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Monday, February 28, 2011

Problems with the Eukaryotic Tree of Life

Here's the ninth question my students have to answer. This is the end of the series since the test is tomorrow.
The positions of animals, fungi, and plants in the eukaryotic tree of life have been clear for decades. So why is there so much controversy today about how to construct a valid tree of eukaryotes? What are the main problems, according to Keeling et al. (2005), and how will those problems be overcome?

Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J., Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol. 20:670-676. [doi:10.1016/j.tree.2005.09.005]

Sunday, February 27, 2011

What's Wrong with This Picture?

Here's my granddaughter Zoë at the Antwerp aquarium. She's learning biology from my daughter, the astrophysicist.

I need to get over to Belgium as soon as possible before it's too late.

Extending the Modern Synthesis at the Molecular Level

Question eight for my students is designed to see if they have read and understood three papers that were assigned to them.
G. Ledyard Stebbins and Francisco Ayala wrote in 1981,
During the last decade no other issue has been more actively debated among evolutionists than the role of random drift. Molecular studies have shown that protein polymorphisms are pervasive in natural populations and that protein changes accompany the evolution of species. The neutrality theory of protein evolution proposes that evolution at the molecular level is largely due to random drift rather than being impelled by natural selection. But many evolutionists maintain that natural selection plays an essential role even at the molecular level. The “selectionist” and “neutralist” views of molecular evolution are competing hypotheses within the framework of the synthetic theory of evolution.
Why do they refer to “selectionist” and “neutralist” views “of molecular evolution”? Is there no debate over the role of random genetic drift except at the molecular level? Do you agree with Stebbins and Ayala that Neutral Theory and the role of random genetic drift are usually included in the description of the Modern Synthesis? Did Gould agree when he wrote his 1980 paper?
The quotation is from a paper published in response to Gould's famous Paleobioogy paper where he said that, "I have been reluctant to admit it—since beguiling is often forever—but if Mayr's characterization of the synthetic theory is accurate, then that theory, as a general proposition, is effectively dead, despite its persistence as textbook orthodoxy." (see Good Science Writers: Stephen Jay Gould for a description of what Gould thought of his own claim in 2002.) This paper is now available online. In the past, lots of people referred to it but never read it.

Gould responded to the Stebbins and Ayala paper in Gould (1982). The three papers illustrate the core of the debate over the Modern Synthesis and its possible extensions. I think it's fair to say that modern evolutionary theory has moved away from the hardened version of the 1960s but still not addressed some of the issues that Gould raised thirty years ago.

[Photo Credit: Photograph of Stephen Jay Gould by Kathy Chapman from Lara Shirvinski at the Art Science Research Laboratory, New York (Wikipedia)]

Gould, S.J. (1980) Is a New and General Theory of Evolution Emerging? Paleobiology 6:119-130. [PDF]

Gould, S.J. (1982) Darwinism and the Expansion of Evolutionary Theory. Science 216:380-387. [PDF]

Stebbins, G.L. and Ayala, F.J. (1981) Is a new evolutionary synthesis necessary? Science, 213: 967-971. [PDF]

Extending the Modern Synthesis

Question seven for my students is very difficult. I gave it to them as a possibility for next Tuesday's exam but I've almost decided not to us it. How many of you, dear readers, could come up with a good answer?
Which of the current proposed “extensions” of the Modern Synthesis come from studies of molecular evolution? Which one of them would you definitely include if you were proposing Evolutionary Theory (version 2011)?
Think in terms of what has to be in the textbooks ten years from now when they are discussing fundamentals of evolutionary theory.

Debating the Existence of Junk DNA

The sixth question for my students is ...
Do you think that most of the DNA in our genome is junk? Explain your answer.
This requires that the students take a position and defend it. That means they have to understand both sides of the argument in order to engage in truly critical thinking. It doesn't matter which side you take—I'll even accept a wait-and-see position if it's well argued.

We've seen repeatedly in the scientific literature and on the blogs that many professional scientists couldn't pass this question on an exam. Is it naive to think that undergraduates can master a topic like this?

[Dog Ass Plots] [Genome Size, Complexity, and the C-Value Paradox]

Accelerated Human Evolution: Models and Data

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

Here's the fifth question.
In their 2007 paper Hawks et al. conclude,
The rate of adaptive evolution in human populations has indeed accelerated within the past 80,000 years. The results above demonstrate the extent of acceleration: the recent rate must be one or two orders of magnitude higher that the long-term rate to explain the genomewide pattern.
If the actual results demonstrate that human evolution has accelerated then why are there still scientists who dispute the conclusion?
The point of the question is the conflict between how scientists deal with data that conflicts with their model. In this case, it's scientists (like me) who are uncomfortable with the conclusions of Hawks et al. (2007). If the data they published is valid then this should be a situation where all scientists abandon their former models it light of a "nasty little fact."

But that never happens. Why?

I'd also like to discuss another topic. How many people who read the Hawks et al. paper are actually capable of evaluating the data to see if it supports the conclusions? Are we in a new age of biology where the complexity of the databases and the sophistication of the computer algorithms make it impossible for the average scientist to judge the quality of the experiments? How about reviewers, can they evaluate the methods and results?

Note: The issues get bound up with the adaptationist/pluralist debate because two of the authors on the paper published a book to promote their views. You can read some examples of the adaptationist views of Cochran and Harpending at: Examples of Accelerated Human Evolution. I don't think John Hawks supports such an adaptationist position but I'm hoping he will chime and tell us. (John is a really smart guy—on more than one occasion he has demonstrated that my arguments are full of holes. It's embarrassing.)

Another Note: Here are some blogs that you might enjoy reading if this question interests you.

Signals of recent positive selection in a worldwide sample of human populations…maybe

Signals of Positive Selection in Humans?

Overstating the obvious

SEED Reviews The 10,000 Year Explosion

Did biologists really think that human evolution stopped?

Are Humans Still Evolving?

John Hawks doesn't like random genetic drift

Genetic differences between human populations: more drift than selection?

Is Evolution Linked to Environmental Change?

Accelerated Human Evolution

Human evolution has accelerated

Are humans evolving faster?

Hawks, J., Wang, E.T., Cochran, G.M., Harpending, H.C., and Moyzis, R.K. (2007) Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. (USA) 104:20753-20758. Epub 2007 [PubMed] [DOI:10.1073/pnas.0707650104]

Hofer, T., Ray, N., Wegmann, D., and Excoffier, L. (2009) Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection Annals of Human Genetics 73:95-108 [doi: 10.1111/j.1469-1809.2008.00489.x]

Pickrell, J.K., Coop, G., Novembre, J., Kudaravalli, S., Li, J.Z., Absher, D., Srinivasan, B.S., Barsh, G.S., Myers, R.M., Feldman, M.W., and Pritchard, J.K. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Research 23 published in advance March 23, 2009 [DOI: 10.1101/gr.087577.108]

Thursday, February 24, 2011

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]

Wednesday, February 23, 2011

What Does "Prokaryote" Mean?

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

Here's the fourth question.
Norman Pace (2006) says,
I believe it is critical to shake loose from the prokaryote/eukaryote concept. It is outdated, a guesswork solution to an articulation of biological diversity and an incorrect model for the course of evolution. Because it has long been used by all texts of biology, it is hard to stop using the word, prokaryote. But the next time you are inclined to do so, think what you teach your students: a wrong idea.
Outline the main reasons why Pace wants to ban the word “prokaryote.” Do you agree with him?
My students have a copy of the Nature article and we've also discussed the Three Domain Hypothesis. You can learn about some of the controversy at The Three Domain Hypothesis.

Norman Pace is currently Distinguished Professor of Molecular, Cellular and Developmental Biology at the University of Colorado, Boulder.

Part of this discussion is about taxonomy and the proper way to classify organisms. We didn't talk about that in class but for completeness here's what Ernst Mayr has to say about Pace's idea (Mayr, 1998).
In contrast to a Hennigian cladification, the Darwinian classification uses two sets of criteria. Although all taxa must be monophyletic, that is, descended from the nearest common ancestor, they are ranked according to the degree of difference from each other. Therefore, one must ask, are the archaebacteria as different from the eubacteria as from the eukaryotes or are they much more similar to the eubacteria, thus justifying the inclusion of both kinds of bacteria in the prokaryotes and confirming the two-empire classification?

Mayr, E. (1999) Two empires or three? Proc. Natl. Acad. Sci. (USA) 95:9720-0723. [PNAS Free PDF]

Pace, N.R. (2009) Time for a change. Nature 441:289. [doi:10.1038/441289a]

Monday, February 21, 2011

Dawkins, Darwin, Drift, and Neutral Theory

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

Here's the third question.
Read the following statements by Richard Dawkins from his latest book, The Greatest Show on Earth (2009, pages 332 and 333).
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 the 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!

... When a gene mutates into one of its synonyms, you might as well not bother to call it a mutation at all. Indeed, it isn’t a mutation, as far as the consequences on the body are concerned. And for the same reason it isn’t a mutation at all as far as natural selection is concerned. But it is a mutation as far as molecular geneticists are concerned, for they can see it using their methods.
Dawkins doubts that any mutation giving rise to a visible phenotype can be neutral ("ultra-Darwinists like me incline against the idea"). Such mutations are only important in molecular evolution. Do you agree with him? Does Neutral Theory only apply to invisible mutations that can only be detected by molecular geneticists? Be sure to bring up the enormous variations in phenotypic characteristics among different human populations.
My students have read the Spandrel's paper so they are aware of the arguments made by Gould & Lewontin. Some of you may not be as familiar with those arguments so let me remind you of what Gould & Lewontin said back in 1978-79.
At this point, some evolutionists will protest that we are caricaturing their view of adaptation. After all, do they not admit genetic drift, allometry, and a variety of reasons for non-adaptive evolution? They do, to be sure, but we make a different point. In natural history, all possible things happen sometimes; you generally do not support your favored phenomenon by declaring rivals impossible in theory. Rather, you acknowledge the rival but circumscribe its domain of action so narrowly that it cannot have any importance in the affairs of nature. Then, you often congratulate yourself for being such an undogmatic and ecumenical chap. We maintain that alternatives to selection for best overall design have generally been relegated to unimportance by this mode of argument. Have we not all heard the catechism about genetic drift: it can only be important in populations so small that they are likely to become extinct before playing any sustained evolutionary role?
To which I would add the following argument: "We've all heard about Neutral Theory but it only applies to inconsequential mutations detectable only by molecular geneticists."

Jerry Coyne's Opinion

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

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

Sunday, February 20, 2011

Quotations from Richard Lewontin

Darwin's theory of evolution by natural selection in particular is hopelessly metaphysical, according to the rules of etiquette laid down in the Logic of Scientific Inquiry and widely believed in by practicing scientists who bother to think about the problem. The first rule for any scientific hypothesis ought to be that it is at least possible to conceive of an observation that would contradict the theory. For what good is a theory that is guaranteed by its internal logical structure to agree with all conceivable observations, irrespective of the real structure of the world? If scientists are going to use logically unbeatable theories about the world, they might as well give up natural science and take up religion. Yet is that not exactly the situation with regard to Darwinism? The theory of evolution by natural selection states that changes in the inherited characters of species occur, giving rise to differentiation in space and time, because different genetical types leave different numbers of offspring in different environments... Such a theory can never be falsified, for it asserts that some environmental difference created the conditions for natural selection of a new character. It is existentially quantified so that the failure to find the environmental factor proves nothing, except that one has not looked hard enough. Can one really imagine observations about nature that would disprove natural selection as a cause of the difference in bill size? The theory of natural selection is then revealed as metaphysical rather than scientific. Natural selection explains nothing because it explains everything.

“Testing the Theory of Natural Selection” Nature March 24, 1972 p.181

It is the great irony of modern evolutionary genetics that the spirit of explanation has moved more and more towards optimal adaptation, while the technical developments of population genetics of the past 30 years have been increasingly to show the efficacy of non adaptive forces in evolution.

"A natural selection" Nature May 11,1989 p.107

Theodosius Dobzhansky, the leading empirical evolutionary geneticist of the twentieth century, who spent most of his life staring down a microscope at chromosomes, vacillated between deism, gnosticism, and membership in the Russian Orthodox Church. He could not understand how anyone on his or her deathbed could remain an unrepentant materialist. I, his student and scientific epigone, ingested my unwavering atheism and a priori materialism along with the spinach at the parental dinner table.

"The Wars Over Evolution" New York Review of Books October 20, 2005

As to assertions without adequate evidence, the literature of science is filled with them, especially the literature of popular science writing. Carl Sagan's list of the "best contemporary science-popularizers" includes E.O. Wilson, Lewis Thomas, and Richard Dawkins, each of whom has put unsubstantiated assertions or counterfactual claims at the very center of the stories they have retailed in the market. Wilson's Sociobiology and On Human Nature5 rest on the surface of a quaking marsh of unsupported claims about the genetic determination of everything from altruism to xenophobia. Dawkins's vulgarizations of Darwinism speak of nothing in evolution but an inexorable ascendancy of genes that are selectively superior, while the entire body of technical advance in experimental and theoretical evolutionary genetics of the last fifty years has moved in the direction of emphasizing non-selective forces in evolution. Thomas, in various essays, propagandized for the success of modern scientific medicine in eliminating death from disease, while the unchallenged statistical compilations on mortality show that in Europe and North America infectious diseases, including tuberculosis and diphtheria, had ceased to be major causes of mortality by the first decades of the twentieth century, and that at age seventy the expected further lifetime for a white male has gone up only two years since 1950. Even The Demon-Haunted World itself sometimes takes suspect claims as true when they serve a rhetorical purpose as, for example, statistics on child abuse, or a story about the evolution of a child's fear of the dark.

"Billions and Billions of Demons" a review of Carl Sagan's
The Demon-Haunted World: Science as a Candle in the Dark
, New York Review of Books, Jan. 9, 1997

Third, it is said that there is no place for an argument from authority in science. The community of science is constantly self-critical, as evidenced by the experience of university colloquia "in which the speaker has hardly gotten 30 seconds into the talk before there are devastating questions and comments from the audience." If Sagan really wants to hear serious disputation about the nature of the universe, he should leave the academic precincts in Ithaca and spend a few minutes in an Orthodox study house in Brooklyn. It is certainly true that within each narrowly defined scientific field there is a constant challenge to new technical claims and to old wisdom. In what my wife calls the Gunfight at the O.K. Corral Syndrome, young scientists on the make will challenge a graybeard, and this adversarial atmosphere for the most part serves the truth. But when scientists transgress the bounds of their own specialty they have no choice but to accept the claims of authority, even though they do not know how solid the grounds of those claims may be. Who am I to believe about quantum physics if not Steven Weinberg, or about the solar system if not Carl Sagan? What worries me is that they may believe what Dawkins and Wilson tell them about evolution.

"Billions and Billions of Demons" a review of Carl Sagan's
The Demon-Haunted World: Science as a Candle in the Dark
, New York Review of Books, Jan. 9, 1997

If Darwin's revolution was not in proclaiming evolution as a fact, then it must have been in his theory of its mechanism. And what was that theory? Why, "natural selection," of course, which then makes the theory of natural selection the very essence of Darwinism and any doubt about the universal efficacy of natural selection anti-Darwinian. There is a form of vulgar Darwinism, characteristic of the late nineteenth century and rejuvenated in the last ten years, which sees all aspects of shape, function, and behavior of all organisms as having been molded in exquisite detail by natural selection—the greater survival and reproduction of those organisms whose traits make them "adapted" for the struggle for existence. This Panglossian view is held largely by functional anatomists and comparative physiologists who, after all, make a living by explaining what everything is good for, and by sociologists who are self-consciously trying to win immortality by making their own small revolution. Evolutionary geneticists, on the other hand, who have spent the last sixty years in detailed experimental and theoretical analysis of the actual process of evolutionary change, and most epistemologists take a more pluralistic view of the forces driving evolution.

An occasional philosopher has allied himself or herself with the "adaptationists," who give exclusive emphasis to natural selection., and one such, Michael Ruse, makes a characteristic presentation in Darwinism Defended. Darwinism, the representative of objective modern science, is under ideologically motivated attack. Professor Ruse is alarmed: "'Darwinism,' as I shall refer to Darwin-inspired evolutionary thought, is threatened from almost every quarter." Well, not from every quarter, just the right and left flanks, it seems. First, the fundamentalists, supported by Ronald Regan, make a know-nothing assault from the right. No sooner have real evolutionists wheeled to face this attack than they are fallen upon by subversive elements from the left, "biologists with Marxist sympathies" and their "fellow travelers" among philosophers who argue "that any evolutionary theory based on Darwinian principles—particularly any theory that sees natural selection as the key to evolutionary change—is misleadingly incomplete."

Onto the field, mounted upon his charger perfectly adapted for the purpose, with weapons carefully shaped by selection to spread maximum confusion among the enemy, not to mention innocent civilians, comes Professor Ruse, "trying to rescue ... from the morass into which so many seem determined to drag them," "Darwin's life and achievements." In all fairness to Professor Ruse, he did not invent this version of events. The theory that evolutionary science is being brutally beaten and cut with crosses, hammers, and sickles made its first appearance in E.O. Wilson's On Human Nature as the only plausible explanation he could imagine for the failure of sociobiology to achieve instant, universal, and lasting adherence. The situation of evolutionary theory, however, is rather more complex and more interesting than Professor Ruse's Manichaean analysis suggests....

What vulgar Darwinists fail to understand, however, is that there is an asymmetry in Darwin's scheme. When adaptation is observed, it can be explained by the differential survival and reproduction of variant types being guided and biased by their differential efficiency or resistance to environmental stresses and dangers. But any cause of differential survival and reproduction, even when it has nothing to do with the struggle for existence, will result in some evolution, just not adaptive evolution.

The Panglossians have confused Darwin's discovery that all adaptation is a consequence of variational evolution with the claim that all variation evolution leads to adaptation. Even if biologists cannot, philosophers are supposed to distinguish between the assertion that "all x is y" and the assertion that "all y is x," and most have. This is not simply a logical question but an empirical one. What evolutionary geneticists and developmental biologists have been doing for the last sixty years is to accumulate a knowledge of a variety of forces that cause the frequency of variant types to change, and that do not fall under the rubric of adaptation by natural selection. These include, to name a few: random fixation of nonadaptive or even maladaptive traits because of limitations of population size and the colonization of new areas by small numbers of founders; the acquisition of traits because the genes influencing them are dragged along on the same chromosome as some totally unrelated gene that is being selected; and developmental side effects of genes that have been selected for some quite different reason.

from a review of Darwinism Defended: A Guide to the Evolution Controversies by Michael Ruse. It was first published in The New York Review of Books on June 16, 1983 and reprinted in It Ain't Necessarily So: The Dream of the Human Genome and Other Illusions.

It is time for students of the evolutionary process, especially those who have been misquoted and used by the creationists, to state clearly that evolution is a FACT, not theory, and that what is at issue within biology are questions of details of the process and the relative importance of different mechanisms of evolution. It is a FACT that the earth with liquid water, is more than 3.6 billion years old. It is a FACT that cellular life has been around for at least half of that period and that organized multicellular life is at least 800 million years old. It is a FACT that major life forms now on earth were not at all represented in the past. There were no birds or mammals 250 million years ago. It is a FACT that major life forms of the past are no longer living. There used to be dinosaurs and Pithecanthropus, and there are none now. It is a FACT that all living forms come from previous living forms. Therefore, all present forms of life arose from ancestral forms that were different. Birds arose from nonbirds and humans from nonhumans. No person who pretends to any understanding of the natural world can deny these facts any more than she or he can deny that the earth is round, rotates on its axis, and revolves around the sun.

The controversies about evolution lie in the realm of the relative importance of various forces in molding evolution.

"Evolution/Creation Debate: A Time for Truth" Bioscience 31, 559 (1981) reprinted in Evolution versus Creationism J. Peter Zetterberg ed., ORYX Press, Phoenix AZ 1983

To say that genetic differences are relevant to hetero- and homosexuality is not, however, to say that there are "genes for homosexuality" or even that there is a "genetic tendency to homosexuality." This critical point can be illustrated by an example I owe to the philosopher of science, Elliott Sober. If we look at the chromosomes of people who knit and those who do not, we will find that with few exceptions, knitters have two X chromosomes [women], while people with one X and one Y chromosome [men] almost never knit. Yet it would be absurd to say that we had discovered genes for knitting. ... [I]n our culture, women are taught to knit and men are not. The beauty of this example is its historical (and geographical) contingency. Had we made our observations before the end of the eighteenth century (or even now in a few Irish, Scottish and Newfoundland communities), the results would have been reversed. Hand knitting was men's works before the introduction of knitting machines around 1790, and was turned into a female domestic occupation only when mechanization made it economically marginal.

Letter to the editor, New York Review of Books, Nov. 2, 1995

Listen to Richard Lewontin

Here's an interview with Richard Lewontin from Nov. 20, 2003. He talks about all sorts of things that are relevant to what we debate on the blogs and he's a lot smarter than we are.

Saturday, February 19, 2011

Dan Dennett Replies

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

I look forward to your reply.

Best wishes,

Dan Dennett

Revolution in Wisconsin

You'd been reading about revolutions in the Middle East. The people there want freedom and democracy. Now the revolution has spread to Wisconsin. It's a complicated situation that seems totally bizarre to those of us living outside America. Apparently the Democratic legislators have left the state and remain in hiding in order to prevent the Republicans from crushing unions. The teachers are on strike and the schools are closed. Strange.

Here's a 30 minute explanation for those of you who want to know. The situation reminds me a great deal of Alice in Wonderland.

Friday, February 18, 2011

Daniel Dennett's View of Adaptationism

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

Here's the second question.
Discuss the following statement by Daniel Dennett from his book Darwin’s Dangerous Idea (1995, p. 238). Do you agree or disagree? Pay particular attention to the kind of reasoning required in the field of molecular evolution.
Adaptationist reasoning is not optional, it is the heart and soul of evolutionary biology. Although it may be supplemented, and its flaws repaired, to think of displacing it from its cental position in biology is to imagine not just the downfall of Darwinism but the collapse of modern biochemistry and all the life sciences and medicine. So it is a bit surprising to discover that this is precisely the interpretation that many readers have placed on the most famous and influential critique of adaptationism, Stephen Jay Gould and Richard Lewontin’s oft-cited, oft-reprinted, but massively misread classic, “The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Program” (1979).
My students all have a copy of the Spandrels paper and they should be familiar with it. In case you're not (shame), it seems to me that Lewontin & Gould are advocating a pluralist approach to evolution. They criticize the adaptationist program and really would like to see it disappear. Is Dennett making a distinction between the adaptationist program and adaptationist reasoning? I don't think so because here's what he says on the same page as the quotation above.
The biologists' name for this style of reasoning is adaptationism. It is defined by one of its most eminent critics as the "growing tendency in evolutionary biology to reconstruct the evolutionary events by assuming that all characters are established in evolution by direct natural selection of the most adapted state, that is, the state that is an optimum solution to a problem posed by the environment" (Lewontin 1983). These critics claim that, although adaptationism plays some important role in biology, it is not really all that central or ubiquitous—and, indeed, we should try to balance it with other ways of thinking. I have been showing, however, that it plays a crucial role in the analysis of every biological event at every scale from the creation of the first self-replicating molecule on up. If we gave up adaptationist reasoning, for instance, we would have to give up the best textbook argument for the very occurrence of evolution (I quoted Mark Ridley's version of it on page 136): the widespread existence of homologies, those suspicious similarities of design that are not functionally necessary.
Dennett is a philosopher so he might not be as familiar with modern biochemistry as his statement implies. Can anyone figure out why biochemistry would collapse if we stop attributing everything to adaptation? I wonder how adaptationist thinking helps us understand sequence-based phylogenetic trees and the molecular clock? At the other extreme, how crucial a role does adaptationism play in deciding whether birds are dinosaurs or punctuated equilibria are the dominant pattern in the fossil record?

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

UPDATE: Dan Dennett Replies.

Let me close, for no particular reason, with a few quotations from one of my personal heroes, Betrand Russell.
A stupid man's report of what a clever man says can never be accurate, because he unconsciously translates what he hears into something he can understand.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Science is what you know, philosophy is what you don't know.
That last one is for John Wilkins.

UPDATE: See Dan Dennett Replies