What Causes Speciation?

 
The latest issue or Science magazine contains a number of articles on speciation.

The one that most interests me is Schluter (2009), a paper that discusses mechanisms of speciation. Schulter begins with ...

It took evolutionary biologists nearly 150 years, but at last we can agree with Darwin that the origin of species, "that mystery of mysteries" (1), really does occur by means of natural selection (2–5). Not all species appear to evolve by selection, but the evidence suggests that most of them do. The effort leading up to this conclusion involved many experimental and conceptual advances, including a revision of the notion of speciation itself, 80 years after publication of On the Origin of the Species, to a definition based on reproductive isolation instead of morphological differences (6, 7).

I've heard this a lot recently but it doesn't make sense to me. How could the evolution of reproductive isolation be selected?

The main question today is how does selection lead to speciation? What are the mechanisms of natural selection, what genes are affected, and how do changes at these genes yield the habitat, behavioral, mechanical, chemical, physiological, and other incompatibilities that are the reproductive barriers between new species? As a start, the many ways by which new species might arise by selection can be grouped into two broad categories: ecological speciation and mutation-order speciation. Ecological speciation refers to the evolution of reproductive isolation between populations or subsets of a single population by adaptation to different environments or ecological niches (2, 8, 9). Natural selection is divergent, acting in contrasting directions between environments, which drives the fixation of different alleles, each advantageous in one environment but not in the other. Following G. S. Mani and B. C. Clarke (10), I define mutation-order speciation as the evolution of reproductive isolation by the chance occurrence and fixation of different alleles between populations adapting to similar selection pressures. Reproductive isolation evolves because populations fix distinct mutations that would nevertheless be advantageous in both of their environments. The relative importance of these two categories of mechanism for the origin of species in nature is unknown.

Is there an expert on speciation out there who can explain this? I understand how two incipient species can adapt to different environments and become morphologically distinct but I don't understand how this kind of adaptation leads to selection for reproductive isolation. This is a problem that we discussed earlier [Testing Natural Selection: Part 2].

The second mechanism is even more difficult for me. I understand how chance mutations can arise and become fixed but to my mind this isn't natural selection. It's speciation by random genetic drift. It's just an accident that the mutations being fixed in the separated populations happen to lead to reproductive isolation.

Schluter tells us that mutation-order speciation is "distinct from genetic drift." He seems to refer to it as "selection" of some sort without explaining why. ("The unidentified component of speciation, if built by selection and not genetic drift, could be the result of either ecological or mutation-order mechanisms.") He says that the mutations that give rise to reproductive isolation are "advantageous" in both populations but they just happened to occur in one of them and not the other. Again, the question is what sort of mutations favoring reproductive isolation would be "advantageous," and therefore selected?

If the mutation arises later on in the other species will it sweep to fixation and remove the reproductive isolation barrier?

It's not clear to me that we have identified the mechanisms of reproductive isolation in a large number of examples. Schluter seems to agree,

The most obvious shortcoming of our current understanding of speciation is that the threads connecting genes and selection are still few. We have many cases of ecological selection generating reproductive isolation with little knowledge of the genetic changes that allow it. We have strong signatures of positive selection at genes for reproductive isolation without enough knowledge of the mechanisms of selection behind them. But we hardly have time to complain. So many new model systems for speciation are being developed that the filling of major gaps is imminent. By the time we reach the bicentennial of the greatest book ever written, I expect that we will have that much more to celebrate.

Given our lack of knowledge how can biologists be so confident that Darwin was right? How do they know that most speciations are due to natural selection and not random genetic drift—especially since drift and accident seem to be intuitively more likely?

Is this an example of adaptationist bias or is there really lots of evidence to support speciation by natural selection?

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Schluter, D. (2009) Evidence for Ecological Speciation and Its Alternative. Science 323: 737 - 741 [DOI: 10.1126/science.1160006]

A Confused Philosopher

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

More calls to extend the defunct Modern Synthesis

Once again, a group of scientists want to extend and revise the Modern Synthesis version of evolutionary theory in order to bring their pet projects into the mainstream. Once again, these scientists seem to have missed the real revolution that took place 45 years ago so they are attacking a strawman. And, once again, they seem to think that the core principles of evolutionary theory can be defined by how complex animals evolve, ignoring bacteria and single-cell eukaryotes that have been at the heart of the history of life for 3.5 billion years.

But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown.
 &nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp &nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbspCarl SaganThe paper by Laland et al. (2015) was published in Proceedings of the Royal Society (UK) Series B just this month (August, 2015). The usual suspects are included in the author list including three of the Altenberg 16: Eva Jablonka, Gerd B. Müller, and John Odling-Smee. This is the same group that defended the "yes" side when Nature posed the question, "Does evolutionary theory need a rethink?" back in October, 2014 [see Rethinking evolutionary theory ].

Facts and theories of evolution according to Dawkins and Coyne

Sometime back in the pre-Cambrian (before blogs) there was a newsgroup called talk.origins—it still exists. In 1993 I wrote a little essay that tried to convince creationists¹ of the difference between facts of evolution and evolutionary theory [Evolution is a Fact and a Theory]. I relied heavily on Stephen Jay Gould's essay on "Evolution as Fact and Theory" originally published in Discover magazine in 1981 and re-printed in Hen's Teeth and Horse's Toes.

I updated my thoughts on Gould's essay in 2007 [Evolution Is a Fact and a Theory] and added some more comment on the 30th anniversary [Evolution Is a Fact and a Theory].

Lot's of other people have presented their take on the facts and theories of evolution. Here's one from Richard Lenski and another from Ryan Gregory.

Top Ten Evolution Articles from New Scientist

 
In my opinion, New Scientist is the best of the current crop of science magazines for the general public, although, in all honesty, the competition is not very challenging.

New Scientist has published Darwin's dangerous idea: Top 10 evolution articles. Most of them are fairly respectable. The main exception is an article on epigenetics [Rewriting Darwin: The new non-genetic inheritance]. That article is an embarrassment.

One of the best articles is Evolution: 24 myths and misconceptions. I've already posted my kudos at: Evolution: 24 myths and misconceptions. One of the nicest things about the series of articles is their description of random genetic drift as an important player in evolution; for example, Evolution myths: Natural selection is the only means of evolution.

Which brings me to the last article in the top ten list: Freedom from selection lets genes get creative. Here's what it says about random genetic drift.

Natural selection, first identified by Charles Darwin in On the Origin of Species, occurs when genetic mutations cause changes in the body and behaviour of an animal that affect its ability to survive and pass on its genes. Some mutations will have positive effects, others may kill an animal outright or somehow affect its offspring's ability to survive and reproduce. Harsh climates, sparse food and relentless predators destroy many individuals, leaving only those that survive best under exactly those pressures. As a result, the more intense the pressure of natural selection, the tighter the fit between a species and its niche.

So, what happens when the pressure is off? You might think there would be little impetus to adapt, so that species would pretty much stay the same. Not so, says Deacon. Animals still change because genes mutate all the time. The constant rewriting of DNA supplies the raw material from which natural selection picks its winners and losers, and when selection is relaxed, the process of weeding out is less ferocious. Instead, a process called genetic drift kicks in as mutations proliferate and animals with a much wider variety of traits are able to survive and reproduce. Some of the classic traits of a species may be lost, while others can arise for no reason other than that it simply doesn't matter if they do.

Close, but it doesn't quite merit a cigar. Drift does not "kick in" when selection pressure is lifted. Drift occurs all the time. It even competes with natural selection.

And while it's partially true that, "the more intense the pressure of natural selection, the tighter the fit between a species and its niche" it's also true that intense "pressure" increases the chance of extinction.

It seems strange that popular journals can publish articles about evolution that disagree with each other and nobody (editors?) seems to notice.

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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.

Motoo Kimura calculates a biochemical mutation rate in 1968

I recently had occasion to re-read a paper by Motoo Kimura from 1968. (Kimura, 1968). I noticed, for the first time, that he estimates a mutation rate based on his understanding of the error rate of DNA replication. He also makes a comment about creationists.

Remember, this was in 1968 and we didn't know as much then as we do now. Kimura took note of the fact that evolutionary trees based on comparing amino acid sequences gave rates of amino acid substitutions that seemed far too high. His conclusion is in the abstract.

Answering creationist questions about Neutral Theory

Many of the creationists are just learning about Neutral Theory for the first time in their lives. (The basics were published in the late 1960s—over 45 years ago.)

Vincent Torley (vjtorley), a philosopher from Australia, has struggled with the idea for several weeks and now he thinks he has some challenging questions for evolutionary biologists. Those creationists are really fast learners. It took me several years of study before I really grasped the basic concepts and the theory behind population genetics. Torley's questions are at: Will the real Neutral Theory please stand up?. The obligatory piling on by "News" is at: Is there a real neutral theory of evolution?.

Torley begins with ...

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.

The Evolution Poll of Sandwalk Readers

 
The poles are closed and the results are in. Richard Dawkins is the clear winner (boo!).

The good news is that 87% (499/573) Sandwalk readers have legitimate scientific views of evolution (Dawkins + Gould + Futuyma). Only a small number of readers are creationists or proponents of theistic evolution.

The bad news is that most readers are split between three different views of evolution. Some people have asked me to explain these three views so here's a brief summary of how I distinguish between Dawkins, Gould, and Futuyma.

Richard Dawkins holds the Charles Simonyi Chair for the Public Understanding of Science at Oxford University (UK). In his first book, The Selfish Gene (1976), he promoted the idea that evolution can be viewed as a competition between genes. This concept was amplified in The Extended Phenotype (1982) where he also answered the main criticism of the selfish gene concept. Dawkins' most popular book was The Blind Watchmaker, first published in 1986. In that book he made the case for design by natural selection and attempted to dismiss, or minimize, all other mechanisms of evolution. The emphasis on the power of natural selection was expanded in Climbing Mt. Improbable (1996).

Dawkins is the leading exponent of adaptationism—or Ultra-Darwinism—the idea that everything interesting in evolution can be explained by adaptation. This is especially true of traits that give rise to visible phenotypes. Dawkins is not very interested in macroevolution and he dismisses punctuated equilibria and species sorting. He believes, along with most adaptationists, that macroevolution is just an extension of natural selection acting on populations. (See RichardDawkins,net for a complete list of books and articles.)

Stephen Jay Gould was Alexander Agassiz Professor of Zoology at Harvard University from 1967 until his death in 2002.

He published Ontogeny and Phylogeny in 1977 where he made the case for a relationship between development and evolution. In The Mismeasure of Man (1981) he criticized biological determinism. Wonderful Life (1989) described the Burgess Shale fossils and explained Gould's ideas about the role of chance and contingency in evolution. In 2002, Gould published The Structure of Evolutionary Theory where he attempts to explain macroevolution, punctuated equilibria, and species sorting. These are part of Gould's hierarchical approach to evolutionary theory. Gould identifies himself as a pluralist—one who recognizes many different mechanisms of evolution that can give rise to important and interesting features. He tends to place much more emphasis on chance and accident in evolution than Dawkins.

Gould, along with Niles Eldredge, is famous for the concept of punctuated equilibrium. This is the idea that much of the change in the characteristics of species is concentrated in brief speciation (by cladogenesis) events.

Gould wrote a regular column for Natural History magazine and many of his articles have been collected in a series of anthologies: Ever Since Darwin, The Panda's Thumb, Hen's Teeth and Horse's Toes, The Flamingo's Smile, Bully for Brontosaurus, Eight Little Piggies, Dinosaur in a Haystack, Leonardo's Mountain of Clams and the Diet of Worms, The Lying Stones of Marrakech, and I Have Landed. Some of his essays and some of his scientific articles are widely cited. (For a complete list see SJG Archive.)


Douglas J. Futuyma is a Professor of Ecology & Evolution at the State University of New York at Stoney Brook. He is best known for his textbooks on evolution; Evolutionary Biology (1998) and Evolution (2005). His major research interests are evolutionary theory [see Hypotheses, Facts, and the Nature of Science] and the interactions of plants and insects [see Insect Pests: Resistance and Management].

Futuyma's view of evolution is different from that of Richard Dawkins because Futuyma is interested in random genetic drift and speciation. Futyuma is much more aware of population genetics than Dawkins or Gould and he (Futuyma) frequently refers to it in his books and papers. Unlike Gould, Futuyma is skeptical of punctuated equilibria and particularly species selection/sorting, although, ironically, he is credited with proposing the best explanation of the connection between cladogenesis and evolution.

You can check out some of Futuyma's ideas in this interview. In response to the question, "Is natural selection the only mechanism of evolution?", Futuyma replies,

No, certainly not. There cannot be evolution without genetic variation in the first place. So there must be mutation and often recombination to generate the different genotypes or the different versions of the genes, known as alleles, which then may or may not make a difference in the ability of an organism to survive and reproduce. You can’t have any evolutionary change whatever without mutation, and perhaps recombination, giving rise to genetic variation. But once you have genetic variation, there are basically two major possibilities:

First, there is simply no difference between the different genotypes or different genes in their impact on survival or reproduction, and in that case, you can have random changes of one versus the other type in a population or a species until eventually one replaces the other. That is an evolutionary change. It happens entirely by chance, by random fluctuations. That is what we call the process of genetic drift.

Genetic drift is very different from possibility number two, natural selection, which is a much more consistent, predictable, dependable change in the proportion of one gene vs. another, one genotype vs. another. Why? Simply because there is some consistent superiority, shall we way, of one genotype vs. another in some feature that affects its survival or some feature affecting its reproductive capabilities.

Neither Gould or Dawkins would respond in this way. Dawkins would admit to random genetic drift but downplay its importance. Gould would focus on higher mechanisms of evolution like species sorting.

Futuyma also thinks about the role of mutation in a different way than either Dawkins or Gould, especially Dawkins. While Dawkins is very much opposed to crediting mutations per se with any substantial influence on evolution, Futuyma is more sympathetic to a limited mutationism point of view. For example, when asked what would happen if the tape of life were re-played he says.

Of course, it wouldn’t be the same, because first of all, random processes are involved in the evolutionary process. For example, the origin of new mutations: a lot of evolution is dependent on particular mutational changes in genes that were very, very rare or unlikely, but that just happened at the right time, in the right species, in the right environment, but it need not happen that way. So, there’s this unpredictability.

This is very unlike Dawkins who is more inclined to think of evolution as design and strongly resists any attempt to sneak randomness into the equation. For the most part, Dawkins believes that all possible mutations will be available for selection so mutations can never determine the direction of evolution. Gould prefers to focus on developmental constraints as possible limits to the effectiveness of natural selection.

Don't call it "The Theory of Evolution"

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

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

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

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

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

Here's how Futuyma explains the concept of theory in his book Evolution 2nd ed. p. 613.

So is evolution a fact or a theory? In light of these definitions, evolution is a scientific fact. That is, descent of all species, with modification, from common ancestors is a hypothesis that in the past 150 years or so has been supported by so much evidence, and so successfully resisted all challenges, that it has become a fact. But this history of evolutionary change is explained by evolutionary theory, the body of statements (about mutation, selection, genetic drift, developmental constraints, and so forth) that together account for the various changes that organisms have undergone. [my emphasis ... LAM]

He makes the same point in the opening pages of his book where he uses both terms when discussing the history of evolutionary theory. (Note that when Darwin used the word "theory" to describe natural selection he was not using it in the same sense as Gould and Zimmer to describe a modern scientific theory. That's why Futuyma uses "hypothesis" in the quote below.)

We now know that Darwin's hypothesis of natural selection on hereditary variation was correct, but we also know that there are more causes of evolution than Darwin realized, and that natural selection and hereditary variation themselves are more complex than he imagined. A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitute our current theory of evolution, or "evolutionary theory." Like all theories in science, it is a work in progress, for we do not yet know the causes of all of evolution, or all the biological phenomena that evolutionary biology will have to explain. Indeed, some details may turn out to be wrong. But the main tenets of the theory, as far as it goes, are so well supported that most biologists confidently accept evolutionary theory as the foundation of the science of life. p. 14 [my emphasis ... LAM]

When you're talking about the mechanisms of evolution, please use "evolutionary theory" instead of "the theory of evolution."

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

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Razib Khan defends old-fashioned evolution theory

Razib Khan writes at Gene Expression. He's a big fan of personal genetics and genome sequencing and, in the past, has been a defender of the Modern Synthesis version of evolutionary theory. In light of the recent Nature discussion on "Does evolutionary theory need a rethink?" (Laland et al. 2014), Razib thought he would re-state his position [Evolution Ever Evolves].

I laid out my position in: Rethinking evolutionary theory. I don't think any of the new ideas like epigenetics, plasticity, facilitated variation etc. are about to change evolutionary theory significantly. However, I do think that the standard version of the 1940s Modern Synthesis was far too rigid and that a modern emphasis on population genetics (including Neutral Theory and more emphasis on random genetic drift) have significantly changed evolutionary theory—something close to a "revolution." The problem is that many scientists, and even many evolutionary biologists, haven't really integrated this change into their way of thinking. This resistance was very well described in a paper by Stephen J. Gould and Richard Lewontin over 45 year ago (Gould and Lewontin, 1978) [What Does San Marco Basilica Have to do with Evolution?]

I think there's already been a "revolution" but most people didn't notice and are still stuck in the 1940s adhering to an old-fashioned version of evolutionary theory that emphasizes adaptation.

Razib Khan doesn't like Gould and doesn't like new-fangled ideas like "neutralism" and "random genetic drift". Let's see what he thinks of the latest kerfluffle.

It seems that rather regularly there is a debate within evolutionary biology, or at least in public about evolutionary biology, where something new and bright and shiny is going to revolutionize the field. In general this does not pan out. I would argue there hasn’t been a true revolution in evolutionary biology since Mendelian genetics and classical Darwinism were fused in the 1920s and 1930s during the period when population genetics as a field was developed, and the famous "synthesis" developed out of the interaction of the geneticists with other domains of evolutionary relevance. This does not mean that there have not been pretenders to the throne. Richard Goldschmidt put forward his "hopeful monsters," neutralism reared its head in the 1970s, and evo-devo was all the rage in the 2000s. Developments that bore scientific fruit, such as neutralism, were integrated seamlessly into evolutionary biology, while those that did not, such as Goldschmidt’s saltationism fell by the wayside. This is how normal science works.

The main point here is whether Neutral Theory and an increased emphasis on random genetic drift "were integrated seamlessly" into the Modern Synthesis view that was popular in the 1960s. Is it true that the way modern population geneticists look at evolution is just a little bit different from the way evolutionary biologists thought about evolution in the 1920s, 1930s, and 1940s? I don't think so. I think there's been a significant shift—so much so that we can no longer refer to the "Modern Synthesis" as the most modern version of evolutionary theory.

Unlike Razib Khan, I am not convinced that most evolutionary biologists have made the shift. At my university, for example, the students must take a first-year course on evolution taught by members of the Dept. of Evolution & Ecology. I see these students in subsequent years and they don't understand the basics of population genetics. Nor do they appreciate the role of neutral alleles and random genetic drift. They are being taught the evolutionary theory of the Modern Synthesis (circa 1960).

Also the debates we are having over junk DNA suggests strongly that most scientists are not familiar with modern population genetics and Neutral Theory.

But every now and then you have a self-declared tribune of the plebs declaring that the revolution is nigh. For decades the late Stephen Jay Gould played this role to the hilt, decrying "ultra-Darwinism," and frankly misrepresenting the state of evolutionary theory to the masses from his perch as a great popularizer. More recently you have had more muted and conventional revisionists, such as Sean Carroll, who promote a variant of evo-devo that acclimates rather well to the climes of conventional evolutionary biology.

I do not believe that Gould misrepresented evolutionary theory to the masses. I believe that Richard Dawkins misrepresented evolutionary theory to the masses.

Like Razib, I'm not a big fan of evo-devo and I don't think it contributes much to fundamental evolutionary theory.

Nature now has a piece out which seems to herald the launching of another salvo in this forever war, Does evolutionary theory need a rethink? It’s written in the form of opposing dialogues. I’m very much in the camp of those believe that there’s no reason to overturn old terms and expectations. Evolutionary biology is advancing slowly but surely into new territory. There’s no problem to solve. The one major issue where I might have to make a stand is that it focusing on genetics is critical to understanding evolution, and dethroning inheritance from the center of the story would eviscerate the major thread driving the plot. The fact that evolutionary biologists have the conceptual and concrete gene as a discrete unit of information and inheritance which they can inspect is the critical fact which distinguishes them from fields which employ similar formalisms but have never made comparable advances (such as economics).

I agree with Razib Khan that genetics (population genetics) is the key to understanding evolutionary theory at the population level. I think we disagree on exactly what version of population genetics we support and on the importance of adaptation.

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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]

Laland, K., Uller, T., Feldman, M., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G. A., Hoekstra, H. E., Futuyma, D. J., Lenski, R. E., Mackay, T. F. C., Schluter, D. and Strassmann, J. E. (2014) Does evolutionary theory need a rethink? Nature 514, 163-165. [PDF]

The Cost of Introns

Michael Lynch estimates that the cost of adding an intron to an intronless gene is equivalent to adding about 31 bp of essential target (Lynch, 2010). This is roughly the number of base pairs in an average intron that have to be preserved in order for the intron to be properly spliced. Adding an intron increases the chances that a gene will be inactivated by mutation.

In spite of this deleterious cost, introns have spread in certain genomes; notably, in mammals and flowering plants. How do we explain the spread of introns? Is it consistent with the null hypothesis of random genetic drift?

According to Lynch the answer could be, yes. Here's what he says in his book The origins of genome architecture.

For newly arisen introns having no functional significance for the products of their host genes, the primary force opposing their ability to spread throughout a population is their excess mutation rate to defective allele(s), and because this force is expected to be quite weak, selection will be ineffective in preventing intron colonization in populations experiencing substantial levels of random genetic drift.

The selection coefficient for intron deletion has to be above a certain threshold in order to prevent introns from spreading. This threshold depends on the population size: in large populations the deleterious effect of introns is sufficient to ensure that they will be kept to a minimum, or eliminated entirely.

For species with small populations there will be a cutoff where the selection coefficient cannot overcome the effect of random genetic drift and intron insertion is effectively neutral.

Lynch calculates the cost of the extra target nucleotides as a function of the mutation rate (μ) and explains why the cutoff is 2N_gμ = 0.04 (N_g is the effective number of genes ~ 2N_e). You can estimate 2N_gμ by counting the nucleotide diversity at silent sites in protein-encoding genes (π_s). Thus, a plot of number of introns vs π_s [2N_gμ] is a test of the hypothesis.

Here's the figure from Lynch's book.

The data indicates that species with small values of π_s the spread of introns cannot be prevented even though introns may be deleterious. The cutoff is about 0.04 as predicted.

This does not prove that intron proliferation in some species is due to random genetic drift but it does show that the hypothesis cannot be ruled out. There's no need to invoke adaptive explanations for the initial spread of introns in vertebrate and plants genomes.

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Lynch, M. (2010) Rate, molecular spectrrum, and consequences of human mutation. Proc. Natl. Acad. Sci. USA 107:961-968. [doi: 10.1073/pnas.0912629107]

New Scientist doesn't understand modern evolutionary theory

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

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

Human Y Chromosome Mutation Rates

 
One thing men are really good at is making mistakes—just ask any woman. When it comes to mutations we are ten times better than women at ensuring the evolution of the species.

Knowing the actual rate of mutation in humans—or any other species—is important for many reasons. For one thing, it tells us about the maximum possible rate of evolution. For another, it gives us an important clue about the differences between beneficial, detrimental, and neutral alleles.

It's a lot more difficult to measure mutation rates than you might imagine. In theory, you could sequence the genomes of hundreds of parents and their offspring and identify mutations that must have occurred in the germ lines of the parents. In practice, this is far too expensive and time-consuming and, besides, it will miss any severely detrimental mutations.

But let's say you did the experiment in spite of the time and money. If the measured mutation rate turned out to be close to the calculated value, then you could assume that most of the mutations were neutral. A few might be beneficial.

Another possibility is to measure the number of differences between two individuals who are separated by a large number of generations. In this case you are measuring the combined effect of mutation and the fixation of alleles in a population. This is what we do whenever we compare gene sequences from different species.

Alleles can be fixed by natural selection or by random genetic drift. If most are fixed by natural selection (adaptation) then you'll learn very little about the overall mutation rate aside from a minimum estimate. That's because you don't know the fitness of every allele and how fast it became fixed in the population and you don't know how many mutations were detrimental or neutral, and what happened to them.

Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations must be neutral ones.

Motoo Kimura (1968)
However, you have a fighting chance if most mutations give rise to neutral alleles. In that case, the overall rate of fixation by random genetic drift is the same as the mutation rate [see: Random Genetic Drift and Population Size]. The data suggest that this is the correct scenario. When we compare individual genes from different species, the observed differences are consistent with the expected result if most of the differences are due to the fixation of neutral alleles by random genetic drift.

For the comparison between humans and chimpanzees, the estimated rates are remarkably consistent. They range from about 2 × 10^-8 to about 5 × 10^-8 mutations per nucleotide (base pair) per generation (Nachman, 2004; Britten, 2002). This agrees with the known error rate of DNA replication, which is about 10^-10 per nucleotide per replication. Since there are about 400 DNA replications between the male zygote and mature sperm, this translates to 4 × 10^-8 mutations per nucleotide per generation [see, Mutation Rates].

This is where men come in. There are many fewer cell divisions in the female line—about 30—so the egg contributes fewer mutations than the sperm. In fact, for most purposes we can ignore women in these calculations. Men have another big advantage. They have a Y chromosomes that's passed down directly from father to son and it doesn't recombine with any female chromosomes.¹ You don't need to worry about fixation.

If you sequence Y chromosomes from related men you can get a direct estimate of the mutation rate provided most of the alleles are neutral. It's best to choose men who are distantly related since there won't be many differences between closely related men. Two sons, for example, are likely to have identical Y chromosomes.

Xue et al. (2009) did the experiment [Human mutation rate revealed]. They sequenced the Y chromosomes of two men who were separated by 13 generations. After eliminating repetitive regions, the relevant region of comparison was 10.15 × 10⁶ nucleotides (base pairs, 10.15 Mb). The men differ at four confirmed sites. This gives a mutation rate of 3.0 × 10^-8 per generation or 0.75 × 10^-10 per nucleotide per DNA replication.

The agreement is remarkable. What this means is that we have a good handle on the mutation rate in humans and we have growing evidence that most mutations are neutral (i.e. most of our genome is junk).

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1. This isn't strictly correct but you can ignore the small regions where recombination is possible.

Britten, R.J. (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc. Nat. Acad. Sci. USA 99:13633-13635. [doi: 10.1073/pnas.172510699]

Nachman, M.W. (2004) Haldane and the first estimates of the human mutation rate. J Genet. 83:231-233. [PubMed]

Xue, Y., Wang, Q., Long, Q., Ng, B.L., Swerdlow, H., Burton, J., Skuce, C., Taylor, R., Abdellah, Z., Zhao, Y.; Asan, Macarthur, D.G., Quail, M.A., Carter, N.P., Yang, H., Tyler-Smith, C. (2009) Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree. Curr Biol. Aug 26. [Epub ahead of print] [doi: 10.1016/j.cub.2009.07.032]

Xue, Y., Wang, Q., Long, Q., Ng, B., Swerdlow, H., Burton, J., Skuce, C., Taylor, R., Abdellah, Z., & Zhao, Y. (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree Current Biology DOI: 10.1016/j.cub.2009.07.032

What is the Modern Synthesis?

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

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

Elizabeth Pennisi writes about Richard Lenski's long-term evolution experiment

Elizabeth Pennisi has written about the long-term evolution experiment of Richard Lenski [The Man Who Bottled Evolution]. The experiment is in it's 25th year and it is entirely appropriate that Science magazine devotes several pages to describing the results. There have been some remarkable discoveries.

But I want to focus on a couple of things that Pennisi says in her article. There has also been a discussion on Panda's Thunb: Lenski’s experiment: 25 years and 58,000 generations. Pennisi writes ...

Lenski's humble E. coli have shown, among other things, how multiple small mutations can prepare the ground for a major change; how new species can arise and diverge; and that Gould was mistaken when he claimed that, given a second chance, evolution would likely take a completely different course. Most recently, the colonies have demonstrated that, contrary to what many biologists thought, evolution never comes to a stop, even in an unchanging environment.

Let's talk about two issues in that paragraph.

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.]