Pharyngula

I must disagree with Larry Moran, who accuses the field of evo-devo of animal chauvinism — not that it isn’t more or less true that we do tend to focus on metazoans, but I disagree with an implication that this is a bad thing or that it is a barrier to respectability. Larry says we need to cover the other four kingdoms of life in greater breadth, which I agree is a fine idea. I would like to have a complete description of the genome of every species on earth, a thorough catalog of every epistatic interaction between those genes during development, a hundred labs working on each species, and a massive collection of papers for each one documenting every step and every protein and every variation in their development. I would like it tomorrow.

I think we all agree that that would be impractical. The question is how we will focus our research to maximize our use of limited resources, and get us useful answers that will lead us in productive directions. Larry is advocating maximizing our phyletic breadth by following organisms representative of the greatest amount of diversity. He is proposing this in opposition to the proposal from Jenner and Wills, who suggest a different strategy — and I find myself agreeing more with Jenner and Wills than with Moran.

Their suggestion is that instead of picking our model organisms by where they are on the phylogenetic tree, we ought to select them by their suitability for answering specific questions in evo-devo. If we want to “discover law-like generalities (nomothetics)” we need to emphasize the pursuit of conceptual themes rather than haring off to collect another organism in the stamp book. That sounds like a good path to intellectual respectability to me.

Along those lines, Jenner and Wills recommend several species that deserve expanded study; they all happen to be animals, but they all also happen to present illustrations of interesting concepts in evo-devo. They even offer a handy list of these central evo-devo concepts that we should be pursuing.

  • Developmental programming. Allometry of horns in the beetle Onthophagus nigriventris.

  • Developmental bias. Variation in body size in C. elegans.

  • Developmental constraint. Shell morphology in the gastropod Cerion.

  • Redundancy. Anterior-posterior axis development in Drosophila melanogaster.

  • Modularity. Sense organs in the cavefish Astyanax mexicanus.

  • Evolvability. In silico cell-lineage evolution.

  • Origin of evolutionary novelties. The sea anemone Nematostella vectensis (bilateral symmetry, triploblasty).

  • Relationship between micro- and macroevolution. The three-spined stickleback and Heliconius butterfly wing patterns.

  • Canalization and cryptic genetic variation. D. melanogaster phenotypic variation increase during HSP90 impairment.

  • Developmental and phenotypic plasticity, polyphenism. Ant caste polyphenism and caste determination by primordial germ cells in the parastic wasp Copidosoma floridanum.

Larry mentions that there has been a significant foundation of research in gene regulation that is of great importance in understanding development, work that has been done in viruses and bacteria. I agree that all of that is important — I’ve read Ptashne, too — and that understanding those seminal ideas from people like Jacob and Monod ought to be a required element of beginning workers in evo-devo. But the real question ought to be whether we can better address the concepts listed above with a test tube full of bacteria, or with the animal species described. I suspect the latter, but Larry can explain to me otherwise; I fear, though, that understanding modular interactions between fields of tissues requires an experimental subject that has tissues.

One complaint I would have with Jenner and Wills, though, is that while their concept-focused approach is laudable, it is a little peculiar that plants are so poorly represented in their list of model organisms, and that is an unnecessary exclusion. Plants ought to be excellent subjects for studying modularity and the origin of novelties, for instance, so I suspect some bias towards animal models that isn’t entirely based on their applicability to specific questions.

Still, it’s not enough to tell us that bacteria exhibit properties of gene regulation just like metazoans — the question is whether they exhibit higher-level properties of multicellularity, tissue organization, and organismal patterning that are the subjects of interest to people doing evo-devo. Try as one might, I just don’t see bacteria as being entirely useful subjects for studying the evolution of body plans, except maybe as an outgroup that lacks a body plan.


Jenner RA, Wills MA (2007) The choice of model organisms in evo-devo. Nat Rev Genet. 8:311-314. Epub 2007 Mar 6.

Comments

  1. #1 Keith Douglas
    March 31, 2007

    I’m not a biologist, never mind a specialist in evolution or development. But it seems to me that one should simply investigate whatever seems interesting and affordable and slowly knit the pieces together.

  2. #2 mark
    March 31, 2007

    How about J. Craig Venter? He does his amazing survey of ocean life, (and what do the creationists say? That we can’t use evolutionary theory to interpret biology because we haven’t effectively catalogued the specific evolutionary pathway of every animal that has ever lived, ha!)

    Anyway, besides the point. The Sorcerer II expedition is, I think, one of the most interesting biological experiments ever undertaken, because Venter is not just focusing on the smaller creatures, but is taking on the ambitious idea of surveying the current state of ocean life. It also is leading to the discovery of thousands of new genes, new biochemical pathways, maybe even new useful biomolecules and antibiotics.

    I guess my response to Moran is that his focus is too narrow. I don’t think we can predict what experimental animal may ultimately prove the concept or give us the most informative answers. I’m kind of suspicious of these top-down strategies that would attempt to coordinate a field (reminds me of Zerhouni’s roadmap for some reason). We should continue to shotgun across multiple species (and plants, and even ocean life) because the scientific breakthroughs come from unexpected places. Just look at taq.

  3. #3 Stuart Coleman
    March 31, 2007

    As with all fields, there will be disagreements as to how best to answer the questions that need to be answered. I agree with you more than Larry (it seems like plants and animals should be the first organisms we understand). But the animal bias is understandable, I think, because it can lead to discoveries that pertain to us, which seems like the best way to get funding, (and maybe discover the next great therapy for some disease).

  4. #4 Ford
    March 31, 2007

    I wasn’t aware that evo-devo wasn’t considered respectable. Maybe it’s the eye patch?

    But there’s certainly a lot more to evolutionary biology than evo-devo. I’ve pretty much ignored it in This Week in Evolution, figuring you’ve got it covered, and I haven’t run short of topics yet.

  5. #5 Ken C.
    March 31, 2007

    “Their suggestion is that instead of picking our model organisms by where they are on the phylogenetic tree, we ought to select them by their suitability for answering specific questions in evo-devo.”

    Wasn’t it always this way? I don’t think it was a bias toward the lovable fruitfly, the adorable squid, the enchanting aplysia, or the cute-but-feisty horseshoe crab that led to their study, but rather their fast reproduction, big axons, not-too-large-ganglia, and nice compound eyes, respectively. Yes?

  6. #6 Torbjörn Larsson
    March 31, 2007

    Ah, the never ending argument about research strategies with finite resources.

    Yes, concentrating resources on some areas may make us miss things and distort the picture for a while. I remember Pharyngula’s posts on the non-general, compressed and tightly orchestrated development in Drosophila.

    But concentration, competition and feedback are good things (to use a PZism, for once) in science, at least in a developing field.

    Being a layman, I can only assume that Jenner and Wills review means that the field has matured enough to start to ask specific questions. It sounds like there are exciting times ahead here. I suspect PZ would wish he had more arms. Ooops, I forgot, he already does!

  7. #7 Torbjörn Larsson
    March 31, 2007

    Ah, the never ending argument about research strategies with finite resources.

    Yes, concentrating resources on some areas may make us miss things and distort the picture for a while. I remember Pharyngula’s posts on the non-general, compressed and tightly orchestrated development in Drosophila.

    But concentration, competition and feedback are good things (to use a PZism, for once) in science, at least in a developing field.

    Being a layman, I can only assume that Jenner and Wills review means that the field has matured enough to start to ask specific questions. It sounds like there are exciting times ahead here. I suspect PZ would wish he had more arms. Ooops, I forgot, he already does!

  8. #8 Magister Ludi
    March 31, 2007

    PZ – Moran’s right – you are an animal chauvinist. The world was strictly the domain of bacteria, archaea, and microbial eukaryotes for more than 3.5 billion years and they still dominate in number, diversity, biomass, and biogeochemical significance. Microbes frequently use multicellular communication (e.g. quorum sensing) and some are obligately multicellular (e.g. multicellular magnetotactic bacteria). Microbes are metabolically-diverse, using every conceivable energy-yielding electron donor/acceptor pair including metals – not just organics and O2 (boring). Metazoans are really just an afterthought in the scheme of life and not all that interesting in terms of fundamental biochemical diversity. If it’s been done, a microbe probably did it first. And if you really can’t pry yourself away from eukaryotes, it would also be nice if you would think beyond the stuff you see everyday (plants and animals) and remember your fungi and microbial euks! I’m not saying that the questions that you want to answer aren’t interesting (they are fascinating), but it does seem that your evo-devo view of what the fundamental questions in evolutionary biology should be (even in terms of the biology of cellular interaction) is too narrowly focused on metazoan life.

  9. #9 PZ Myers
    March 31, 2007

    Errm, no. I’m saying the fundamental questions in general evolutionary biology and the fundamental questions in evo-devo are different — I don’t think anyone is saying they’re the same. The conflict arises when people assume that an interesting problem in bacteria is what ought to be studied instead of an interesting problem in butterflies because, for some reason of reverse elitism, butterflies are third-rate organisms compared to E. coli.

  10. #10 Torbjörn Larsson
    March 31, 2007

    Ooh, a fight!

    You know that the public always cheers on the small guys, don’t you? Animals may not be the cuddly crowd pleaser that it seems at first sight. 🙂

  11. #11 Torbjörn Larsson
    March 31, 2007

    Ooh, a fight!

    You know that the public always cheers on the small guys, don’t you? Animals may not be the cuddly crowd pleaser that it seems at first sight. 🙂

  12. #12 Norman Doering
    March 31, 2007

    mark wrote:

    The Sorcerer II expedition is, I think, one of the most interesting biological experiments ever undertaken, because Venter is not just focusing on the smaller creatures, but is taking on the ambitious idea of surveying the current state of ocean life.

    Venter seems to be doing for the ocean’s single celled critters what Darwin on the Beagle did for multicellular island species.

    I’ve got some more links Venter’s Sorcerer II expedition and his new start-up called Synthetic Genomics in a blog I wrote to tear into Vox Day’s ignorant ideas about what science is:

    http://normdoering.blogspot.com/2007/03/religions-war-on-science-part-1.html

    I think, for the near future, the money will be in microbes. Bio-fuels, drugs and more… so don’t worry about a lack of interest.

  13. #13 GS
    March 31, 2007

    Although there may be a research bias towards certain creatures as opposed to others, I tend to believe this is a result of the amount of work that has already been done on them. We can’t start asking complex questions until we know the basic parameters of the organism we are working on. There are some ‘standard’ lab organisms that are used over and over again because we know how to raise them and what we can do with them. I think that there will be more organisms available to answer complex questions, after we figure out how to work with them first.

    However, I will say that there is an incredible bias in the courses that are taught! Not only towards metazoans, but they are also very ‘vertebrate-centric’. For example, at my institution, the introductory level bio course spends 3 classes on animal diversity (a.k.a everything except vertebrates) and 12 on vertebrates and vertebrate systems.

  14. #14 Scott Hatfield
    March 31, 2007

    What self-respecting animal *wouldn’t* be an animal chauvinist?

    More to the point, while studying the diversity of all life is clearly one of biology’s long-term projects, *IF* forced to prioritize, with limited resources, I think we should focus on those species that will provide the greatest insights into our own evolutionary history, our own pathologies, etc.

    We have two compelling reasons to focus on this task, to work toward that day when ‘much light will be thrown on the origin of man and his history’, as follows:

    First, to meet our moral obligation to relieve pain and suffering amongst members of our own species;

    Secondly, that by better understanding our own ‘nature’ we can reign in the pathological excesses of our own behaviour as a species, behavior which continually menaces the very diversity that Prof. Moran is concerned is underserved.

    In this context, it is worth noting that Dr. Venter’s survey of oceanic microbial diversity is being funded by the Department of Energy. The effort has been sold to DOE not as pure research, but as part of a comprehensive search for new enzymes for the synthesis of industrially-desirable compounds, leading (if we might dare to dream) to a cheap, clean, sustainable hydrogen economy.

    Such a result would entirely justify a major program in non-metazoan genomics, but the point I’m trying to make is that we should always focus on such applications in terms of building public support for scientific research, rather than mounting a campaign on general principles as to the utility of pure research.

    We must first preserve that diversity in order to study it, and as a whole we are unlikely to act in ways that will preseve that diversity without stabilizing the manner in which human populations expand, diversify and exploit the planet’s resources.

    Respectfully submitted…SH

  15. #15 Rienk
    March 31, 2007

    What surprises me is that unicellular organisms are even considered suitable for evo-devo: especially when it comes to bacteria! Microbiology is a highly funded field and almost every study done can be tied in with evolutionary science, whether it is resistance, both inter- and intracellular communication, metabolic processes, signaling pathways, et cetera. It’s already being done anyway and so why divert investments from other organisms to organisms already so well studied. Spread your chances.

    And a slight transgression: although his research is quite impressive, I still think that Craig Venter is an egotistical, selfish, money hungering, megalomaniac scientist. He practically invented the idea of patenting sequences to keep academia from doing research.

  16. #16 PonderingFool
    March 31, 2007

    I am a big advocate for baterial and archaeal research. We do tend to focus on pathogenic bacteria when studying prokaryotes but there is a lot we can learn about life on this planet (and on/in us) by studying more of these organisms. That said such resaerch should not take away from the work of those working with multicellar eukaryotic organisms. A model organism to use is the best one you can find to answer the question you are asking. Moran comes across as a little petty and sounding jealous of what is being learned/grants acquired by the evo-devo crowd.

    Side question- PZ are you with Moran on archaea being lumped with bacteria? I ask because you refer to the 5 kingdom system.

  17. #17 Torbjörn Larsson
    March 31, 2007

    He practically invented the idea of patenting sequences to keep academia from doing research.

    I’m not well versed in the background of this, but off hand it seems patenting is done to attract funding and venture capital. Wouldn’t that, and the added market pressure, lead to faster, albeit differently constrained, results? When you do an agreement with a devil, willingly or not, it isn’t often only the devil gets something.

    Another question is if what is mostly (today) discovery should be grouped under a system concerning development and, traditionally, construction. Perhaps it has some moral problems. But it seems to work.

  18. #18 Torbjörn Larsson
    March 31, 2007

    He practically invented the idea of patenting sequences to keep academia from doing research.

    I’m not well versed in the background of this, but off hand it seems patenting is done to attract funding and venture capital. Wouldn’t that, and the added market pressure, lead to faster, albeit differently constrained, results? When you do an agreement with a devil, willingly or not, it isn’t often only the devil gets something.

    Another question is if what is mostly (today) discovery should be grouped under a system concerning development and, traditionally, construction. Perhaps it has some moral problems. But it seems to work.

  19. #19 Chet
    March 31, 2007

    Yeah! And how dare physicians focus on the anatomy of only one species? I recommend we boycott all the doctors and get checkups from veterinarians, instead.

  20. #20 coturnix
    March 31, 2007

    I am on PZ’s side on this issue, mainly because I don’t even think it is an issue. The Jenner paper poses some much more important and interesting questions.

  21. #21 jimmiraybob
    March 31, 2007

    … bacteria, archaea, and microbial eukaryotes … and they still dominate in number, diversity, biomass, and biogeochemical significance.

    Shhhhhhhhhhhhh! You give too much away too soon. Wait until the signal for the revolution to begin.

  22. #22 Larry Moran
    March 31, 2007

    PZ says,

    Try as one might, I just don’t see bacteria as being entirely useful subjects for studying the evolution of body plans, except maybe as an outgroup that lacks a body plan.

    Here’s the problem. Is the field of evolutionary developmental biology (evo-devo) confined to the study of body plans and animal tissues? Or, is it about development in all kinds of species, including bacteria?

    If it’s restricted to complex animals then please tell the evo-devo people to stop making general claims about the importance of their field in evolution. You can’t have it both ways. If evo-devo is restricted to one small twig on the tree then it doesn’t apply elsewhere. If it covers all of development then the theories and generalizations may have wider significance. Pick one or the other.

    To put things in perspective, look at where the animal twig is in this eukaryotic tree. Is that where the entire field of evo-devo is located?

  23. #23 Colugo
    March 31, 2007

    I’m all for studying archaea, bacteria, and protists … solely as models for the physiology, inter-cellular communication, and life cycles of the really interesting and important organisms: the eumetazoa.

    I jest.

    On a more serious note, here’s another central concept that Jenner and Wills should have added: somatic selection.

  24. #24 Magister Ludi
    March 31, 2007

    … bacteria, archaea, and microbial eukaryotes … and they still dominate in number, diversity, biomass, and biogeochemical significance.

    Shhhhhhhhhhhhh! You give too much away too soon. Wait until the signal for the revolution to begin.

    It doesn’t matter. PZ’s cephalopod army is no match for our Borg-like bacterial nanowires:

    http://www.physorg.com/news71777718.html

  25. #25 buglady
    March 31, 2007

    Microbial research is definitely better funded now than evo-devo: so many different ways to link the diverse lifestyles of microbes to human health, is what it come down to. Evo-devo might be getting some specialized funding from NSF at the moment, but we are talking about some pretty pathetic grant amounts- maybe $300,000 for three years max. Hardly enough for a postdoc or technician, a grad student, and some basic supplies. I would like to move into molecular biology in my own work, but would have a hard time procuring the funds from NSF to set up the necessary laboratory environment to do so.
    The Jenner and Wills list of to-dos concerned me a bit on one front: no mention of nervous system evolution. I may be a bit biased as a neuroethologist, but I think that we are on the cusp of breaking some big ground in terms of the developmental modifications behind brain architectures that generate novel behaviors. Put some money behind us, oh program directors!!

  26. #26 Colugo
    April 1, 2007

    Another way to think of that tree of life diagram that shows the alleged marginality of plants and animals.
    http://scienceblogs.com/evolgen/2006/08/phylogeny_friday_25_august_200.php

    Consider these measures:

    Diversity: There is more functional diversity – measured by the internal and secreted products of various specialized cells – proteins, lipoproteins, calcified matrix, membranes, ribozymes, etc. – in a single multicellular organism than in whole taxonomic groups of simple unicellular organisms.

    Complexity: The most complex unicellular organisms, even colonial ones, have far less functional complexity – structured interaction between cells, ability to respond to various environmental and internal states, levels of biological organization etc. – than multicellular organisms. Complexity would of course include functional diversity.

    Imagine pie charts including all of the taxa in that tree of life diagram with slices of the pie determined by total functional diversity or functional complexity. Plants and animals wouldn’t look so marginal.

    To say that animals and plants are not particularly important because they are just two branches of many in the tree of life is like saying that ordinary matter is unimportant because most of the universe is dark matter and dark energy.

    http://en.wikipedia.org/wiki/Image:DarkMatterPie-590.jpg

  27. #27 Ken C.
    April 1, 2007

    Maybe it doesn’t change things significantly, but wouldn’t a more “fair” comparison on the eukaryotic tree be to consider the different *kinds* of cells in a multicellular organism? If you’re counting each kind of single-celled organism by itself, shouldn’t you count each kind of human-liver, frog-eye, and squid-nerve cell on its own? Put another way, what is the total information in the relevant parts of the animal genetic endowment, vs. other eukaryotes? If you wrote out the sequences of bacteria, and then compressed them as strings, how big would the result be, as compared to the same exercise as applied to animals?

  28. #28 Heleen
    April 3, 2007

    How nice to see The Plausibility of Life by Marc Kirschner and John Gehart called wide-eyed speculation in Sandwalk. I found this book ignorant of anything beyond vertebrates (even if they do know a lot about vertebrate development), ignorant about evolutionary biology and especially ignorant about the topic they said they wanted to write about, the origin of novelty. After all, The Plausility of Life contains no account of the origin of any new trait or part.

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