Molecular Evolution Exam - April 2015

Here's the final exam in my course. Students have to answer the first two questions and three of the next five questions. How would you do?

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1. Choose a subtopic from your essay and explain it better than you did in your essay and/or rebut the comments and criticisms made by the marker/grader.


2. Michael Lynch says in The Origins of Genome Architecture ....
   

   Nothing in Evolution Makes Sense Except in the Light of Population Genetics
   Evolution is a population genetic process governed by four fundamental forces, which jointly dictate the relative abilities of genotype variants to expand through a species. Darwin articulated a clear but informal description of one of those forces, selection (including natural and sexual selection), whose central role in the evolution of complex phenotypic traits is universally accepted, and for which an elaborate formal theory in terms of changing genotype frequencies now exists. The remaining three evolutionary forces, however, are non-adaptive in the sense that they are not the function of the fitness properties of individuals: mutation (broadly including insertions, deletions, and duplications) is the fundamental source of variation on which natural selection acts; recombination (including crossing-over and gene conversion) assorts variation within and among chromosomes; and random genetic drift insures that gene frequencies deviate a bit from generation to generation independently of other forces. Given the century of theoretical and empirical work devoted to the study of evolution, the only logical conclusion is that these four broad classes of mechanisms are, in fact, the only fundamental forces of evolution. Their relative intensity, directionality, and variation over time define the way in which evolution proceeds in a particular context.

   Do you agree with Lynch that “Nothing in Evolution Makes Sense Except in the Light of Population Genetics”? If so, why isn’t population genetics taught in introductory biology courses? If not, why not?


3. Imagine that identical female twins were born to a woman in 1000 AD. Imagine that you could find a direct descendant of each twin in 2015. If you sequence the complete genomes of the descendants, approximately how many differences would you expect to find? How do these compare to the differences between any two randomly selected individuals from the same part of the world? Explain your reasoning and describe any assumptions you make. Think carefully before you answer. The second question is the most important one. (Human mutation rate = 130 mutations per generation. Haploid genome size = 3.2 × 10⁹ bp.)


4. Why do some scientists think that there is no unique tree of life?


5. Many people believe that recombination evolved because it increases genetic variation in a population and this provided a selective advantage over species that didn’t have recombination. Do you agree with this explanation for the evolution of recombination? Why, or why not? What are the other possibilities?


6. What is “evolvability ”and why could it be important in evolution? Why are some scientists skeptical of this claim?


7. Richard Dawkins once wrote,
   

   Even the most ardent neutralist is quite happy to agree that natural selection is responsible for all adaptation. All he is saying is that most evolutionary change is not adaptation. He may well be right, although one school of geneticists would not agree. From the sidelines, my own hope is that the neutralists will win, because this will make it so much easier to work out evolutionary relationships and rates of evolution. Everybody on both sides agrees that neutral evolution cannot lead to adaptive improvement, for the simple reason that neutral evolution is, by definition, random, and adaptive improvement is, by definition, non-random. Once again, we have failed to find any alternative to Darwinian selection, as an explanation for the feature of life that distinguishes it from non-life, namely adaptive complexity.
   
   Richard Dawkins (1986) The Blind Watchmaker. p. 304

   Can you describe situations in Richard Lenski’s ongoing evolution experiment where neutral or deleterious alleles were essential for adaptive change?

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P-ter Accuses Me of Quote Mining

 
There are many adaptationists who recognize that random genetic drift exists. They will, when pressed, admit that neutral alleles can be fixed in a population. However, these adapationists pften maintain that visible phenotypes cannot be neutral with respect to survivability. Thus all visible phenotypes, with rare exceptions, are adaptations.

Several people have expressed this point of view in the comments on Sandwalk but the most prominent proponent is Richard Dawkins. I often use a quotation from The Extended Phenotype to demonstrate how Dawkins thinks about this issue. It comes from a chapter titled Constraints on Perfection. Here's the complete paragraph; I often use just the part that begins "The biochemical controversy ....[Richard Dawkins on Visible Changes and Adaptationism].

I have tried to show that adapatationism can have virtues as well as faults. But this chapter's main purpose is to list and classify constraints on perfection, to list the main reasons why a student of adaptation should proceed with caution. Before coming to my list of six constraints on perfection, I should deal with three others that have been proposed, but which I find less persuasive. Taking first, the modern controversy among biochemical geneticists about "neutral mutations", repeatedly cited in critiques of adaptationism, it is simply irrelevant. If there are neutral mutations in the biochemist's sense, what this means is that any change in polypeptide structure which they induce has no effect on the enzymatic activity of the protein. This means that the neutral mutations will not change the course of embryonic development, will have no phenotypic effect at all, as a whole-organism biologist would understand phenotypic effect. The biochemical controversy over neutralism is concerned with the interesting and important question of whether all gene substitutions have phenotypic effects. The adaptationism controversy is quite different. It is concerned with whether, given that we are dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist's 'neutral mutations' are more than neutral. As far as those of us who look at gross morphology, physiology and behaviour are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976b) wrote: "I interpret 'rate of evolution' as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution ..." If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.

Natural selection is the only explanation we know for the functional beauty and apparently "designed" complexity of living things. But if there are any changes that have no visible effect—changes that pass right under natural selection's radar—they can accumulate in the gene pool with impunity and may supply just what we need for an evolutionary clock.

Richard Dawkins
The Extended Phenotype (2005)I have discussed this quotation with Richard Dawkins and I am convinced that it fairly represents his viewpoint. The only quibble would be that Dawkins would probably admit of one or two exceptions where neutral alleles might produce a phenotypic effect. In other words, his statement above is perhaps an example of hyperbole but that's how I always read it anyway. Almost all popular science writers make generalizations of this sort and it's not a great crime.

The bottom line is that Dawkins thinks that neutral mutations cannot have an effect on embryonic development; therefore, they cannot result in a visible phenotype. Dawkins believes that almost all visible mutations will have either a beneficial or a detrimental effect on the survivability of an organism and that neutral mutations are a phenomenon that's confined to the molecular level where they may not even count as evolution.

P-ter thinks that I misrepresent Dawkins by quote mining [Larry Moran caught quote mining]. Here's what P-ter says,

This certainly seems to place Dawkins as an "adaptationist", one who thinks that all differences in phenotypes are adaptations. I was a little surprised by this, but the quote seemed clear, and I wasn't going to take the time to find my original.

Luckily, another commenter pointed out that The Extended Phenotype is searchable at Google Books [The Extended Phenotype]. And funny, the very next line after Moran stops quoting is possibly relevant:

The next lines P-ter is referring to is the beginning of a new paragraph ...

He might, nevertheless, be dealing with a neutral character in the sense of an earlier controversy (Fisher & Ford 1950; Wright 1951). A genetic difference could show itself at the phenotypic level, yet still be selectively neutral.

P-ter then continues with ...

Dawkins goes on to express some skepticism about some arguments for evolution by drift, but he's certainly not an "adaptationist" in the Moran sense.

I suppose I'm somewhat naive: distorting someone's argument through selective quotation is a classic creationist tactic, and Moran has written a bit about the propaganda techniques used by that crowd. Little did I know his familiarity is not of an entirely academic sort.

[1] As opposed to "pluralists", as he likes to call himself. For someone who (rightfully, in my opinion) is disdainful of "framing" (the view that scientists need to spin their results in order to resonate better with the public), he certainly knows how to frame.

This is a very serious charge. I'm accused of deliberately distorting Dawkins' position by selective quotation. According to P-ter, Dawkins does not believe what he says in the quoted paragraph. (And elswhere, I might add.) According to P-ter Dawkins believes that mutations with a visible phenotype can be neutral. (We're not talking about one or two exceptions here, we're talking about the generality that applies to a significant percentage of mutations.)

P-ter's evidence of the crime of quote mining is the first two sentences of a paragraph that appears on the bottom of page 32. You can read it for yourself but it seems obvious to me that Dawkins is raising a possible objection to his claim and then dismissing it. Here are the first few (not just two) sentences of that paragraph: I think they convey the correct intent.

He might, nevertheless, be dealing with a neutral character in the sense of an earlier controversy (Fisher & Ford 1950; Wright 1951). A genetic difference could show itself at the phenotypic level, yet still be selectively neutral. But mathematical calculations such as those of Fisher (1930b) and Haldane (1932a) show how unreliable human subjective judgement can be on the "obviously trivial" nature of some biological characters. Haldane, for example, showed that, with plausible assumptions about a typical population, a selection pressure as weak as 1 in a 1000 would take only a few thousand generations to push an initially rare mutation to fixation, a small time by geological standards. It appears that in the controversy referred to above, Wright was misunderstood (see below) ...

A careful reading of Dawkins shows that the objection to his claim doesn't stand because people misunderstood Wright. Thus, according to Dawkins, characters that appear to be neutral really aren't.

I maintain that my original characterization of the Dawkins' position is accurate and his words reflect his true beliefs. I resent P-ter's accusation that I deliberately tried to misrepresent Dawkins by quoting that passage.

Incidentally, P-ter puts words in my mouth. I recognize several different kinds of adaptationist. The worst of them are those who think every visible phenotype is an adaptation of some sort but there are many who do not hold this extreme position. It's simply not true that I say every adaptationist must deny the fixation of neutral alleles with a visible phenotype. Some are easier to mock than others, but it's pretty easy to get most of them going whenever I point out that Dawkins is an adaptationist.

What would happen if Intelligent Design Creationists understood evolution?

There's an interesting phenomenon taking place over on one of the main Intelligent Design Creationist websites. It started when a philosphopher, Vincent Torley, tried to understand how the sequences differences between chimpanzees and humans could be explained by evolution. In the beginning, he was skeptical of the explanation I offered and he was supported by a biochemist creationist named Branko Kozulic. Kozilic assured him that his skpeticism was justified and the population geneticists were wrong.

Then an amazing thing happened. Salvador Cordova, another well-known creationist, posted a comment on one of Torley's blog posts. You can see it as comment #39 on Branko Kozulic responds to Professor Moran. Cordova was responding to comments posted by Nick Matzke and "WD400" on that same post. Here's what Sal Cordova said,

Michael Lynch on modern evolutionary theory

Of the Five Things You Should Know if You Want to Participate in the Junk DNA Debate, the most difficult to explain is "Modern Evolutionary Theory." Most scientists think they understand evolution well enough to engage in the debate about junk DNA. However, sooner or later they will mention that junk DNA should have been deleted by selection if it ever existed. You can see that their worldview leads them to believe that everything in biology has an adaptive function.

It's been a few years since I posted Michael Lynch's scathing comments on panadaptationism and how it applies to understanding genomes [Michael Lynch on Adaptationism and A New View of Evolution]. You're in for a treat today.

Here's what you need to know about evolution in order to discuss junk DNA. The first quotation is from the preface to The Origins of Genome Architecture (pages xiii-xiv). The second quotations are from the last chapter (page 366 and pages 368-369.

Contrary to popular belief, evolution is not driven by natural selection alone. Many aspects of evolutionary change are indeed facilitated by natural selection, but all populations are influenced by nonadaptive forces of mutation, recombination, and random genetic drift. These additional forces are not simple embellishments around a primary axis of selection, but are quite the opposite—they dictate what natural selection can and cannot do. Although this basic principle has been known for a long time, it is quite remarkable that most biologists continue to interpret nearly aspect of biodiversity as an outcome of adaptive processes. This blind acceptance of natural selection as the only force relevant to evolution has led to a lot of sloppy thinking, and is probably the primary reason why evolution is viewed as a soft science by much of society.

A central point to be explained in this book is that most aspects of evolution at the genome level cannot be fully explained in adaptive terms, and moreover, that many features could not have emerged without a near-complete disengagement of the power of natural selection. This contention is supported by a wide array of comparative data, as well as by well-established principles of population genetics. However, even if such support did not exist, there is an important reason for pursuing nonadaptive (neutral) models of evolution. If one wants to confidently invoke a specific adaptive scenario to explain an observed pattern of comparative data, then an ability to reject a hypothesis based entirely on the nonadaptive forces of evolution is critical.

The blind worship of natural selection is not evolutionary biology. It is arguably not even science.

Michael Lynch

Despite the tremendous theoretical and physical resources now available, the field of evolutionary biology continues to be widely perceived as a soft science. Here I am referring not to the problems associated with those pushing the view that life was created by an intelligent designer, but to a more significant internal issue: a subset of academics who consider themselves strong advocates of evolution but who see no compelling reason to probe the substantial knowledge base of the field. Although this is a heavy charge, it is easy to document. For example, in his 2001 presidential address to the Society for the Study of Evolution, Nick Barton presented a survey that demonstrated that about half of the recent literature devoted to evolutionary issues is far removed from mainstream evolutionary biology.

With the possible exception of behavior, evolutionary biology is treated unlike any other science. Philosophers, sociologists, and ethicists expound on the central role of evolutionary theory in understanding our place in the world. Physicists excited about biocomplexity and computer scientists enamored with genetic algorithms promise a bold new understanding of evolution, and similar claims are made in the emerging field of evolutionary psychology (and its derivatives in political science, economics, and even the humanities). Numerous popularizers of evolution, some with careers focused on defending the teaching of evolution in public schools, are entirely satisfied that a blind adherence to the Darwinian concept of natural selection is a license for such activities. A commonality among all these groups is the near-absence of an appreciation of the most fundamental principles of evolution. Unfortunately, this list extends deep within the life sciences.

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... the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer (without any direct evidence). True, we have actually seen natural selection in action in a number of well-documented cases of phenotypic evolution (Endler 1986; Kingsolver et al. 2001), but it is a leap to assume that selection accounts for all evolutionary change, particularly at the molecular and cellular levels. The blind worship of natural selection is not evolutionary biology. It is arguably not even science. Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.

Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.It should be emphasized here that the sins of panselectionism are by no means restricted to developmental biology, but simply follow the tradition embraced by many areas of evolutionary biology itself, including paleontology and evolutionary ecology (as cogently articulated by Gould and Lewontin in 1979). The vast majority of evolutionary biologists studying morphological, physiological, and or behavioral traits almost always interpret the results in terms of adaptive mechanisms, and they are so convinced of the validity of this approach that virtually no attention is given to the null hypothesis of neutral evolution, despite the availability of methods to do so (Lande 1976; Lynch and Hill 1986; Lynch 1994). For example, in a substantial series of books addressed to the general public, Dawkins (e,g., 1976, 1986, 1996, 2004) has deftly explained a bewildering array of observations in terms of hypothetical selection scenarios. Dawkins's effort to spread the gospel of the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, and because more people have probably read Dawkins than Darwin, his words have in some ways been profoundly misleading. To his credit, Gould, who is also widely read by the general public, frequently railed against adaptive storytelling, but it can be difficult to understand what alternative mechanisms of evolution Gould had in mind.

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A Confused Philosopher

Darwinism and Its Discontents, by Michael Ruse, Cambridge University Press (2006)

Ruse defines Darwinism as the idea that natural selection is the chief causal process behind all organisms (p.2). He identifies a whole list of people who oppose Darwinism. Some of these are creationists—this book is not about them.

The main "discontents," according to Ruse, are misguided social scientists with their irrational fear of genetic determinism; philosophers who "can't handle the awful truth;" and evolutionary biologists whose objections "cannot be grounded purely in theory or evidence" (p.3). Many of discontent evolutionary biologists are (gasp!) Marxists.

I am one of those scientists who question Darwinism, so this book is all about me.

What does Michael Ruse have to say about us "discontents?"

At the risk of damning myself in the eyes of sound scholarship and of God, let me be categorical. All of the critics of Darwinism are deeply mistaken.

Wrong. It is Michael Ruse who is mistaken and this damn book is full of sloppy scholarship.

Chapters 1-4 cover the basic facts of evolution. Ruse establishes the important contribution of Darwin in discovering natural selection. He points out that natural selection is the "single best idea anyone ever had" (Dennett, 195). I agree.

The "fact" of evolution is explained and the history of life is briefly described. None of this is controversial as far as scientists are concerned but Ruse is setting the stage for the most important part of the book.

Before continuing, it's worth pointing out one of the major failings of the book: the lack of any solid definition of evolution. It seems clear that Ruse is confused about the difference between evolution and one of the main mechanisms of evolution, namely, natural selection. This confusion haunts the last part of the book and makes it very difficult for Ruse to come to grips with the ideas of the "discontents."

Chapter 5 ("The Cause of Evolution") is all about natural selection. Ruse builds the case for natural selection using all the old examples that we are familiar with. Only in Chapter 6 ("Limitations and Restrictions") does he begin to address the objections to classical Darwinism.

First in the dock is adaptationism as a flawed strategy. The adaptationist fallacy is a direct frontal attack on old-fashioned Darwinian thinking. The attack was first launched by Gould and Lewontin in the famous Spandrels of San Marco paper (1979). What does Ruse have to say about this?

Now, what is to be said by the Darwinian in response to this charge? Simply this: whoever doubted the point that Gould and Lewontin are making? It has always been recognized by evolutionists—certainly from the "Origin of Species" on—that however common or ubiquitous adaptation may be, it is only part of the story. (p.135)

Bravo! In two sentences Michael Ruse admits there's more to evolution than natural selection and, therefore, the discontents have a good case. Now let's see if he understands what these other things are and why they are important. (Don't hold your breath.)

Several examples follow. In all of them, Ruse makes the case that adaptation isn't necessarily optimal. Sometimes there just hasn't been enough time for adaptation to succeed, this is why some bird species haven't yet adjusted to being parasitized by cuckoos. Sometimes natural selection has done a good, but not perfect, job; as in the circuitous route followed by mammalian sperm ducts that loop over the ureter. Sometimes natural selection is even maladaptive, as in the large antlers of the extinct Irish Elk. All of these examples are intended to show that Gould and Lewontin were wrong.

What about group selection? That's a major challenge to Darwinism and natural selection. Not a problem. Hamilton solved it by coming up with kin selection. Kin selection has been the greatest gift to adaptationist thinking since natural selection itself.

What about random genetic drift? Now, that's a real issue since there's very little doubt about its importance. (It's by far the main mechanism of evolution, properly defined.) Does Ruse agree? Nope. Ruse notes that random genetic drift was first proposed by Sewall Wright back in 1931 and expanded by Moto Kimura in 1968. But after some initial excitement Ruse concludes,

Wright's theory is not very Darwinian. Natural selection does not play an overwhelming role. Genetic drift is the key player in Wright's world. However, although many of these ideas were taken up by later thinkers, especially by Theodosuis Dobzhansky in the first edition of his influential "Genetics and the Origin of Species," drift soon fell right out of fashion, thanks to discoveries that showed that many features formerly considered just random are in fact under tight control of selection. Today no one would want to say that drift (at the physical level) is a major direct player, although in America particularly, there has always been a lingering fondness for it. (p.150)

There you have it. One of the most decisive and well studied alternatives to natural selection is dismissed as a fad. This is sloppy scholarship. Ruse clearly does not know what he's talking about. He's probably read too much of Richard Dawkins and his fellow philosopher Daniel Dennett, and not enough evolutionary biology textbooks.

Now we turn to punctuated equilibria. If Ruse is an opponent of Gould you would expect to see the standard references to saltation in this part of the book. You won't be disappointed. Although saltation and hopeful monsters have nothing to do with punctuated equilibria—and certainly nothing to do with the challenge to Darwinism—they are obligatory strawmen whenever you want to discredit Stephen Jay Gould. It's another indicator of poor scholarship.

Species selection, the real hierarchical challenge to Darwinism, isn't even mentioned. This omission is all the more remarkable since Ruse recognizes that in order to make a case for evolution at higher levels a non-Darwinian mechanism is needed; one that will decouple macroevolution and microevolution.

[Gould proposes] that at upper levels there are other mechanisms that the microevolutionists miss. Which of course might be so, but until some convincing alternatives are supplied, Darwinians continue to argue that in important respects macroevolution is microevolution writ large. Natural selection working on random mutation is the key to evolutionary change, long term as well as short term. (p.159)

What a remarkably crude way of dismissing all the work done by a large number of paleontologists, not to mention a 1433 page book called The Structure of Evolutionary Theory. Ruse may have good reason for rejecting species selection but we'll never know. Sloppy scholarship, Ruse should be ashamed.

Chapter 6 is the most important chapter since it covers the main objections of the discontented. Ruse fails to meet any of those objections; indeed, he fails to understand most of them. The rest of the book doesn't get any better.

I'll finish this off by quoting from the concluding paragraph of Chapter 6.

What is our end point? It is just plain silly to say that Darwinism is an exhausted paradigm or that selection is a trivial cause of change—or even that it calls for significant revision or augmentation. It is a powerful mechanism and has proven its worth time and time again. It is not all-powerful. Natural selection has its limits—limits that have been recognized since the time of Darwin (he himself noted many of them)—but taken as a whole, it is the key to understanding the organic world. There is no call for theory change yet, nor is there any prospect of such change in the near future. (p.165)

Speaking for the discontents, I beg to differ. Random genetic drift is by far the most common mechanism of evolution and modern evolutionary theory fully acknowledges this fact. Darwinism (natural selection) is important but it ain't the only game in town. Darwin knew nothing about random genetic drift. That's why it's wrong to describe modern evolutionary theory as Darwinism.

Gould and his colleagues have proposed a hierarchical theory of evolution in which natural selection is only one mechanism and it operates at only one level (individuals within a population). Hierarchical theory may not be correct but you'll never know from reading this damn book.

The "Null Hypothesis" in Evolution

There's been a lot of discussion about the proper way to engage in thinking about evolution. When faced with a new problem, some people think that it's proper to begin by investigating adaptationist explanations. Others think that the proper way to begin is by assuming that the character in question is mostly influenced by random genetic drift. We are having a lively debate about this at Dawkins, Darwin, Drift, and Neutral Theory.

Part of the discussion boils down to a debate about the proper "null hypothesis" in evolutionary theory.

Here are some explanations from the textbooks that may help explain the "null hypothesis."

The most widely used methods for measuring selection are based on comparisons with the neutral theory, in which variation is shaped by the interaction between mutation and random genetic drift (Chapter 15). The neutral theory serves as a well-understood null hypothesis, and deviations from it may be caused by various kinds of selection. In the following sections, we examine ways of detecting and measuring selection by comparison with neutral theory.

EVOLUTION by Nicholas H. Barton, Derek E.G. Briggs, Jonathan A. Eisen, David B. Goldstein, and Nipam H. Patel, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2007 (p. 530)

The first step in a statistical test is to specify the null hypothesis. This is the hypothesis that there is actually no difference between the groups. In our example, the null hypothesis is that the presence or absence of wing markings does not effect the way jumping spiders respond to flies. According to this hypothesis, the true frequency of attack is the same for flies with markings on their wings as for flies without markings on their wings.

The second step is to calculate a value called a test statistic....

The third step is to determine the probability that chance alone could have made the test statistic as large as it is. In other words, if the null hypothesis were true, and we did the same experiment many times, how often would we get a value for the test statistic that is larger than the one we actually got?

EVOLUTIONARY ANALYSIS by Scott Freeman and Jon C. Herron, Prentice Hall, Upper Saddle River, New York 1998 (p. 73)

Genetic drift and natural selection are the two most important causes of allele substitution—that is, of evolutionary change—in populations. Genetic drift occurs in all natural populations because, unlike ideal populations at Hardy Weinberg equilibrium, natural populations are finite in size. Random fluctuations in allele frequencies can result in the replacement of old alleles by new ones, resulting in non-adaptive evolution. That is, while natural selection results in adaptation, genetic drift does not—so this process is not responsible for those anatomical, physiological, and behavioral features of organisms that equip them for survival and reproduction. Genetic drift nevertheless has many important consequences, especially at the molecular genetic level: it appears to account for much of the differences in DNA sequences among species.

Because all populations are finite, alleles at all loci are potentially subject to random genetic drift—but all are not necessarily subject to natural selection. For this reason, and because the expected effects of genetic drift can be mathematically described with some precision, some evolutionary geneticists hold the opinion that genetic drift should be the "null hypothesis" used to explain an evolutionary observation unless there is positive evidence of natural selection or some other factor. This perspective is analogous to the "null hypothesis" in statistics: the hypothesis that the data does not depart from those expected on the basis of chance alone. According to this view, we should not assume that a characteristic, or a difference between populations or species, is adaptive or has evolved by natural selection unless there is evidence for this conclusion.

EVOLUTION by Douglas Futuyma, Sinauer Associates Inc., Sunderland, MA, USA 2009 (p. 256)

Here are some papers from the scientific literature that illustrate how one goes about using the null hypothesis to ask questions about evolution.

Duret, L. and Galtier, N. (2007) Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends in Genetics 23:273-27 [doi:10.1016/j.tig.2007.03.011]

Orr, H.A. (1998) Testing Natural Selection vs. Genetic Drift in Phenotypic Evolution Using Quantitative Trait Locus Data. Genetics 149:2099-2104. [Abstract]

Brown, G.B. and Silk, J.B. (2002) Reconsidering the null hypothesis: Is maternal rank associated with birth sex ratios in primate groups? Proc. Natl. Acd. Sci. (USA) 99:11252-11255. [doi: 10.1073/pnas.162360599]

Nachman, M.W., Boyer, S.N., and Aquadro, C.F. (1994) Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice. Proc. Natl. Acd. Sci. (USA) 91:6364-6368. [Abstract]

Fincke, O.M. (1994) Female colour polymorphism in damselflies: failure to reject the null hypothesis. Anìm. Behav. 47:1249-1266. [PDF]

Roff, D. (2000) The evolution of the G matrix: selection or drift? Heredity 84:135–142. [doi:10.1046/j.1365-2540.2000.00695.x]

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A New View of Evolution

There have been lots of new books about evolution in the past decade or so. I tend to divide them into three categories:

1. The Standard View: These are books that basically support the Modern Synthesis with some small tweaks here and there. They do not advocate major shifts in the way we look at evolution. Books by Richard Dawkins (The Greatest Show on Earth: The Evidence for Evolution), Jerry Coyne (Why Evolution Is True), Sean B. Carroll (Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution), and Ken Miller (Only a Theory) fall into this category.
2. The New View: Some books make the case for a new way of looking at evolution. I'll call it the "New View." Many of Stephen Jay Gould's books fall into this category (The Structure of Evolutionary Theory). He refers to it as extending the modern synthesis. Most of the "extension" is based on a pluralist, rather than an adaptationist approach but other modifications are important. Two recent books by Michael Lynch (Origins of Genome Architecture) and Eugene Koonin (The Logic of Chance: The Nature and Origin of Biological Evolution) fall into this category. It's a view that I share.
3. The Radical View: Some books advocate a more-or-less complete overthrow of the Modern Synthesis, replacing it with the author's pet theory. Examples are: Marc Kirschner, and John Gerhart (The Plausibility of Life: Resolving Darwin's Dilemma), James Shapiro (Evolution: A View from the 21st Century), Lynn Margulis and Dorion Sagan (Acquiring Genomes: A Theory Of the Origin Of Species), Massimo Pigliucci and Gerd B. Müllerand (editors) (Evolution - the Extended Synthesis), many others.

Darwin and Design by Michael Ruse

 
In Darwin and Design Michael Ruse tackles a tough problem; namely "Does evolution have a purpose?" Unfortunately the correct answer is "no" but Ruse muddles, misdirects, and misunderstands so thoroughly that by the time you reach the end of the book you just want to throw it against the wall.

The main theme of the book is teleological thinking or the idea that things happen in order to achieve a goal. We are familiar with this way of thinking in religion. Ruse spends some time describing the history, culminating in the natural theology of William Paley.

Paley and others argued that the presence of design in nature demanded a God who was the designer. The teleological part of this argument is the recognition that designed species, especially humans, represent a clear goal that needs an explanation. Life has meaning and purpose, according to believers, and it is God who gave it to us.

A teleological argument, or argument from design, is an argument for the existence of God or a creator based on perceived evidence of order, purpose, design and/or direction in nature. The word "teleological" is derived from the Greek word telos, meaning end or purpose. Teleology is the supposition that there is purpose or directive principle in the works and processes of nature.
"Teleological Argument" WikipediaCharles Darwin explained how life could appear to be designed by invoking natural selection, thus removing God from the equation. Nevertheless, teleology remains an important part of science, according to Ruse, because nature is designed by natural selection. It is quite appropriate, he says, to argue from design (the eye for example) to cause (adaptation).

This then is the paradox to which Darwin and Design is directed. Darwin seems to have expelled design from biology, and yet we still go on using and seemingly needing this way of thinking. We still talk in terms appropriate to conscious intention, whether or not we believe in God. In biology we still use forward-looking language of a kind that would not be deemed appropriate in physics or chemistry. Why is this?

Ruse seems to be at his best when describing the history of philosophy—as long as that history pre-dates Charles Darwin. His book is worth reading if you want a good summary of the design argument up to 1859. From that point on things begin to fall apart because Ruse does not understand modern evolution and he does not understand the controversies over evolutionary theory that persist to this day. Consequently, all of his history from Darwin on is biased and wrong.

The essence of Ruse's argument is as follows. Life evolves by natural selection. This leads to species and characteristics that are well-adapted. These characteristics have the appearance of design because they are, in fact, designed by natural selection. Because we know that everything is an adaptation it's perfectly legitimate to look at a species or an organ and assume that it as been designed by natural selection. While this adaptationist program may seem teleological because it assumes a purpose, it is, in fact a very legitimate way to do biology because design is a fundamental part of biology.

There are times when one thinks that Michael Ruse must have slept through the last half of the twentieth century. Has he never heard of Gould & Lewontin and The spandrels of San Marco? Is he unaware of the controversy over the validity of the adaptationist program?

Yes and no. He's heard of the controversy but he just wasn't listening. Everyone else who has addressed this question recognizes that the Gould & Lewontin challenge is not going to go away. They attempt to deal with it—usually not very successfully.

To his credit, Ruse seems to have picked up on the rumors that something important was going on so he does mention the spandrels paper and the attack on the adaptationist program. It's right there on pages 234-239. Five pages on structural constraints as introduced by Gould & Lewontin in their famous 1979 paper. Structural constraints? Surely there's more to the argument than that? Yes, there is but Ruse can easily dismiss it,

The point is whether they [Gould & Lewontin] introduce a whole new dimension into the discussion, by showing that much in the organic world is fundamentally nonadaptive. Darwinians have failed to see this and still continue not to see it.

That's it. Ruse is blind to modern evolutionary theory and quite proud of it. According to Ruse everything is an adaptation and "Darwinism" and "evolution" are synonyms.

The rest of the five pages on Gould & Lewontin are no more enlightening. Lest you think I'm being too harsh on Ruse, I assure you I'm not. He really doesn't get it. There are two pages devoted to random genetic drift. Two pages! After acknowledging that drift can sometimes cause evolution he dismisses it out of hand with,

Over time, however, random drift would be expected to average out more smoothly than differences due to the ever-changing forces of selection. For this reason the hypothesis that most molecular difference is due to drift has not been well received. Time and time again, measurements have shown that molecular differences are not what we would expect were drift the sole or main cause of change. In fruit flies, we see how random drift was ruled out as a significant factor in changing levels of the Adh gene.(p. 201)

Having summarily dismissed all objections to the ubiquity of adaption, Ruse can defend the argument from design by invoking adaptation as the sole driving force of evolution. In a chapter on "Design as Metaphor" he outlines his version of the adaptationist program. It's not only appropriate to attribute design to living things but it's a very productive way of advancing scientific knowledge.

Organisms produced by natural selection, have adaptations, and these give the appearance of being designed. This is not a chance thing or a miracle. If organisms did not seem to be designed, they would not work and hence would not survive and reproduce. But organisms do work, they do seem to be designed, and hence the design metaphor, with all the values and forward-looking, causal perspective it entails, seems appropriate.(p. 276)

Critics of the adaptationist program—I am one—argue that it begs the question. When you see something in nature it is reasonable to assume that it arose by evolution. The question we want to answer is what kind of evolution gave rise to that particular characteristic?

Take the fact that some people can roll their tongue as a simple example. We know there is a genetic basis to tongue-rolling. Some people have the allele that allows it, and some don't. We want to know why tongue-rolling exists.

     Once you have the metaphor of design in play, then of course you can ask questions about borderline instances and extensions and so forth. The real question, though, is whether, in the first place, the metaphor itself is an appropriate one. The question is not whether metaphors should be used at all but whether the specific metaphor of design should be used to explain evolution.

     Darwinians argue strenuously that it must be used. Richard Dawkins speaks to precisely this issue, asking what job we expect an evolutionary theory to perform. ... Dawkins agrees with John Maynard Smith that the "main task of any theory of evolution is to explain adaptive complexity, i.e. to explain the same set of facts which Paley used as evidence of a Creator."
Michael Ruse p. 278If you are a modern evolutionary biologist then you are aware of several possibilities. It could be just an accident that has no great significance at all. Maybe tongue-rollers and non-tongue-rollers have an equal chance of leaving offspring and the alleles will be fixed or eliminated by random genetic drift. Or maybe one of these groups has a selective advantage. Maybe tongue-rollers are more successful at having children and that's why the allele persists in the population. Eventually everyone will be a tongue-roller because natural selection is operating.

If you are a committed adaptationist then you begin by assuming that the ability to roll your tongue is designed. Your task is then to explain how this design arose and you have only one choice—evolution by natural selection. Thus, your choice of the design metaphor has blinded you to the possibility that tongue-rolling may not be an adaptation at all. This is a very restrictive research program because the question pre-supposes the answer. In other words, by imposing design and purpose on the natural world—albeit natural and not divine purpose—Ruse and his colleagues are avoiding the very question they should be asking; namely, "is this an adaptation?" This bias leads to fanciful just-so stories as the adaptationists struggle to come up with imaginary ways of explaining the design that they think they see in nature.

Does Ruse have an answer to this objection? Yes he does,

The critic might respond that one has here a circular situation: Darwinians make searching for adaptation central to their program, and then when they find the adaptations they so fervently seek, they use them as support for Darwinism. But a better term than "circularity" might be "self-reinforcement." Darwinism is a successful theory—our scientific examples show that—and at the moment (and for the foreseeable future, whatever the qualifications) it is the only game in town, on its own merits. Fruit flies, dunnocks, dinosaurs, fig wasps—this is a theory on a roll. It has earned the right to set the agenda. (p. 280)

As far as I'm concerned this is dead wrong. Darwinism is not the only game in town and we've known that for almost fifty years. At the very least you have to consider fixation of alleles by random genetic drift. If this is how a character actually evolved then there is no design. The metaphor is inappropriate. The program is useless. (There are other non-Darwinian processes.)

The entire thrust of Ruse's argument for design and purpose in evolution is absolutely dependent on one critical assumption: that natural selection is the only significant mechanism of evolution. If this isn't true then his whole argument falls apart. It isn't true.

I accept Ruse's challenge when he says,

Of course, Lewontin and his school do not care for many of the findings of the adaptationists. But to say that we should not play the game at all, or that we should count all as equal, requires some persuasive arguments. Better than arguments would be examples. Let those who worry about explanatory adaptationism show their dunnnocks and dinosaurs and fig wasps. When they demonstrate that they can do science which explains and predicts without invoking adaptation even implicitly, then we can start taking their position seriously. (p. 281)

There are literally dozens of examples of non-adaptive evolution that have been widely discussed in the scientific literature. It is more than "silly" of Ruse to issue a challenge like this. It's just plain ignorant.

Scientists who study junk DNA, for example, are doing very legitimate science when they predict that junk DNA sequences will not be conserved between species. Scientists who study blood type in humans are doing real science when they test the null hypothesis by asking whether the alleles conform to the Hardy-Weinberg distribution. (They do, suggesting strongly that they are not under selection.) Scientists who study speciation in birds ask whether the founder effect is real. (It is, and this shows that morphological changes during speciation are not due to adaptation.) The late Stephen Jay Gould and his colleagues have done good science by developing theories of punctuated equilibria and species sorting without assuming that natural selection and adaptation are essential. Ruse needs to take their position seriously. Meanwhile Ruse has demonstrated that we don't need to take him seriously.

The entire field of molecular evolution is based largely on explanations and predictions that rely on random genetic drift of neutral alleles. As far as I know, the people who work in that field are good evolutionary biologists even though they don't assume design when constructing their phylogenies.

And lets not forget about one of Lewontin's favorite examples. The African rhinoceros has two horns while the Indian rhinoceros has only one. Why? If you accept the modern theory of evolution then your choices of explanation can range from adaptive to accidental. If you restrict yourself to Darwinism then you must assume design and your explanation has to invoke natural selection. Somehow you have to come up with ways to explain why African rhinos were better off with two horns while Indian rhinos were better off with only one.

Using the metaphor of design and purpose forces you to assume the answer to the very question you are asking. It forces you to reject known evolutionary mechanisms such as random genetic drift. This may be good philosophy but it's not good science.

Getting back to the title of the book. Is nature designed? Partly, but there are lots of things that don't look designed and are not the end product of natural selection. Our genome is a good example. It's more like a Rube Goldberg apparatus than a well-tuned machine. It is not particularly helpful to say that living things are designed, or even that they have the appearance of design. If we stop saying that everything is designed then we will be better prepared to consider other possibilities, like evolution by accident.

Species Diversity

 
Some of you might recall my series of postings last year on the top Science questions. One of them was What Causes Species Diversity?. This is an important unanswered question in evolutionary biology even if it's conflated with speciation. We don't really have a good handle on what causes speciation.

That doesn't mean that we are completely ignorant. There are several candidates that, singly or in combination, account for much of what we understand about speciation and diversity. I'd like to quote Richard Dawkins from Unweaving the Rainbow since, as an admitted adaptationist, his view carries much more weight than that of a pluralist. (The reason will become apparent.) Here's how Dawkins describes the problem ...

The standard neo-Darwinian view of the evolution of diversity is that a species splits into two when two populations become sufficiently unalike that they can no longer interbreed. Often the populations begin diverging when they chance to be geographically separated. The separation means that they no longer mix their genes sexually and this permits them to evolve in different directions. The divergent evolution might be driven by natural selection (which is likely to push in different direction because of different conditions in the two geographical areas). Or it might consist of random evolutionary drift (since the two populations are not genetically held together by sexual mixing, there is nothing to stop them drifting apart). In either case, when they have evolved sufficiently far apart that they no longer interbreed even if they were geographically united again, they are defined as belonging to separate species.

Either, or both, of the two main mechanisms of evolution—natural selection and random genetic drift—can lead to speciation and diversity.

One could also argue that diversity depends ultimately on mutation. In this case, the main role of natural selection and random genetic drift is to reduce diversity by eliminating unfit and neutral alleles.

This has always been similar to my understanding of speciation and diversity. I was surprised, therefore to learn that one of my colleagues at the University of Toronto, Spencer Barrett, doesn't think random genetic drift plays a role in speciation [see Darwinism at the ROM]. Barrett is one of the featured presenters in a video at the Darwin exhibit at the Royal Ontario Museum.

In a display on the evolution/creation controversy, I copied down the following statement ...

Darwin's Theory of Evolution by Natural Selection is the only scientific explanation for the spectacular diversity of life on Earth.

So, here's the question of the day. Do you agree with that statement? Do you agree that natural selection is the only scientific explanation of diversity? Spencer Barrett seems to agree. Richard Dawkins would not agree. What do you think?¹

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1. If you disagree with the statement then please try and explain why it is featured so prominently in the Darwin exhibit. Is this an example of framing, or ignorance?

Good Science Writers: Douglas J. Futuyma

 
Douglas J. Futuyma is Distinguished Professor in the Department of Ecology and Evolution at the State University of New York at Stony Brook [Douglas Futuyma]. He is best known for his textbooks on evolution, Evolutionary Biology, beginning with the first edition in 1979. The latest version is a shorter textbook entitled Evolution (2005).

Futuyma has also published a trade book on the evolution/creation controversy. The first edition of Science on Trial: The Case for Evolution was published in 1983 and the second edition was published in 1995. Since Futuyma is a professional scientist, he meets all the qualifications for inclusion in Richard Dawkins' book: The Oxford Book of Modern Science Writing. But he is not there.

Douglas Futuyma is a brilliant textbook author. This kind of science writing is not usually recognized, but it should be. Futuyma's ability to accurately explain complex ideas is head-and-shoulders above that of most other textbook authors—no matter what their subject. I've chosen two excerpts from Evolution (2005) to illustrate this ability. You may find them familiar—that's because they have been widely quoted and paraphrased to the point where they seem trivial. Let's not forget that it is Futuyma who first began to explain evolution in this manner.

What Is Evolution?
The word evolution comes from the Latin evolvere, "to unfold or unroll"—to reveal or manifest hidden potentialities. Today "evolution" has come to mean, simply, "change." It is sometimes used to describe changes in individual objects such as stars. Biological (or organic) evolution, however, is change in the properties of groups or organisms over the course of generations. The development or ONTOGENY, or individual organisms is not considered evolution: individual organisms do not evolve. Groups of organisms, which we may call populations, undergo descent with modification. Populations may become subdivided, so that several populations are derived from a common ancestral population. If different changes transpire in the several populations, the populations diverge.

The changes in populations that are considered evolutionary are those that are passed via the genetic material from one generation to the next. Biological evolution may be slight or substantial: it embraces everything from slight changes in the proportions of different forms of a gene within a population to the alterations that led from the earliest organism to dinosaurs, bees, oaks, and humans. (p. 2)

Good Science Writers

Good Science Writing
David Suzuki
Helena Curtis
David Raup
Niles Eldridge
Richard Lewontin
Steven Vogel
Jacques Monod
G. Brent Dalrymple
Eugenie Scott
Sean B. Carroll
Richard Dawkins

Evolution as Fact and Theory
In The Origin of Species, Darwin propounded two major hypotheses: that organisms have descended, with modification, from common ancestors; and that the chief cause of modification is natural selection acting on hereditary variation. Darwin provided abundant evidence for descent with modification, and hundreds of thousands of observations from paleontology, geographic distributions of species, comparative anatomy, embryology, genetics, biochemistry, and molecular biology have confirmed this hypothesis since Darwin's time. Thus the hypothesis of descent with modification from common ancestors has long had the status of a scientific fact.

The explanation of how modification occurs and how ancestors gave rise to diverse descendants constitutes the theory of evolution. 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 incomplete, for we do not yet know the causes of all of evolution, and some details may turn out to be wrong. But the main tenets of the theory are well supported, and most biologists accept them with confidence. (pp. 13-14)

I've also chosen an excerpt from Science on Trial (1995). In order to appreciate it, you will need a bit of background. The passage below comes from a chapter on "Chance and Mutation." The chapter opens with a brief description of a play by Tom Stoppard celled Rosencrantz and Guildenstern Are Dead. For those of you not intimately familiar with Shakespeare's Hamlet, Rosencrantz and Guildenstern are two minor characters who are tricked by Hamlet and end up sailing to England where, contrary to their expectations, they will be executed. Stoppard's play is about fate and inevitability.

But just as gravity and Brownian movement may both affect the motion of an airborne particle, chance and natural selection often work simultaneously, and certain evolutionary phenomena can be understood only if we take both into account. Many populations of houseflies throughout the world have evolved a resistance to DDT—an adaptation that has come about by natural selection. In some populations, however, the adaptation is provided by a dominant gene; in some by a recessive gene; in some by a number of genes, each with a small effect. The physiological mechanism by which the genes act also varies: flies can be resistant, for example, either by having developed an enzyme that degrades DDT or by having altered the cell membrane so that DDT is less able to penetrate the tissues. These are alternative adaptive mechanisms. Which one developed in a particular population must have depended on which mutations happened to be present in the population when it became exposed to DDT—and this is very much a matter of chance. Thus, chance initially determines what genetic variations will be acted on by natural selection to develop an adaptation.

When we extrapolate this principle of indeterminacy to long-term evolution, we can understand why different organisms have evolved different "solutions" to similar adaptive "problems." By chance, they had different genetic raw materials to work with. It is doubtless adaptive for male frogs to have a vocal sac that enables them to produce resonant calls that attract females. But whether a frog developed a single sac in the middle of the throat, as in the bullfrog, or a pair of sacs on either side, as in the leopard frog, may have been affected by what mutations first occurred by chance in the ancestor of each species.

If chance is a name for the unpredictable, them almost any historical event is affected by chance. Would Hamlet's mother, watching him stab Polonius through the arras, have predicted that this would be one in a chain of events leading to the death of Rosencrantz and Guildenstern? If you had been on the island of Mauritius in the mid-Tertiary, would you have predicted that the pigeons there would evolve into flightless dodos and then become extinct in the seventeenth century because they were easy prey for sailors? If you had seen a bipedal ape on the plains of Africa in the Pliocene, could you have predicted that this feature would prove crucial in the evolution of a larger brain and the development of human culture? Probably not; for in all such instances, the event that we recognize in hindsight as a "cause" might have been followed by other events leading to a different outcome. All of evolution, like all of history, seems to involve chance, in that very little of what has happened was determined from the beginning.

The mind that cannot abide uncertainty is troubled by the idea that the human species developed by "chance." But whether we evolved by chance or not depends on what the word means. We did not arise by a fortuitous aggregation of molecules, but rather by a nonrandom process—natural selection favoring some genes over others. But we are indeed a product of chance in that we were not predestined, from the beginning of the world, to come into existence. Like the extinction of the dodo, the death of Rosencrantz and Guildenstern, or the outbreak of World War I, we are a product of a history that might have been different. (pp. 146-147)

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Moran on Miller

Over at EVOLUTIONBLOG, Jason Rosenhouse has written a little essay criticizing my interpretation of Ken Miller's beliefs. [Moran on Miller]

I suggested that Miller's God can tweak evolution and John Rosenhouse replies,

I am not aware of any instance where Miller argued that God tweaks mutations to get what He wants. In fact, it seems to me that Miller's view of evolution is almost indistinguishable from that of Richard Dawkins. For example, in Finding Darwin's God Miller has nothing but praise for Dawkins' description of evolution in The Blind Watchmaker.

Miller lays out his case in Finding Darwin's God: A Scientist's Search for Common Ground between God and Evolution. Chapter 7 ("Beyond Materialism") sets the tone for the last half of the book. Here, Miller stresses the importance of the Heisenberg uncertainty principle (p.200). This is the basis for his statement that, materialism is wrong at its core (p.203).

Miller then goes on to his main point; namely, that ...

... the fact that mutation and variation are inherently unpredictable means that the course of evolution is, too. In other words, evolutionary history can turn on a very, very small dime—the quantum state of a single subatomic particle.

This is an important part of Miller's argument. Let's make sure everyone understands it. Miller is saying; (a) tiny changes can have profound effects, and (b) there is fundamentlal uncertainly at the subatomic level so we can never be sure of what caused something to happen. It's important for Miller's argument that evolution appear to be fundamentally a random process. I know from personal experience that Richard Dawkins does not agree.

The dénouement comes in Chapter 8 ("The Road Back Home"). The goal in that chapter is to find a way where God can be present and active in the world without being detectable by science. The solution is very ingenious,

Fortunately, in scientific terms, if there is a God, He has left Himself plenty of material to work with. To pick just one example, the indeterminate nature of quantum events would allow a clever and subtle God to influence events in way that are profound, but scientifically undetectable to us. Those events could include the appearance of mutations, the activation of individual neurons in the brain, and even the survival of individual cells and organsisms affected by the chance processes of radioactive decay. Chaos theory emphasizes the fact that enormous changes in physical systems can be brought about by unimaginably small changes in initial conditions; and this, too could serve as an undectable amplifier of divine action. (p.241)

So, God can guide evolution and perform miracles and we have no way of knowing it that he meddled. But meddle he does. That's an absolute requirement in Miller's religion.

Jason Rosenhouse continues,

It is likewise absurd to say that Miller's view of evolution is nearly indistinguishable from Behe's. Miller believes that God set up the initial conditions for making evolution possible, but then natural forces took over. He is quite clear in his book that the course of evolution was not foreordained by anything God did. This fact is crucial to Miller's view of Christian theology. He argues that a world in which God constantly intervenes, or one in which the course of evolution was foreordained by God, would also be a world that could not be viewed as truly separate from God Himself.

Miller's God has to perform miracles; that's an essential part of the Roman Catholic faith. What Miller is trying to do is explain how his God can do it while not conflicting with science. The passage that I just quoted is the answer. But let's be clear about one thing. Miller's religion is not deism, in spite of what you (John) might have thought.

Yes, it's true that Miller doesn't want a God who intervenes all the time. That's why he says that "God's miracles are not routine subversions of the laws of nature" (p.239). But that doesn't mean that miracles are forbidden—not by any reading of Miller than I can see. Instead, Miller argues that "when God does act in the world, He does so with care and subtlety."

Jason, the answering of prayer is another example of a God who is active in the present-day world. This is not consistent with your claim that Miller believes in a God who set up the initial conditions then stepped aside. Miller says,

... any traditional believer must agree that God is able to influence the thoughts and actions of individual beings. We pray for strength, we pray for patience, and we pray for understanding. Prayer is an element of faith, and bound within it is the conviction that God can affect us and those for whom we pray in positive ways.

That's not a deist God. That's not even the God of Michael Denton. At the risk of beating a dead horse, let's quote Miller once again to prove to you that he believes in an active God who intervenes in nature,

Remember, once again, that people of faith believe their God is active in the present world, where He works in concert with the naturalism of physics and chemistry. A God who achieves His will in the present by such means can hardly be threatened by the discovery that He might have worked the same way in the past.

According to Miller, the end result of evolution is to have "given the Creator exactly what He was looking for—a creature who would know Him and love Him ..." (p.239). Miller says that "... we can certainly see God's will emerging in the grand and improbable tree of life" (p.238). It's true, as you say, that Miller never explicitly states that God guided evolution. Instead, what he does is explain that there's a purpose behind the universe and that God is active in the world today and has been in the past. Miller then describes ways in which God could have undetectably guided things if He had wanted to, by fiddling with quantum indeterminacy. You are left to draw your own conclusions.

The most important difference between Behe and Miller is that Behe thinks you can actually detect God's handiwork while Miller thinks it is so well hidden that scientists can can never detect it. Miller recognizes it only through his faith.

Denis Noble writes about junk DNA

I have read Dance to the Tune of Life. It's a very confusing book for several reasons. Denis Noble has a very different perspective on evolution and what evolutionary theory needs to accomplish. He thinks that life is characterized by something he calls "Biological Relativity." I don't disagree. He also thinks that evolutionary theory needs to incorporate everything that has ever happened in the history of life. That's where we part company.

I'm working slowly on a book about genomes and junk DNA so I was anxious to see how Noble deals with that subject. I tend to judge the quality of books and articles by the way they interpret the controversy over junk DNA. Here's the first mention of junk DNA from page 89. He begins by saying that it's difficult to explain development and the diversity of tissues in multicellular organisms. He continues with,

What Is Evolutionary Theory? Futuyma vs Coyne

I've been under the impression that the distinction between the fact of evolution and evolutionary theory is not controversial—at least among evolutionary biologists. Ever since Gould, the point has been that the facts of evolution include things like common descent and the history of life on Earth. Evolutionary theory attempts to provide a mechanism that accounts for those fact and observations.

Richard Dawkins makes this clear in his book The Greatest Show on Earth (p. 17).

Biologists often make a distinction between the fact of evolution (all living things are cousins) and the theory of what drives it (they usually mean natural selection, and they may contrast it with rival theories such as Lamarck's theory of 'use and disuse' and 'the inheritance of acquired characteristics'). ... Nowadays it is no longer possible to dispute the fact of evolution itself—it has graduated to become a theorum or obviously supported fact—but it could still bedoubted (just) that natural selection is its major driving force.

The distinction is important. Things like common descent and the history of life are the facts that demonstrate evolution. Evolutionary theory offers a solid, widely-accepted, explanation of how evolution happens.

Douglas Futuyma has written one of the most respected textbooks on evolution. He agrees with this distinction—as do all other textbook authors that I know of. Here's what Futuyma says in Evolution 2nd ed. p. 4.

The explanation of how modification occurs and how ancestors gave rise to diverse descendants constitutes the theory of evolution. 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.

No doubt you're puzzled about the purpose of this posting. You are probably saying to yourself. "So what? We all know that, already."

Apparently, not all of us agree. In an otherwise excellent review of Richard Dawkin's book, Jerry Coyne says the following [see: The Improbability Pump].

Demonstrating the truth of natural selection is just one of Dawkins's aims, for the theory of evolution is composed of several more or less independent parts, which I like to describe in one longish sentence: "Life on earth evolved gradually, beginning with one primitive species; it then branched out over time, throwing off many new and diverse species--and the process producing the illusion of design in organisms is natural selection." This sentence constitutes a scientific theory, which is not just a guess but an informed statement about the general principles that explain many observations about nature.

I think that's very wrong. First, it's wrong because it states that the history of life is a theory. Second, it's wrong because it states that the "illusion of design" is part of modern evolutionary theory (it isn't). Third, it's wrong because it only mentions natural selection and modern evolutionary theory is much more than that.

I hope this was just an attempt to (over-)simplify evolution for the readers of The Nation. In that case it might be (just) excusable. But I can't wait until the creationists get a hold of this review. They'll be delighted to learn that, according to Jerry Coyne, the gradual descent and diversification of life is only a theory.

They'll also be happy to learn from a prominent evolutionary biologist that design is part of modern evolutionary theory.

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Jason Rosenhouse Doesn't Understand Pluralists

 
Jason Rosenhouse has posted some comments on a recent book review by Richard Lewontin. In that book review, Lewontin—who along with Gould is the co-author of the spandrels paper—questions the emphasis on natural selection and the use pf "Darwinism" as a synonym for evolution. Read Lewontin on Darwin to see what Jason thinks of the book review.

I want to focus on a specific question that Jason Rosenhouse asks.

I've never really understood what it is exactly that anti-selectionists are complaining about. If they agree that complex adapations arise as the result of gradual accretion mediated by natural selection, then I fail to see how they are really so different from people like Richard Dawkins or Daniel Dennett (two people often described as being beknighted uber-selectionists). If they do not agree then I would like to hear their proposed alternative mechanism.

The original paper by Gould and Lewontin, The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme, explains the problem very well. The authors begin their criticism with ...

We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm. It is rooted in a notion popularized by A.R. Wallace and A. Weismann, (but not, as we shall see, by Darwin) toward the end of the nineteenth century: the near omnipotence of natural selection in forging organic design and fashioning the best among possible worlds. This programme regards natural selection as so powerful and the constraints upon it so few that direct production of adaptation through its operation becomes the primary cause of nearly all organic form, function, and behavior. Constraints upon the pervasive power of natural selection are recognized of course (phyletic inertia primarily among them, although immediate architectural constraints, as discussed in the last section, are rarely acknowledged). But they are usually dismissed as unimportant or else, and more frustratingly, simply acknowledged and then not taken to heart and invoked.

The anti-selectionists—I am one—do not question the fact that adaptations are produced by natural selection. What we question is whether everything in evolution is an adaptation. We question those who think that "evolution" and "natural selection" are synonyms. And since "Darwinism" is equivalent to evolution by natural selection we question whether evolution is the same as Darwinism.

We pluralists like to point out that much of evolution is due to random genetic drift. Since Darwin's name is not associated with the theory of evolution by random genetic drift, it is inappropriate to say that all of evolution is Darwinist.

It's not that complicated. It was all explained in the classic spandrels paper published 30 years ago. Complex biological structures may be due entirely to adaptation, or they may be mostly an accident that's arisen by random genetic drift, or they may be due to combinations of drift and selection.

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An Adaptationist in Piazza San Marco

John Wilkins of Evolving Thoughts is currently in Venice, Italy. He has just visited the Basilica San Marco (St. Mark's Basilica) according to What I am doing on my holidays….

This visit is significant since the Spandrels of San Marco are famous in evolutionary biology. They are part of the attack on adaptationism launched in 1979 by Gould and Lewontin. This is a paper that every student of evolution should read. Here's an online version: The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.

John has been struggling with adaptationism for almost fifteen years. When he first began studying evolutionary biology he, like many others, was unaware of the importance of random genetic drift and other anti-adaptationist perspectives. He certainly didn't know that random genetic drift is by far the dominant mechanism of evolution in terms of frequency of allele fixation. Over time John has developed an unusual perspective on adaptionism—one that I don't really understand.

Here's how he explains it in his latest posting ...

This is interesting, I think, in the context of Gould’s and Lewontin’s paper. It shows that claims of things being adaptive or not depend crucially on what one counts as the “task” of a structure. Since I think that everything is subjected to selection pressure at all times (sometimes not enough to overcome the noise of statistical properties), counting what is, and what isn’t, adaptive is a bit of a personal call, in the absence of access to the historical processes of particular traits. I am becoming more of an adaptationist these days.

The idea that many alleles might be slightly beneficial or slightly detrimental isn't very controversial. But that's not what John is saying. As I understand him, he's saying there can be no such thing as a truly neutral allele. He seems to be saying that anyone who believes otherwise is making a "personal call." A personal call that he believes is wrong since he thinks (i.e. his personal call) that everything is subject to natural selection.

He's also making a somewhat trivial point that doesn't contribute to the debate, as far as I'm concerned. Many alleles that are slightly beneficial are lost due to random genetic drift and many alleles that are slightly deleterious are fixed by random genetic drift. To me, that says that adaptationism can't explain all of evolutionary biology. To call yourself an adaptationist while knowing that slightly deleterious alleles can be fixed by random genetic drift seems somewhat unsatisfying.

John has a paper in the latest issue of Biology and Philosophy, an issue devoted to Adaptationism. It's not a very enlightening issue, from my perspective. The main problem with adaptationism isn't that it can't explain adaptation and it isn't that some just-so stories are wrong. The main problem is that adaptationists don't even consider any other alternatives to fixation by natural selection. Everything, especially everything with a visible phenotype, is automatically assumed to be adaptive and the arguments proceed from there.

One of the papers I liked was Seven Types of Adaptationism by Tim Lewens (Lewens, 2009). The seven types are:

A Empirical adaptationisms

1. Pan-selectionism–natural selection is the most significant of the evolutionary forces that act on populations.
2. Good-designism–evolutionary processes tend to result in organisms with suites of well-designed traits. Most lineages are highly evolvable.
3. Gradualism–adaptation is always the result of selection acting on gradual
variation.

B Methodological Adaptationisms

4. Weak heuristic adaptationism–those traits that are adaptations are likely to be correctly recognised as such only if we begin by assuming that all traits are adaptations.
5. Strong heuristic adaptationism–only by beginning to think of traits as adaptations can we uncover their true status, whether they are adaptations or not.

C Disciplinary Adaptationism

6. Explanatory adaptationism–an evolutionary biologist’s proper business is the study of adaptations.

D Epistemological Adaptationism

7. Epistemological optimism–investigators have access to the data that reliably discriminate between conflicting evolutionary hypotheses.

There are problems with all seven forms of adaptationism but the nice thing about Lewens' paper is that he effectively refutes #4, #5, and #7. In the case of methodological adaptationism it's just not true that the default assumption has to be adaptation. Evolutionary biology will be just as productive in the long run if drift is the default assumption and adaptation has to be proven.

In explanatory adaptationism, the assumption is that all of the interesting parts of evolution are adaptations and fixation of alleles by random genetic drift is so boring that it might as well not even be evolution. This is the stance taken by many adaptationists, like Richard Dawkins. As you might imagine, it doesn't take much effort to refute that kind of argument. One's personal opinion about what's interesting and what's not interesting should not play a role in determining how everyone else should go about studying evolution.

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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.

Lewens, T. (2009) Seven types of adaptionism. Biol. Philos. 24:161–182. [doi: 10.1007/s10539-008-9145-7]

The Mutationism Myth, IV: Mendelian Heterodoxies

This is the sixth 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.

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.

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The Curious Disconnect

Last month, we debunked the Mutationism Myth and learned why the discovery of genetics in 1900 led "Mendelians" to reject Darwin's view. These same Mendelians went on to lay the foundations of a genetics-based view of evolution, during a period of rapid innovation from 1900 to 1915. But this begs another question: if the Mendelians invented the 20th-century consensus, and just left it to others to work out the math, why aren't they lauded as "founders" of modern neo-Darwinism, instead of being derided as fools? We'll find out in part 4 (today), and part 5, here on on The Curious Disconnect (credits).

The Mutationism Myth, part 4. Mendelian Heterodoxies

The reader who has been following our story so far may be baffled. As we found out in part 3, the Mendelians understood how to conceptualize a population as a dynamic system of allele and genotype frequencies (the Bateson-Saunders equilibrium), how to see evolutionary change as a probabilistic 2-step process of the introduction and acceptance-or-rejection of mutations, and how to think about selection-driven changes in a quantitative trait.

Why don't the Mendelians get credit for laying the foundations of the 20th-century consensus?

As we will learn today and in part 5, the Mendelian view is not the 20th-century "neo-Darwinian" consensus. The Mendelians combined genetics with selection. By contrast, the 20th-century consensus combines genetics with Darwinism, i.e., the Modern Synthesis invokes the principles of genetics to prop up 19-century doctrines of Darwin and his followers, such as natura non facit salta, the creativity of selection, the idea of evolution as a process of adaptive adjustment initiated by changed conditions, and the notion that the course or direction of evolution is determined by selection but not by "random" variation.

When I mock the Modern Synthesis for its Darwinian excesses, I don't want to give the impression that its wrong for a theory₁ to go beyond what is demanded by the facts. All theories₁ must go beyond the facts, taking risks. While most theories, it seems, take risks in the service of conceptual simplicity, the Modern Synthesis takes risks in the service of 19th-century Darwinian doctrines. On the basis of these commitments, e.g., its rejection of the "lucky mutant" view necessary to understand molecular evolution, the Modern Synthesis later failed.

But that's getting ahead of ourselves. Our task right now is to begin sorting out why the Modern Synthesis is Darwinian, while the Mendelian view it replaced was not.

"Mutationism" vs the Mendelian "view"

My understanding of the evolutionary views of "Mendelians" is based on the works of Bateson (1894, 1900, 1902, 1909), Johannsen (1903, 1909), de Vries (1905), Morgan (1903, 1916, 1925, 1932), Punnett (1911), Vavilov (1922), Shull (1936) and, with some reservations, Goldschmidt (1940). Every time I research the Mendelians, I find new material and revise my views, e.g., I am resolving more and more to avoid the label "mutationism", which I see increasingly as a pejorative term preferred by opponents rather than supporters.

I also have come to understand more confidently that, while the Mendelians had much to say about evolution— indeed, many of them were motivated to study heredity precisely because of their interest in evolution—, they didn't have a unified "view". With the exception of de Vries, the Mendelians did not propose what we would call "a theory of evolution", i.e., a Grand Unified Theory₁ of Evolution (GUTE) that purports to be comprehensive. Instead they argued that we need to rethink how evolution works, and follow the implications of genetics wherever they led— typically away from a more Darwinian view emphasizing infinitesimalism, determinism, and selective control.

Thus, while "Mendelism" (in contrast to "mutationism") does not sound like a very good name for a theory of evolution, that's ok, because it's not: Mendelism is a theory of genetics, and the "Mendelian view of evolution" is simply what the early Mendelian geneticists thought about evolution.

Recognizing the lack of a Mendelian GUTE helps us to appreciate more fully the role of the "Modern Synthesis" in the development of evolutionary thinking, and in the Mutationism Story. In the 19th century, before the discovery of genetics, scientists divided their allegiance among multiple GUTEs, most importantly, Darwinism and Lamarckism. By 1910, it was clear to leading thinkers that genetics had undermined all 19th-century GUTEs (including de Vries's "MutationsTheorie" ¹). The geneticists (for whatever reason) did not fill this gap by proposing a new GUTE. Thus, while the Mendelian era from 1900 to 1930 was not a stagnant period, it may be seen as a GUTE-less period that ended with the rise of the Modern Synthesis.²

Initiative

The view that events of mutation initiate evolutionary change contrasts with the view that evolutionary change is a series of adjustments or responses to external stimuli, as in the views of Buffon or Darwin. Punnett writes:

"With the advent of heredity as a definite science we have been led to revise our views as to the nature of variation, and consequently in some respects as to the trend of evolution. Heritable variation has a definite basis in the gamete, and it is to the gamete, therefore, not to the individual, that we must look for the initiation of this process. Somewhere or other in the course of their production is added or removed the factor upon whose removal or addition the new variation owes its existence." (p. 141)

Variation (mutation) is the locale of evolutionary initiative, to the extent that both 1) the possibilities or directions of future evolutionary change are established at the moment of the mutation (i.e., mutation as a source of creativity or direction, as addressed below); and 2) the dynamics of evolutionary change depend on the times of appearance of mutations. This second sense depends somewhat on the "new mutations" conception of evolution as a 2-step process of the introduction of a variant followed by its acceptance or rejection.

In this view, one may expect that the dynamics of evolution (adaptive or not) will depend on mutation rates. In fact, the Mendelians sometimes recognized this kinetic dependence, as when Shull (1936, p. 140) argues, "a gene produced twice by mutation has twice as good a chance to survive as if produced only once" (see also Morgan 1925, p. 142). This non-Darwinian idea that propensities of variation could make an evolutionary change more or less likely was not a new thought (indeed it was understood as the potential mechanistic basis of "orthogenesis"), but now it could be given a more precise interpretation.

The architects of the Modern Synthesis later ridiculed what they called the "lucky mutant" view (Mayr 1963, p. 101), but it was hardly an unsophisticated appeal to chance, as we saw in part 3 with the quotation illustrating Morgan's stunning grasp of the probability of acceptance of new mutations. Punnett made a similar statement in his 1911 book (online source):

"The new variation springs into being by a sudden step, not by a process of gradual and almost imperceptible augmentation. It is not continuous but discontinuous, because it is based upon the presence or absence of some definite factor or factors— upon discontinuity in the gametes from which it sprang. Once formed, its continued existence is subject to the arbitrament of natural selection. If of value in the struggle for existence[,] natural selection will decide that those who possess it shall have a better chance of survival and of leaving offspring than those who do not possess it. If it is harmful to the individual[,] natural selection will soon bring about its elimination. But if the new variation is neither harmful nor useful[,] there seems no reason why it should not persist."

By rejecting this component of the Mendelian view of evolution, the Modern Synthesis disallowed a direct link between the rate of mutation and the rate of evolution, making the theory incompatible with the results of studies of "molecular evolution" that began to emerge a half-century after the insights of Punnett and Morgan.

Discontinuity

To understand the issue of discontinuity or discreteness, again we must distinguish 2 senses. In the passage quoted above from Punnett, it's clear that Punnett is talking about what we might call a "mechanistically" discontinuous change in the sense that the mutant factor comes into existence at a specific point in time, due to an event of mutation, rather than gradually, due to an ongoing process of "imperceptible augmentation".

Mayr and others frequently misinterpret the Mendelian commitment to mechanistic discontinuity as a commitment to dramatic phenotypic saltations, but this is a different issue entirely.

In fact, the Mendelians entertained a range of views on the sizes of evolutionary changes important in evolution, excluding only the Darwinian extreme of relying wholly on "insensible" or "infinitesimal" changes. De Vries adopted an antithetical position emphasizing dramatic changes that create new species (with intra-specific variation and selection playing only a minor role). Bateson challenged

"the crude belief that living beings are plastic conglomerates of miscellaneous attributes . . . and that by Variation any of these attributes may be subtracted or any other attribute added in indefinite proportion" (Bateson 1894, p. 80)

Bateson's view was that, if we wish to understand evolution, we must move beyond speculative reconstructions of past events based on assuming variability and then assuming some adaptive rationale, and start studying what variations actually tend to occur. In pursuit of a less speculative approach to evolution, Bateson traveled the world to catalog 886 cases of discontinuous variation, published in his volume "Materials for the Study of Variation" (Bateson 1894); he planned a second volume on continuous variation but never completed it. Morgan argued that "even the smallest changes that add to or subtract from a part in the smallest measurable degree" may arise by mutation, and these are "the most probable variants that make a theory of evolution possible" (Morgan 1925, p. 129).

Both senses of "discontinuity" represent departures from late-19th-century and 20th-century versions of Darwinism. The mechanistically discretized view of the mutationists clashed with the incipient Modern Synthesis view in Punnett's (1930) Nature review of Fisher's The Genetical Theory of Natural Selection:

Throughout the book one gets the impression that Dr. Fisher views the evolutionary process as a very gradual, almost impalpable one, in spite of the discontinuous basis upon which it works. Perhaps this is because he regards a given population as an entity with its own peculiar properties as such, whereas for the geneticist it is a collection of individuals.

Much of the neo-Darwinian antipathy to "mutationists" was based on a negative reaction to the "saltationism" of de Vries and Goldschmidt, even though their views do not represent a shared commitment of the Mendelians. However, the mere fact that the Mendelians allowed some large changes distinguished them from the Darwinian view that "Natural selection can act only by the preservation and accumulation of infinitesimally small inherited modifications" (Darwin, Ch. 4, Origin of Species).

Creativity

The mutationists held that "the function of natural selection is selection and not creation. It has nothing to do with the formation of new variation" (Punnett 1911). Likewise, Bateson (1909) writes:

"we must relegate Selection to its proper place. Selection permits the viable to continue and decides that the nonviable shall perish; just as the temperature of our atmosphere decides that no liquid carbon shall be found on the face of the earth: but we do not suppose that the form of the diamond has been gradually achieved by a process of Selection. So again, as the course of descent branches in the successive generations, Selection determines along which branch Evolution shall proceed, but it does not decide what novelties that branch shall bring forth."

The creativity of mutation or, more properly, of mutation-and-altered-development (Stoltzfus, 2006), may be illustrated (in the extreme case) by Goldschmidt's concept of a "macromutation", akin to Galton's concept (invoked repeatedly by Bateson, 1894) of a shift between "positions of organic stability". If a variant toad arises with fully formed eyes in the roof of its mouth, such that it must open its mouth to see— as in the actual toad pictured on p. 97 of Dawkins (1996)— this is an extreme yet coordinated change, and a "macromutation" if it is heritable. If such a variant supplants the parental form or becomes a separate species, this is a non-Darwinian, saltational change in which creativity is due largely to mutation-and-altered-development. In the case of less dramatic transformations, the creative role of mutation-and-altered-development is correspondingly less dramatic.

In spite of Goldschmidt's notorious belief that distinctive phenotypic transformations suggested major genetic reorganizations ("systemic mutations"), he insisted that the complexity of the underlying genetic change is not the decisive issue:

It does not make any difference whether a single macroevolutionary step is caused by a major change within the chromosomal pattern, [that is,] a systemic mutation, or by a special kind of gene mutation with generalized effect, if such is imaginable. The decisive point is the single change which affects the entire reaction system of the developing organism simultaneously, as opposed to a slow accumulation of small additive changes. (Goldschmidt 1940, p. 251)

The claim that selection is creative is one of the key claims of Darwinism, advanced and defended by supporters of Darwinism, and rejected by its critics, as Gould (1977) documents extensively. We see this argument arising again and again up to the present day, e.g., the authors of a recent "evo-devo" book echo the century-old rhetoric of Mendelians, claiming that selection is not creative and is merely a "sieve" (Kirschner and Gerhardt, 2005), and in response (in the Nature review of this book), a dyed-in-the-wool Darwinist defends the ancient orthodoxy that selection is creative (Charlesworth, 2005). Later on, we will devote an entire post (probably more than one) to the Darwinian doctrine of selective creativity, and its relation to the Darwinian doctrine known as "gradualism".

Directionality

On a one-dimensional scale of fitness or adaptedness, every change is either "up" (beneficial) or "down" (deleterious), but in a multi-dimensional space of phenotypes, every change has a distinctive direction.

Punnett invoked mutation as a source of direction in considering features such as lepidopteran wing patterns (Punnett 1911, p. 145). A more typical statement was to draw a contrast with the views of Weissman, Fisher, and others who imagine variation in all directions. For instance, in the book review cited earlier, Punnett (1930) chides Fisher for denying to mutations "any importance in determining the direction of evolutionary change"; likewise Shull takes aim at Fisher's view:

"To assert, as Fisher does, that mutation has nothing to do with the direction of evolution is like assuming that a tetrahedron may fall, at different times, with ten or a hundred points uppermost. The ten points and ten opposite sides to fall upon do not exist. How great a restriction is placed upon the course of evolution by the inability of genes to mutate in certain ways it is impossible to tell; but it may easily be much greater than any of us suppose." (Shull, 1936, p. 448)

A clearer Mendelian concept of the influence of mutation emerges in regard to parallel evolution, which was assumed to indicate non-random tendencies of variation, since "it strains one's faith in the laws of chance to imagine that identical changes should crop out again and again if the possibilities are endless and the probabilities equal" (Shull 1935, p. 448). Vavilov noted that the same varieties or polymorphisms often occur in parallel, even in distantly related species in the same genus or family, and he argued for a causal role of this "law of homologous variation" (Vavilov 1922) in parallel evolution. As an example, Vavilov reports that lentils (Ervum lens), a food crop, and vetch (Vicia sativa), a weed, have many homologous variations, and notes that vetches sometimes mimic lentils so closely in cultivated fields that their seeds cannot be separated by mechanical sorters:

the role of natural selection in this case is quite clear. Man unconsciously, year after year, by his sorting machines separated varieties of vetches similar to lentils in size and form of seeds, and ripening simultaneously with lentils. The same varieties certainly existed long before selection itself, and the appearance of their series, irrespective of any selection, was in accordance with the laws of variation. (Vavilov 1922, p. 85)

Darwin preceded Vavilov in recognizing a principle of "analogous variation" due to a similar "inherited constitution", but denied it any influence on evolutionary change:

But characters thus gained [by analogous variation] would probably be of an unimportant nature, for the presence of all important characters will be governed by natural selection, in accordance with the diverse habits of the species, and will not be left to the mutual action of the conditions of life and of a similar inherited constitution. (ch. 5, Darwin 1859)

That is, while we might recognize a kind of dualism in Darwin's view, in the sense that both fluctuation and selection are required for change as opposed to non-change, Darwin insists that selection "governs" the course of evolution, over-ruling variation. Darwin's followers, likewise, emphasize that selection, while not sufficient to cause change by itself, is the proper cause of the manner of change (that is, its directionality, dynamics, creativity, and so on). Darwin's followers have an ideological commitment to giving selection a power to control or dominate "random" mutation, and a commitment to denying internal causes of direction in evolution (if you have these commitments, you are probably a Darwinian; if you don't, you are not— or maybe you're just confused). The Mendelians did not share these ideological commitments.

Nonetheless, the Mendelians were a long way, as we still are, from having a clear view of this issue. Shull once remarked "What the world most needs, then, is not a good five-cent cigar, but a workable— and correct— theory of orthogenesis" (p. 449), "orthogenesis" being the idea of a trend or direction due to intrinsic tendencies of variation. The Mendelians did not develop such a theory. In spite of knowing that some variations occur more often than others, they often spoke as though any conceivable variation were either possible or impossible, which I see— and I see it almost everywhere— as a sign of immature thinking on this topic.

Of course, we are not much better off today. The evo-devo field clearly needs an idea of developmental tendencies in variation as a source of direction, and leading thinkers have called (vaguely) for such an idea for 30 years, but the evo-devo field still has no theory and instead is schlepping around its clunky old "toolbox" metaphor. Apparently, this toolbox contains the tools that selection uses to build structures, revealing that evo-devoists remain Darwinians who personify selection as a craftsman. Elsewhere (Stoltzfus, 2006; Stoltzfus and Yampolsky, 2009; online source), I have argued that we manifestly need a causal theory of orthogenesis, linking tendencies of variation to tendencies of evolution, and I have outlined the conceptual and mechanistic basis for such a theory, including population-genetics modeling.

In a series of later posts, we will take up the issue of "source laws and consequence laws" of variation, i.e., source laws governing the emergence of variation, and consequence laws governing its influence on evolutionary change.

Synopsis

Upon the discovery of genetics in 1900, a new breed of scientists rejected Darwin's theory and began developing a new understanding of evolutionary change based on Mendelian principles. They combined genetics with Darwin's principle of selection, but departed from Darwin's view in arguing that evolutionary change is not composed entirely of infinitesimal increments, and in representing mutation as a source of discontinuity, directionality, creativity and initiative.

Yet, somehow, "Darwinism" returned in the form of the Modern Synthesis. This new view included all the principles of Mendelian genetics, yet rejected all the non-Darwinian innovations of the Mendelians. The restoration of Darwinism in the Modern Synthesis— an accomplishment based more on rhetorical sleight-of-hand than on population genetics theory— will be our topic next time.

References

Bateson, W. 1894. Materials for the Study of Variation, Treated with Especial Regard to Discontinuity in the Origin of Species. Macmillan, London.

Bateson, W. 1900. Problems of Heredity as a Subject for Horticultural Investigation. Journal of the Royal Horticultural Society 25:54-61.

Bateson, W. 1902. Mendel's Principles of Heredity: A Defense. Cambridge University Press, Cambridge.

Bateson, W. 1909. Heredity and Variation in Modern Light. Pp. 85-101 in A. C. Seward, ed. Darwin and Modern Science: Essays in Commemoration of the Centenary of the Birgh of Charles Darwin and of the Fiftieth Anniversary of the publication of the Origin of Species. Cambridge, London.

Bateson, W., and E. R. Saunders. 1902. Experimental Studies in the Physiology of Heredity. Reports to the Evolution Committee. Royal Society.

Charlesworth, B. 2005. On the Origins of Novelty and Variation. Science 310:1619-1620.

Dawkins, R. 1996. Climbing Mount Improbable. W.W. Norton and Company, New York.

De Vries, H. 1905. Species and Varieties: Their Origin by Mutation. The Open Court Publishing Company, Chicago.

Goldschmidt, R. 1940. The Material Basis of Evolution. Yale University Press, New Haven.

Gould, S. J. 1977. Ever Since Darwin. W.W. Norton & Co., New York.

Kirschner, M. W., and J. C. Gerhart. 2005. The Plausibility of Life: Resolving Darwin's Dilemma. Yale University Press, New Haven.

Johannsen, W. L. 1903. Erblichkeit in Populationen und in reinen Linien. Gustav Fischer, Jena.

Mayr, E. 1963. Animal Species and Evolution. Harvard University Press, Cambridge, Massachusetts.

Morgan, T. H. 1903. Evolution and Adaptation. Macmillan, New York.

Morgan, T. H. 1916. A Critique of the Theory of Evolution. Princeton University Press, Princeton, NJ.

Morgan, T. H. 1925. Evolution and Genetics. Princeton University Press, Princeton.

Morgan, T. H. 1932. The Scientific Basis of Evolution. W.W. Norton & Co., New York.

Punnett, R. C. 1911. Mendelism. MacMillan.

Punnett, R. C. 1915. Mimicry in Butterflies.

Punnett, R. C. 1930. Genetics, Mathematics, and Natural Selection. Nature 126:595-597.

Shull, A. F. 1936. Evolution. McGraw-Hill, New York.

Stoltzfus, A. 2006. Mutationism and the Dual Causation of Evolutionary Change. Evol Dev 8:304-317.

Stoltzfus, A., and L. Y. Yampolsky. 2009. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered 100:637-647.

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

Footnotes

¹ Although de Vries continued to promote his "MutationsTheorie" for some years after 1900, it actually was a 19th-century theory of species-selection based on his work on Oenothera varieties, not on his work as one of the 3 re-discoverers of Mendel's principles.
² The perceived need for a dominant GUTE, and the ideological immunity that develops around a dominant GUTE, are issues that we will address in a future post.

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_myth4 (Arlin Stoltzfus, ©2010)

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