About Rationally Speaking

Rationally Speaking is a blog maintained by Prof. Massimo Pigliucci, a philosopher at the City University of New York. The blog reflects the Enlightenment figure Marquis de Condorcet's idea of what a public intellectual (yes, we know, that's such a bad word) ought to be: someone who devotes himself to "the tracking down of prejudices in the hiding places where priests, the schools, the government, and all long-established institutions had gathered and protected them." You're welcome. Please notice that the contents of this blog can be reprinted under the standard Creative Commons license.

Thursday, August 21, 2008

Hurrah! Yet another controversy in evolutionary biology!

I have made the point several times on this blog that creationists (among whom I squarely classify so-called intelligent design proponents) simply don’t get it (or refuse to get it) when they claim that scientific controversies are a sign that there is something seriously wrong with science. Au contraire, mes amis, science makes conceptual progress largely through discussions and disagreements among scientists, which eventually get settled because of new empirical discoveries. Now, controversies about the Bible, on the other hand... But I digress.

The latest round of vigorous debate in evolutionary biology has been featured in Science by reporter Elizabeth Pennisi, and it deals with the role of cis-regulatory sequences in evolution. cis what?, you might say. A cis regulatory sequence is a piece of DNA that is located outside of a gene proper (typically upstream of it), but located next to it on a chromosome. The cis element does not code for a protein or enzyme, unlike the gene itself, but rather alters the timing (during development) and place (which tissue) the gene itself gets expressed. cis is in opposition to another type of regulation of gene activity, known as trans, where a molecule produced in one part of the nucleus (by a particular sequence of DNA) affects the regulation of a gene far away, on a different part of the genome.

cis-regulatory sequences have received much attention lately, for instance by evolutionary biologist Sean Carroll of the University of Wisconsin-Madison, who is one of the leading researchers on so called “evo-devo” (evolutionary developmental biology). In 2005, Carroll wrote an influential paper in PLoS Biology, in which he argued that the action of cis-regulatory elements is crucial to morphological evolution in animals (though why only morphological? What about physiology, biochemistry, or other aspects of the phenotype?). The implication is that cis-regulatory evolution may be directly involved with the origin of several major “phenotypic novelties,” the sort of structures whose detailed explanation is one of the holy grails of evolutionary biology.

Just like in any good controversy, though, there is a group of people pushing for new ideas and another one playing the part of the intellectual conservative, resisting the change and declaring that what is being trumpeted as new is either already known or not much of a big deal. Sure enough, in 2007 the journal Evolution published a response to Carroll’s paper, co-authored by Jerry Coyne (University of Chicago) and Hopi Hoekstra (Harvard). Coyne, incidentally, has appeared in the role of the skeptic several times lately, most recently in another piece by Pennisi in Science, the one commenting on the so-called “Altenberg 16” meeting which I organized in Austria this summer (more on that meeting will soon appear in Nature magazine, again featuring Jerry as the counterpoint, in that case to my own positions).

Coyne and Hoekstra’s paper, according to Pennisi and some comentators, was sharply worded (indeed, Hoekstra herself regretted the strong language in the Science interview), and the Scientific American’s web site recently hosted an article by Carroll and colleagues that led to an interesting exchange (in the comments section) between Carroll and some readers (Coyne did not participate). However much the verbiage may have bruised egos or raised hairs, of course, the real controversy is about the empirical evidence and its interpretation: are cis-regulatory sequences that important in morphological evolution or not?

In part the answer depends on what one means by “important.” We do not have reliable data about the frequency of evolutionary changes triggered by mutations in cis-regulators vs. standard protein-coding genes, and it is unlikely that a large unbiased sample of enough genomes will be available any time soon to settle the matter in that sense. Then again, “importance” in biology is hardly a matter of sheer numbers: some evolutionarily relevant phenomena happen very rarely, and yet they are arguably very important in the sense that they affect the subsequent course of life’s history on the planet in remarkable ways. Think of impacts of extraterrestrial bodies and their link to mass extinction: sure, they happen once every several tens or even hundreds of millions of years, but the one at the end of the Cretaceous helped wipe out the dinosaurs and arguably led to the rapid ecological takeover of mammals.

In the cis dispute, Carroll brings up what I think is in fact compelling evidence that cis-regulation does play a crucial role in morphological evolution, at least some of the time. Coyne’s response is to demand more direct (less correlational) evidence before jumping to conclusions, and he has a point too. The reality is probably somewhere in the middle, as my colleague Gunter Wagner (one of the Altenberg 16) told Science: “There are clearly well-worked-out examples where microevolutionary changes can be traced back to cis-regulatory changes.” Greg Wray (another middle ground voice of reason, and yet another Altenberg 16 co-conspirator) said “I think we are on the threshold of a very exciting time.”

There are two points to be taken from this story, I think. First, social scientists ought to do serious studies of the role of personality in scientific disputes (it has probably been done already). Why is it, for instance, that people like Jerry Coyne tend to find themselves very often defending the conservative position, while people like, hum, me, find themselves on the other side of the barricade? Obviously, some of the times the conservatives will be right, at other times the progressives will be, so finding yourself more frequently than not in one category must have to do more with your psychology than with whether you tend to be right or not.

The second point, however, is about how science makes progress: we need both the Sean Carrolls and the Jerry Coynes of the world, not just because they make science more personal and, frankly, exciting, but because it is the tension between ideas that drives the whole enterprise. Some scientific controversies get settled by the data, others remain in permanent suspension because pertinent data isn’t forthcoming, and yet others change in nature over time because people shift conceptual framework and therefore come to think about old issues in new ways. This is entirely different from pseudosciences like intelligent design, where controversy undermines the ideological message, and where empirical facts have nothing to do with it. Of course, a psychological study of the creationist mind would also be fascinating, I can see the title of an fMRI paper already: “This is your brain on creationism”...

[Note: this post has been slightly modified from the original, thanks to comments from Jerry Coyne]


  1. Excellent post. If I recall correctly, Marc Kirschner and his colleague John Gerhart have also had some strong criticism for their take on 'facilitated variation', which is also dependent on the cis-regulatory sequence.

  2. First, social scientists ought to do serious studies of the role of personality in scientific disputes (it has probably been done already).

    I'm not sure if David Hull's Science as a Process counts as being from the social sciences but it sure covered the topic a lot.

    Excellent explanation why scientists spat (and should!) and why creationists display ignorance and/or duplicity when they try to exploit that.

  3. My advice to Coyne and Carroll: shut up and get some data. This is the frustrating thing about these personality fights...it's not about the data (of which there's precious little in this case), it's about self-aggrandizing superimposition of your own will or version of reality on others. I think any biologist backed into a corner will admit that both are "important." Relative importance is a ridiculous argument at this stage.

  4. This is a good healthy spat, seems to me. I'm very interested in the role of personality in determining the direction (or misdirection) of science, and not in-house, bit the popularizers (who shape the ideas of future scientists and tend to be generalists). Would punctuated equilibrium have gotten as much notice had it been proposed by someone other than Gould? Would evo-devo be more advanced if there had been no Haeckel, or if von Baer had been more outgoing? What would creationism look like without the beautiful prose of Agassiz, he of the diamond plated CV?

  5. Nice post Massimo, I think that controversies are very important for the progress of science. I have a paper related to the topic (but it talks about ecology not evolution...). Controversies are definitely and interest areas and even some researchers don't like then and even avoid them.

  6. Au contraire, mon amis...
    Max, I know you're an Italian speaker and all, but in French, that should read "au contraire, MES amis..." (plural "friends", you see).
    C'est le plus marrant erreur que je n'ai jamais entendu...

  7. Kimpatsu,

    thanks for the correction! The text is now French-passable :)

  8. Feeling magnanimous today, Massimo? Calling ID even a pseudoscience is quite generous of you... :O)

    The controversy. Cool... These things can be fun, but can also be frustrating.

    I don't know if it's the case here, maybe it is still early in the field, but what Miko says might hit it. More data, less talking.

    I myself say this based on the fights I used to follow in the field of phylogenetics, basically "cladists" versus "everyone else". All the "philosophy" thing justifying cladistics, and the long and endless exchanges... but hardly any data backing anything up either way (that came here and there later, but people would mostly ignore or disqualify it for whatever reason they could conjure). As the warring camps get old and die, the "controversy" dies out. Nowadays, the systematic wars are mostly a thing of the past as far as I can tell, as new generations just see that each method will have its strengths and weaknesses in different situations, etc. And then people get to work instead of throwing more wood at the fire of the "controversy".

  9. J,

    as you might expect, I disagree with the simple "let's get more data" response. Many scientific controversies, and the one about cladism is a perfect example, hinge on conceptual issues and therefore require quite a bit of theoretical discussion, not just more data. Of course more (relevant) data is always a good thing, but scientific theories don't just emerge from stockpiling data.

  10. Massimo, but as far as postmodernism is concerned, you are a "conservative", right? My stake on this is that classifying the science one does by the political view one holds will bring more harm than good, vide science studies.

    I don't have a problem with their discussions "on the vacuum", as long as:
    1) they don't stop working (for a broad definition of "working") in order to devote to their vendetta (IOW, talking is good, but working is not bad either);
    2) they don't prevent other people from doing the work (for the same bogus definition of work as above).

    Point (2) is certainly not the case, unless it affects their objectivity in reviewing etc. - which is very unlikely. Actually by exposing the controversy is more likely that other people feel attracted by the subject: visibility is always a good thing.
    As for point (1) it should not be an issue, but it soon came to my mind the sad story of Peter Duesberg (the guy who was too proud or too stupid to recognize HIV as the cause of AIDS).

  11. Massimo,
    Regarding your idea about social scientists doing research in this area:
    I think something could be done if we could conduct a study on self-reported scientific radicals/progressives, moderates, and conservatives and administer the MMPI to them. Just a thought.


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