Wednesday, January 14, 2015

Looking for Spandrels

I've just assigned the Spandrels paper to the students in my molecular evolution class. A few of them will have read it already but most haven't. It's such an important paper that it should be required reading for every undergraduate in the biological sciences.

I've mentioned this before on Sandwalk (see links below). While searching through my old posts I came across one from 2008 titled In Search of Spandrels. I'd forgotten about it completely. It reproduced a post that I wrote for talk.origins on Aug. 20, 1998. Nobody knows about talk.origins these days but some of us have fond memories. (It still exists.) Here's what I wrote 17 years ago. It was a different era.
I recently found myself in the catacombs of the library archive far away from the stress of students writing their summer exams. It was very peaceful. It was also a place where creationists never go.

I must confess that my primary motivation for being there was work avoidance—I hate marking exams—but there was another reason as well. My secondary mission was to retrieve a pristine copy of the "Spandrels" paper so I could hand it out to my students. (My own copy had some embarassing margin notes that weren't fit for young eyes.)

There were many bound volumes of the Proceedings of the Royal Society of London (Series B). Did you know that this journal goes back over one hundred years? (That's even before I was born.) Did you know that you have to look in the stacks under "R", for "Royal", and not "P", for "Proceedings"? Did you ever wonder why librarians do that? My own theory is that they really don't want us to take out their books so they make it as difficult as possible to find something.

I was looking for volume 205 (1979). As usual, it was on the bottom shelf; way down at the level of my shoes. I had to get down on one knee and that's a lot of work. But at least volume 205 wasn't missing. With trembling hands I flipped the pages looking for the sacred text. Would it be there or would the pages have been cut out with a razor blade? Chances were good—pre-med students don't read about evolution.

Yes! There it was: "The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptionist programme" by S.J. Gould and R.C. Lewontin. They even spelled "programme" correctly! Off I went to the photocopy machine. Off I went to buy a new photocopy card. Back I came to the photocopy machine. Let's see now ... how much magnification will I need to fill an 8x11 page so I don't have to close the damn lid every time I copy a page? 125% should do it. Wrrrrr .... flash .... swish .... splat.

Maybe 120% would work ...

At last, page 598 was perfect. (Anyone want extra copies of the references from this paper?) I worked my way forward to page 581 fending off the librarian who insisted that I had to close the lid or I would ruin the photocopier—and my eyes (I'm not sure which was more important to her).

I was lucky there were three or four students to distract her. Behind my back I heard some mumblings about "eccentric" and "stubborn" but unfortunately I couldn't see exactly what was going on.

Hope I didn't miss anything interesting.

I knew that Gould had presented the paper at a meeting in London in December, 1978. Lewontin wasn't there because you have to fly to get to England and Lewontin thinks that if humans were made to fly then we would have evolved wings. So, who else was at the meeting? Did they publish papers in the same issue of the journal? Let's see ...

My thoughts were interrupted by some shouting in the line behind me. Guess I'd better get away from the photocopier. The machine seems to be making people angry.

Off I went to find a desk to sit down at. Found one. Off I went to the photocopier to retrieve my photocopy card. Back I came to the desk.

Someone was there. Found another desk. It had a banana peel on it.

Cool. All the papers are here. The meeting was called "The Evolution of Adaptation by Natural Selection" and it was organized by John Maynard Smith and R. Holliday. Orgel has a paper on evolution in vitro. The Charlesworths write about sex in plants. There's a paper by Maynard Smith on game theory and the evolution of behaviour. George Williams was present (more about him later). And guess who else? - Richard Dawkins!

The Dawkins' paper is titled "Arms races between and within species" (R. Dawkins and J.R. Krebs). It goes on and on about the adaptive significance of arms races and the optimization of animals. I bet the Gould talk was not well received by Dawkins in 1978. :-)

The Williams paper is very interesting ("The question of adaptive sex ratio in outcrossed vertebrates"). He examines two popular theories of the adaptive control of sex ratio (why there are 50% males and 50% females). After looking at the detailed models and the available data he concludes,
Evidence from vertebrates is unfavourable to either theory and supports, instead, a non-adaptive model, the purely random (Mendelian) determination of sex.
Good for him. I wish I could have been at the meeting. Maybe there was a discussion. Flipping to the back of the book I find a petulant summary of the meeting written by A.J. Cain. You can tell he's really annoyed at something that went on in the meeting,
Ever since natural selection appeared on the scene, there have been those who voiced an a priori and dogmatic dislike of it. One classic example is George Bernard Shaw ... I suspect from my own work that natural selection may have been very much more important than anyone has realized up to now. If so, can these emotional and other rejections of it, or, more generally, the tendency of the human race to take a non-objective view of evolution and kindred topics, be explained by natural selection?

There is a possible evolutionary explanation, as yet untested, and no other scientific one that I know of.
Whew! The discussion must have been exciting. Let's see, it should be right at the end. Ah, here it is,
[It has not been possible to include the general discussion in this publication.]
Damn.

Gotta go, the banana peel is making me ill—it looks like it's been here since the day before yesterday. Is that a fruit fly? Off I go.

Back again. (Forgot my pen.) See ya.

Larry Moran

What Does San Marco Basilica Have to do with Evolution?

A Critique of the Adaptationist Programme

An Adaptationist in Piazza San Marco

The Spandrels of San Marco and the Panglossian Paradigm


Gould, S. J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proc. R. Soc. Lond. B 205:581-598. [doi: 10.1098/rspb.1979.0086

41 comments :

  1. And now you can just click on that doi and get a pristine pdf on your desktop. No banana peels. Technology is wonderful.

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  2. I have an ambivalent reaction to this article. On the one hand, hurrah for ridiculing adaptationism and detailing how it discards one failed story and immediately grasps for another without bothering to question the pattern in which every story has the same hero.

    On the other hand, this is a meta-scientific argument, and so are the alternatives. What about science? The alternative to a scientific theory is a scientific theory, but they have none to offer. The alternative to one perspective (adaptationism) is another perspective. The whole gist of the article, which eventually becomes maddening, is that we ought to be liberal children of the 1960s like the authors. We ought to be self-critical and try on different perspectives. We ought to be "pluralistic" like his holiness Lord Darwin.

    I remain deeply disappointed that it never gets beyond this, and ends up being rather conservative and wishy-washy about causation and mechanisms. Darwin's alternative mechanisms were mistaken. Yet we should adopt his attitude. That's lame. Mechanisms and scientific theories matter, and they ought to matter more to us than a metaphysical attitude like "pluralism".

    For instance, look at how they refer to the issue of drift. Rather than talking about rigorous predictions of a theory, they criticize the meta-scientific strategy of allowing drift as a theoretical possibility but excluding it in practice. This was done by pigeon-holing its domain of relevance to that of extremely small populations that are probably about to go extinct anyway, a la Lande. This framing of things still appears sometimes (Charlesworth, 2013, Genetics 194: 955-971. doi: 10.1534/genetics.113.151555), but actually the shift in perspective G & L advocate has happened. In the past, evolutionary geneticists could be relied on to assert that evolution is deterministic except in unusually small populations. Today they tend to say that drift is important and evolution is stochastic except in unusually large populations. The "normal" case and the exceptional case have switched. Many scientists are willing to treat neutrality, rather than adaptation, as the null hypothesis.

    When commentators and Extended Synthesis advocates reflect on this kind of shift, they say that we assign a greater role to "chance" in evolution.

    In some ways I think that is a good thing, but in other ways this is metaphysical baby-talk. A shift in thinking has taken place without any real comprehension. Chance and constraints are not causes. A constraint is not the cause of an outcome, it is the non-cause of a non-outcome. Chance is not a cause. By critiquing "chance" I don't mean to suggest that we should believe everything has a meaning. Evolution used to have a theory that seemed to guarantee that we would live in the best of all possible worlds. Now we have notions like "chance", "contingency" and "constraints" which are by their nature antithetical and cannot stand on their own. They merely signal that the old view is not correct.

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  3. I love this bit: Did you know that you have to look in the stacks under "R", for "Royal", and not "P", for "Proceedings"? Did you ever wonder why librarians do that? My own theory is that they really don't want us to take out their books so they make it as difficult as possible to find something.

    That attitude lives on in this digital age. If I want to find something in Nature it's no good typing "Nature" in the search box because if I do I'll get 89 hits including such important journals as Archives néerlandaises des sciences exactes et naturelles Série 3 b, Sciences naturelles and I won't get to the journal that everyone calls Nature until I get near the bottom of the first page. So I need to specify "exact title". However, the librarians have thought up another gotcha to make sure that that isn't straightforward (though to be fair to them, when I just checked I found that after about ten years of the madness I'm about to describe they have finally decided that it doesn't matter whether you include "the" in the title of the Journal of Biological Chemistry.

    Until very recently, If I specified "the Journal of Biological Chemistry" it would find it, but if I specified "Journal of Biological Chemistry" it would say that there were no journals of that name. OK, so let's always include "the", but for some journals it still works the other way around. Searching for "Biochemical Journal" works, but searching for "the Biochemical Journal" returns no hits. So you need to know which it considers to be the exact title of which journal.

    (I did read the more important parts of your post as well, but my eye was caught by the remark about librarians.)

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  4. I've always found the paper rather self-important and sententious. "We fault the adaptationist programme ...". Oh, do ya now? It has the flavour of Party Central criticism of a region's crypto-capitalistic leanings.

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    1. Well, it was written during Lewontin's Marxist phase after all. A few years after that, he co-wrote "The Dialectical Biologist" with Richard Levins where, as the title suggests, the authors attempt to apply the Marxist idea of the dialectic to biology

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  5. Hey Larry, did you ever see the book Understanding Scientific Prose (editor Jack Selzer, U. of Wisconsin Press 1993)? It's a bunch of 'Science Studies' people dissecting the spandrels paper from their (to me) exotic perspectives.

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  6. Betcha none of these papers will matter in 15 years. Evolutionary biology is under attack, MORE, then it was in the 1970's. The attack is progressing.
    These papers will be footnotes to errors that quickly become obscure.

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    1. Yep. Any day now. Just you wait. Evolution will be dead by 1870. I mean 1910. OK, 1940 [...] 2015 ... OK, say 2030. Any day now ...

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  7. I once found myself in a library with archives of the Royal Society going to back to day one ( and this was in the regular stacks!). Depressing, as many of the volumes were in deplorable condition. And so was the scientific quality of much of the early days of the discipline. Read more like the diary of a collegiate sadists club. Stuff like "How long will a mature male terrier survive with his liver removed?" Quite a historical documentation.

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  8. There are many contemporary non-population geneticists that dislike the spandrel paper; an example can be found here: https://dynamicecology.wordpress.com/2011/08/26/why-the-spandrels-of-san-marco-isnt-a-good-paper/

    At the time (1979) I was a youngish faculty member and I remember the paper as a breath of fresh air. In my earlier education the "just so" stories were rampant and L&G punctured their balloon nicely, I thought, even if they were a little short on providing an explicit solution to the "everything is adaptive" problem."

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    1. There are many contemporary non-population geneticists that dislike the spandrel paper ...

      Of course there are still many biologists who don't like the Spandrels paper. Most of them don't "get" it, like the one you link to.

      This is the problem.

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    2. Hmmm. The world (or that portion who has read 'Spandrels') divides into one of two camps: those who think it one of the most important evolutionary papers of the last 35 years, and those who don't 'get' it? OK, I saw that word 'most', but are you aware of anyone who 'gets' it and doesn't like it?

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    3. I saw that word 'most', but are you aware of anyone who 'gets' it and doesn't like it?

      No, are you? I know people who see it (correctly) as a personal attack on their way of thinking bu those people tend to focus on the meanings of the word "spandrel" and/or "bauplan" instead of on the main point. They often claim that nobody is an adaptationist, especially them.

      Whenever you see someone complaining about "rhetoric" and "metaphors" in the Spandrels paper you can bet your life that they see no rhetoric or metaphors in The Selfish Gene.

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    4. I do have a question in line with Gould's Panda's Thumb and Zebra stripes.

      Clearly much/most of the genome is indeed junk

      I have no problem with any claim that the vast majority (>99%) of genetic variation is neutral. After all, most of that is junk.

      I also have no problem that a great deal of morphological variation is neutral.

      And as Larry & Gould clearly elucidate; organisms are NOT perched on adaptive peaks.

      so far so good...

      So what makes a Chimpanzee different from a Human? That is truly an interesting question.

      Well most of the H/C difference is about junk DNA (uninteresting) and most of the remainder is due to neutral alleles (similarly uninteresting).

      But I (to my embarrassment) have taken a (probably misguided) evodevo approach suggesting that very minor differences in regulatory genes can effect huge changes in phenotype and that these interesting bits and pieces were identified for the precise reason they were subject to strong selection pressures resulting in significant DNA variation...

      ... and this version of evodevo makes for the interesting stuff.

      I am thinking of Human accelerated regions (eg. enhancers such as HACNS1)

      http://en.wikipedia.org/wiki/Human_accelerated_regions

      Reading up some more on this I now realize that much of this hyper-variability that I had presumed a result of strong selection pressure could be actually a result of nonallelic or ectopic gene conversion.


      Ouch! I never realized this before. So I guess my question now is how many of these Human accelerated regions clearly represent adaptation??? … and how many are neutral or “nearly neutral”?

      Again and as always – my gratitude to one and all for their patient indulgence.

      Ps to Allan: Thanks for those text recommendations http://sandwalk.blogspot.ca/2015/01/evolutionary-biochemistry-and.html?showComment=1421090792036#c6932462644922708598

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    5. They often claim that nobody is an adaptationist, especially them.

      Meh. It's a label. Call me what you like. I have a tendency to assume that phenotypically visible characters have a good chance of being adaptive. So shoot me. One could equally claim that people who diss The Selfish Gene don't 'get it'. But that's not much of an argument. I think people are generally bright enough to understand both perspectives, and simply disagree on the emphasis. More problematic, I think, are people who misunderstand what selection is. From the Wikipedia article on Spandrels: "It is thought in the scientific community today that everything an animal has developed that has a positive effect on that animal’s fitness was due to natural selection or some adaptation." That pushes so many buttons, I barely know where to begin.

      Whenever you see someone complaining about "rhetoric" and "metaphors" in the Spandrels paper you can bet your life that they see no rhetoric or metaphors in The Selfish Gene.

      I doubt that.

      One of my principal beefs with 'Spandrels' is that there are no decent examples of a spandrel given, in the terms they implicitly demand - ie, where the selective effect of the assumed spandrel has been evaluated and found to be nonadaptive. It becomes (in a phrase I might be in danger of over-using) a 'just-ain't-so' story.

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    6. The fact that men have nipples is a potential spandrel. It would be almost impossible to prove the negative ... i.e. that there was absolutely no fitness benefit. That's why Gould and Lewontin say that the default hypothesis should be nonadaptive and the burden of proof lies with those who claim that it is an adapation. You should not assume that it has a good chance of being adaptive in men just because it is phenotypically visible.

      We discussed this in class today. We discovered that half the class could roll their tongues and the other half couldn't. That's a phenotypically visible character. Should we automatically assume that one half of the class is less fit than the other? Or, is it more reasonable to conclude, tentatively, that the phenotypes are neutral?

      What about other phenotypically visible characters like eye color, the shape of your nose, and male pattern baldness? Should we assume that one of the alleles governing each of these characters is adaptive? Which ones?

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    7. The fact that men have nipples is a potential spandrel. It would be almost impossible to prove the negative ... i.e. that there was absolutely no fitness benefit.

      I don't think sexually dimorphic characters are a very good example. Bimodal adaptation is still adaptation. Adaptation sums over many generations, and genes spend half their existence in one gender and half in the other. Even if the fitness contribution of breast tissue genes to males is zero, those genes are very likely to be under selection in the population. The evolutionary and developmental explanation for nipples in males cannot exclude the fact that these genes are under selection in females.

      Gould and Lewontin say that the default hypothesis should be nonadaptive and the burden of proof lies with those who claim that it is an adapation.

      There is not a single ‘nonadaptive cause’. Drift, hitchhiking, gene conversion, recombination, mutation, ‘selfish DNA’ – they all have a part to play. “Prove it’s an adaptation, or we declare it to be … er … one of these”.

      We discussed this in class today. We discovered that half the class could roll their tongues and the other half couldn't. That's a phenotypically visible character. Should we automatically assume that one half of the class is less fit than the other? Or, is it more reasonable to conclude, tentatively, that the phenotypes are neutral?

      When a gene is polymorphic, that conclusion is more likely than if it is fixed. Still, such arguments cut both ways. Adaptationists don’t say “there are no nonadaptive characters”, any more than ‘Accidentalists’ say there are no adaptive ones.

      What about other phenotypically visible characters like eye color, the shape of your nose, and male pattern baldness? Should we assume that one of the alleles governing each of these characters is adaptive? Which ones?

      Show me your selection coefficients and I’ll show you mine.

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    8. I would like to draw Larry's attention to an interesting paper (just published yesterday) that I wager merits attention by participants in this forum

      http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3196.html

      According to their analysis, it would appear that only about 7% of the letters in the human genome are functionally important!!!!!

      ... and constitutes a resounding contradiction of ENCODE as hyped in the popular press.

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    9. Allan Miller says,

      The evolutionary and developmental explanation for nipples in males cannot exclude the fact that these genes are under selection in females.

      Exactly. The reason men have nipples has nothing to do with whether they have a function in men and everything to do with the fact they have a function in females. In men, it's an accident and there's no reason why male nipples couldn't disappear.

      There is not a single ‘nonadaptive cause’. Drift, hitchhiking, gene conversion, recombination, mutation, ‘selfish DNA’ – they all have a part to play. “Prove it’s an adaptation, or we declare it to be … er … one of these”.

      Allan, you said, "I have a tendency to assume that phenotypically visible characters have a good chance of being adaptive." I don't have that tendency. I have a tendency not to jump to conclusions about adaptations and that means considering lots of other possibilities. I do NOT "declare" that something is an accident, I simply like to point out to adapationists that they are making unwarranted assumptions.

      When a gene is polymorphic, that conclusion is more likely than if it is fixed.

      So, a more correct statement of your position is that you have a " tendency to assume that phenotypically visible characters have a good chance of being adaptive but only if they have become fixed in the population." Right?

      At some point in the future either the ability or the lack of ability to roll your tongue will become fixed in the population even if it's nonadaptive. This will be true of all phenotypically visible character that are neutral. Is it true that you will then have a tendency to think of them as adaptations?

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    10. Tom Mueller says,

      According to their analysis, it would appear that only about 7% of the letters in the human genome are functionally important!!!!!

      Not quite correct. It says that only a small percentage of the genome is conserved but it doesn't rule out DNA that is functionally important but the sequence is irrelevant. There are known examples that I've described many times in previous posts.

      This is not a new result. We've known this for fifteen years.

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    11. re: Not quite correct.

      I was wondering about that myself!

      Here is what some google-whacking got me:

      The scientists found that, at most, only about 7% of the letters in the human genome are functionally important. "We were impressed with how low that number is," says Siepel. "Some analyses of the ENCODE data alone have argued that upwards of 80% of the genome is functional, but our evolutionary analysis suggests that isn't the case." He added, "other researchers have estimated that similarly small fractions of the genome have been conserved over long time evolutionary periods, but our analysis indicates that the much larger ENCODE-based estimates can't be explained by gains of new functional sequences on the human lineage. We think most of the sequences designated as 'biochemically active' by ENCODE are probably not evolutionarily important in humans."

      http://tinyurl.com/kjs4wgf

      Is it safe then to presume that Siepel is guilty of hype and over-stating his case?

      re: ... but it doesn't rule out DNA that is functionally important but the sequence is irrelevant. There are known examples that I've described many times in previous posts.

      Exactly what I was wondering.

      I raised this question more than once when speculating whether parasitic DNA can be co-opted into becoming symbiotic DNA in different lineages even when discussing different sequences.

      I was thinking of course of human Alu and murine B1

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    12. Have you guys seen a man without nipples? Even worst seeing a woman without nipples and breasts. I've seen it. Apparently men get breast cancer too. I didn't know that. Ugly views

      Delete
    13. "One of my principal beefs with 'Spandrels' is that there are no decent examples of a spandrel given, in the terms they implicitly demand - ie, where the selective effect of the assumed spandrel has been evaluated and found to be nonadaptive."

      How about Goulds umbillicus example? It's a feature of all shells that are produced by the particular form of secretion used by all Mollusks, is present in all Mollusks as a side effect of having that type of shell and is used to protect eggs in some clades of snails. But it's somewhat silly to argue that the trait itself was adaptive when it arose.

      "There is not a single ‘nonadaptive cause’. Drift, hitchhiking, gene conversion, recombination, mutation, ‘selfish DNA’ – they all have a part to play."

      But they aren't what the spandrels paper is about, really. The spandrels paper is primarily about traits(!) and their non-independence. Which as it happens is mostly the same as developmental constraints. The key papers to look at (and if there's one thing I really dislike about Gould is that he cites them to rarely where they are relevant. Nothing Gould wrote after these makes sense without understanding them, yet they are mostly not cited):
      Raup et al. 1973. "Stochastic Models of Phylogeny and the Evolution of Diversity"
      Raup and Gould 1974. "Stochastic Simulation and Evolution of Morphology-Towards a Nomothetic Paleontology"
      Schopf et al. 1975. "Genomic Versus Morphologic Rates of Evolution: Influence of Morphologic Complexity"
      Gould et al. 1977. "The Shape of Evolution: A Comparison of Real and Random Clades"

      To sum these up shortly:
      Raups earlier work had shown that most of the diversity of mollusk shell morphology could be represented by just 4 parameters (later work showed that there are better choices for these parameters, but you still end up with 4). That's somewhat surprising, because you could take a lot more morphometric measures. But because the developmental process is constraint, these are not independent. In the 4 MBL papers simulations were run in which clades were produced by simple BD models and in which the parameters were allowed to vary among lineages assuming no "net" selection (note that this is not the same as "no selection anywhere", just independence of changes for each taxon and a mean change of 0). The results were compared to the real fossil record and this null model in many ways matches the fossil record.

      It's worth noting, no, it's absolutely vital to note, that this is a null model for morphological change across lineages in deep time. Which is quite removed from population genetics. If one takes these results and tries to infer something about the role of drift, then one is making a couple of very problematic assumptions and Gould would have (rightly) pointed out that this was "extrapolationism". There are assumptions about the relationship between genetic and morphological change in there that are often unwarranted and there are assumptions about the cause for global trends in there that are usually wrong.

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    14. Larry, So, a more correct statement of your position is that you have a " tendency to assume that phenotypically visible characters have a good chance of being adaptive but only if they have become fixed in the population." Right?

      Weelll ... I don't take a dichotomous view. A population possesses a set of fixed traits, and a set of polymorphic ones. I don't think it unreasonable to assume that the polymorphic set will contain more drifting alleles than the fixed portion, so this is another factor that increases the likelihood, not any kind of certainty.

      At some point in the future either the ability or the lack of ability to roll your tongue will become fixed in the population even if it's nonadaptive. This will be true of all phenotypically visible character that are neutral. Is it true that you will then have a tendency to think of them as adaptations?

      I don't think of traits becoming fixed, but their underlying genes. Even then, it is not so much a particular allele, but descendants of a particular copy. These may be mutated descendants, even more likely in the neutral case. Assuming for the sake of argument that tongue-rolling is controlled by 2 alleles of 1 ancestral sequence, we are looking for the day when the B form becomes extinct. Will the population, on that day, be all-rolling? Probably not, in a population of this size. The population will consist of descendants of the A form, but in the time it has taken for neutral drift to fix 'not-B' (ancestral A), A may have generated neutral versions C, D, E, some of which may be functionally B. Time to fix does depend upon effective population size, of course. But it also depends on s and u, and so fixed traits should (on balance) contain more of the adaptive than polymorphic ones.

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    15. Simon, The spandrels paper is primarily about traits(!) and their non-independence. Which as it happens is mostly the same as developmental constraints.

      Well, that's another beef! Evolution is all about metazoan somas! (And, one suspects, the nature/nurture debate in a particularly self-important species of such).

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    16. I have a suggestion for a spandrel: Skincolour of caucasians. It seems to be nothing but a byproduct of the selection for reduction in melanin. In other words, it is not that the yellowpinkish colour of the skin of "white people" is adaptive, that's just the colour skin has when melanin production is downregulated.
      Increasing the potential to absorb light for vitamin D production doesn't require(afaik) any particular colour of the skin, only that light of specific wavelengths can pass through.

      The brown/dark colours of "black people" might not even be directly adaptive, in that we can easily imagine other dark colours(dark green, dark red, dark purple etc.) providing the same protection agains UV light. In this sense it is only the darkness of it that is of adaptive benefit, not that it is some specific hue and shade of brown.

      Once the selection for protection against UV light is relaxed, so adsorption of light for vitamin-D synthesis can remain high, the skin's colour is free to change within the range of colours and hues the cells and biological substances the skin is made of(fats, collagen and so on) just happen to have.

      Thoughts and criticisms welcome.

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    17. Well, similar work has since been done for Foraminifers as well as some colonial organisms (and branching morphologies of plants have been around for a while as well). Apart from that: I find it silly to fault paleontologists for investing research effort in groups that have a decent fossil record. There is work on geobiochemistry where we can detect decay products of some organic substances, but it's not as if there was a fossil record of - say - archea that could be identified as such.

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    18. In men, it's an accident and there's no reason why male nipples couldn't disappear.

      No, it's not an 'accident' if it is under selection in females - that maintains the alleles in the population. There is in fact an allele suppressing female-style breasts in men, under hormonal control. I reckon that's probably an adaptation!

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    19. Simon - I know, I was being silly on purpose. Nonetheless, soma-centric bias is kind of a key distinction between what might be called the 'Gouldian' and 'Dawkinsian' approaches.

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    20. Mikkel - being picky, a 'spandrel' should perhaps be some feature of organismal architecture, to be in line with Gould & Lewontin's explicit connection, though it tends to have become anything to which one could attach the label 'nonadaptive consequence of something else'.

      Your skin colour example is interesting. There is a pretty good correlation between skin colour and latitude, among those races that have occupied their ancestral positions for a reasonable period. The 'adaptationist' following Williams, Maynard Smith et al would argue that the s values of the coloration genes are under differential selection in different regions, and the balance between UV sensitivity and Vitamin D photochemistry are both very plausible selective agents (is that a 'just-so story'? What about sexual selection? Drift?). But what they don't argue is that 'it has to be this colour', any more than they argue that the optimal human digit number per limb is 5.

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    21. s values [..] are under differential selection

      I meant *are different*

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    22. LM : What about other phenotypically visible characters like eye color, the shape of your nose, and male pattern baldness? Should we assume that one of the alleles governing each of these characters is adaptive? Which ones?

      Larry, I need to thank you for re-igniting my enthusiasm for Stephan Jay Gould. I just downloaded the Panda’s Thumb on my kobo and was struck by mention of “beanbag genetics” in the prologue.

      That reminded me of P Z Myers’ blogpost
      http://scienceblogs.com/pharyngula/2011/12/19/steve-pinkers-hair-and-the-mus/

      “Beanbag Genetics”?! Some quick google-whacking and I had an aha moment:

      http://en.wikipedia.org/wiki/Ernst_Mayr#Mayr.27s_ideas

      The question about Allan’s response to Mikkel got me wondering whether you are asking the wrong question.

      It is not about whether blonde/milk complexion is adaptive as say compared to red hair/freckles; but rather whether any decrease in melanin deposition was at any point in our history adaptive. If the answer to that question is yes – then different versions of a variety of eye/hair colors are indeed adaptive compared to the original default setting that was disadvantageous.

      But even if they were not – the point becomes moot according to Mayr:

      In many of his writings, Mayr rejected reductionism in evolutionary biology, arguing that evolutionary pressures act on the whole organism, not on single genes, and that genes can have different effects depending on the other genes present

      At this point we need to invoke high school notions of polygenic & pleiotropic. Maybe male pattern baldness is not adaptive when considered in isolation, but the network of different gene interactions that cause male pattern baldness also result in a cluster of other phenotypes not immediately obvious to the observer and such a constellation of cause-effect gene interactions considered as a whole together are indeed adaptive.

      Considering just one effect (male pattern baldness in this case) would constitute the ignoratio elenchi aka "Beanbag Genetics"

      I must be getting something wrong here and I suspect that I am merely restating your thesis from a different angle perhaps

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    23. I don't know why so many feel that pleiotropy and polygeny should cause any problem for reductionism. This is the essence of Denis Noble's critique as well.

      G&L's critique too is at phenotypic level - their cartoon adaptationist will try and explain any and every feature in terms of the adaptive value of that feature. But those taking the 'gene's-eye-view' are looking at it from the inside out (or, as I would put it, the right way round! ;) ). The genetic material is digital, and persistent through copying. Fitness is enhanced, or not, through the net resultant of all phenotypic consequences and circumstantial constraints (including gender-specific features under hormonal override, recessiveness, epistasis etc). There does not need to be a 1:1 mapping, nor consistent s, for an allele to benefit or hinder its own spread. Evolutionary haplotypes are not developmental units, nor coding ones.

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    24. Which of course does not prevent one from trying to make causal statements, sometimes unwisely, to try and pin down a reason for fixation or extinction.

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    25. Hi Allan and thank you for your patient response

      I fear that I may simply be restating the obvious and I beg your patience and indulgence.

      But when attempting to translate all of the above (especially Simon’s insights) into terms that a high school student could understand, I still wonder if reductionistic over-thinking may be posing a problem.

      I wonder outloud whether Larry Moran is guilty of creating a strawman argument or as you phrased it “ cartoon adaptationist”?

      Let’s try this one step at a time and first things first:

      Regarding for example hair colour: “Should we assume that one of the alleles governing each of these characters is adaptive? Which ones?

      Well, it isn’t just about different alleles for ONE gene now is it… but leaving even that aside for the moment; I can still repose the question whether the original default setting of melanin deposition in my ancestors’ epidermis during the last ice-age presented a problem or not.

      Harking back to the vitamin D story, let’s say yes.

      That would mean any evolutionary strategy (forgive my teleological turn of phrase) would present a selective advantage. The fact there exist a variety of different phenotypes that present this selective advantage should not distract us from the benefit of any version of reduced melanin deposition during the last ice age.

      If one wants to consider the blond phenotype in isolation then the paramount question is whether blond conveyed an advantage or compared to melanin deposition during the last ice age or alternatively whether red hair conveyed a similar advantage or not etc…

      To my way of thinking it becomes illogical to then rephrase the question whether the red hair phenotype is advantageous compared to the blonde phenotype TODAY… and failing to detect any selective advantage (let’s shrug off 1/Ns) claim the existence of these various phenotypes today represent confirmation of Neutral Theory.

      At a minimum – some other phenotype other than hair color should be cited to buttress Neutral Theory.

      Maybe Larry’s thesis is more subtle than I am able to discern and perhaps I am again merely rephrasing his thesis, but from a different angle.

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    26. Tom - my take is that the debate hinges on a phenotypic vs a genetic reductionism. There is only so far one can 'atomise' organismal traits. There’s only so far one can usefully atomise the genetic material as well, but it is at a somewhat lower level. Genes (as simply linear subdivisions of the raw genome) form part of the environment of other genes, so you get coevolutionary relationships.

      Many different genotypes may respond to the selection of a coarse phenotypic ‘trait’. Against each other, they might largely drift. But against that which they collectively replaced, less certain. Selection is a continual matter of ‘running to stay still’, as Van Valen put it. Once selection has fixed an allele, the relative fitness wrt that locus is back at 0. But attempts to knock that allele off its perch on the adaptive hillside have a reduced chance of success, because more of genetic space is now ‘downhill’. Whereas a drift- fixed allele has no particular barrier stopping it from drifting back towards polymorphy. And if mildly deleterious into the bargain, it must persist against active selective pressure also.

      Having said which, I think non-adaptive factors are responsible for a significant amount of phyletic change and divergence!

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  9. Ghee whiz Allan

    That reminds me:

    I always did think there were three kinds of people on this planet: those who can count and those who can't!

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  10. As a student of one of the authors of "Spandrels" I am a bit biased. But I think that it did a useful service. I know one of the people whose work was savaged in "Spandrels". He immediately became much more defensive and much less fast-and-loose with imagined adaptive scenarios.

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    1. The students in my molecular evolution class are about to graduate in a few months. A few weeks ago, they were completely unaware of the fact that random genetic drift plays a significant role in evolution and they had never heard of the controversy over adaptationism.

      By the way, some of the students had heard of a guy named Joe Felsenstein because they used the PHYLIP package in another course. One students knew who Stephen Jay Gould was and none of them had heard of Richard "Dick" Lewontin.

      This is surprising since they have all taken at least one previous course on evolution. Why do you think we a giving out degrees in the biological sciences to students who see nothing wrong with the adaptationist position because they don't even know there are other options?

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