Do Some IDiots Actually Question the Existence of Natural Selection?

Paul Nelson has been challenging the pervasiveness of adaptationism by pointing out that many evolutionary biologists promte nonadaptive evolution. See the discussion and comments on Jerry Coyne's blog website: A Marshall McLuhan moment with creationist Paul Nelson. Nelson has been accused, falsely, of claiming that some evolutionary biologists deny that natural selection is an important mechanism in evolution.

Paul Nelson doesn't deny that natural selection is a real phenomenon. He may be an IDiot (and a YEC) but he's not THAT stupid. On the other hand, one didn't have to wait too long before getting confirmation that some other IDiots really are THAT stupid.

And guess what? They are allowed to post on the main Discovery Institute blog, Evolution News & Views (sic)!!! You have to read How "Real" Is Natural Selection? by Tom Bethell ... otherwise you'd never believe me.

Here's what Tom Bethell says about natural selection.

Tomoko Ohta and Nearly Neutral Theory

There's an interview with Tomoko Ohta in the August 21, 2012 issue of Current Biology: Tomoko Ohta.

You should know who she is but in case you don't, here's part of the brief bio ...

In 1973, she presented her first major paper entitled ‘Slightly deleterious mutant substitutions in evolution’. This theory was an expansion of Kimura's ‘neutral theory’, which Ohta called the ‘nearly neutral theory’ of molecular evolution. Her theory emphasizes the importance of interaction of drift and weak selection, and hence the role of slightly deleterious mutations in molecular evolution. With the accumulation of genome data, some of the predictions of the nearly neutral theory have been verified. The theory also provides a mechanism for the evolution of complex systems. Her other subject is to clarify the mechanisms of evolution and variation of multigene families. She has received several honors, including the foreign membership of the National Academy of Sciences, USA and Person of Cultural Merit, Japan.

It's very important to understand the essence of Nearly Neutral Theory since it explains the relationship between fitness and population size. Everyone needs to understand that Ohta demonstrated how slightly deleterious alleles can be fixed in a population. Her work showed that an allele can become effectively neutral in small populations even though it may actually lower the fitness of an individual. It's a way of explaining the limits of natural selection and of extending the Neutral Theory of Kimura.

She describes what happened when she joined Kimura's group at Tokyo.

At that time, Kimura was thinking of combining the theory of stochastic population genetics, the field he had been working on, with biochemical data on the nature of the genetic material. He proposed his now famous ‘neutral theory of molecular evolution’ in 1968. The ‘neutral theory’ proposed that most evolutionary changes at the molecular level were caused by random genetic drift rather than by natural selection. Note that the neutral theory classifies new mutations as deleterious, neutral, and advantageous. Under this classification, the rate of mutant substitutions in evolution can be formulated by the stochastic theory of population genetics. Kimura's theory was simple and elegant, yet I was not quite satisfied with it, because I thought that natural selection was not as simple as the mutant classification the neutral theory indicated, and that there would be border-line mutations with very small effects between the classes. I thus went ahead and proposed the nearly neutral theory of molecular evolution in 1973. The theory was not simple, and much more complicated, but to me, more realistic, and I have been working on this problem ever since.

This has nothing to do with Darwinism even though it's a fundamental part of modern evolutionary theory. You can't have an intelligent discussion about genome evolution, adaptationism, molecular evolution, or junk DNA without a firm grasp of Nearly Neutral Theory.

It's a shame there's no Nobel Prize for evolution.

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Michael Lynch on Evo-Devo

Michael Lynch had some cogent (and provocative, and true) words on adaptationism in his book The Origins of Genome Architectue [Michael Lynch on Adaptationism].

Here's what he has to say about evo-devo.

Consider the steady stream of recent books by authors striving to define a new field called evolutionary developmental biology (e.g., Arthur 1997; Gerhart and Kirschner 1997; Davidson 2001, 2006; Carrol et al. 2001; West-Eberhard 2003; Carrol 2005a; Kirschner and Gerhart 2005). The plots of all these books are similar: first, it is claimed that observations from developmental biology demonstrate major inadequacies in current evolutionary theory, and then a new view of evolution that eliminates many of the central shortcomings of the field is promised. Developmental biologists are correct in pointing out that evolutionary theory has not yet specifically connected genotype to phenotype's in a molecular/cell biological sense. However, extraordinary claims call for extraordinary evidence, and none of these treatises provide any formal example of the fundamental inability of evolutionary theory to explain patterns of morphological diversity. Those who argue that microevolutionary theory has made no contributions to our understanding of the evolution of form may wish to consult the substantial body of quantitative genetics literature on multivariant evolution. Such work is by no means fully satisfactory, as it is couched in terms of statistics (variances and covariances) rather than the molecular features of individual genes, but a more precise evolutionary framework for linking genes and morphology not be possible until a critical mass of generalities on the matter has emerged at the molecular, cellular and developmental levels.

For the vast majority of biologists, evolution is nothing more than natural selection. This view reduces the study of evolution to the simple documentation of differences between species, proclamation of a belief in Darwin, and concoction of a superficially reasonable tale of adopting the divergence (...). A common stance in cellular and developmental biology is that the elucidation of differences in molecular genetic pathways between two species (usually very distant species) completes the evolutionary story. No need to dig any deeper—because natural selection surely produce the end products, the population genetic details do not matter. In individual cases, this type of informal thinking may do little harm, but in the long-run it undermines the very scientific basis of with the evolutionary biology.

There are two fundamental issues here. First, the notion that interspecific differences at the molecular level reveal the mechanism of evolution ignores the fundamental distinction between the outcome of evolution and the events that lead to such changes. For example, although most animal developmental biologists argue that it was shocking to discover that the development of all animals is based on modifications of the same sets of ancient genes, many evolutionary biologists regard this view with some surprise. It is, of course, easy to criticize based on 20/20 hindsight, but we have known for decades that all eukaryotes share most of the same genes for transcription, translation, replication, nutrient uptake, core metabolism, cytoskeletal structure, and so forth. Why would we expect anything different for development? Although knowing that HOX genes play a central role in the development of all animals provides insights into the genetic scaffold from which body plans are built, it does not advance our knowledge of the evolutionary process much beyond noting that all vertebrates share a heritage of calcified skeletons. It need not even tell us that such genes were involved in the initial stages of differentiation (Alonso and Wilkins 2005). A vast chasm of stepwise (and partially overlapping) changes may separate today's products of evolution, and understanding those steps is what distinguishes evolutionary biology from comparative biology.

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Michael Lynch on Adaptationism

I've been studying Michael Lynch's book The origins of Genome Architecture. It's a marvelous book, I wish everyone interested in evolution could read it and understand it.

The last chapter is very interesting. Lynch talks about the importance of understanding modern population genetics.

... I will comment on the current state of affairs in evolutionary biology, particularly the perception of softness in the field that has been encouraged by the propagation of evolutionary ideas by those with few intentions of being confined by the constraints of prior knowledge.

He also talks about adaptationism/panselectionism and about evolutionary-developmental biology. I'll get to evo-devo in another post [Michael Lynch on Evo-Devo] but here are some choice words about adapationism.

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.

....

... 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.

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.

I agree with everything Lynch writes except that I have a pretty good idea what alternative mechanisms Gould proposed.

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Dinner with Bjørn

Bjørn Østman of Pleiotropy and Carnival of Evolution was in town for a visit on Monday, Aug. 8, 2011. We talked about evolution, accommodationism, atheism, PZ, education, visas, politics, carnivals, the USA, adaptationism, blogging, and careers in science.

I think he was happy to learn that I agreed with him on almost everything.

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Junk & Jonathan: Part 4—Chapter 1

I received a copy of the book a few days ago and this is my first posting on its contents. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

This is a very small book. There's only 114 pages of text—it's more like a large pamphlet than a book. If I'd read it from front to back in one sitting it would only have taken an hour or so. But I couldn't read it in one go because nobody can put up with IDiot rhetoric for that long!

Chapter 1 is The Controversy over Darwinian Evolution. It has nothing to do with junk DNA.

Wells begins by telling his readers that evolution is a fact. By that he means "microevolution." Wells doesn't believe in macroevolution or common descent and he even challenges the evidence for speciation. As usual, he supports his claims with selected quotations from scientists.

Sixty year after Dobzansky wrote this, biologists had still not observed the origin of a new species ("speciation") by natural selection. In 1997, evolutionary biologist Keith Stewart Thomson wrote: "A matter of unfinished business for biologists is the identification of evolution's smoking gun," and "the smoking gun of evolution is speciation, not local adaptation and differentiation of populations."

Wells is telling his readers that as long as biologists have not directly observed a new species forming then speciation has not been demonstrated. This rules out all evidence from the fossil record and all evidence from molecular phylogeny. Nice trick.

Problem is, there's lots of lots of evidence for speciation, including some examples where speciation has been caught in the act. Wells, like most IDiots, doesn't understand how evolution works. He seems to think that new species will form overnight and that all biologist have to do is keep their eyes open and record the examples.

I don't know for sure whether Wells intends to emphasize speciation by natural selection when he claims that, "biologists had still not observed the origin of a new species ("speciation") by natural selection." If that's his intent then it's true that there are very few examples of true speciation (biological species concept) that can be attributed directly to natural selection. As Jerry Coyne points out, reproductive isolation is mostly due to accident (random genetic drift) and not natural selection [The Cause of Speciation]. That's in line with modern evolutionary theory and Coyne should know because he's one of the world's leading experts on speciation. [UPDATE: Coyne and some commenters have corrected me. Coyne actually does think that most speciation is due to natural selection. I'll stick with Futuyma as my authority. He's much more open to the idea of speciation by random genetic drift (Evolution 2nd ed. p. 447)]

There are two possibilities here. Either Wells is deliberately misleading his readers by emphasizing that speciation must occur by natural selection or he's ignorant of modern evolutionary theory. Since most IDiots have a concept of evolution that dates back to the nineteenth century, I'll go with the second explanation. However, there's almost certainly an element of deception in his remarks since Jonathan Wells has a long history of deliberately misrepresenting evolution.

Theme

Genomes
& Junk DNASo, Wells is dead wrong about the first point in his book. There's abundant evidence of speciation (and macroevolution) and, furthermore, modern evolutionary theory does not attribute speciation exclusively to adaptation (i.e. there's more to evolution than Darwinism).

The importance of Wells' rejection of macroevolution will become obvious later on in the book when he argues that Intelligent Design Creationism does not rule out common ancestry. He agrees that someone like Michael Behe can believe in common descent and still be a card-carrying IDiot.

By the way, Wells is clever enough to cover his bases in case speciation is ever observed.

Of course, even if scientists eventually observe the origin of a new species by natural selection, the observation would not mean that natural selection can also explain the origin of significantly new organs or body plans. But the fact that scientists have not observed even the first step in macroevolution means that "evolution's smoking gun" is still missing.

The rest of the chapter (three pages) is a re-hash of arguments Wells made in Icons of Evolution and elsewhere.

• The Cambrian Explosion "contradicts Darwin's theory that major differences should arise only after millions of years of evolution ...."
• Molecular evolution isn't accurate: "molecular evidence is plagued with inconsistencies." The rejection of molecular evidence as unreliable is going to cause problems for Wells later on since he relies on it for some of his arguments about junk DNA. As usual, the IDiots want to have their cake and eat it too.
• Homology is a circular argument, according to Wells, so you can't use homology as evidence for evolution. That's correct. Similarity is the evidence and homology is the conclusion. This flaw in Wells' reasoning has been pointed out to him repeatedly over the past decade but he ignores all criticism and continues to use arguments that have been refuted.
• The Haeckel drawings were fakes and, "The truth is that vertebrate embryos start out looking very different from each other, then they converge somewhat in appearance midway through development before diverging as they mature." This has nothing to do with junk DNA so I won't discuss the massive amount of embryological evidence for evolution.

Wells closes with,

So microevolution is a fact, supported by overwhelming evidence, but macroevolution remains an assumption, illustrated with icons that misrepresent the evidence or rely on circular reasoning. The icons are not science, but myth.

This sets the tone for the rest of the book. Even though it is filled with references to the scientific literature there's never any discussion of alternative hypotheses or conflicting data. This is not a book where the author wants to inform his readers about the exciting controversies and conflicts within science. This is a book where the author wants to promote creationism by attacking and misrepresenting evolution using faulty logic and untruths.

The next paragraph is quite interesting. He invokes the beliefs of Americans as support for his claims. Apparently they're much more perceptive that the typical evolutionary biologist. (I wonder what he thinks of Australians and Europeans?)

This may be one reason why—despite the Darwinists' near-monopoly over science education—most Americans still reject the doctrine that human beings evolved from ape-like ancestors by unguided processes such as random variation and survival of the fittest.

I think this means that Wells also rejects common ancestry. If so, it will mean that he can't use it to support any of his arguments later on in the book, right?

Finally, at the very end of the chapter we get to the point,

In the 1950s, neo-Darwinists equated genes with DNA sequences and assumed that their biological significance lay in the proteins the encoded. But when molecular biologists discovered in the 1970s that most of our DNA does not code for proteins, neo-Darwinists called non-protein-coding DNA "junk" and attributed it to molecular accidents that have accumulated in the course of evolution. Like peppered moths, Galapagos finches, Darwin's Tree of Life, homology in vertebrate limbs, and Haeckel's embryos, "junk DNA" has become an icon of evolution. But is it science of myth?

I've discussed Wells' ignorance of history in previous postings but, for the record, here are the facts.

• By the 1970s molecular biologist were well aware of the fact that non-protein coding genes existed (e.g. ribosomal RNA genes, tRNA genes etc.)
• By the 1970s molecular biologists knew of several functions of DNA sequences that weren't genes. Origins of replication and regulatory sequences were well-known but there were others.
• Even in the 1970s no knowledgeable molecular biologist could ever defend the idea that all non-coding DNA was junk. (It's true that there were some stupid scientists who weren't aware of tRNA genes and regulatory sequences and made silly statement because of their ignorance but they don't count.)
• By the 1970s junk DNA was a fact. The scientific controversy was over how much of our genome is junk. Is it the majority or only a small percentage?
• By the 1970s knowledgeable evolutionary biologists were well aware of the fact that most of our genome was mutating and evolving as though most changes were neutral (genetic load arguments). This didn't mean that most of our genome was junk but it did mean that the sequence couldn't be important or we would never be able to tolerate the genetic load. This was not common knowledge among biologists—still isn't.
• By the 1970s most molecular biologists were aware of the so-called "C-value paradox" where very closely related species have very different genome sizes. They correctly interpreted this to mean that the species with the large genomes probably didn't need all that extra DNA. (Up until now, Intelligent Design Creationists have not offered a reasonable answer to The Onion Test. Wells tries on Chapter 8.)
• The proponents of large amounts of junk DNA in our genome would hardly ever have referred to themselves as "Darwinist" or "neo-Darwinists." In fact, they tended to be among those evolutionary biologists who opposed adaptationism and favored Neutral Theory and random genetic drift. Pluralist concepts were much more compatible with the idea of significant amounts of junk DNA than strict "Darwinist" interpretations of genome evolution.

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The Problem with Evolutionary Psychology

Jesse Bering is an evolutionary psychologist at Queen's University, Belfast, Northern Ireland (UK). He blogs at Bering in Mind on the Scientific American website. Read his latest post: Natural homophobes? Evolutionary psychology and antigay attitudes.

In that post, Bering takes seriously the idea that homophobia could be a character that evolved in our ancestors. The idea is that parents who were homophobic were more likely to be concerned about the sexual orientation of their children. If this led to more heterosexual children then the parents would have more grandchildren and the allele for homophobia would increase in the population.

To my mind this idea is so ridiculous it doesn't even merit discussion and it certainly should never be published in a "scientific" journal. Why is it that respected evolutionary psychologists think these just-so stories are an important part of their discipline? Does this mean that the entire discipline is suspect?¹

Jesse Bering is the author of The God Instinct. I haven't read this book but I'm going to order a copy. Here's what he says on his website.

Why does even the most committed atheist turn to God when a family member falls seriously ill, or they find themselves in close personal danger? Using the latest scientific evidence, Jesse Bering explores how people's everyday thoughts, behaviours and emotions betray an innate tendency to reason as though God were deeply invested in their public lives and secret affairs.

In this entertaining and thought-provoking book, he argues that this religious reflex is not an irrational aberration, and that God is not a cultural invention or an existential band-aid, but an intrinsic human trait, developed over millennia, that carries powerful evolutionary benefits.

Breaking new ground, The God Instinct uses hard science to show that God is not a delusion, but a sophisticated cognitive illusion. Bering reveals the roots of religion in our ability to think beyond our immediate surroundings, and explains why this capacity for belief sets us apart from other animals.

Jesse Bering sounds like a complicated person with interesting perspectives on evolution and religion. Here's what he says about himself on the website.

Jesse Bering is Director of the Institute of Cognition and Culture at the Queen's University, Belfast. An evolutionary psychologist, he is one of the principal investigators on the Explaining Religion Project.

The Institute's research focuses primarily on human social behaviour, and current topics range from people's belief in the afterlife to moral disgust over social offences. Funded by the EU, the John F Templeton Foundation and the US Air Force, it has projects running all over the world, including India, Mali and Cyprus.

Jesse writes a weekly column for Scientific American, ‘Bering in Mind’. The members of The International Academy of Digital Arts and Sciences named the column an official 2010 Webby Honoree in the “blog­cultural” category.

As well as being an acknowledged expert in his field, Jesse Bering is well known for his approachable and engaging popular writing. Born in the USA, he now lives in Northern Ireland.

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1. Perceptive readers will see a connection between evolutionary psychology and adaptationism.

[Hat Tip: Joe at Canadian Atheist]

Jerry Coyne's Opinion

No, I'm not referring to his opinion on adaptationism. He hasn't weighed in on that subject even though he's a former student of Lewontin and surely has something to say.

I'm referring to Coyne's selections of the best popular singers of our time. His top two are Frank Sinatra and Barbra Streisand. Some of my friends and relatives are interested in these things. it's hard to argue with his selections so far.

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Dan Dennett Replies

This is Daniel Dennett's reply to my earlier post: Daniel Dennett's View of Adaptationism.

Dear Larry,

Your blog was drawn to my attention today, and I decided it was well worth a response. Thanks for leading with your chin.

I’ve been wondering whether anybody would respond vigorously enough, and with enough authority, to my statement about the central importance of adaptation in evolution and the centrality of adaptationist thinking in biology to make it worth my time and energy to expand and explain. You have done so, and your commentators—especially anonymous and z—have already done a good job expressing at least a large part of my response, and I am grateful to them. I particularly endorse anonymous in his comment on the huge space of possible proteins and the fact that “functional proteins” are what inhabit that space.

You already accept the centrality of adaptation, as you say yourself in response to anonymous: “We agree that adaptation is a very important part of evolution and to ignore it completely would be ridiculous.” You need to remember that a great many non-biologists do not agree about this, and many of them have read the Gould & Lewontin essay (reputedly one of the most-cited papers in academia) as showing that (as Jerry Fodor once said to me, years ago) “adaptationism is completely bankrupt.” One of my chief aims in Darwin’s Dangerous Idea was to redress the balance, showing philosophers and other humanists and social scientists that they had to take evolutionary thinking (chiefly adaptationist thinking) seriously. Pluralism is not the lesson Fodor took from Gould & Lewontin’s essay, as his recent book with Piatelli-Palmarini makes clear. The “Spandrels” essay was the chief inspiration for his preposterous claim that “Darwin was wrong”. So I must ruefully admit that my efforts to squelch this widespread misreading of the message of “Spandrels” failed utterly to reach some thinkers.

But what about your biology students and their examination question about my notorious hymn to adaptationist reasoning? I wish you had also given them the passage in the same book, a few pages later, inwhich I quote Niles Eldredge and Michael Ghiselin, who make incautious claims about how we can replace “what is good” (adaptationism) with the more sober question “What has happened?” (pp240-41) I point out there that the very examples they cite depend, tacitly, on adaptationist assumptions—obvious assumptions but so much the better. I have much the same message for you, in response to your paragraph:

“I wonder how adaptationist thinking helps us understand sequence-based phylogenetic trees and the molecular clock. At the other extreme, how crucial a role does adaptationism play in deciding whether birds are dinosaurs or punctuated equilibria are the dominant pattern in the fossil record? I’m thinking that it might be a problem grading the answer to this question. Can a student defend Dennett’s statement and still get a passing grade?”

So let me take your wonders in turn. Nobody can reason about sequence-based phylogenetic trees without some assumptions about what historical processes created the data we now have available in the DNA of living and—in some cases—recently extinct species where DNA can be extracted. Those assumptions include, trivially, assumptions about the relative high fidelity of DNA replication and transmission, the role of DNA expression in (partially) determining phenotypic features, and the tendency of selection to weed out dysfunctional mutations and combinations.

Consider in particular how, for instance, biologists identify and explain gene duplication events. The uncontroversial interpretation of two suspiciously similar sequences in today’s DNA is as evidence—often considered conclusive—of a (roughly datable) duplication event followed by the preservation of one copy for its old (functional) role, freeing up the “extra” copy for exploitation/pruning for some new (functional) role. Duplication events just happen, of course, and not for any reason. The vast majority of them, we may safely suppose, disappear in a few generations or even sooner, but when they persist, it is because they get exploited and preserved for their functional roles. I suppose it is the obvious safety of the adaptationist assumptions here that hides them from view, creating the illusion, apparently, that there is no dependence on adaptationist premises here at all.

As for the molecular clock, it too cannot be relied on without help from adaptationist distinctions For one thing, you can’t distinguish Kimura’s neutral theory from Ohta’s “nearly neutral theory” without taking on board the role of slightly harmful gene differences that are subject to selection (which changes the rate at which such mutations go to fixation). And Ohta’s theory can explain some data that Kimura’s cannot. There are many other complications that arise for the molecular clock, regarding different rates in different taxa, that call for—and receive—clarification from adaptationist reasoning. For instance, molecular evolution in bacteria is faster than molecular evolution in mammals like us. Why? We have elaborate proof-reading systems the bacteria lack, and this raises the high fidelity of our replication processes. Trying explaining that without any appeal to function.

So there’s the answer to your first wonder. IF you want to avail yourself of the standard account of gene duplication events (to take just one uncontroversial example), and the limits on the utility of the molecular clock, you have to give adaptationist reasoning an essential role in your explanation—so central and unchallenged that it need not be mentioned.

Second wonder: “how crucial a role does adaptationism play in deciding whether birds are dinosaurs”? Well, unless you are asking a deliberately “philosophical” (as opposed to scientific) question about “where we draw the line” between (true) dinosaurs (with dinosaur essences) and true birds, a question that does not require or deserve an answer, you are asking for the evidence that birds descended, by a gradual sequence of intermediaries, from dinosaurs, and that is, I think, well established on multifarious grounds. All of those grounds depend, trivially, on assumptions about the absence (or huge unlikelihood) of hopeful monsters, on the necessary viability or fitness of all the intermediate forms, and so forth. Those are adaptationist assumptions. Perhaps because they are so uncontroversial they are not recognized as adaptationist, but there is no other reasoning that supports them. Those who think genetic drift explains a great deal—and of course it does—don’t make the mistake of holding that it can permit gene migrations across deep fitness valleys in adaptive landscapes. This shows the centrality, the non-optionality, of adaptationist reasoning even for the account of the birds-from-dinosaurs history. You cannot answer the “What has happened?” question without adding (sotto voce) “assuming that the descendants obeyed the fundamental constraints of natural selection”.

And lest anyone think that there is no more detailed role for adaptationist reasoning in the dinosaur-to-bird story, consider the question of how wings evolved and why they have the shapes they do. Now you don’t have to consider such questions, and the relevance to them of, say, the independent evolution of (functional) wings in insects and mammals, but it does seem to be an important part of the story.

What, then, of the question of whether “punctuated equilibria are the dominant pattern in the fossil record’? I haven’t encountered any reasoning about this issue that doesn’t involve discussion of whether the equilibria are due to stabilizing selection or other factors, and whether the punctuation episodes are driven by novelties in the environment (in adaptive radiations, for instances) or have some more endogenous trigger. So I guess I am unfamiliar, as a non-biologist, with the alternative settings of these issues that somehow avoid those adaptationist topics. I hope you will enlighten me.

Your final question is whether a student could agree with me and get a passing grade. Well, that is for you to answer: Is there is enough material in the various comments on your blog, and in my response here, to support a passing response on your examination? I have tried to answer your questions. Here is a question for you:

You preface the paragraph I quoted above with this question: “Can anyone figure out why biochemistry would collapse if we stop attributing everything to adaptation?” My question is: can you see that this is an unsympathetic caricature of my claim? I never say we need to “attribute everything to adaptation” or anything close to that. You agree that adaptation is important; and I expect you will agree with me now that (obvious) adaptationist reasoning undergirds all explanation of historical process in biology. That is what I mean by saying that adaptationist reasoning is “not optional, it is the heart and soul of evolutionary biology.”

I look forward to your reply.

Best wishes,

Dan Dennett

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Daniel Dennett's View of Adaptationism

I've prepared a bunch of exam questions for my students and given them out two weeks before the exam. I promised them that I would post some of these questions on my blog to see how you would answer them. I'm hoping that you, dear readers, will show my students that there really is some controversy.

Here's the second question.

Discuss the following statement by Daniel Dennett from his book Darwin’s Dangerous Idea (1995, p. 238). Do you agree or disagree? Pay particular attention to the kind of reasoning required in the field of molecular evolution.

Adaptationist reasoning is not optional, it is the heart and soul of evolutionary biology. Although it may be supplemented, and its flaws repaired, to think of displacing it from its cental position in biology is to imagine not just the downfall of Darwinism but the collapse of modern biochemistry and all the life sciences and medicine. So it is a bit surprising to discover that this is precisely the interpretation that many readers have placed on the most famous and influential critique of adaptationism, Stephen Jay Gould and Richard Lewontin’s oft-cited, oft-reprinted, but massively misread classic, “The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Program” (1979).

My students all have a copy of the Spandrels paper and they should be familiar with it. In case you're not (shame), it seems to me that Lewontin & Gould are advocating a pluralist approach to evolution. They criticize the adaptationist program and really would like to see it disappear. Is Dennett making a distinction between the adaptationist program and adaptationist reasoning? I don't think so because here's what he says on the same page as the quotation above.

The biologists' name for this style of reasoning is adaptationism. It is defined by one of its most eminent critics as the "growing tendency in evolutionary biology to reconstruct the evolutionary events by assuming that all characters are established in evolution by direct natural selection of the most adapted state, that is, the state that is an optimum solution to a problem posed by the environment" (Lewontin 1983). These critics claim that, although adaptationism plays some important role in biology, it is not really all that central or ubiquitous—and, indeed, we should try to balance it with other ways of thinking. I have been showing, however, that it plays a crucial role in the analysis of every biological event at every scale from the creation of the first self-replicating molecule on up. If we gave up adaptationist reasoning, for instance, we would have to give up the best textbook argument for the very occurrence of evolution (I quoted Mark Ridley's version of it on page 136): the widespread existence of homologies, those suspicious similarities of design that are not functionally necessary.

Dennett is a philosopher so he might not be as familiar with modern biochemistry as his statement implies. Can anyone figure out why biochemistry would collapse if we stop attributing everything to adaptation? I wonder how adaptationist thinking helps us understand sequence-based phylogenetic trees and the molecular clock? At the other extreme, how crucial a role does adaptationism play in deciding whether birds are dinosaurs or punctuated equilibria are the dominant pattern in the fossil record?

I'm thinking that it might be a problem grading the answer to this question. Can a student defend Dennett's statement and still get a passing grade?

UPDATE: Dan Dennett Replies.

Let me close, for no particular reason, with a few quotations from one of my personal heroes, Betrand Russell.

A stupid man's report of what a clever man says can never be accurate, because he unconsciously translates what he hears into something he can understand.

I think we ought always to entertain our opinions with some measure of doubt. I shouldn't wish people dogmatically to believe any philosophy, not even mine.

If a man is offered a fact which goes against his instincts, he will scrutinize it closely, and unless the evidence is overwhelming, he will refuse to believe it. If, on the other hand, he is offered something which affords a reason for acting in accordance to his instincts, he will accept it even on the slightest evidence. The origin of myths is explained in this way.

In all affairs it's a healthy thing now and then to hang a question mark on the things you have long taken for granted.

It has been said that man is a rational animal. All my life I have been searching for evidence which could support this.

Passive acceptance of the teacher's wisdom is easy to most boys and girls. It involves no effort of independent thought, and seems rational because the teacher knows more than his pupils; it is moreover the way to win the favour of the teacher unless he is a very exceptional man. Yet the habit of passive acceptance is a disastrous one in later life. It causes man to seek and to accept a leader, and to accept as a leader whoever is established in that position.

Patriots always talk of dying for their country but never of killing for their country.

So far as I can remember, there is not one word in the Gospels in praise of intelligence.

The universe may have a purpose, but nothing we know suggests that, if so, this purpose has any similarity to ours.

The whole problem with the world is that fools and fanatics are always so certain of themselves, but wiser people so full of doubts.

This is one of those views which are so absolutely absurd that only very learned men could possibly adopt them.

This is patently absurd; but whoever wishes to become a philosopher must learn not to be frightened by absurdities.

When one admits that nothing is certain one must, I think, also admit that some things are much more nearly certain than others. It is much more nearly certain that we are assembled here tonight than it is that this or that political party is in the right. Certainly there are degrees of certainty, and one should be very careful to emphasize that fact, because otherwise one is landed in an utter skepticism, and complete skepticism would, of course, be totally barren and completely useless.

Aristotle maintained that women have fewer teeth than men; although he was twice married, it never occurred to him to verify this statement by examining his wives' mouths.

The fact that an opinion has been widely held is no evidence whatever that it is not utterly absurd; indeed in view of the silliness of the majority of mankind, a widespread belief is more likely to be foolish than sensible.

It is undesirable to believe a proposition when there is no ground whatsoever for supposing it is true.

A process which led from the amoeba to man appeared to the philosophers to be obviously a progress though whether the amoeba would agree with this opinion is not known.

Advocates of capitalism are very apt to appeal to the sacred principles of liberty, which are embodied in one maxim: The fortunate must not be restrained in the exercise of tyranny over the unfortunate.

Almost everything that distinguishes the modern world from earlier centuries is attributable to science, which achieved its most spectacular triumphs in the seventeenth century.

I would never die for my beliefs because I might be wrong.

In America everybody is of the opinion that he has no social superiors, since all men are equal, but he does not admit that he has no social inferiors, for, from the time of Jefferson onward, the doctrine that all men are equal applies only upwards, not downwards.

It is possible that mankind is on the threshold of a golden age; but, if so, it will be necessary first to slay the dragon that guards the door, and this dragon is religion.

There is something feeble and a little contemptible about a man who cannot face the perils of life without the help of comfortable myths.

Men are born ignorant, not stupid. They are made stupid by education.

Religion is something left over from the infancy of our intelligence, it will fade away as we adopt reason and science as our guidelines.

Science is what you know, philosophy is what you don't know.

That last one is for John Wilkins.

UPDATE: See Dan Dennett Replies

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What Does San Marco Basilica Have to do with Evolution?

Everyone interested in evolution should read the famous critique of the adaptationist program by Stephen Jay Gould (1941-2002) and Richard Lewontin (1929 - ). Whether you agree with them or not, it's essential that you become informed about the adpatationist-pluralist controversy—also known as the neutral-selectionist controversy. That controversy is still very much a part of the debates over evolution, although the adaptationist side tends to argue that the controversy has been settled.

It's no secret that I'm a huge fan of Gould and if I had my druthers I'd make students read every one of his books, including, The Structure of Evolutionary Theory. I'm a pluralist.

My friend John Wilkins, a philosopher, visited St. Mark's Square and the Basilica last year. He's on the opposite side of this debate and he offers the best defense of adaptationism that I've seen in recent years. You should keep an eye on his blog, Evolving Thoughts, it's a must-read for anyone who's serious about evolution. I blogged about John's version of adaptationism [An Adaptationist in Piazza San Marco].

This is a rich topic for undergraduates and there are many potential essay topics.

Michael Ruse Defends Adaptationism
Richard Dawkins' View of Random Genetic Drift
Naked Adaptationism

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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. Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 205, No. 1161, The Evolution of Adaptation by Natural Selection (Sep. 21, 1979), pp. 581-598. [AAAS reprint] [printable version]

Shoddy But Not "Junk"?

Philip Ball is a freelance science writer based in London (UK). He frequently writes for Nature. His latest article is a review of a recently published paper by John Avise [What a shoddy piece of work is man]. Apparently Avise has just published a paper in PNAS where he points out that our genome does not look like it was designed. It's an attack on Intelligent Design Creationism and Adaptationism.

I can't find the paper but I have read Avise's book, Inside the Human Genome so I'm familiar with his thesis—and I agree with it.

The purpose of this posting is not to review the points that John Avise makes but to comment on one of the points made by Philip Ball. At the end of his Nature review he says,

However — although heaven forbid that this should seem to let ID off the hook — it is worth pointing out that some of the genomic inefficiencies Avise lists are still imperfectly understood. We should be cautious about writing them off as 'flaws', lest we make the same mistake evident in the labelling as 'junk DNA' genomic material that seems increasingly to play a biological role. There seems little prospect that the genome will ever emerge as a paragon of good engineering, but we shouldn't too quickly derogate that which we do not yet understand.

THEME

Genomes & Junk DNA

I just gave a talk on junk DNA where I explained to my audience the nature of the scientific controversy. We know for a fact that our genome is littered with pseudogenes of all sorts and we know for a fact that more than 50% of our genome is repetitive DNA of one kind or another. A good hunk of that is degenerative transposons and fragements of transposons [Junk in your Genome: LINEs]. Another large hunk is Alu sequences: fragments of an ancient primate transposon derived from 7SL RNA [Transcription of the 7SL Gene].

We also know a great deal about introns and that knowledge leads to the conclusion that most intron sequences are dispensable. it's part of the junk in our genome. We know about the genetic load argument [Genetic Load, Neutral Theory, and Junk DNA] and we know about the C-Value Paradox. Most scientists who study the problem of junk DNA know about The Onion Test.

My point is that it's extremely misleading to suggest that our identification of junk DNA is based on a lack of understanding. That's simply not true. There are some very good scientific reasons for maintaining that most of our DNA is junk based on over 40 years of work on genome organization.

Yes, it's true that there have been some scientific challenges questioning the conclusion of those studies. There is a group of scientists who claim that vast amounts of our genome serve some mysterious purpose that's only vaguely defined. It could be regulation of some sort or even an entire new class of RNA-encoding genes that make us human.

These claims make the debate over junk DNA a scientific controversy but they certainly haven't succeeded in disproving the hypothesis. None of the recent claimants can explain pseudogenes and degenerative transposons, which make up more than half of our genome. None of the opponents can refute the genetic load argument.

Science writers like Philip Ball can be forgiven for not delving into the problem. It's easy to fall for the latest articles that purport to show function for a large part of what we call junk DNA. After all, those anti-junk proponents don't do their homework either and they gloss over all the data that contradicts their "new" hypothesis.

My point is that the idea of junk DNA is alive and well in spite of what modern science writers seem to think. It's just not true that today's scientists think we made a big mistake in the past by calling it junk DNA. This is still very much a scientific controversy and it's too soon to tell how it will pan out.

Personally, I think the evidence in favor of a large amount of junk in our genome is persuasive and I'd be very, very surprised if a significant amount of it turns out to be functional. I wish science writers would stop behaving as though the issue had been resolved and junk DNA is dead.

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Michael Ruse Defends Adaptationism

Jerry Fodor and Massimo Piattelli-Palmarini have just published a book called What Darwin Got Wrong. I haven't read the book but from the reviews I've seen, it's not something that I'm looking forward to. However, their main thesis is that natural selection has been oversold as an explanation for evolution and I have a great deal of sympathy for that point of view. Furthermore, I think that adaptationism—the assumption that adaption is the default explanation for everything that evolves—is a scientifically bankrupt position. I'm a pluralist.

Michale Ruse has reviewed the book for boston.com and I'd like to analyze his review in order to reveal where he goes wrong.

Origin of the specious
This new critique intends to rebut Darwin’s ideas but seems largely to misunderstand evolutionary theory.

“What Darwin Got Wrong’’ is an intensely irritating book. Jerry Fodor, a well-known philosopher, with coauthor Massimo Piattelli-Palmarini, a cognitive scientist, has written a whole book trashing Darwinian evolutionary theory - the theory that makes natural selection the main force of change in organisms through the ages.

Like I said, I haven't read the book so I can't really comment on the specifics. But I can comment on what Micahel Ruse says about the book.

He begins by claiming that the authors misunderstand evolutionary theory. That may be true but it will become painfully obvious that Michael Ruse is not enough of an authority to make such a claim.

Let's begin by seeing how Ruse describes evolution. He says that "Darwinian evolutionary theory" is the theory proposing that natural selection is the main force of evolution. Strictly speaking, that's correct. What we're interested in debating is whether "Darwinian evolutionary theory" is correct as defined.

The answer is clearly "no." Random genetic drift is the most common mechanism of evolution as long as you define evolution properly. Thus, as a explanation of evolution, Darwinism is not as good as a pluralistic evolutionary theory. Although Ruse isn't clear on this, it's well known from his previous writings that he thinks of Darwinism as the preferred explanation of evolution and not just of adaptation. In fact, he rarely distinguishes between the two.

I conclude, right from the beginning of the review, that Michael Ruse has a poor understanding of evolutionary theory.

You would think that somewhere in the pages there would be one - just one - discussion of the work that evolutionists are doing today to give a sense of how the field itself has evolved. Peter and Rosemary Grant on Darwin’s finches for example; Edward O. Wilson and Bert Hölldobler on ant social structures perhaps; David Reznick on Trinidadian guppies perchance? But no such luck. A whole book putting in the boot and absolutely no serious understanding of where the boot is aimed.

Aren't those interesting examples? Just what you'd expect from a myopic adaptationist. What about studies of molecular evolution which are almost entirely based on neutral changes and random genetic drift. You'd think that someone who claims to be on top of modern evolutionary theory would recognize the growing evidence of non-adaptive change, wouldn't you?

Why write such a book? The authors would respond in two ways. First, in a section that would be better described as “What Darwin Didn’t Know,” rather than “What Darwin Got Wrong,” they tell us that today’s cutting-edge biology has all sorts of explanations of organic origins that make Darwinism otiose. We learn that life is constrained by the laws of physics and chemistry, and that something like natural selection, which supposedly molds organic life into sophisticated bundles of adaptations, simply cannot get off the ground. To the contrary, evolution is all a matter of molecular development, guided by the self-organizing laws of the physical sciences.

To which Darwinians can only respond, wearily again, that they have known about constraints since “The Origin of Species.’’ Because body weight cubes as length increases, you cannot build a cat the size of an elephant. The elegant feline legs needed for jumping must be replaced by tree trunks able to carry many pounds. And examples of plausible self organization have been fitted into the Darwinian picture for many years. A favorite example is the way that many flowers and fruits (like pine cones) exhibit patterns following the Fibonacci series, made famous by “The Da Vinci Code.’’ Chauncey Wright, a 19th century pragmatist, discussed these patterns in detail, showing how formal rules of mathematics can nevertheless yield organisms that are highly adapted and that natural selection is the vital causal element. The rules give the skeleton, and then selection fills in the details. The order of a plant’s leaves may be fixed, but how those leaves stand up or lie down is selection-driven all of the way.

In their various published articles Fodor and Piattelli-Palmarini have over-emphasized "constraints" and they come off sounding like some new-agers who have just discovered molecular biology.

But the fundamental point about constraints is interesting and it's true that adaptationists have been forced to recognize it every since Gould and Lewontin published the Spandrels paper back in 1977. Most adaptationist still don't get it and Ruse is no exception, although in this case he probably gets it better than Fodor and Piattelli-Palmarini. Ruse admits that there are certain physical constraints on the way plant leaves evolve, for example, but he then goes on to say that everything else is an adaptation. How does he know this? How does he know for sure that the differences in the leaves of red maples, silver maples, and sugar maples are all due to natural selection?

The second half of the book is a frontal attack on natural selection itself. The main argument is very odd. It is allowed that there is differential reproduction. Some organisms have many offspring, and some have just a few. It is even allowed that the reason why some succeed and others don’t might have to do with the superior features possessed by the winners and not the losers. At which point you might think: Darwinism wins, because what else is there to natural selection?

Not so fast, however. Our authors take as gospel the argument of the late Stephen Jay Gould and the geneticist Richard Lewontin that although some features may be adaptive others may not. This argument is then used to say that if an organism succeeds in life’s struggles, you can never conclude that a particular feature was essential for this success, because there may be other features linked to it. Perhaps it was the latter features that were essential. Natural selection fails therefore as a mechanism of change.

I take it as "gospel" that random genetic drift is an important mechanism of evolutionary change. Why do I get the impression that Michael Ruse has doubts about this? Why does he use the word "gospel" to refer to the ideas of Gould and Lewontin but not Dawkins and E.O. Wilson? Isn't that strange?

Hundreds of evolutionary biologists have written about random genetic drift and other possible mechanisms of evolution (e.g., molecular drive, species sorting). They do not claim, as Ruse implies, that non-adaptive traits become fixed because they are "linked" to adaptive ones. Is this how Ruse dismisses random genetic drift—by treating it as a by-product of natural selection?

In fairness, Fodor and Piattelli-Palmarini do go on about linkage in their published articles so Ruse is right to mock those silly claims. However, I wish he didn't make things worse by implying that hitchhiking is the explanation for drift.

The existence of random genetic drift does not mean that natural selection "fails. " It just means that natural selection by itself is not a sufficient explanation for evolutionary change. Perhaps Fodor and Piattelli-Palmarini are confused about this—other reviews suggest that this is the case—but Michael Ruse seems to be trashing the very idea that something other than natural selection could be at play.

I read all of this stuff a couple of times. I am just not used to people giving the opposition everything for which they have asked and then plowing on regardless. But, even if you ignore the apparently shared belief that selection is at work - we may not know which features were crucial, but that hardly stops us saying that there was selection at work - the other points hardly crush the Darwinian. It has long been known that features get linked. And in any case, we can ferret out which features are most useful and which are just along for the ride. Suppose eyes, which are surely necessary, are linked to tufts of hair, which may not be. Well, experiment and see how the organisms get along without eyes and then without hair.

Non-adaptive features can arise even if they are completely unlinked to adaptive feature. Ruse doesn't seem to understand this basic concept of population genetics. And Ruse needs to take his own advice. Rather that just assume that a feature is an adaptation, you need to do the experiments. This applies to the leaves on a tree and the beaks of the finch.

Fodor and Piattelli-Palmarini will not allow this, because apparently we are now ascribing conscious intentionality to the nonconscious world. We are saying the eyes were designed for seeing in a way that the tufts were not. And they stress that the whole point of a naturalistic explanation, to which the Darwinian is supposedly committed, is that the world was not designed.

In response, one can only say that this is a misunderstanding of the nature of science. The Darwinian does not want to say that the world is designed. That is what the Intelligent Design crew argues. The Darwinian is using a metaphor to understand the material nonthinking world. We treat that world as if it were an object of design, because doing so is tremendously valuable heuristically. And the use of metaphor is a commonplace in science.

Darwinist are always saying that the world has the appearance of design. Of course it's a metaphor but it's a metaphor based on the idea that natural selection, and not God, is the designer.

Ruse and his fellow adaptationists treat the world as if it were an object of design because they are psychologically committed to the idea that natural selection is responsible for almost everything. They cannot adjust to the fact that much of what we see in living things could be due to accident, or even the fixation of deleterious mutations. That's one of the reasons they have so much trouble with junk DNA and it's why they can't account for so much diversity in populations.

Here's a clue. Life doesn't actually look terribly designed. Get over it. Abandon the metaphor—it just feeds into a false notion of evolution and, incidentally, lends support to the IDiots.

Why then do we have these arguments? The clue is given at the end, when the authors start to quote - as examples of dreadful Darwinism - claims that human nature might have been fashioned by natural selection. At the beginning of their book, they proudly claim to be atheists. Perhaps so. But my suspicion is that, like those scorned Christians, Fodor and Piattelli-Palmarini just cannot stomach the idea that humans might just be organisms, no better than the rest of the living world. We have to be special, superior to other denizens of Planet Earth. Christians are open in their beliefs that humans are special and explaining them lies beyond the scope of science. I just wish that our authors were a little more open that this is their view too.

This is despicable. Evolutionary psychology is a broken discipline. And it's not because there is no genetic components to behavior—of course there is. It's because the field is dominated by adaptationist explanations and crazy "just-so" stories that would make Rudyard Kipling proud.

If you accept, as I do, that humans do all kinds of silly things just because of their culture and superstitions, and not necessarily because they are adaptive, then that makes us more like the other animals and not more special. If you accept that we are products of evolution by accident and not "design" (metaphorically) then that makes us farther removed from a potential designer and not closer to God as Ruse would have you believe.

Ruse and the adaptationists are the ones who skate close to the edge when it comes to supporting Christian concepts of life. They do this by conceding that we look designed when that's simply not the full story.

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[Image Credit: The photo is from Paul Nelson on the Intelligent Design website. It refers to Ruse's idea that evolution is a form of religion. There's something to be said for this idea, especially when it's applied to confirmed Darwinists.]

Good News from Gent

While in Gent I got a chance to meet up with some members of the Department of Philosophy at the University of Gent. Jan Verbeeren (right) is a regular reader of Sandwalk. Stefaan Blanke (below left) and Maarten Boudry (below right) are graduate students who I met at the Darwin conference in Toronto in November.

It was easy to convince Maarten to join Jan and I for a beer because Jan was buying. Unfortunately, Stefaan couldn't make it so I'll have to go back for another visit.

There are at least 500 different beers made in Belgium—or so I'm told [Belgium beers]. I doubt that I'll be able to sample all of them before I leave. The ones I had in Gent were "Delirium Tremens" and "Tripel Karmeliet." They were excellent.


We talked about adaptationism vs. pluralism. It seems to be a difficult controversy to grasp if you haven't been trained as a scientist. I think the problem is that the concept of random genetic drift as a mechanism of evolution is not widely accepted among philosophers.

We also spent an hour or so talking about methodological naturalism and philosophical naturalism. This was the subject of Maarten's talk in Toronto last November and I think he's on to something (with Stefaan). I'll write a separate post on this topic.

The title of this post is from How They Brought the Good News from Ghent to Aix by Robert Browning.

I SPRANG to the stirrup, and Joris, and he;
I gallop’d, Dirck gallop’d, we gallop’d all three;
“Good speed !” cried the watch, as the gate-bolts undrew;
“Speed!” echoed the wall to us galloping through;
Behind shut the postern, the lights sank to rest,
And into the midnight we gallop’d abreast.

...

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A Philosopher's View of "Darwinism"

 
Most people think of "Darwinism" as equivalent to "evolution" but that can't be right. There are some mechanisms of evolutionary change—like random genetic drift—that clearly don't fall under the general beliefs of Darwin and his modern followers.

In today's terminology, Darwinism refers to a worldview that emphasizes natural selection as the most important mechanism of evolutionary change. Some extreme Darwinists even deny that change by random genetic drift counts as evolution.

Those of us who adhere to a broader view of evolution are called "pluralists" because we we consider several different mechanisms of evolution and several different levels of evolutionary change.

Jim Lennox is a philosopher. He has written a revised version of the "Darwinism" entry in Stanford Encyclopedia of Philosophy [Darwinism]. Now we all know that philosophers can be wordy, if it can be said by a normal person in two paragraphs then a philosopher can't possible write anything less than a small book. However, at the very least you expect to see a conclusion that makes sense. Is "Darwinism" a viable position in the 21st century? What does "pluralism" mean?

And wouldn't you expect a serious discussion of adaptationism and how it relates to Darwinism? I would.

Read the entry and see if you can decide whether "Darwinism" is a good synonym for "evolution."

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[Hat Tip: John Wilkins]

Richard Dawkins' View of Random Genetic Drift

The Greatest Show on Earth is Richard Dawkins' latest book. It's his eighth book on evolution: the others are The Selfish Gene (1976), The Extended Phenotype (1982), The Blind Watchmaker (1986), River Out of Eden (1995), Climbing Mount Improbable (1996), Unweaving the Rainbow (1998) and The Ancestors Tale (2004).

I'm interested in the evolution of Richard Dawkins' ideas about evolution; in particular, his ideas about random genetic drift and mechanisms of evolution other than natural selection.

In Chapter 1 Dawkins says, "All reputable biologists go on to agree that natural selection is one of its most important driving forces, although—as some biologists insist more than others—not the only one."

This looks promising. Dawkins is saying— in chapter 1—that there are two mechanisms (driving forces) of evolution. He implies that he accepts random genetic drift as a "driving force" of evolution. (Assuming that random genetic drift is what he has in mind.) It's clear that "some biologists" have influenced him, although it's not clear from the sentence whether those biologists are "reputable"!

Since this is a book about the evidence for evolution, I eagerly anticipated his explanation of random genetic drift. Would it be as good as Jerry Coyne's?¹ In fact, I was so eager that I couldn't wait. I jumped to the index to look under "random."

Nothing. Not to worry. The other important mechanism must be here somewhere. Is it indexed under "genetic"? No. What about "drift"? No, not there either.

What gives? How can you write a book about evolution in the 21st century without mentioning random genetic drift as an important mechanism of evolution? Even the other adaptationist, Jerry Coyne, has it in the index to Why Evolution Is True.

Maybe Dawkins uses another term for the second mechanism of evolution. I recalled that he often gets mixed up about the difference between neutral theory and random genetic drift. Let's see if "Neutral Theory" is in the index. Nope.

What about "Kimura"? Success at last! Check out page 332.

Page 332 is in the middle of a section on The Molecular Clock in Chapter 10. It seems a bit late to begin discussing the second mechanism of evolution, but, as I said before, it's promising that Dawkins even concedes that there is one.

Dawkins explains that the reason why there's a molecular clock is because the majority of changes at the genetic level are neutral and these changes are fixed in a regular, clock-like, albeit stochastic, process. He then goes on to say...

When the neutral theory of molecular evolution was first proposed by, among others, the great Japanese geneticist Motoo Kimura, it was controversial. Some version of it is now widely accepted and, without going into the detailed evidence here, I am going to accept it in this book. Since I have a reputation as an arch-"adaptationist" (allegedly obsessed with natural selection as the major or even only driving force of evolution) you can have some confidence that if even I support the neutral theory it is unlikely that many other biologists will oppose it!

I can't think of any serious biologists who would deny that neutral mutations exist. The essence of Neutral Theory, or Nearly Neutral Theory as it is currently called, is undoubtedly correct. The fact that Richard Dawkins accepts it in this book is not remarkable. What's remarkable is that he has to tell us that he accepts it, especially in a book about the evidence for evolution.

Meanwhile, we are still waiting for the explanation of the "other" mechanism of evolution. The one that was mentioned in Chapter 1 when he said that natural selection does not account for all of evolution. He can't have been thinking about "Neutral Theory" since that's not a mechanism of evolution. And he can't just have been thinking about a mechanism for fixing neutral mutations since he surely knows that the "other" mechanism can result in the loss of beneficial alleles and the fixation of detrimental ones.

Still waiting. What we see in Chapter 10 is an explanation of neutral mutations but no mention of random genetic drift—the mechanism responsible for fixing neutral mutations in a population. He does briefly mention on page 335 that neutral mutations can "go to fixation by chance." I get the impression that he goes out of his way to not name the other mechanism of evolution. You know what I'm referring to, it's the mechanism that gets a whole chapter to itself in all the evolutionary biology textbooks [Evolution: Table of Contents].

Dawkins concedes that the vast majority of the human genome consists of sequences that aren't genes. Here's how he puts it ...

It is a remarkable fact that the greater part (95% in the case of humans) of the genome might as well not be there, for all the difference it makes. The neutral theory applies even to many of the genes in the remaining 5%—the genes that are read and used. It applies even to genes that are totally vital for survival. I must be clear here. We are not saying that a gene to which the neutral theory applies has no effect on the body. What we are saying is that a mutant version of the gene has exactly the same effect as the unmutated version.

In other words, the vast majority of the DNA in our genome is junk. Mutations that occur in junk DNA will become fixed in spite of the fact that they are not seen by natural selection. This is what he means when he says that most mutations are neutral and it's equivalent to saying that the dominant mechanism of evolution, in terms of overall frequency, is random genetic drift and not natural selection. I just wish he'd come right out and say it.

It's a shame that Dawkins does not actually mention the mechanism by which those neutral mutations become fixed but instead continuously refers to neutral theory as the alternate mode of evolution. The general public needs to hear about random genetic drift and Dawkins is—like it or not—the most prominent evolutionist on the planet.

Dawkins has not changed his mind about the existence of these neutral mutations and he has not changed his mind about their importance. While they may exist, they are not important as far as evolution is concerned. He makes this very clear—once again—in this book.

As it happens, it is probably true to say that most mutations are neutral. They are undetectable by natural selection, but detectable by molecular geneticists; and that is an ideal combination for an evolutionary clock.

None of this is to downgrade the all-important tip of the iceberg—the minority of mutations that are not neutral. It is they that are selected, positively or negatively, in the evolution of improvements. They are the ones whose effects we actually see—and natural selection "sees" too. They are the ones whose selection gives living things their breathtaking illusion of design. But it is the rest of the iceberg—the neutral mutations which are in the majority—that concerns us when we are talking about the molecular clock.

As geological time goes by, the genome is subjected to a rain of attrition in the form of mutations. In that small portion of the genome where the mutations really matter for survival, natural selection soon gets rid of the bad ones and favors the good ones. The neutral mutations, on the other hand, simply pile up, unpunished and unnoticed—except by molecular geneticists.

This is the way the adaptationist dismisses non-adaptive evolution. It's not really of interest to real biologists. It's only interesting to molecular geneticists. And we all know that those people are not real evolutionary biologists!

Now we come to one of the most interesting sentences in the entire book; at least as far as I'm concerned. As most Sandwalk readers know, we have long debated whether or not visible mutations can be neutral. Once you have an observed phenotype, can you ever attribute it to neutrality? Many adaptationists argue that you can't.

Here's what Richard Dawkins says in his latest book.

It is also possible (although "ultra-Darwinists" like me incline against the idea) that some mutations really do change the body, but in such a way as to have no effect on survival, one way or the other.

This is progress. Back when he wrote The Extended Phenotype, in 1982, Richard Dawkins said.

The adaptationism controversy is quite different. It is concerned with whether, given that we're 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 behavior are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976) 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 differences among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.

Finally, in 2009, Richard Dawkins admits that it is "possible" that visible mutations could be neutral. Hallelujah!

I'm looking forward to book #9.

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1. Jerry Coyne's View of Random Genetic Drift

Naked Adaptationism

 
Most other mammals think that humans are excessively ugly. They probably see us in the same way we see naked mole rats. We (mostly) have no hair.

What happened to our hair? There are many explanations for human hairlessness but they all share one common characteristic—they are adaptationist just-so stories.¹

If you're looking for the best example of an adaptationist then you need look no further than Elaine Morgan, author of the Aquatic Ape speculation [see Elaine Morgan and Aquatic Apes]. She has written an article for last week's issue of New Scientist: Why are we the naked ape?. It won't come as a big surprise to learn that she dismisses all of the speculations about the evolution of hairlessness, except one: we lost our hair because our ancestors lived in the water.

That's not the point I want to make. Here's what Elaine Morgan says in the first few sentences.

RIGHT from the start of modern evolutionary science, why humans are hairless has been controversial. "No one supposes," wrote Charles Darwin in The Descent of Man, "that the nakedness of the skin is any direct advantage to man: his body, therefore, cannot have been divested of hair through natural selection."

If not natural selection, then what?

The idea that our lack of hair might just be an accident is completely foreign to someone like Elaine Morgan. She's probably being deadly serious when she asks the question, "If not natural selection, then what?" For adaptationists, natural selection is the only game in town and no other sorts of explanation are possible.

If it's genetic and visible, then it must be an adaptation. If one just-so story is refuted then make up another one to take it's place. That's what the article is all about. One by one, she dismisses sexual selection, overheating on the savannah, neoteny, avoiding parasites, evaporating sweat, leaving only aquatic ape speculation that hasn't been refuted, or so she claims.

One of the problems with the adaptationist program was described by Gould and Lewontin (1979), "If one adaptationist argument fails, assume that another must exist ...." Why not start thinking about other, non-adaptationist explanations?

Why is that so hard?

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1. The one exception is the idea that our nakedness is an epiphenomenon resulting from neotony.

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.

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]