Tuesday, February 15, 2011

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.

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.


  1. I appreciate Sean B. Carroll's assistance in elucidating for interested laypersons some of the bases for morphological change in the animal kingdom from the Cambrian through the present. His explanations of change occurring through common types of mutations in regulatory genes helped me understand species changes on a level other than the usual (at least in what I read and was taught) "Here's a flower with a really deep throat, and wouldn't ya know it, here's a moth with a really long tongue." I'd certainly wondered how, from a genetic and biomolecular point of view, such morphological changes came about.

    On a deeper level, others evidently wondered as well. I still remember Gould asking near the end of Wonderful Life why the post-Cambrian hadn't seen more diversification in basic animal body plans.

    In helping raise awareness of how factors on the molecular level play an important role in what sorts of changes we see on a morphological level, I think of Carroll's and Arlin Stoltzfus' work as analogous.

  2. Thank you for pointing out the problems with Evo-devo as theory. I have been reading the New Science of Evo-Devo. For me personally, many of the points made by Carroll were revolutionary, but that is because I learned to believe that evolutionary theory in general is highly complex and full of holes. That a "small set of genes can produce drastically different body types" was news to me (sadly enough), and incredible news at that. That you could learn about furry things (or an elephant) from fruit flies fascinates me. Either I did not learn this in high school/college, or I just did not listen very well, which could be the case (I do feel embarrassed for my lack of knowledge in this seemingly fundamental area of biology).

    It is very good to know that the big ideas presented in the book are not as new or revolutionary as Carroll seems to imply. I will admit that I like how he presents the information---I can sense his excitement and I, too, feel that same excitement. I thought, "why didn't I learn this stuff in school?" However, I also felt led to believe that this "revolutionary" science can explain everything in the fields of biology and evolution, that it is foundational. So, this blog post helped me to see the book within the bigger picture of scientific thought. Thank you!

  3. Tammy posted:
    "I thought, 'why didn't I learn this stuff in school'?"

    I agree.
    The idea that very small changes can have very large effects is very significant.
    It turns the usual idea of gradual accumulation of random mutations on its head.

    This should be taught from the beginning, instead of young people being given the outdated, old ideas that so many people take as given.

    It seems to me that this is the sort of curriculum change that ID folk promote and that makes perfect sense.