Daniel Dennett's View of Adaptationism

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

Here's the second question.

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

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

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

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

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

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

UPDATE: Dan Dennett Replies.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

That last one is for John Wilkins.

UPDATE: See Dan Dennett Replies

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The Hollies

Ms Sandwalk [Are you young enough, My favourite song of the year] and my friend Elliot Schiller [The Ronettes, Poco] have been posting videos of their favorite songs. Here's a group they "forgot" [The Hollies].

Turn up the volume—especially bass—for the first one. Look for Graham Nash in the third video.

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Mankind Has Stopped Evolving

We discussed this topic in class. Here's a physicist named Machio Kaku pontificating about evolution. Kaku is an expert on string theory. I wonder how he'd feel if a typical evolutionary biologist answered a question about string theory?

A curious aspect of the theory of evolution is that everybody thinks he understands it.
                                                                                     Jacques Monod

UPDATE: John Hawks weighs in with Kaku cockup.

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[Hat Tip: Pharyngula:Why do physicists think they are masters of all sciences?]

Facilitated Variation

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 first question. It's based on Gerhart and Kirschner (2007).

What do you think of Kirschner and Gerhart’s "Theory of Facilitated Evolution." Is this something that has to be incorporated into a new extended version of evolutionary theory? What, if any, are the limitations of the theory and what, if any, new insights into evolution does it provide?

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Gerhart, J., and Kirschner, M. (2007) The theory of facilitated variation. Proc. Natl. Acad. Sci. USA 104 Suppl 1:8582-8589. [doi: 10.1073/pnas.0701035104]

Sean Carroll's View of Evo-Devo

I'm trying to teach students about different ways of looking at evolution in my course on molecular evolution. One of the myths about molecular evolution is that it applies only at the level of molecules and "real" evolutionary biologists don't have to think about it when they are out in the field studying flowers, fruit flies, or small fish.

This is a profound misunderstanding on many levels but one of the most important is that many biologists don't appreciate the contributions molecular studies have made to our understanding of phenotypic diversity. All biologists need to learn about the way genes produce diversity.

The combination of evolution and developmental biology (evo-devo) has provided considerable insights into the problem of phenotypic diversity. We now understand how a small set of genes can produce drastically different body types. Sean Carroll has written several books on this subject but if you don't have time to read them you can listen to a 37 minute lecture he gave last Fall: How Bugs Get Their Spots: Genetic switches and the evolution of form. Keep in mind that this lecture is partly about how to teach evolution to undergraduates and high school students.

Does evo-devo have to be incorporated into an extended evolutionary synthesis? If you listen to some of the main proponents of evo-devo you'd have to answer "yes" to this question. These proponents think that the Modern Synthesis cannot deal with the discoveries of evo-devo and it needs to be extended to cover the idea that small changes in regulatory genes can have large effects on morphology.

Unfortunately, there are two serious problems with evo-devo when presented as a theory. They both detract from the main message. The most important problem to do with perspective. The fundamentals of evolutionary theory ("extended" or not) have to be broad enough to cover all of biology. Evo-devo doesn't really do that because it focuses almost exclusively on large multicellular animals. To put this into perspective, look at the diagram below. It's from Keeling et al. (2005).


Find the "Kingdom" of "animals" on this tree of eukaryotes. When you see the small branch that defines the most important subject matter of evo-devo you'll begin to appreciate why some of us don't think this generalizes to a major extension of evolutionary theory. (Note that prokaryotes are not included in this tree so the problem is even worse than you imagine.)

The second problem has to do with the unfortunate hype that seems to come with promoting evo-devo. As I said above, much of it detracts from the important and valuable lessons we can learn from developmental biology. Here are some examples from Sean Carroll's talk.

He talks about evo-devo discoveries that "shattered expectations" and gives a few examples.

Expectation: Different Sets of Genes Build Different Body Forms

He claims that his advisers believed you could never learn about furry things from studying fruit flies. He's talking about regulatory genes, especially HOX genes, as though that was a truly shocking discovery.

Maybe it was to some people but I grew up in the world of Jacques Monod and a whole bunch of molecular biologists who were convinced that what we learned about bacteria and bacteriophage would apply to elephants (and fruit flies). And it did.

Sean is talking about a different set of people who, forty years ago, may not have been on top of molecular biology. It's time to stop using these bogeymen to make your field look more revolutionary than it is. He says that the discovery of HOX genes is a finding that no biologist on the planet anticipated as though the idea that you might have similar regulatory genes shared by a small cluster of species (see diagram above) was revolutionary.

Why was that revolutionary? By the time the first HOX genes were sequenced (in the early 1980s) we already knew that all living organisms (prokaryotes and eukaryotes) shared a number of genes in basic metabolic pathways including DNA replication, transcription, and translation. The first homeobox sequences were thought to be similar to the helix-turn-helix motif in bacterial regulatory proteins and none of my friends were shocked. Were yours?

Expectation: Vastly different structures with similar functions such as animal eyes, appendages, etc evolved from scratch via independent genetic paths.

This is mostly correct. We knew in the 1980s that insect legs and vertebrate legs, for example, were not homologous so we expected that some of the genes for these structures would be different.¹ This expectation has been confirmed in spite of what Sean Carroll might imply in his talk. The fact that regulatory genes controlling the expression of these different genes might be conserved is not a surprise.

Insects and mammals needed to evolve separate unique genes (from scratch) for their different appendages. These genes were easily brought under the control of existing regulatory proteins. They did not need to evolve new regulatory proteins, and they didn't.

So, if evo-devo represents a real challenge to evolutionary theory then what, exactly, is being challenged and how does evo-devo provide an answer? It seems to me that evo-devo is helping us understand some of the details about the history of life—especially animal life—but I'm not sure this is the same thing as making a contribution to evolutionary theory.

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1. Nobody expected the muscle and nerve cell genes to be different but we would have been truly shocked to find that insects contained the genes for making bones or that mammals had the genes for making chitinous exoskeletons.

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.

Hugh Ross Teaches Us about Evolution

There's been a lot of talk recently about teaching evolution. The IDiots want us to teach the "controversies" in evolution. I'm happy to oblige. For all you students out there, here's an example of the intellectual opposition to evolution. I think we need to expose every university student to this sort of controversy. It would do wonders for science education.

(Hugh Ross is an Old Earth Creationist. He has a Ph.D. in astronomy from the University of Toronto that qualifies him as an expert on evolution. He is Canadian, but please don't spread that around.)

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[Hat Tip: Pharyngula]

Christianity Today: Unreasonable Doubt

Jim Spiegel is a philosophy professor at Taylor University (a Christian College in Indiana, United States). He has published an article in Christianity Today: Unreasoanble Doubt, "The reasons for unbelief are more complex than many atheists let on."

It's interesting to see what a philosophy professor/Christian apologist has to say about why we have failed to be convinced about the existence of supernatural beings.

Paul provides at least part of the answer in the same Romans passage, noting that some people "suppress the truth by their wickedness" (1:18). We all suffer from intellectual blind spots created by personal vices and immoral desires. To the extent that we succumb to these, we may be tempted to adopt perspectives that enable us to rationalize perverse behavior.

In this regard, scholars are no different from anyone else. The 20th-century ethics philosopher Mortimer Adler (who was baptized quietly at age 81) confessed to rejecting religious commitment for most of his life because it "would require a radical change in my way of life, a basic alteration in the direction of my day-to-day choices as well as in the ultimate objectives to be sought or hoped for …. The simple truth of the matter is that I did not wish to live up to being a genuinely religious person."

Historian Paul Johnson's fascinating if disturbing book Intellectuals exposed this pattern in the lives of some of the most celebrated thinkers in the modern period, including Rousseau, Shelley, Marx, Ibsen, Hemingway, Russell, and Sartre. In their private (and often public) lives, these Western intellectual stars were moral wrecks. Could their rejection of God—and, in particular, Christianity, with its exacting moral standards—have been entirely intellectual and dispassionate? Or might the same desires confessed by Nagel and Adler have played a role in their atheism?

Damn him! He's discovered the secret. My life is a moral wreck and that's why I have to reject God. Can you imagine how my life would be transformed if I ever became a Christian? I'm just not ready for that kind of morality.¹

(I assume this is one of those "sophisticated" arguments for religion that we hear so much about.)

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[Hat Tip: Canadian Atheist]

1. The University expects its members to use discretion and discernment in their choices of entertainment and recreation (some examples include media, Internet usage, and games). Social dancing is not permitted on or away from campus. However, acceptable forms of expression may include sanctioned folk dances, dances that are designed to worship God, dancing at weddings, and the use of choreography in drama, musical productions and athletic events. Activities and entertainment that are of questionable value or diminish a person's moral sensitivity should be avoided.

Happy Valentine's Day!

Who was Saint Valentine and why do we (males) have to buy flowers and chocolates today?¹ Nobody really knows very much about the Saints Valentine (there were about a dozen of them). The whole idea of romantic Valentine's day seems to have been invented by Geoffrey Chaucer sometime around 1380.

It seems like people in England just wanted to enjoy a bit of debauchery fun on February 14th so they connected their frolics with a Roman Catholic saint in order to get the permission of the church! Pretty clever, eh?

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1. And why don't women have to reciprocate?

A New Way of Regulating Human Genes?

ScienceDaily is all over this revolutionary discovery [Primates' Unique Gene Regulation Mechanism: Little-Understood DNA Elements Serve Important Purpose].

Scientists have discovered a new way genes are regulated that is unique to primates, including humans and monkeys. Though the human genome -- all the genes that an individual possesses -- was sequenced 10 years ago, greater understanding of how genes function and are regulated is needed to make advances in medicine, including changing the way we diagnose, treat and prevent a wide range of diseases.

"It's extremely valuable that we've sequenced a large bulk of the human genome, but sequence without function doesn't get us very far, which is why our finding is so important," said Lynne E. Maquat, Ph.D., lead author of the new study published February 9 in the journal Nature.

The actual paper is ...

Gong, C. and Maquat, L.E. (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470:284–288. [doi:10.1038/nature09701]

It's just one more example of how a transcribed Alu sequence can screw up gene expression. There's an outside chance that this is significant and has been selected as a regulatory mechanism but the most probable explanation is that it's just an accident. In any case, there's no reason to generalize from this single example.

This statement is unworthy of a scientist.

"Previously, no one knew what Alu elements and long noncoding RNAs did, whether they were junk or if they had any purpose. Now, we've shown that they actually have important roles in regulating protein production," said Maquat, the J. Lowell Orbison Chair, professor of Biochemistry and Biophysics and director of the Center for RNA Biology at the University of Rochester Medical Center.

The correct statement is that we've known for decades that the vast majority of Alu elements in the genome do absolutely nothing. However, there are a dozen examples already in the scientific literature of Alu sequences that affect transcription, RNA processing, mRNA, or translation. They've all proven to be unique, rare, cases. We strongly suspect that most long noncoding RNAs are junk but there are some excellent examples of ones that are functional.

Lynne Maquat has shown an effect of a transcribed Alu sequence but it's simply not true that every obscure phenomenon reveals an important role in regulating protein production. And it's simply not true that this example has any implications for the vast majority of Alu sequences in the genome. Save the hype for your grant application.

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[Hat Tip: Ryan Gregory at Genomicron: Grumble grumble… media… evolution… junk DNA… grumble.]

iPhone App

I have friends and relatives who love iPhone and Blackberry apps. Here's just the gift for someone who has everything and it's only $1.99.

This app is sanctioned by the Pope and it will guide you through confession by helping to list all your sins [Catholic church gives blessing to iPhone app].

There's something a little troubling about the screen shot. Do you see that box beside "Have I been involved with superstitious practices ..."? Isn't there something strange about leaving it unchecked while filling out a form like this?

I wonder how many sins there are and whether they have a box for "check all."

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[Hat Tip: RichardDawkins.net]

Evolution's Hidden Force

I was really excited (not) when the January 8th edition of New Scientist arrived. The cover story was bound to be something I could use in my course when we discussed modern views of evolution. Even the title was provocative: Uncertainty principle: How evolution hedges its bets.¹

The article was written by freelance science writer Henry Nicholls. He lives in London UK and he has a Ph.D. (2007) in Evolutionary Ecology. Here's how the article begins ...

A man walks into a bar. "I have a new way of looking at evolution," he announces. "Do you have something I could write it down on?" The barman produces a piece of paper and a pen without so much as a smile. But then, the man wasn't joking.

The man in question is Andrew Feinberg, a leading geneticist at Johns Hopkins University in Baltimore; the bar is The Hung, Drawn and Quartered, a pub within the shadow of the Tower of London; and what's written on the piece of paper could fundamentally alter the way we think about ... evolution ....

Let's turn this into a quiz.

What did Andrew Feinberg write about on that piece of paper?

1. the importance of small RNAs
2. random genetic drift
3. epigenetics
4. species sorting
5. hierarchical theory
6. evo-devo
7. evolvability
8. mutationism
9. developmental constraints
10. contingency
11. alternative splicing
12. selfish DNA
13. the demise of the Central Dogma
14. facilitated variation
15. group selection
16. phenotypic plasticity
17. molecular chaperones
18. genome complexity and the myth of junk DNA
19. horizontal gene transfer
20. the death of trees
21. molecular drive
22. endosymbiosis
23. mass extinctions
24. punctuated equilibria
25. genomics
26. proteomics
27. systems biology
28. the high cost of a beer in London

All of these things have been touted as new ways of looking at evolution. Which one did he choose?

Here's a hint ...

Before setting foot in the pub, Feinberg had taken a turn on the London Eye, climbed Big Ben and wandered into Westminster Abbey. There, as you might expect, he sought out the resting place of Isaac Newton and Charles Darwin. He was struck by the contrast between the lavish marble sculpture of a youthful Newton, reclining regally beneath a gold-leafed globe, and Darwin's minimalist floor stone.

As he looked round, Feinberg's eyes came to rest on a nearby plaque commemorating physicist Paul Dirac. This set him thinking about quantum theory and evolution, which led him to the idea that ... XXX ... might inject a Heisenberg-like uncertainty into the expression of genes, which would boost the chances of species surviving. That, more or less, is what he wrote on the piece of paper.

Hmmm ... Hung, Drawn and Quartered ... that gives me an idea. Let me write it down ....

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[Photo Credit: Jaunted]

1. Most of you can't follow the link because it's behind a paywall.

Sing the National Anthem

Ms. Sandwalk has a thing about singing our national anthem, O, Canada. Not only does she think that every Canadian should sing along whenever it's played but they should do so in TWO languages!

It's really not that difficult. The words and the music are widely available on the internet and everyone sings from the same page.

Not so true in the USA as we see below. Christina Aguilera is singing just one of the hundreds of versions that are popular. You'd have to know in advance what version she was going to use if you want to sing along. Ms. Sandwalk is not happy.

Oh, say, can you see, by the dawn's early light,
What so proudly we hail'd at the twilight's last gleaming reaming?
Whose broad stripes and bright stars, thro' the perilous fight,
O'er the ramparts we watch'd, were so gallantly streaming?
Oh so proudly we washed at the twilight's last reaming
And the rockets' red glare, the bombs bursting in air,
Gave proof thro' the night that our a flag was still there.
O say, does that star-spangled banner yet wave
O'er the land of the free and the home of the nuh brave?

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[Hat Tip: Greg Laden's Blog: Sing along with Christina Aguilera]

A Changing Society

This is really funny ... "Name Something That Gets Passed Around."

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[Hat Tip: Friendly Atheist]

A Challenge to Homeopathy

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Evolution Made Us All

This is from Ben Hillman at Vimeo [Evolution Made Us All]. I appreciate the intent but I can't help but wonder whether such videos don't do more harm than good. It makes me very uneasy to see evolution presented in such a manner and I really don't like the glorification of Charles Darwin that we see in popular views on evolution.

If we're truly interested in advancing the goal of science education then videos such as this are part of the problem, not part of the solution.

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[Hat Tip: RichardDawkins.net]