The "Null Hypothesis" in Evolution

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution

Theme

Better BiochemistryTansey et al. (2013) have described the five core concepts in biochemistry and molecular biology. These are the fundamental concepts that all biochemistry instructors must teach and all biochemistry students must understand.

The five core concept categories are:

1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
5. macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]

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]

What Is Darwinism?

Over on the thread Close, but no cigar we're having a little discussion about the meaning of the term "Darwinian." I explained it as "evolution by natural selection."

Pete Dunkelberg is one of those people who emphasize natural selection in their discussion of evolution and he didn't like my description of Darwinian evolution. Pete said,

Misbegotten terminology. "darwinian processes" is creationist coinage with no meaning.

Talking of "darwinism" in biology is akin to talking of "newtonism" in physics: a bad idea. Aren't you glad physicists don't use terms like that to make polemics against each other?

wolfwalker asks: Larry, what do people mean by [these unneeded terms]? Larry tells him what Larry means. But the terms have no standard meaning. Larry's official ruling is that Darwin never heard of variable rates of morphological evolution and also thought selection was all.

It is patently untrue that the term "Darwinian" has no meaning in biology. Pete's position is that "Darwinist" refers to evolutionary biologists who no longer exist. He seems to think that everyone has become a pluralist these days. I beg to differ.

Core Darwinism, I shall suggest, is the minimal theory that evolution is guided in adaptively nonrandom directions by the nonrandom survival of small hereditary changes.... Adaptive does not imply that all evolution is adaptive, only that core Darwinism's concern is limited to the part of evolution that is.

Dawkins, R. (2003) The Devil's Chaplain p. 81 In physics, everyone knows that Newtonian physics has been extended in the twentieth century so that it's no longer accurate to refer to oneself as a Newtonian physicist since it implies ignorance of relativity. But this is a bad analogy since there are a great many evolutionary biologists (and even more of the other kinds of biologists) who are proud to call themselves Darwinists. Modern Darwinists place a great deal of emphasis on adaptation and natural selection as the main mechanisms of evolution.

Pete is dead wrong when he claims that, "Larry's official ruling is that Darwin never heard of variable rates of morphological evolution and also thought selection was all." I never said any such thing. I'm well aware of the fact that Darwin considered variable rates of natural selection and I'm well aware of the fact that he accepted other mechanisms of evolution, such as a watered down version of Lamarckism. The problem here seems to be that Pete doesn't understand the meaning of gradualism and he doesn't understand that modern Darwinists do not attribute everything in biology to selection.

As for the standard meaning of "Darwinism," Pete is correct to say that there is no universally accepted definition but that shouldn't be a surprise to anyone. There's hardly anything that all biologists can agree on.

However, there is a considerable group of evolutionary biologists who agree with Ernst Mayr when he says ...

After 1859, that is, during the first Darwinian revolution, Darwinism for almost everybody meant explaining the living world by natural processes. As we will see, during and after the evolutionary synthesis the term "Darwinism" unanimously meant adaptive evolutionary change under the influence of natural selection, and variational instead of transformational evolution. These are the only two meaningful concepts of Darwinism, the one ruling in the nineteenth century (and up to about 1930) and the other ruling in the twentieth century (a consensus having been reached during the evolutionary synthesis). Any other use of the term Darwinism by a moder author is bound to be misleading.

Mayr, E. (1991) What Is Darwinism? in One Long Argument p. 107.

See Why I'm Not a Darwinist for an earlier use of this quotation. The point is that the modern meaning of Darwinism is usually taken to mean an emphasis on natural selection.

Mayr explains the standard adaptationist view of random genetic drift by equating it with Neutral Theory and mischaracterizing the entire controversy. (This seems to be a very common trait among the defenders of strict Darwinism.)

The neutralists are reductionists, and for them the gene—more precisely the base pair—is the target of selection. Hence, any fixation of a "neutral" base pair is a case of neutral evolution. For the Darwinian evolutionists, the individual as a whole is the target of selection, and evolution takes place only if the properties of the individual change. A replacement of neutral genes is considered merely evolutionary noise and irrelevant for phenotypic evolution. (ibid p. 152)

I'm not making this up. I'm trying to do my best to represent the standard—but not universal—description of the adaptationist position. It's quite wrong for Pete Dunkelberg to pretend that the definition of Darwinism and the adaptationists is something that I created. (BTW, most pluralists treat the individual as the unit of evolution. They just believe that populations can fix alleles, even alleles with visible phenotypes, by random genetic drift as well as natural selection.)

Mayr continues,

The Darwinian wonders to what extent it is legitimate to designate as evoluton the changes in gene frequencies caused by nonselected random fixation. In some of the older (particularly nineteenth century) literature on evolution, one finds discussions on how to discriminate between evolution and mere change. There it was pointed out that the continuing changes in weather and climate, the sequences of the seasons of the year, the geomorphological changes of an eroding mountain range or a shifting river bed, and similar changes do not qualify as evolution. Interestingly, the changes in nonselected base pairs and genes are more like those nonevolutionary changes than they are like evolution. Perhaps one should not refer to non-Darwinian evolution but rather to non-Darwinian changes during evolution. (ibid p. 153)

While this position may seem extreme by 2007 standards, I believe that there are many evolutionary biologists who tend to dismiss all nonselected evolutionary change as uninteresting and unimportant. They are Darwinists. The extremists among this group attribute all kinds of things to adaptation, including most animal behavior. They are the ultra-Darwinians.

Many books have been written about the controversy in evolutionary biology between the adaptationists and the pluralists. Michael Ruse, for example, tried to explain it all last year (2006) in Darwinism and Its Discontents. Ruse is a firm believer in Darwinism, which he defines as "natural selection as the chief causal process behind all organisms." This is a common definition as explained above. However, one must read between the lines to see how Darwinists interpret that definition. A key point is what they think about random genetic drift. Here's how the Darwinist Ruse treats Sewall Wright's concept of random genetic drift.

Wright's theory is not very Darwinian. Natural selection does not play an overwhelming role. Genetic drift is a key player in Wright's world. However, although many of these ideas were taken up by later thinkers, especially by Theodosius 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 (Lewontin, 1981). 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.

Michael Ruse is not an evolutionary biologist but he represents the views of Dawkins and, to a lesser extent, E.O. Wilson. They have no use for drift especially when it comes to visible characteristics. That's the hallmark of modern Darwinism.

So, is it true that no evolutionary biologist would want to say that drift is a major player in evolution? Of course not. There are lots of them who say exactly that in spite of what Michale Ruse would have you believe. Does Ruse have an answer to these "discontents?" Yes, he does ...

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

To which I reply, you took the risk and your scholarship has been discredited. I can't speak for God.

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 ...

Teaching Evolution in Natural History Museums

 
In an article published last November in Trends in Ecology & Evolution, Bruce MacFadden urges that natural history museums explore the use of new displays, such as those involving genomics and molecular biology, to educate the general public [Evolution, museums and society].

He writes ...

Public understanding of evolution has changed little over the past quarter-century [4]. The challenge therefore remains for natural history museums to improve communication about evolution, particularly the more difficult concepts.

MacFadden notes that museum visitors are more likely to accept evolution. Museums need to do a better job of taking advantage of this fact in order to enhance understanding of evolution.

Evolution represents a complex array of concepts, some of which are well understood whereas others are poorly understood by museum visitors. If an institution is committed to improving public understanding about evolution, then additional resources and effort should be directed toward more effectively communicating the more poorly understood concepts such as natural selection.

Yes, natural selection is difficult but random genetic drift is even more difficult. Unfortunately, I don't get the impression that MacFadden is counting random genetic drift as one of the basic concepts that museum visitors need to learn about.

One solution is to create displays about molecular evolution.

In this regard, there is much room to highlight research traditionally not considered to be natural history, such as genomics and molecular biology [9], although these subjects are not usually specimen based and therefore potentially less attractive to the public. In these instances, visitors are more likely to grasp difficult concepts when they have some prior understanding of a topic [10], or can place these concepts in a modern-day societal context. For example, disease vectors such as influenza and malaria mutate rapidly to become drug resistant, and therefore have negative consequences for world health.

This is a good idea. I recently visited the American Natural History Museum in New York and it had an excellent display on molecular evolution. It showed how you could compare DNA sequences and it explained that many of the mutations were just accidents that became fixed in the population by genetic drift. It even mentioned junk DNA and messy genomes.

It was a very popular display. Not only did it highlight some of the most important evidence for the history of life, it also explained the two main mechanisms of evolution. There were more people reading the material in the molecular evolution area than in the more traditional fossil areas. DNA is exciting.

Kotiaho et al. (2009) disagree. In the June issue of Trends in Ecology & Evolution they write [Evolution education in natural history museums ] ...

In his essay, MacFadden advocates the allocation of resources into novel contents, such as genomics or molecular biology, in order to increase the public understanding of evolution. We argue that museums should concentrate more on demonstrating the basic principles and outcomes of natural selection, rather than presenting fashionable novel contents such as genomics (which, it seems, even scientists often have a hard time understanding [4]).

It's clear that Kotaiho et al. see natural selection as the main (only?) mechanism of evolution. What they want is the kind of display that illustrates natural selection. They like dioramas.

If we want to educate the visitors of natural history museums about evolution by means of natural selection, we should aim at delivering the message that across species there is enormous within-species variation, that some of this variation is likely to cause differences among individuals in their lifetime reproductive success and that these differences will result in a constant change – evolution. In museums, we have a great opportunity to do this; as well as the exhibits open to the public, museums usually have extensive collections containing numerous individuals of each species. A simple illustration of the replacement of one generation by the next generation might work in making the operation of natural selection more tangible. With such an illustration, we can easily see why and how a population can undergo constant change, and thus grasp the basic principles of evolution by means of natural selection.

Natural history museums are our collective memory of the past. Their collections can, and have been, used to study evolution (e.g. [7]). Perhaps even more importantly, however, they could also be used to illustrate to the general public the evolutionary changes that have taken place. We challenge the exhibit designers of natural history museums to emphasize variation within species, and to demonstrate change due to natural selection, rather than stasis in nature.

Here's the problem. It might be fine to mount a display showing variation within a population. It might be possible to construct a display where the next generation has a different degree of variation. But it would be wrong to attribute that to natural selection unless you could present evidence that there were fitness differences associated with those variants.

I fear that these authors are not distinguishing between evolution and natural selection. They think that evidence of evolution is evidence of natural selection.

I don't understand why Kotaiho et al. would want to ignore molecular evolution and genomics. There's no better way to illustrate random genetic drift and there's no excuse for eliminating one of the most important fields in modern evolutionary biology.

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Michael Ruse Defends Adaptationism

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

A philosopher's view of random genetic drift

Random genetic drift is a process that alters allele frequencies within a population. The change is due to "random" events. It differs from natural selection where the change is due to selection for alleles that confer selective advantage on the reproductive success of an individual. Here's one description,

If a population is finite in size (as all populations are) and if a given pair of parents have only a small number of offspring, then even in the absence of all selective forces, the frequency of a gene will not be exactly reproduced in the next generation because of sampling error. If in a population of 1000 individuals the frequency of "a" is 0.5 in one generation, then it may by chance be 0.493 or 0.505 in the next generation because of the chance production of a few more or less progeny of each genotype. In the second generation, there is another sampling error based on the new gene frequency, so the frequency of "a" may go from 0.505 to 0.501 or back to 0.498. This process of random fluctuation continues generation after generation, with no force pushing the frequency back to its initial state because the population has no "genetic memory" of its state many generations ago. Each generation is an independent event. The final result of this random change in allele frequency is that the population eventually drifts to p=1 or p=0. After this point, no further change is possible; the population has become homozygous. A different population, isolated from the first, also undergoes this random genetic drift, but it may become homozygous for allele "A", whereas the first population has become homozygous for allele "a". As time goes on, isolated populations diverge from each other, each losing heterozygosity. The variation originally present within populations now appears as variation between populations.

Suzuki, D.T., Griffiths, A.J.F., Miller, J.H. and Lewontin, R.C.
in An Introduction to Genetic Analysis 4th ed. W.H. Freeman (1989 p.704)

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.

Richard Dawkins' View of Random Genetic Drift

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The adaptationism controversy is quite different. It is concerned with whether, given that we're dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist's "neutral mutations" are more than neutral. As far as those of us who look at gross morphology, physiology and behavior are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976) wrote: "I interpret 'rate of evolution' as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution ..." If a whole organism biologist sees a genetically determined differences among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.

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

I'm looking forward to book #9.

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1. Jerry Coyne's View of Random Genetic Drift

Have Humans Stopped Evolving?

Yesterday's Quirks & Quarks radio show had a segment on human evolution. Here's the description from their website:

January 6, 2007: Are Humans Still Evolving?

Evolution has made us what we are today, and we're increasingly learning what made modern humans different from our ancestors. But many scientists think that we have now removed nature's control over our genetic legacy. Our technology allows us to control our environment and survival to the degree that we may have stopped human evolution altogether. Is our growth and development as a species at a standstill? If not, what will we become in the future? Find out this week on Quirks & Quarks.

Listen to the podcast. The segment on human evolution starts about one third of the way through the show.

The idea that humans have stopped evolving is ridiculous. It reflects a deep and fundamental misunderstanding of evolutionary theory.

Fortunately, the blurb on the website doesn't reflect what was broadcast. The host, Bob McDonald actually does a very good job of sorting through the rhetoric and the show is an excellent summary of current scientific thinking. It's by far the best thing about the rate of human evolution that I've ever heard on public radio.

One of the people interviewed on the show is Steve Jones from University College, London. Jones claims that almost everyone is reproducing these days so natural selection isn't affecting humans any more. He contrasts the situation today with that in Shakespeare's time when 2 out of 3 babies didn't survive to adulthood.

This is one of the weaker parts of the show. The claim that natural selection isn't working on humans is false. It is refuted by Jones himself later on in the broadcast, and by Noell Boaz from Ross University in Dominica.

Let's deal with the increase in longevity that we've seen in some societies over the past 500 years. We'll dismiss the obvious bias in equating what happens in Caucasian societies with evolution of the entire species. What about the fact that people in London live longer today that they did in 1600? Does this have anything to do with evolution?

Jones thinks so. He says,

Now a lot of those deaths in the old days were due to genetic differences but if everybody stays alive, everybody gets through, no more natural selection.

I don't think so. It isn't obvious to me that people were surviving in 1600 because they had better genes. People died for all kinds of reasons that had nothing to do with genes. A famous example from the nineteenth century was the London cholera outbreak. In that case, you died if you were close to the contaminated Broad Street Pump and not because you had bad genes.

If you died of infection or malnutrition in 1600 it was probably due to bad luck and not bad genes. As living conditions improved, everyone benefited equally, not just those who might have been genetically susceptible. Thus, natural selection wasn't all that important back then and most of the improvements in health in developed countries have affected evolution directly. (The quibblers are waiting to pounce, so let me address two objections to that statement. First, there are other, more modern, medical advances that do affect selection—wait for them. Second, there are some examples of genetic effects on whether you survive disease. Some people might have been more resistant to the Black Plague, for example. Such examples are exceptions to the rule. The common assumption that most deaths in the past had something to do with natural selection is what I'm addressing here.)

So, let's be skeptical about the specific argument that Jones is making, namely that increased longevity, per se, is proof that the effect of natural selection is diminished in modern societies. A lot of negative selection—selection against less fit individuals—is still taking place in utero just as it always has. Lethal mutations result in spontaneous abortion or failure to produce viable sperm and eggs. This form of natural selection hasn't changed significantly. Also, even though severely handicapped children born today may survive longer, they probably won't reproduce.

On the other hand, there are medical advances that do affect natural selection. The most obvious one is the invention of eyeglasses. As Jones points out in the show, people with a genetic disposition for bad eyesight can now survive whereas back in the hunter-gatherer days it might have been much more difficult. Thus, natural selection in favor of good eyesight has been relaxed because of eyeglasses.

What does that mean for human evolution? To its credit, the Quirks & Quarks show doesn't jump to the false conclusion so common among the general public. Evolution hasn't stopped, it has increased! The removal of negative selection causes previously detrimental alleles to survive in the population; therefore, their frequency increases. Thus, evolution is happening today but was blocked by negative selection in the past.

The same argument applies to all medical advances that allow for previously handicapped individuals to survive in modern society. Human evolution is being accelerated. This is a point worth emphasizing because the opposite conclusion is so common. Most people think that removing strong negative selection means that evolution has stopped when, in fact, the exact opposite is true! The misconception arises because the general public thinks of evolution as a progressive improvement in the gene pool. Modern medicine is allowing "defective" individuals to survive. This can't be evolution according to that false understanding of evolution. (There are other things wrong with that false argument; namely, the concept that people with myopia or diabetes are somehow lesser citizens. This isn't the place to get into that discussion.)

Strong negative selection acts as a brake on evolution. It slows evolution down. Remove the brake, and evolution speeds up.

There's more to evolution than natural selection. Bob McDonald interviews Katherine Pollard from the University of California, Davis. She points out that much of evolution is due to random genetic drift. Drift has nothing to do with natural selection, so whether or not selection has decreased will play only a minor role in whether humans are evolving. You can't stop drift and you can't stop mutations. You can't stop human evolution. As McDonald puts it, "we still will evolve ... it's not the kind of evolution we imagine."

Evolution is not just the result of survival of the fittest. Furthermore, it is not progressive in spite of the fact that this misconception is widespread. As McDonald says in closing, "... this is an illusion about the way that evolution works. Evolution has never guaranteed improvement or progress, just change."

Change is good. It's good that humans are evolving. Things can only get better, right?

Teaching IDiots About Evolution

 
The National Academies (Science, Engineering, Medicine) (USA) have just published their latest book on the evolution/creationism controversy. You can download it for free on their website [Science, Evolution, and Creationism].

The book attempts to define evolution and it doesn't do a bad job of describing a minimal definition that would be acceptable—that is if you only look at the actual definition. Here it is from page 5.

Evolution consists of changes in the heritable traits of a population of organisms as successive generations replace one another. It is populations of organisms that evolve, not individual organisms.

Sandwalk readers will know that this is the kind of definition that I prefer as well [What Is Evolution?]. This sort of definition is neutral with respect to mechanisms. It doesn't matter whether evolution occurs by natural selection, random genetic drift, of something else entirely. That's just as it should be because the explanation of how evolution occurs lies properly in the domain of evolutionary theory. Thus, we can say that evolution is a fact because we see it happening and we have overwhelming evidence that has happened in the past. We can be confident that it is a fact even though we may not be as certain about how it happened.

Once we start committing to an explanation we can no longer talk about facts, in many cases, since the exact mechanism of evolution is often disputed. The National Academies book begins with a wonderful description of Tiktaalik, a fossil animal that shares characteristics of both fish and primitive tetrapods. It is strong evidence in support of the evolution of tetrapods from fish and that lineage is now considered to be a well established fact.

However, it would be wrong to use Tiktaalik as support for a particular mechanism of evolution. The fossil suggests that natural selection is playing a role but random genetic drift is not ruled out. We know from other sorts of data that natural selection and random genetic drift are facts, as well as being part of evolutionary theory, but it's a good idea to draw a distinction between evolution, the process, and theories about how it occurs. This is especially true when trying to explain things to IDiots.

Unfortunately, the authors of Science, Evolution, and Creationism don't do as good a job in this regard as they should have. For example, the (reasonably correct) definition that I quoted above is found at the end of a paragraph that weakens it considerably. Here's the entire paragraph ...

If a mutation increases the survivability of an organism, that organism is likely to have more offspring than other members of the population. If the offspring inherit the mutation, the number of organisms with the advantageous trait will increase from one generation to the next. In this way, the trait — and the genetic material (DNA) responsible for the trait — will tend to become more common in a population of organisms over time. In contrast, organisms possessing a harmful or deleterious mutation are less likely to contribute their DNA to future generations, and the trait resulting from the mutation will tend to become less frequent or will be eliminated in a population. Evolution consists of changes in the heritable traits of a population of organisms as successive generations replace one another. It is populations of organisms that evolve, not individual organisms.

The next paragraph then goes on to describe natural selection. There is no mention of random genetic drift anywhere in the book, although there is a passing reference to the fact that neutral mutations can be fixed. This reference is found on page 29 near the end of the book.

The net result is that evolution the process, is intimately connected to the mechanism of natural selection in this book. Readers will assume that scientists equate evolution with natural selection and use the terms interchangeably.

Why is this a problem? Well, for one thing, it's wrong. Normally that should be a good enough reason to avoid such errors, but these days there's a movement afoot to frame evolution in a way that resonates with the general public. Perhaps it's okay to define evolution as natural selection if it helps educate the average person? I object to such reasoning in the strongest possible terms. The essence of science is being honest and accurate and those goals should never be sacrificed for political gain. It may be easier to avoid confusion by not mentioning other mechanisms of evolution but the end result is that the public is not being educated correctly about evolution. You can't then turn around and complain that the public doesn't understand evolution.

The IDiots are upset about this book. They have found many ingenious ways of criticizing the contents. Here's a perfect example from Casey Luskin [The Facts about Intelligent Design: A Response to the National Academy of Sciences’ Science, Evolution, and Creationism].

I don't have the time, or the patience, to correct everything that's wrong with this article but there's one point I'd like to address. Here's what Casey Luskin says about evolution.

The NAS unscientifically elevates evolution to the status of unquestionable dogma.

The NAS defines evolution as evolution by natural selection and claims that “[t]here is no scientific controversy about the basic facts of evolution,” asserting that evolution is “so well established that no new evidence is likely to alter” it. In doing so, the NAS treats Neo-Darwinian evolution like an unquestionable dogma, not like a science. Such proclamations from the NAS are dangerous because they threaten the prestige of the NAS as an objective and trustworthy voice advising society.

Moreover, the NAS’s claim that there is no controversy over evolution is a bluff, for there is significant scientific dissent from the view of evolution by natural selection. Leading biologist Lynn Margulis, who opposes ID, criticizes the standard Darwinian mechanism by stating that the “Darwinian claim to explain all of evolution is a popular half-truth whose lack of explicative power is compensated for only by the religious ferocity of its rhetoric.”[7] She further observes that “new mutations don’t create new species; they create offspring that are impaired.”[8] In 2001, biochemist Franklin Harold admitted in an Oxford University Press monograph that "there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”[9] Other scientists have gone much further.

Over 700 doctoral scientists have signed a public statement asserting their agreement that they "are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life."[10] But what are these scientists to do when the top scientific organization in the U.S. proclaims that evolution is as unquestionable as the existence of atoms or the heliocentric model of the solar system? Clearly the NAS’s statements threaten the academic freedom of scientists to dissent from Neo-Darwinian evolution.

In the past it has been easy to show that the IDiots are either mistaken or lying when they make comments like this. I've said many times that they deliberately try to confuse people by making it seem as though evolution, the fact, is the same as natural selection, the mechanism. They know full well that there's a difference between controversies over the sufficiency of natural selection and whether evolution, per se, is overwhelmingly support by hard evidence. They know that evolution is not the same as Darwinism and attacks on Darwinism are not the same thing as attacks on evolution.

This rebuttal is now a bit more difficult with the publication of Science, Evolution, and Creationism. Nowhere in the book do the authors deliberately make the distinction between natural selection and evolution and nowhere do they mention any other mechanism of evolution (e.g., random genetic drift). When reading the book, most of us recognize that there are abundant, oblique, references to the fact that the authors are not stupid, but that is only apparent to scientists who know about evolution.

Casey Luskin has taken advantage of this lost opportunity on the part of the National Academies to make it look like they are being dogmatic and forcing everyone to accept Darwinism. When I decided to write about Luskin's silly article, I thought it would be easy to refute what he was saying by referring back to the book. I thought the book would make it clear that evolution is not the same as natural selection. Unfortunately, there's nothing I can quote from the book that explicitly makes that point even though it's there implicitly. That's a missed opportunity that I hope can be remedied in future printings.

---

On being outed as a closet Darwinist, again

I can understand why the Intelligent Design Creationists want to label me as a Darwinist, but John Wilkins? What's his motive?

He writes [Closet Darwinism, and definitions],

Larry’s argument is roughly this: modern evolutionary theory includes a host of ideas that do not rely upon the ubiquity of natural selection. "Darwinism" and cognates is basically a focus upon natural selection (and hence adaptationist views of biology). Ergo, modern evolutionary theory is not “Darwinian” in the main. I would say both of these premises are correct (of course – Larry is a very clever and erudite man), but that the conclusion doesn’t follow.

Well, it follows for me. If the term "Darwinist" has become associated with an adaptationist view of evolution then I don't want to be called a "Darwinist."

There are plenty of other terms that are just as suitable. You could refer to everyone who studies evolution as an "evolutionary biologist." What's wrong with that?

Austin Hughes and Neutral Theory

Austin Hughes (1949 - 2015) died a few years ago. He was one of my favorite evolutionary biologists.

Chase Nelson has written a nice summary of Hughes' work at: Austin L. Hughes: The Neutral Theory of Evolution. It's worth reading the first few pages if you aren't clear on the concept. Here's an excerpt ...

When the technology enabling the study of molecular polymorphisms—variations in the sequences of genes and proteins—first arose, a great deal more variability was discovered in natural populations than most evolutionary biologists had expected under natural selection. The neutral theory made the bold claim that these polymorphisms become prevalent through chance alone. It sees polymorphism and long-term evolutionary change as two aspects of the same phenomenon: random changes in the frequencies of alleles. While the neutral theory does not deny that natural selection may be important in adaptive evolutionary change, it does claim that natural selection accounts for a very small fraction of genetic evolution.

A dramatic consequence now follows. Most evolutionary change at the genetic level is not adaptive.

It is difficult to imagine random changes accomplishing so much. But random genetic drift is now widely recognized as one of the most important mechanisms of evolution.

I don't think there's any doubt that this claim is correct as long as you stick to the proper definition of evolution. The vast majority of fixations of alleles are likely due to random genetic drift and not natural selection.

If you don't understand this then you don't understand evolution.

The only quibble I have with the essay is the reference to "Neutral Theory of Evolution" as the antithesis of "Darwinian Evolution" or evolution by natural selection. I think "Neutral Theory" should be restricted to the idea that many alleles are neutral or nearly neutral. These alleles can change in frequency in a population by random genetic drift. The key idea that's anti-Darwinian includes that fact plus two other important facts:

1. New beneficial alleles can be lost by drift before they ever become fixed. In fact, this is the fate of most new beneficial alleles. It's part of the drift-barrier hypothesis.
2. Detrimental alleles can occasionally become fixed in a population due to drift.

In both cases, the alleles are not neutral. The key to understanding the overall process is random genetic drift not the idea of neutral alleles—although that's also important.

Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.

I would just add that it's Neutral Theory PLUS the other effects of random genetic drift that make evolution much more random than most people believe.

Austin Hughes was a skeptic and a creative thinker who often disagreed with the prevailing dogma in the field of evolutionary biology. He was also very religious, a fact I find very puzzling.

His scientific views were often correct, in my opinion.

In 2013, the ENCODE (Encyclopedia of DNA Elements) Project published results suggesting that eighty per cent of the human genome serves some function. This was considered a rebuttal to the widely held view that a large part of the genome was junk, debris collected over the course of evolution. Hughes sided with his friend Dan Graur in rejecting this point of view. Their argument was simple. Only ten per cent of the human genome shows signs of purifying selection, as opposed to neutrality.

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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.