1) = 0.5 + d, and ultimately to fixation, f(A1) = 1. Likewise, there is some rate of mutation from A1 to A2, and another rate for the reverse pathway, and this rate can be understood to shift the relative frequencies to the point where f(A1) = 0.5 + d.

The key innovation in this view is its identification of mathematically continuous shifts in allele frequency as the common currency underlying a theory of causal agency. In classical physics, the displacement of a particle in continuous space (over continuous time) plays a similar role as the common currency of causal effects: multiple forces can cause such displacement, and their effects can be combined or decomposed. Likewise, in the MS, selection, drift, and mutation are identified as "forces" because they can cause shifts in frequencies.

Accordingly, the founders of population genetics looked at mutation as a "force" or "pressure" that, if powerful enough, could cause or "drive" evolution. From the mutation-selection balance equation and available data on mutation rates, Fisher (1930) and Haldane (1932) argue that, because mutation rates are so small, the opposing "force" of selection rules and mutation "pressure" cannot drive an allele to fixation. The conclusion of this "opposing pressures" argument 9 is that mutation is not an effective evolutionary force. Thus, in classical population-genetics modeling, its quite common to simply leave out mutation rates, on the grounds that they don't have substantial effects on the behavior of the model (e.g., as in the seminal analysis of 2-locus models by Lewontin & Kojima, 1960).

Having ruled out mutation as a "force", this left the idea of mutation as a source of "raw materials". That is, the architects of the MS looked at mutation in two ways, as a material cause, and as an efficient cause (agent, force). As just noted, the schematization of mutation as a "force" led to its rejection as an important "force", while its role as a material cause was addressed with the metaphor of "raw materials", as in several quotation given above, and in the following:
"The process of mutation supplies the raw materials of evolution, but the tempo of evolution is determined at the populational levels, by natural selection in conjunction with the ecology and the reproductive biology of the group of organisms" (Dobzhansky, 1955, p. 282)
"Mutation as an evolutionary force. In the early days of genetics it was believed that evolutionary trends are directed by mutation, or, as Dobzhansky (1959) recently phrased this view, 'that evolution is due to occasional lucky mutants which happen to be useful rather than harmful.' In contrast, it is held by contemporary geneticists that mutation pressure as such is of small immediate evolutionary consequence in sexual organisms, in view of the relatively far greater contribution of recombination and gene flow to the production of new genotypes and of the overwhelming role of selection in determining the change in the genetic composition of populations from generation to generation." (p. 101 of Mayr, 1963)
In this way, following the arguments of Fisher (1930), population genetics was believed to undermine any and all non-Darwinian theories of "evolution worked by mutation".

The keys to the kingdom

As we have seen, the restoration of "Darwinism" depended on several key innovations.

The first innovation was the change in attitude that inaugurated the process of redefining "Darwinism" that, for better or worse, continues today. For literally decades after the re-discovery of Mendelian genetics in 1900, the generality of Mendelian inheritance was disputed by biologists who, loyal to 19th century views of Darwin and Lamarck, reacted to genetics as though it must be some kind of misleading laboratory artefact, inapplicable in "nature".

Nevertheless, by 1930, Mendelian inheritance had been shown in a wide variety of macroscopic organisms, while experimental support for the hereditary laws of Darwin and Lamarck was trivial in comparison. The architects of the MS took Mendelian genetics as a given and simply ignored Darwin's laws of heredity, or treated them as an unimportant detail. In a sense, Darwin's followers had switched their allegiance from Darwin's specific theory1 to a more abstract view, which we might call Darwinian selectionism, in which selection has a kind of causal pre-eminence, and all other issues are negotiable. Darwin's followers quietly backed away from his risky position of natura non facit salta, and ignored the fact that their new idea of the maintenance of abundant variation in the gene pool was not isomorphic with Darwin's concept of indefinite variability (hereditary fluctuation).

The second key innovation was this "gene pool". Even if one deletes from the Origin of Species all the details that are obviously contrary to genetics, the resulting view still makes strenuous and non-arbitrary demands on a theory of variation, as Gould (2002) persuasively argues. Regardless of any other mechanistic details, Darwinian selectionism (the pre-eminence of selection) demands that variation be "copious, undirected, and small in effect" (in Gould's formulation). Darwin's view of evolution as an automatic process of smooth adaptation to altered conditions seemed to require abundant, uniform, and infinitesimal variation, yet the new science of Mendelian genetics seemed to suggest the kind of rare, idiosyncratic, and discrete variants that Darwin rejected.

The key to reconciling the two— at least, rhetorically— is the notional "gene pool". According to an idea first articulated in 1926 by Chetverikov, every species has a "gene pool" that soaks up variation like a "sponge" (Chetverikov 1997), "maintaining" it for later use by selection, and ensuring an abundance of minute heritable variations in every trait, in every generation, as Darwin had conjectured. Thus, in Darwinism 1.0, fluctuation provides fuel "on demand" for selection, which is seen as the engine of evolution; in Darwinism 2.0, the engine has a tank of fuel, the "gene pool", that automagically keeps itself full. Though not equivalent, both views represent variation as merely an abundant source of fuel, with no influence on where evolution goes.

The crowning innovation of the Modern Synthesis was to invoke "population genetics" as a framework of causation that excluded all alternatives to Darwinism (redefined). Viewing evolution from a distance, as a paleontologist or systematist, one sees patterns that might be explained by various modes of evolution: Darwinian, Lamarckian, Buffonian, orthogenetic, saltational, and so on. While Darwinism seems to have been the dominant interpretation, the range of interpretations remained wide at the turn of the century when Mendelism burst onto the scene. While Mendelism revolutionized the evolutionary thinking of those who accepted it, most doubted its relevance to evolution. As late as 1930, one could read in the pages of Nature the view that "a gene is germ damage of which the outward manifestation is a mutation . . In my opinion, mutations and adaptations have nothing to do with one another" (MacBride, 1930).

The architects of the MS, following the original arguments of Fisher (1930), claimed that they could reduce evolution to a causal mechanism based on population genetics, and that this causal mechanism ruled out all modes of evolution but the "Darwinian" one. By the Origin of Species centennial in 1959, the architects of the MS had declared that the debate over evolutionary theory was over, and that they— and Darwin— had won. "Mutationism" came to be seen as discredited:
The genetic work of the last four decades has refuted mutationism (saltationism) so thoroughly that it is not necessary to repeat once more all the genetic evidence against it. (Mayr 1960, p. 355)
if ever it could have been thought that mutation is important in the control of evolution, it is impossible to think so now (Ford 1971, p. 361)
As late as 1932 T.H. Morgan was asserting that 'natural selection does not play the role of a creative principle in evolution', but ten years later all but a very few biologists were agreed on an evolutionary theory based firmly on Darwin's own ideas knitted with subsequent developments in genetics. (Berry 1982, p. 14)
for simplicity we speak of mutation as the first stage in the Darwinian process, natural selection as the second stage. But this is misleading if it suggests that natural selection hangs about waiting for a mutation which is then either rejected or snapped up and the waiting begins again. It could have been like that: natural selection of that kind would probably work, and maybe does work somewhere in the universe. But as a matter of fact on this planet it usually isn't like that. (Dawkins 1996, p. 87)

Looking ahead

Thanks for your forbearance in plowing through all of this history. Ultimately, though, we want to move on to other things. The Curious Disconnect is not a blog about scientific history: its about the current muddle in evolutionary thinking. I'm only explaining the history so that we can take a critical look at the MS and the view of causation that we have inherited from it.

Here is an example of what I mean. Rates of evolution, including adaptive evolution as in Rokyta, et al, 2005, are sensitively dependent on rates of mutation, directly contradicting the MS doctrine that the buffering capacity of the "gene pool" insulates evolution from mutational dynamics 10.

Because the MS is a coherent and integrated view (not just an extendible list of stuff that happens in evolution), and because reality is cohesive as well, fixing the failure of the MS to recognize this dependence is not an arbitrary or isolated error. We can't fix the MS by going through all the works of Mayr, Dobzhansky, Fisher, et al and 1) deleting every explicit claim that the rate or direction of evolution does not depend on mutation and 2) adding the words "And, we think the rate of evolution depends on the rate of mutation". That would not be enough.

For instance, the Gillespie-Orr "mutational landscape" model underlying the analysis of Rokyta, et al, which accounts for the aforementioned rate dependence, is based on a mutationist conception of evolution as a 2-step mutation-fixatioon process. The author of the model writes (Orr, 2003):
Adaptation is a two-step process: (i) alleles having different effects on fitness arise by mutation and (ii) those alleles that improve fitness tend to increase in frequency by natural selection.
thus directly contradicting what Dawkins says (above) about evolution "on this planet" (which, I suppose, raises a question about where Dawkins was when he wrote that statement).

Thus, the problem is not just the specific issue of a rate correlation, but its also the 2-step mutationist view.

To accomodate the observation that the rate of evolution depends sensitively on the rate of mutation, then, we would need to fix the MS view of causation, changing the common currency of causation so that an effect of biases in the origination process can be recognized 11. In turn, to allow a bias in the origination process to affect "evolution" would require us to put the origination process back into "evolution", i.e., we would have to toss out the "shifting gene frequencies" definition. After that, we would have to delete all of the statements rejecting the 2-step "mutationist" view, including all the claims that "selection" never "waits" for a new mutation due to the magical maintenance of variation in the "gene pool". In addition, the effect of mutation biases violates the Darwinian and MS rule that variation is "random" in the sense that the tendencies of variation are unrelated to the realized direction of evolutionary change (this is the sense used in the quotation from Wright given above; see Beatty, 2010 for the analysis of Darwin's view).

The reason that so many changes would be required is that the exclusion of any important formative or directional role for mutation in the MS was not unforeseen or incidental, but utterly deliberate and essential. Real theories make commitments and take risks. Our analysis of the Mutationism Myth shows what these commitments were: the MS represents a commitment to the pre-eminence of selection and the subordination of variation, rejecting Mendelian ideas on mutation as a cause of discontinuity, initiative, creativity, and direction.

Because of this, its rather foolish to talk about "extending", "finishing", or "updating" the Modern Synthesis. We can't "revise" the MS to repudiate Mayr's understanding of evolutionary causation and endorse Morgan's mutationist view instead. To "revise" the MS in that way would be to repudiate the MS itself. Real theories make commitments and take risks. What's wrong about the Modern Synthesis is not a minor detail, but its essential and definitive subordination of the role of variation, and all that comes with it. The MS represents a wager, a bet, that reality would turn out to be a certain way. It didn't. The architects of the MS bet on the wrong horse. End of story.

So, its time to place a new bet, but on what? Just tossing out the MS will not give us that new theory of causation, the one that allows us to compare causal effects across different types of causes. With that, we might be able to address some of the big questions of evolution and confront contemporary challenges relating to "evo-devo". Our goal on the Curious Disconnect is to define issues like this, and to consider what are some of the possible bets. But thats getting ahead of ourselves.

Summary

Darwin's 20th-century followers responded to the Mendelian threat— which (at least partially) called for a stochastic, non-infinitesimal, mutation-driven view of evolution and adaptation— by developing the Modern Synthesis (aka "modern neo-Darwinism" or the "New Synthesis"), a new theory that purported to be consistent both with genetics and with Darwin's 19th-century view of evolution as a process of infinitesimal change controlled, initiated and directed by selection.

The development of this theory, which went on to dominate the 20th century, was based on 3 innovations. The first innovation was to redefine Darwinism. The version of "Darwinism" that the MS restored was not the one that the Mendelians rejected. Instead, Darwinism 2.0 was "Darwinian" in emphasizing the pre-eminence of selection, leaving out the Darwin's non-Mendelian laws of heredity. The second innovation was the notional "gene pool", a populational buffer that insulates ÇevolutionÈ from effects of mutation by churning and mixing and "maintaining" abundant variation. The "gene pool" concept provided a foundation to reject the "lucky mutant" view and argue against Mendelian heterodoxies, e.g., given that evolution begins with the "gene pool", selection (not mutation) initiates evolution, and chooses its direction from the abundance of possibilities.

Finally, the MS included an integrated view of causation in which continuous shifts in allele frequencies are seen as the common currency of causal effects. That is, a factor is identifiable as an evolutionary "force" to the extent that it is capable of causing mass-action shifts in allele frequencies. This view appeared to justify the claim that selection is the driving force in evolution, and that mutation is not a potent force, but merely serves to supply "raw materials" to the "gene pool".

Thus, while the Mutationism Myth wrongly suggests that the MS reconciled genetics and selection (instead, the Mendelians accomplished this), it correctly suggests that the MS restored a "Darwinian" view, and that arguments from population genetics were the key to this restoration, though (as we'll find out later) the crucial arguments from population genetics were based less on mathematics than on metaphors and metaphysics.


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Vavilov, N. I. 1922. The Law of Homologous Series in Variation. J. Heredity 12:47-89.

Wright, S. 1967. Comments on the preliminary working papers of Eden and Waddington. Pp. 117-120 in P. S. Moorehead, and M. M. Kaplan, eds. Mathematical challenges to the neo-Darwinian interpretation of evolution. Wistar Institutional Press, Philadelphia.

Yampolsky, L. Y., and A. Stoltzfus. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev 3:73-83.

Notes

1 The point of this comment is that I don't claim to be presenting the MS in a comprehensive way. This view of the MS is one view. In particular, it represents a kind of dialectic perspective on the MS as a response to Mendelism, focusing on what seems to be a characteristically Darwinian view of the role of variation, and focusing on evolutionary causation.

2 Note that Dobzhansky, in particular, started out as a bit of a heretic on the importance of mutation. In his 1937 book he speculated that different rates of mutation might explain different rates of evolution (p. 37), an idea that later was mocked by Simpson and others, lending credence to Gould's idea of a "hardening" of the Synthesis.

3 Orr and Coyne write "the micromutational view of Darwin, Fisher and others is clear: adaptations arise by allelic substitutions of slight effect at many loci, and no single substitution constitutes a major portion of an adaptation." I think they are right about Fisher and Darwin (ignoring the flagrant anachronism linking Darwin to a position on "allelic substitutions"), but who are the "others"? I can't put Dobzhansky in the same category. He only emphasizes that "small" or "slight" differences predominate in "the majority of cases".

4 Some present-day biologists have an adverse reaction to the term "creativity". Perhaps this is similar to my own adverse reaction to "design": I'd rather that biologists not use the term "design", which smacks of teleology. A similar objection might be made to the term "creativity". Nevertheless, in some sense, a theory of evolution must explain how new things come into existence (creativity) and how they appear to be adapted (design). So, if you are having an adverse reaction to "creativity", then please bear in mind the possibility that there might be ways to re-frame the issues at stake, but that for now, we are going to continue to use the old language of "creativity" because that is what's historically important.

5 This distinction is from Aristotle. His 4-fold taxonomy of causes includes material, efficient, formal (plans, archetypes), and final (goals, intentions) causes.

6 Its hardly ever clear what "random" means in such contexts. This is a topic that we will take up in a future post. The definition that is perhaps the most defensible historically is the one given by Wright, which also corresponds to Darwin's view as discussed in Beatty, 2010. By this definition, "randomness" is not a property of mutation per se, but of its role in evolution.

7 In passing, note how this argument obscures where "new" things come from. In reality, new combinations of pre-existing alleles arise by sexual mixis, by the reassortment of chromosomes, and by intra-chromosomal recombination. These processes, and not future selection, bring the new combinations into existence (and may break it apart again).

8 This passage has been singled out by Gould, 2002 and others. Amundsen (2005) gives a brief explanation of the thinking that underlies this (in his Ch. 11).

9 The "opposing pressures" argument is analyzed in more detail in Yampolsky and Stoltzfus (2001).

10 In the genesis of the MS, this doctrine had no clear basis in theory or experiment. It was not considered in a rigorous way until Maynard Smith tried (and, in my opinion, failed) to justify it in 1976, long after it had become an established orthodoxy.

11 This is explained in more detail in Stoltzfus (2009; see also Yampolsky and Stoltzfus, 2001).

Credits: The Curious Disconnect is the blog of evolutionary biologist Arlin Stoltzfus, available at www.molevol.org/cdblog. An updated version of the post below will be maintained at www.molevol.org/cdblog/mutationism_myth5 (Arlin Stoltzfus, ©2010)


Tuesday, August 31, 2010

The Mutationism Myth, VI: Back to the Future

This is the eighth in a series of postings by guest blogger, Arlin Stoltzfus. You can read the introduction to the series at: Introduction to "The Curious Disconnect". The first part is at: The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion. The second installment is: Theory vs Theory. The third part is: The Mutationism Myth, II. Revolution. The fourth installment is: The Mutationism Myth: III Foundations of Evolutionary Genetics. Part five is The Mutationism Myth, IV: Mendelian Heterodoxies. The sixth installment was The Mutationism Myth, V: The response to Mendelian heterodoxies.

This is Arlin's last contribution. The entire series has been an excellent introduction to the history of evolutionary theory and the concept of mutationism. There are many ways in which the so-called "Modern" Synthesis has to be revised and extended. One of them is to reinstate the concept of mutationism which was purged from evolutionary theory in the 1940s. If you want to understand why this is important then these articles are the place to start.



The Curious Disconnect

Today on The Curious Disconnect (credits), we wrap up our 6-part series on the Mutationism Myth, and set the stage for the future by locating the primary weakness of the 20th century neo-Darwinian consensus in its theory of variation.

I'd like to thank Larry Moran for hosting this series of posts on Sandwalk. If it still seems like a good idea later in the year, I will continue the Curious Disconnect on my own blog site (to be announced).

The Mutationism Myth, part 6. Back to the Future

The Mutationism Myth, a story about how the discovery of genetics affected evolutionary thought, continues to be part of modern neo-Darwinism's monologue with itself (e.g., Charlesworth and Charlesworth, 2009), being used even by leading thinkers calling for an "Extended" Synthesis (e.g., Pigliucci, 2010 1). Since April, we've been deconstructing the Mutationism Myth by exploring what the early Mendelians actually thought, and how their view was replaced by the Modern Synthesis (MS).

Today we'll take the opportunity to review what we've learned and start unpacking its relevance for the future of evolutionary biology.

Review

In the Mutationism Myth (see part 1 for examples), the founders of genetics misinterpret their discovery, concluding that evolution takes place by large mutational jumps, without selection. The false gospel of these "mutationists" brings on a dark period of confusion and error that lasts until the 1930s, when theoretical population geneticists (Fisher, Haldane and Wright) prove that Mendelian genetics is not only compatible with selection, but provides the missing link that completes Darwin's theory and unites all the biological disciplines. The "Modern Synthesis" combining genetics and selection becomes the foundation for all subsequent evolutionary thought.

As we discovered, the Mutationism Myth isn't very accurate. Heredity is not missing from Darwin's theory; selection is not missing from the Mendelian view. Darwin had a theory of heredity both in the sense of a set of phenomenological laws, and in the sense of a mechanism to account for them (part 2). Both were wrong. The Mendelians synthesized genetics and selection, rejecting Darwin's "Natural Selection" theory due to its dependence on fluctuations or "indefinite variability" (defined by Darwin as the subtle variations that arise anew each generation in response to conditions of life). As we know today, such enrivonment-induced fluctuations are non-heritable.

In part 3, we found that the Mendelians laid the conceptual foundations of evolutionary genetics (later formalized mathematically), while part 4 addressed how their view diverged from Darwinian orthodoxy. The Mendelians assumed that new hereditary variants arise rarely and discretely, by mutations whose effects may be large or small. Each new mutation is likely to be rejected, but it may be accepted by chance, especially if it improves fitness. Because, in this view, change depends on discrete events of mutation, the Mendelians (part 4) considered the process of mutation to be a source of initiative, discontinuity, creativity and direction in evolution (Stoltzfus, 2006). This view expanded the role of variation well beyond the subordinate role of raw materials that Darwin had imagined.

The Mendelians were unable to convince naturalists (the majority of their biologist peers) to accept their new view of evolution, nor even a new view of inheritance. Many naturalists remained wedded to Lamarckian and Darwinian views of "soft inheritance".

As we found out in part 5, the "Modern Synthesis" (modern neo-Darwinism) claimed to reconcile Darwin's own view with genetics, though it quietly ignored Darwin's errors while depicting the Mendelians as foolish "saltationists", dismissing their "lucky mutant" view and their ideas about the role of mutation in evolution. In the MS view, each species has a "gene pool" that automatically soaks up and "maintains" hereditary variation, providing abundant "raw materials" for adaptation. The key innovations of this view were to define "evolution" as "shifting gene frequencies" in the "gene pool", to erase the link between "Darwinism" and Darwin's own theory of soft inheritance, and to develop a theory of causation in terms of population-genetic "forces", in which continuous shifts in allele frequencies are the common currency of causation. The new theory put mutation in a subordinate position of supplying infinitesimal "raw materials" for selection. As a result, the MS created a consensus where the Mendelians had failed: naturalists such as Ernst Mayr found that they could accept Mendelian genetics without giving up adaptationist preconceptions.

A bright line

The backdrop for this whole discussion (in case you missed it) is that the MS is strikingly wrong in its neo-Darwinian departures from the Mendelian view. I've implied this several times, and perhaps I've waved my hands and pointed vaguely to mountains of molecular evidence contradicting the MS, but I haven't made this point perfectly clear.

In a moment, I will do that, but first I want to make clear what is at stake.

The Mendelians allowed that evolutionary change could be initiated by an event of mutation, and they interpreted this to mean that mutation was (to an unknown degree) a source of initiative, discontinuity, creativity and direction in evolution. The MS represents a very deliberate rejection of this view, and proposes instead that evolution is a complex sorting out of available variation to achieve a new multi-locus equilibrium, literally by "shifting gene frequencies" in the "gene pool". The rate of evolution, in this view, does not depend on mutation, which merely supplies the "gene pool" with variation; evolution is not shaped by mutation, which is the "ultimate" source of variation, but not the proximate source.

When I made this distinction at a 2007 symposium in honor of W. Ford Doolittle, Joe Felsenstein was in the audience and pointed out that, while Fisher may have looked at things in this way, Wright's stochastic view took into account random events, like new mutations. It's true that Wright's "shifting balance" model assigns a prominent role to random genetic drift, while Fisher's view was deterministic. However, these are just two different flavors of the same "shifting gene frequencies" paradigm: neither view incorporates new mutations. The absence of new mutations from Wright's shifting balance process is apparent from the fact that Patrick Phillips (1996) extended it to include a new starting phase ("phase 0") of "waiting for a compensatory mutation".

The fact that contemporary evolutionary biologists, for the most part, don't understand this aspect of their intellectual heritage is not evidence of a cover-up. Scientists don't get much chance to learn history. The history that they absorb is mainly from stories that appear in scientific writings, like the Mutationism Myth and the Essentialism Story, stories that represent Synthesis Historiography (Amundsen, 2005), the discipline of telling history in ways that make things turn out right for the Modern Synthesis. Synthesis Historiography teaches us that "saltationism" (Mayr's pejorative term for the Mendelian view) and other alternatives to neo-Darwinism are nonsensical, "doomed rivals", supported only by "typologists", creationists, vitalists and other crazies. That is, Synthesis Historiography teaches the TINA doctrine: There Is No Alternative.

As contemporary research drifts away from the "gene pool" theory and the Darwinian doctrines of the MS, each evolutionary biologist remains confident that, due to the TINA doctrine, his own view must be "neo-Darwinian". In reality, alternatives are being explored with increasing vigor in molecular evolution, evo-devo, and evolutionary genetics.

A few folks today are in the reverse situation of being familiar with MS orthodoxy, but not with recent research. Dawkins (2007) stakes his critique of a book by "intelligent design" creationist Michael Behe entirely on his faith in the gene pool theory. Behe claims, in effect, that there was not sufficient time for all the mutations needed to account for evolution. Dawkins responds by attacking the premise that evolutionary rates depend on mutation rates:

"If correct, Behe's calculations would at a stroke confound generations of mathematical geneticists, who have repeatedly shown that evolutionary rates are not limited by mutation. Single-handedly, Behe is taking on Ronald Fisher, Sewall Wright, J.B.S. Haldane, Theodosius Dobzhansky, Richard Lewontin, John Maynard Smith and hundreds of their talented co-workers and intellectual descendants. Notwithstanding the inconvenient existence of dogs, cabbages and pouter pigeons, the entire corpus of mathematical genetics, from 1930 to today, is flat wrong. Michael Behe, the disowned biochemist of Lehigh University, is the only one who has done his sums right. You think? The best way to find out is for Behe to submit a mathematical paper to The Journal of Theoretical Biology, say, or The American Naturalist, whose editors would send it to qualified referees."

With his signature over-the-top rhetoric, Dawkins insists that "mathematical genetics" has proven that evolutionary rates are not limited by mutation. Allowing for some exaggeration, this is an accurate representation of MS orthodoxy ca. 1959, the approximate vintage of Dawkins's views. If Mayr had been alive, he might have said the same thing.

Meanwhile, no one who has been active in evolutionary genetics research in the past 15 years would represent the current state of knowledge in this way. If you want to know what a contemporary researcher would say, take a look at the most recent issue of Evolution in which the article by Douglas Futuyma (famous for his evolution textbook) gives many examples of how evolutionists (including himself) repeated the doctrine that mutation does not "limit" evolution, but argues that we are no longer making this dubious assumption. Another example would be the piece by Ronny Woodruff and James Thompson (1998) that introduces their symposium volume on Mutation and Evolution.2

Yet the MS and its "gene pool" theory have left their mark on evolutionary biology, even if the MS itself has largely disappeared from the collective memory of researchers. One indelible mark is what Gillespie calls "The Great Obsession" of population genetics to understand the "maintenance of variation", but that's a story for another day.

Another indelible mark is the long absence of mutationist models of "adaptation", a topic that has blossomed just in the last dozen years. Allen Orr has achieved well deserved fame for his innovations in this area, and we'll discuss his work briefly in the next section. For now, let us note how other researchers have pointed out the absence of such models:

"Almost every theoretical model in population genetics can be classified into one of two major types. In one type of model, mutations with stipulated selective effects are assumed to be present in the population as an initial condition . . . The second major type of models does allow mutations to occur at random intervals of time, but the mutations are assumed to be selectively neutral or nearly neutral." (Hartl & Taubes, 1998)

"The process of adaptation occurs on two timescales. In the short term, natural selection merely sorts the variation already present in a population, whereas in the longer term genotypes quite different from any that were initially present evolve through the cumulation of new mutations. The first process is described by the mathematical theory of population genetics. However, this theory begins by defining a fixed set of genotypes and cannot provide a satisfactory analysis of the second process because it does not permit any genuinely new type to arise. " (Yedid and Bell, 2002)

These authors are not trying to make a point about history or about the Modern Synthesis: they are simply claiming the novelty of their own models of adaptation that incorporate new mutations. And what they are saying is that the paradigm of 20th-century population genetics is "shifting gene frequencies": overwhelmingly, it's a body of theory about what happens to the variation that is present in a population as an initial condition, not about a larger-scale process in which there are new beneficial mutations.3

One small step for a phage, one giant leap for evolutionary biology

The actual role of mutation in evolution is not what is theorized in the MS. Many arguments could be made to support this contention, but I'm going to make just one argument drawing on one source, namely Rokyta, et al., 2005. I choose this argument because it is particularly compelling and concise. My argument addresses the lucky mutant view of initiative or (to put it another way) dynamics.

Rokyta, et al. is a study of parallel evolution in an experimental population of the bacteriophage phiX174, published in Nature Genetics. It was hailed as "the first empirical test of an evolutionary theory" (Bull & Otto, 2005), where the theory in question is Orr's (2002) ingenious extension of Gillespie's (1984) "mutational landscape" model to take into account predictions of extreme value theory.4

In spite of the fancy name, the "mutational landscape" model of sequence evolution is simple. Rather than considering all conceivable evolutionary changes from a starting sequence, we simplify the problem by considering only changes that occur via 1-bp mutations. That set of possibilities, by definition, is the "mutational landscape" or (my preferred term) the "evolutionary horizon". Each change will shift the evolutionary horizon, but it's easy to recompute the horizon, because it's easy to enumerate (theoretically) all the alternative sequences.

We are going to make this a model of beneficial changes ("adaptation"). A beneficial mutation is introduced into the population of N individuals at some total rate Nu, and faces acceptance with a probability of 2s, based on the classic formula p = 2s for the probability of fixation of a new beneficial mutation.5 For beneficial substitution i with selection coefficient si, the probability6 is just Nu*2si. If we divide an individual Nu*2si by the sum of all such values on the horizon, we get a normalized probability: the probability that the next step in our evolving system is step i. The factor Nu*2 is the same for every step, so it cancels out: only the si values matter. To evolve our sequence, we just sample from this probability distribution of possible steps, then recompute the new evolutionary horizon in preparation for the next step. Easy! 7

From past experiments, Rokyta, et al. know which steps on the horizon are beneficial, and they even know the selection coefficients. They know that sometimes, the same evolutionary steps happen in parallel, in replicate phage populations. They can compare the observed pattern of parallel evolution with the pattern predicted from theory.

Now, the preceding description suggests something fascinating: the cutting edge of evolutionary genetics today, with papers that get published in Nature Genetics with commentaries, uses experimental systems to explore the "lucky mutant" view of parallel evolution.

But the story gets even better. Rokyta, et al actually reject Orr's model, in its original version. They find more parallel evolution than expected. Why? Because the model treats all mutation rates equally. Note above that we canceled out mutation rates on the grounds that they are all the same. But that's not realistic. Some mutations are more likely than others, and this will affect the rate at which they are introduced into the population and subjected to acceptance or rejection. The more heterogeneity in rates of mutation, the more parallel evolution. Rokyta, et al. found that if they revised the model to take into account transition:transversion bias (I think it's about 5-or 6-fold under the experimental conditions), then the predicted amount of parallelism matched the observed amount.

Just let that soak in for a moment. We have an experimental study and a precise model. Evolution in this model is characterized by origin-fixation dynamics, dependent on the rate of mutational introduction of new alleles, and on their probability of fixation. Both factors affect the outcome of evolution; both factors affect the chance of parallelism. The experimental study eliminates (statistically) a model that lacks mutational bias in the introduction of new alleles. Thus the study clearly illustrates the dual causation of evolutionary change, in regard to its dynamics.

Back to the future

The MS is wrong, and not in a small way: it's wrong because reality just looks too much like the antithesis of the MS, i.e., the mutationist view. For instance, as we found out in part 4, Vavilov (1922; see Stoltzfus, 2006) understood the dual causation of parallel evolution, including the role of parallel variation. By contrast, Mayr famously said that the search for homologous genes or homologous mutations was foolish.

This mistaken prediction is repeated ad nauseam in the evo-devo literature. If you have been following along, you now understand why Mayr would make such a prediction. The MS makes substantive claims about evolution, among which are the claim that, while mutation is ultimately necessary to keep the "gene pool" from drying up, selection doesn't need to wait for a new mutation, but draws together a multi-locus optimum from the abundance of raw materials in the gene pool; "evolution" is so far removed from the process of mutation, with so many complex dynamic processes interceding, that the outcome of evolution does not depend on specific events of mutation. If evolution really were like that, parallel mutation would be unimportant. That is, Mayr's prediction accurately reflects the logic of the MS. But as the Rokyta, et al study (and many others) show, the prediction is not fulfilled.

According to Dawkins, "the entire corpus of mathematical genetics" from 1930 to "today" (i.e., about 1959, for Dawkins) would be "flat wrong" if one accepts the premise that evolution depends on new mutations, or that it is limited by the mutation rate. While this view is not often defended, that isn't because it's Dawkins's own personal opinion. Dawkins is accurately characterizing a theory that makes substantive claims about the world, a theory that most of us have forgotten. One of these claims is that "evolution" can be represented mathematically as a process of shifting the frequencies of alleles already present in an initial population, without new mutation; sometimes this doctrine is invoked by saying that "macroevolution" can be extrapolated from "microevolution".

If evolution actually worked like this, then evolutionary change would not exhibit a dependence on the rate of mutation, and Dawkins would be right in his criticism of Behe. But this is wrong. In fact, the dependence is so sensitive that effects of only a few-fold are noticeable, as the Rokyta, et al study (and many others) shows.

I'm not going to mince words. The MS is wrong, and not in a small way: reality looks too much like the mutationist view that we (the scientific community) rejected when we bought into the MS. We need another theory1, perhaps several others.

The road less traveled

What's wrong about the MS, and what its replacement(s) must replace, is its theory of the role of variation in evolution. In future posts on the Curious Disconnect, I intend to focus on this issue. The Mutationism Myth suggests a lesson about how to develop (or rather, how not to develop) a theory of variation.

Darwin knew that hereditary variation played a vital role in evolution. He studied the subject intensely. He found that organisms vary in many different ways, and on many scales, but the evidence on heredity was bewildering and inconclusive. Lacking the means to derive a mechanism of evolution by reasoning upward from genetics, Darwin reasoned downwards from his premises that 1) organisms are exquisitely and pervasively adapted to their niches, 2) selection must have played some role in this, and 3) Mother Nature never makes a jump. Gould argues that Darwin's willingness to posit precise restrictions on variation was a stroke of genius.8 Darwin knew that discrete "sports" (mutants) could be heritable, but he discounted them: they could not make his theory work as desired. Instead, he staked his "natural selection" theory on the heritability of fluctuations, because they were infinitesimal, indefinite (unbiased), and "everywhere present", being induced in abundance whenever organisms encountered altered "conditions of life". Inferring the heritability of fluctuations completed his theory and made it work.

But it was wrong: the fluctuations that made Darwin's theory work are non-heritable, as the Mendelians discovered.

The architects of the MS tried again, with advantages unavailable to Darwin. Not only did they know genetics, they had some mathematical tools to work out unforeseeable implications of genetic concepts. However, they didn't have the knowledge to distinguish among different, genetically consistent modes of evolution. They had to fill in this gap somehow. Their downwards Darwinian reasoning and their upwards Mendelian reasoning met in the middle with the "gene pool": a theory of population genetics that would supply abundant, infinitesimal, "random" variations, in order to rationalize their commitment to the same premises Darwin accepted. That was the genius of the MS.

But again, it was wrong.

If we look at Darwinism in Popperian terms, as a theory1 that takes risks and generates potentially falsifiable claims, then (counterintuitively) it is largely a theory of the role of variation in evolution. The claims that selection is "important", and that it has some inalienable role in adaptation, carry little risk and have been widely accepted for 150 years. By contrast, the restrictions that Darwinism places on variation, in order to make it a subordinate factor that supplies "raw material" to selection, are risky and controversial, e.g., the claim that variation is random with respect to the direction of evolution, or that the rate of evolution does not depend on the rate of mutation, or the "gradualist" claim that variation is not a source of discontinuity. The architects of the MS invested the "gene pool" with nearly magical properties in order to improve the prospects for adaptation. Problematic claims about the role of variation are, and have been for 150 years, the overwhelming basis for scientific criticism of Darwinism.

And this problematic view of variation is based on reasoning from the premise that organisms are exquisitely and pervasively adapted to their niches, to the conclusion that variation must play just the right role of supplying abundant raw materials to make this possible. I believe that there is something fundamentally wrong with this mode of reasoning. Perhaps it betrays a kind of subconscious Panglossian agenda. Every time I give a lecture on mutation-biased evolution, someone suggests that perhaps the mutation biases themselves are adaptive, as though this inference could restore one's faith that everything turns out for the best, and that "the ultimate source of explanation in biology is the principle of natural selection" (Ayala, 1970). Remarkably, the evo-devo-inspired view that seems destined for inclusion in the emerging "Extended Synthesis" is headed down much the same path, with a focus on the idea that the process of variation has been jiggered to make things turn out right for adaptation. What's revealing about this new view is how little attention its proponents have paid to understanding precisely, in terms of population-genetic causation, how the process of variation shapes evolution, before jumping ahead to the shadowy inference that the process of variation itself was shaped by selection for this very role.

We are not going to go down that same road here on the Curious Disconnect, which should make things all the more interesting.

References

Ayala, F. J. 1970. Teleological Explanations in Evolutionary Biology. Philosophy of Science 37:1-15.

Bull, J. J., and S. P. Otto. 2005. The first steps in adaptive evolution. Nat Genet 37:342-343.

Charlesworth, B., and D. Charlesworth. 2009. Darwin and genetics. Genetics 183:757-766.

Dawkins, R. 2007. Review: The Edge of Evolution. Pp. 2. International Herald Tribune, Paris.

Gould, S. J. 2002. The Structure of Evolutionary Theory. Harvard University Press, Cambridge, Massachusetts.

Hartl, D. L., and C. H. Taubes. 1998. Towards a theory of evolutionary adaptation. Genetica 103:525-533.

Medawar, P. B. 1967. The Art of the Soluble. Methuen and Co., London.

Nei, M. 2007. The new mutation theory of phenotypic evolution. Proc Natl Acad Sci U S A 104:12235-12242.

Orr, H. A. 2002. The population genetics of adaptation: the adaptation of DNA sequences. Evolution Int J Org Evolution 56:1317-1330.

Phillips, P.C. 1996. Waiting for a compensatory mutation: phase zero of the shifting-balance process. Genetical Research, Cambridge 67:271-283.

Rokyta, D. R., P. Joyce, S. B. Caudle, and H. A. Wichman. 2005. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet 37:441-444.

Woodruff, R. C., and J. D. Thompson. 1998. Preface in R. C. Woodruff, and J. D. Thompson, eds. Mutation and Evolution. Kluwer, Dordrecht, The Netherlands.

Yedid, G., and G. Bell. 2002. Macroevolution simulated with autonomously replicating computer programs. Nature 420:810-812.


Notes

1 Pigliucci, along with Gerd Muller, edited a book on "the extended Synthesis" with papers from a select group of thinkers who were invited in July, 2008 to a special meeting in Altenberg, Austria. The book is now available in paperback: http://www.amazon.com/Evolution-Extended-Synthesis-Massimo-Pigliucci/dp/0262513676

2 from p. 1 "Although mutation is a key parameter in the genetics of populations, the role of mutation as an evolutionary factor has been debated since the time of Darwin. Early geneticists, who held to the 'classical' view of the genome as being homogeneous with occasional mutant alleles, saw new mutation as a major determining force in adaptive change. When the classical view was replaced with the 'balance' view of the genome, i.e., highly heterogeneous, pre-existing variation became more important as the resource on which selection would act. Many, therefore, began to disregard new mutation as a significant force in evolution, since the level of genetic diversity is already so high that new mutants would generally be expected to add little to that resource . . . Mechanisms responsible for maintaining levels of genetic diversity became the focus of attention, and mutation pressure is now thought by many to have only minor significance, especially when compared to selection, recombination, gene flow, and similar factors. We think this position, like the classical view, is too extreme. While there can be little doubt that mutation per se is not the principle driving force it was once believed to be for phenotypic evolution, we see growing evidence that its role is under-appreciated in important situations. The rate and pattern of mutation can be influenctial variables in adaptive responses, and the role of mutation in evolution deserves to be reexamined."

3 Orr (2002) notes the absence of such models by making a far more sweeping claim that population genetics has ignored, not just new-mutations models of adaptation, but all models of adaptation, and instead has focused on neutral and deleterious alleles. That is an odd thing to say, given that the quantitative genetics of adaptation have been a topic for a long time. In any case, here is what Orr says: "Evolutionary biologists are nearly unanimous in thinking that adaptation by natural selection explains most phenotypic evolution within species as well as most morphological, physiological, and behavioral differences between species. But until recently, the mathematical theory of population genetics has had suprisingly little to say about adaptation. Instead, population genetics has, for both historical and technical resasons, focussed on the fates of neutral and deleterious alleles. The result is a curious disconnect between the verbal theory that sits at the heart of neo-Darwinism and the mathematical content of most evolutionary genetics. "

4 Also known as the theory of records—"record" in the sense of "pinnacle of achievement". Given a series of records, such as the world record in the long-jump, what's the interval of time to the next record, and by how much will it break the previous record? The theory of records addresses such questions. Can you see how this would be useful to make a predictive theory of adaptation?

5 Rokyta, et al. used a different formula for the probability of fixation, because the classic approximation only works for s << 1, whereas the phiX174 populations experience very large s, sometimes s > 1.

6 Formally Nu*2si is not a probability but a steady-state rate (e.g., for an infinite-alleles model). If we treat it as an instantaneous rate, and then compare it to all other instantaneous rates, this makes it a relative probability of choosing step i over a short interval.

7 For our present purposes, we don't need to explain Orr's addition to this model, which was a theory of the distribution of the favorable s values under generalized assumptions (oddly, the commentators on Rokyta, et al. did not mention that Orr's theory wasn't really needed, and that the study really was a test of the mutational landscape model itself).

8 Gould (2002, p. 140) is not endorsing Darwin's error about fluctuation. Darwin's followers think of that mistake as a trivial detail. Instead Gould is endorsing a more general inference. Here is what he writes. "Darwin reasoned that natural selection can only play such a role [as exclusive source of creativity and direction] if evolution obeys two crucial conditions: (1) if nothing about the provision of raw materials—that is, the sources of variation—imparts direction to evolutionary change; and (2) if change occurs by a long and insensible series of intermediary steps, each superintended by natural selection—so that "creativity" or "direction" can arise by the summation of increments.


Under these provisos, variation becomes raw material only—an isotropic sphere of potential about the modal form of a species. Natural selection, by superintending the differential preservation of a biased region from this sphere in each generation, and by summing up (over countless repetitions) the tiny changes thus produced in each episode, can manufacture substantial, directional change. What else but natural selection could be called 'creative,' or direction-giving, in such a process? As long as variation only supplies raw material; as long as change accretes in an insensibly gradual manner; and as long as the reproductive advantages of certain individuals provide the statistical source of change; then natural selection must be construed as the directional cause of evolutionary modification.


These conditions are stringent; and they cannot be construed as vague, unconstraining, or too far in the distance to matter. In fact, I would argue that the single most brilliant (and daring) stroke in Darwin's entire theory lay in his willingness to assert a set of precise and stringent requirements for variation—all in complete ignorance of the mechanics of heredity. Darwin understood that if any of these claims failed, natural selection could not be a creative force, and the theory of natural selection would collapse. "



Credits: The Curious Disconnect is the blog of evolutionary biologist Arlin Stoltzfus, available at www.molevol.org/cdblog. An updated version of the post below will be maintained at www.molevol.org/cdblog/mutationism_myth6 (Arlin Stoltzfus, ©2010)