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.

---

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]

A philosopher tells us how to think clearly about evolutionary causes ... avoid adaptationism

I think philosophy has lost its way. The discipline gives credence to religious philosophers who write about god(s) and to other philosophers who reject determinism and think the mind-body problem is still an open question. Philosophers still debate the validity of the ontological argument. Philosophers of science have not even settled the question of what is science, let alone come up with a valid answer of how to do it. There are few other disciplines that are still respected after several hundred years of trying, and failing, to answer the most fundamental questions in their field. Many academic philosophy department are hotbeds of political correctness and just plain politics.

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

---

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

---

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]

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

---

Why Pigs Don't Have Wings

 
Jerry Fodor publishes a critique of adaptationism in London Review of Books. The title is Why Pigs Don’t Have Wings and it's an excellent read. I wish I could write like this ...

In fact, an appreciable number of perfectly reasonable biologists are coming to think that the theory of natural selection can no longer be taken for granted. This is, so far, mostly straws in the wind; but it’s not out of the question that a scientific revolution – no less than a major revision of evolutionary theory – is in the offing. Unlike the story about our minds being anachronistic adaptations, this new twist doesn’t seem to have been widely noticed outside professional circles. The ironic upshot is that at a time when the theory of natural selection has become an article of pop culture, it is faced with what may be the most serious challenge it has had so far. Darwinists have been known to say that adaptationism is the best idea that anybody has ever had. It would be a good joke if the best idea that anybody has ever had turned out not to be true. A lot of the history of science consists of the world playing that sort of joke on our most cherished theories.

UPDATE: Read Jason Rosenhouse's take on the Foder essay [Fodor on Natural Selection]. Jason makes some good points but I think he misses the main idea; namely that many scientists (and philosophers) have an inordinate confidence in natural selection as the explanation for almost everything in biology that's important (to them).

---

[Hat Tip: Andrew Brown at Helmintholog: Adaptationism contested. Andrew is the author of "The Darwin Wars."]

[Photo Credit: Uncyclopedia.]

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.

Educating an Intelligent Design Creationist: The Meaning of Darwinism

Intelligent Design Creationists love to refer to their opponents as "Darwinists." We all know why they do it. It's a rhetorical device designed to belittle those who accept evolution. The term makes it look like evolutionary biologists worship a man who died 130 years ago and it implies that we still believe in nineteenth century science. The term "Darwinist" also makes it easy to associate modern scientists with social Darwinism. That's a common strategy employed by creationists of all stripes. I get it. It has nothing to do with scientific debates about evolution.

But sometimes rhetoric gets in the way of understanding. There seem to be a few (very few) Intelligent Design Creationists who genuinely want to understand the issues—even if their motive is still to push a scientific view of creationism. They pop up from time to time on the Intelligent Design Creationist websites. Andyjones seems to be one of them. (I'm giving him the benefit of the doubt.)

Visible Mutations and Evolution by Natural Selection

A recent posting [Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift] raised the issue of adaptationism. The controversy is over the main mechanism of genetic change in evolving populations. Adaptationists tend to attribute as much as possible to natural selection while pluralists emphasize the important role of other mechanisms of evolution, like random genetic drift.

There seems to be little doubt that most of the fixed alleles at the molecular level are probably neutral in their effect. Thus, they have been fixed by random genetic drift. This includes many amino acid substitutions in proteins. Even though these substitutions change the structure of a protein by a small amount, it does not seem reasonable to assume that they have all been selected.

Most adaptationists are content to concede this point (although there are holdouts). However, they draw the line at more "visible" mutations. According to this group, the vast majority of "visible" mutations are subject to natural selection and therefore most fixed alleles with a "visible" phenotype are adaptations. The argument seems to be that once a mutation produces a "visible" phenotype then it is not appropriate to suggest that it might be neutral with respect to natural selection. The line seems to be drawn somewhere above differences in the amino acid composition of proteins but it's not clear exactly where.

p-ter is one of those who are very reluctant to admit that a visible character could have been fixed by accident. He has posted a short article on Gene Expression [Do phenotypes evolve neutrally?]. I recommend that you read the comments to see examples of the extreme version of adaptationism. Most of these adaptationists will even argue that human blood types are adaptive. The idea that most native North Americans have type O blood is due to some undefined selective advantage and not to accident.

This argument has been going on for several decades. As usual, it's not about the existence of natural selection or random genetic drift. It's about their relative importance in evolution. To reiterate, the adaptationists believe that almost all mutations with a visible phenotype have been fixed by natural selection. The pluralists think that many of them are neutral and have been fixed by accident. The adaptationists make a distinction between what happens at the molecular level and what happens at the "visible" level while the pluralists think the same mechanims are operating at both levels.

Richard Lewontin uses the example of the Indian and African rhinoceros to focus the debate. The African rhinoceros has two horns while the Indian rhinoceros has only one. The question is whether this difference is due to natural selection—is two horns better than one in Africa? Or, is it just an accident of evolution that one species has two horns while the other has only one?



I don't understand why the adaptationist camp is so reluctant to admit that some visible characters can be fixed by random genetic drift. The idea that every feature of an organism has to be an adaptation seems so out of touch with our modern understanding of evolution that I'm really puzzled by the vehemence with which adaptationists defend their orthodoxy. It seems as though admitting that visible phenotypes might be non-adaptive is a major threat to their worldview.

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.

---

Good Science Writers: Steven Vogel

 
Steven Vogel is a Professor in the Biology Department at Duke University (N.C., USA). His main research interest is comparative biomechanics. He studies things like the design of fly wings and how organisms adapt to fluids (air and water). His secondary interest is science writing and he has published four books: Life's Devices: The Physical World of Animals and Plants (1988); Cats' Paws and Catapults: Mechanical Worlds of Nature and People (1999); Prime Mover: A Natural History of Muscle (2001); Comparative Biomechanics: Life's Physical World (2003).

The excerpt is from Life's Devises. Here, Steven Vogel gives as balanced a description of the use of "design" and "adaptation" as I've seen anywhere.

This book is mainly about organisms, so we will be concerned with a level of biological organization upon which the invisible hand of the selective process should incur fairly immediate consequences. It is the immediacy of operation of that unseen hand that makes organisms appear well designed—as a colleague of mine put it, "The good designs literally eat the bad designs." But it must be emphasized that we mean "design" in a somewhat unusual sense, implying only a functionally competent arrangement of parts resulting from natural selection. In its more common sense, implying anticipation, "design" is a misnomer—it connotes the teleological heresy of goal or purpose. Still, verbal simplicity is obtained by talking teleologically—teeth are for biting and ears for hearing. And the attribution of purpose isn't a bad guide to investigation—biting isn't just an amusing activity incidental to the possession of teeth. If an organism is arranged in a way that seems functionally inappropriate, the most likely explanation (by the test of experience) is that one's view of its functioning is faulty. As the late Frits Went said, "Teleology is a great mistress, but no one you'd like to be seen with in public."

We functional, organismic biologists are sometimes accused of assuming a kind of perfection in the the living world—"adaptationism" has become the pejorative term—largely because we find the presumption of a decent fit between organims and habitat a useful working hypothesis. But the designs of nature are certainly imperfect. At the very least, perfection would require an infinite number of generations in an unchanging world, and a fixed world entails not only a stable physical environment but the preposterous notion that no competing species undergoes evolutionary change. Furthermore, we're dealing with an incremental process of trial and error. In such a scheme, major innovation is not a simple matter—features that will ultimately prove useful are most unlikely to persist through stages in which they are deleterious or neutral. So-called hopeful monsters are not in good odor. Many good designs are simply not available on the evolutionary landscape because they involve unbridgeable functional discontinuities. Instead, obviously jury-rigged arrangements occur because they entail milder transitions. In addition, the constraints on what evolution can come up with must be greater in more multifunctional structures. Finally a fundamentally poorer, but established and thus well-tuned, design, may win in competition with one that is bascially better but still flawed.

I make these points with some sense of urgency since this book is incorrigibly adaptationist in its outlook and teleological in its verbiage. The limitations of this viewpoint will not insistently be repeated, so the requisite grain of salt should be in the mind of the reader as well as the author. Incidentally, the ad hoc character of many features of organisms are recounted with grace and wit in some of the essays of Stephen Jay Gould, not just as an argument against extreme adaptationism but as evidence for the blindly mechanical and thus somewhat blundering process of evolution. His collection entitled The Panda's Thumb (1980) is particularly appropriate here.

---

Richard Dawkins on Visible Changes and Adaptationism

On another thread [Visible Mutations and Evolution by Natural Selection] we are discussing a common adaptationist claim that once a mutation has a visible phenotype it is almost certainly subject to selection. Some people have questioned whether there is anyone who actually believes in such a thing. Here's Richard Dawkins writing in The Extended Phenotype (1982).

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.

In 2007 Dawkins would probably admit to some neutral examples of "genetically determined differences among phenotypes" but his position hasn't changed very much from 1982. For example, in The Ancestor's Tale (2005) he writes,

Contrary to my rather ludicrous reputation as an "ultra-Darwinist" (a slander I would protest more vigorously if the name sounded less of a compliment than it does), I do not think that the majority of evolutionary change at the molecular level is favoured by natural selection. On the contrary, I have always had a lot of time for the so-called neutral theory associated with the great Japanese geneticist Motoo Kimura, or its extension, the "nearly neutral" theory of his collaborator Tomoko Ohta. The real world has no interest in human tastes, of course, but as it happens I positively want such theories to be true. This is because they give us a separate, independent chronicle of evolution, unlinked to the visible features of the creatures around us., and they hold out the hope that some kind of molecular clock might really work.

Just in case the point is misunderstood, I must emphasize that the neutral theory does not in any way denigrate the importance of selection in nature. Natural selection is all-powerful with respect to those visible changes that affect survival and reproduction. 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.

Pluralists believe that all kinds of alleles are neutral or nearly neutral and are fixed in a population by random genetic drift. This includes alleles that produce a visible phenotype. Pluralists do not believe that there is a major distinction between the mechanisms of evolution at the molecular level and the mechanisms at the morphological level.

Contrary to Dawkins, I believe that Neutral Theory has reduced the importance of selection in nature. Prior to 1968 it was common to attribute almost all changes to natural selection and it was common to advocate that the presence of variation in a population was due to balancing selection. Today, one has to consider the evidence for adaptation; you can no longer just assume that it is the only game in town.

Of course it's true that natural selection is the only mechanism that affects allele frequencies once you can demonstrate that a visible change affects survival and reproduction. But Dawkins goes farther than that. He strongly implies that all visible phenotypes are subject to selection and neutral alleles are confined to the molecular level.

Literary Darwinism

 
A reader tells me that Trent University (Peterborough, Ontario, Canada) celebrated Darwin's birthday with a talk by Joseph Carroll on The Historical Position of Literary Darwinism. She asked me what I thought of Literary Darwinism.

I had never heard of it so I asked my good friend "Google" and he (she?) didn't disappoint. There's a Wikipedia entry on Darwinian Literary Studies (aka Literary Darwinism).

As Leda Cosmides and John Tooby indicate in their essay "The Psychological Foundations of Culture," scientific models and theories allow us to sense abstract objects and relationships just as our eyes and ears allow us to sense concrete ones. In Darwinian literary studies, as in evolutionary psychology, "[t]he tools of evolutionary functional analysis function as an organ of perception, bringing the blurry world of human psychological and behavioral phenotypes into sharp focus and allowing one to discern the formerly obscured level of our richly organized species-typical functional architecture."[2] In other words, since the human mind is embodied in evolving organic structures such as the brain, researchers should be able to explain aspects--not only of cognitive systems such as language ability, but of cultural systems such as art and literature--in terms of the environmental factors, or selection pressure, that give rise to them. A chief goal of Darwinian literary studies is to show how the reading and writing of literature contributes to the inclusive fitness of the human organism. In this sense the discipline relates closely to adaptationism, and it shares with the adaptationist social sciences the ultimate goal of understanding human nature.

So it's closely related to adaptationism and evolutionary psychology, eh? I don't think I'm going to like literary Darwinism. Sounds like just another misinterpretation of evolution by a bunch of non-scientists.

Let's look at an example.

A good example of applied Darwinian criticism is Joseph Carroll's reading of Pride and Prejudice, which shows how the fundamental biological problem of mate choice informs the plot of Austen's novel[3]. In this view, the novel narrates a social order in which males compete on the basis of socioeconomic attributes such as money and rank, whereas females compete according to 'personal' attributes such as youth and beauty. The story of Darcy and Elizabeth's courtship establishes a model for partial subversion of this social order, since the couple manage to abide by it even though the proximate causes of their mutual attraction have more to do with the conventionally undervalued attributes of dignity, honesty, kindness, and intelligence. A Darwinian critic might argue that the whole book functions as a tool for humans to perceive, order, and make sense of the conflicting impulses that characterize romantic relationships.

I don't know whether I count as a "Darwinian critic" or not but it seems to me that Austen is pointing out that women can be either smart or stupid when it comes to choosing a mate and so can men. Jane Austin is describing the breakdown of an English social order that existed prior to the nineteenth century. That social order is very different than those in other societies at the same time (e.g. India, China, North American natives), which, in turn, is probably nothing like the society of our ancestors 50,000 years ago. I don't see what this has to do with human evolution—or whatever these English scholars mean by "Darwinism."

---

Is lateral gene transfer (LGT) Lamarckian?

There's an interesting discussion going on about lateral gene transfer (LGT) in eukaryotes. LGT is the process by which DNA from one species invades the genome of another species. It was apparently very common among primitive bacteria several billion years ago and it's still quite common in modern bacteria.

There are many reports of LGT in eukaryotes but some of them seem to be due to contamination from bacteria rather than true LGT. Many scientists are skeptical of these reports; notably Bill Martin (Heinrich Heine Universität, Düsseldorf, Germany) who suggests that almost all of them are artifacts and lateral gene transfer in eukaryotes is extremely rare [see Lateral gene transfer in eukaryotes - where's the evidence?].

Richard Dawkins Is a Scholar and a Gentleman

Most of you think of Richard Dawkins as a "strident atheist" who doesn't suffer fools gladly.¹ The first part of that reputation ("strident atheist") is unjust as Dawkins pointed out on several occasions when he was in Toronto earlier this week.

The second part ("doesn't suffer fools gladly") is quite true. Dawkins thinks that foolish things, like religion and other superstitions, deserve to be ridiculed.

Richard Dawkins and I agree on atheism but disagree on some aspects of evolution. I'm pleased to report that he didn't hold that against me when we met for brunch a few days ago. I guess that means I'm not a fool in his mind!

For those of you who have never had the pleasure of meeting him, I want to assure you that in person he is a very pleasant fellow and lives up to the very British expression, "a scholar and a gentleman."

Some of the people I met were wondering about the reasons why I disagree with some aspects of Richard's views on evolution. They haven't heard of Stephen Jay Gould and I find that very sad. I still believe that everyone interested in evolution has to read and understand the "Spandrels" paper.

Here's a short reading list ....

Michael Lynch on Adaptationism
What Does San Marco Basilica Have to do with Evolution?
Michael Ruse Defends Adaptationism
Richard Dawkins' View of Random Genetic Drift

---

1. The phrase comes from the New Testament [Suffer fools gladly].

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.

---

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.

Ford Doolittle's Critique of ENCODE

Ford Doolittle has never been one to shy away from controversy so it's not surprising that he weighs in against the misleading publicity campaign launched by ENCODE leaders last September (Doolittle, 2013). Recall that Ewan Birney and other prominent members of the consortium promoted the idea that our genome contained an extensive array of regulatory elements and that 80% of our genome was functional [Ewan Birney: Genomics' Big Talker] [ENCODE Leader Says that 80% of Our Genome Is Functional] [The ENCODE Data Dump and the Responsibility of Scientists].

This is the fourth paper that's critical of the ENCODE hype. The first was Sean Eddy's paper in Current Biology (Eddy, 2012). The second was a paper by Niu and Jiang (2012), and the third was a paper by Graur et al. (2013). In my experience this is unusual since the critiques are all directed at how the ENCODE Consortium interpreted their data and how they misled the scientific community (and the general public) by exaggerating their results. Those kind of criticisms are common in journal clubs and, certainly, in the blogosphere, but scientific journals generally don't publish them. It's okay to refute the data (as in the arsenic affair) but ideas usually get a free pass no matter how stupid they are.

In this case, the ENCODE Consortium did such a bad job of describing their data that journals had to pay attention. (It helps that much of the criticism is directed at Nature and Science because the other journals want to take down the leaders!)

The selfish gene vs the lucky allele

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

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

Climbing Mount Improbable as Metaphor

 
One of my postings, Good Science Writers: Richard Dawkins, has been re-posted on RichardDawkins.net. This doesn't happen very often—in fact this may be the very first time. I can't imagine why they would have selected this particular posting.

I mentioned that some of the Dawkins metaphors are misleading and I suggested that Climbing Mount Improbable was one example. That prompted a comment from Richard Dawkins so I replied on his website. In case anyone is interested, I'm reproducing it here.

---

Richard Dawkins asks,

I am interested in the suggestion that Climbing Mount Improbable might not be an ideal title.

Richard, we've been over this ground before but for the benefit of the lurkers let me explain why I think the metaphor is inappropriate.

To begin with, you use the Mt. Improbable image as a metaphor for evolution. This is misleading since evolution encompasses more than just adaptation. It would be difficult to apply the "Climbing Mt. Improbable" metaphor to the organization of our genome, for example, since it's clearly not well-designed and could never be characterized as the peak of an adaptive landscape.

But even as a metaphor for adaptation the image is less than perfect. Most readers will see the peak of Mt. Improbable as a goal of adaptation, implying that evolution somehow recognizes that there is an ultimate perfection that all organisms seek to achieve by reaching the summit. As you well know (I hope) there are very few (any?) species that are perfectly adapted to their environment. If this were true, adaptation would cease because the species resides on the summit of Mt. Improbable.

Thus, in the real world, species tend to move about in the foothills rather than attempt to scale the highest peak. As long as they are good enough to survive and reproduce that's all that's required.

Yes, some individuals within the population might acquire a mutation that makes them a little more fit but in most cases the selective advantage will be too small to make much of a difference. I don't believe there's any great pressure to get to the top of Mt. Improbable. That's why we usually don't see perfection in nature. And it explains why most organisms do not look as though they have been designed by some intelligent being. If anything the "design" looks more like a Rube Goldberg creation, and I doubt that anyone would say that those creations represent the peak of perfection.

I prefer a different view of evolution, one that emphasizes chance and accident [Evolution by Accident]. For me, the metaphor of "Climbing Mt. Improbable" is quite wrong as a metaphor of evolution.

Now, I understand that you disagree about the role of chance and accident. You say, for example, on page 326 of Climbing Mt. Improbable, "It is all the product of an unconscious Darwinian fine-tuning, whose intricate perfection we should not believe if it were not before our eyes" (referring to the evolution of figs and fig wasps). For someone who believes that such a description is characteristic of most evolution (adaptation) the "Climbing" metaphor may seem quite appropriate.

BTW, I agree with you that your case for adaptationism is much stronger in Climbing Mt. Improbable than in The Blind Watchmaker. I especially like the chapter you mention, The Museum of All Shells, where you discuss - among other things - the contrast between your view of evolution and the mutationist view. Ironically, you begin that discussion by pointing out that this is a sophisticated controversy, "... and Mount Improbable, even in its multiple-peaked version, isn't a powerful enough metaphor to explore it."

---