i-68efa548cdb44e33126c5936c96fe3ed-evolution_2008.jpgThe Evolution 2008 conference started out today with a special program for K-12 teachers (mainly life science teachers) organized by the Minnesota Citizens for Science Education (MNCSE). The opening speaker was Scott Lanyon, director of the Bell Museum of Natural History. (The Bell hosted this event.)

i-360cbb04fb3ca5b4766c7598e92870d3-Scott_Lanyon.jpgScott’s objective was to outline several areas of evolutionary biology where fundamental changes had occurred over recent years. This was to provide perspective and food for thought for the Life Sciences teachers attending the event, and Scott was very successful in this effort.

In each case, Scott described a similar trope … “Not so many years ago, understanding [this or that thing] was thought nearly impossible…. but today, look what we have….”

Specifically, Scott, a bird phylogeny expert, outlined four areas of research corresponding to four major areas of evolutionary biology:

1) Phenotype
2) Genotype
3) Speciation
4) History (Phylogeny)

Comparing evolutionary thinking of a couple decades ago to the present, the genotype-phenotype one-to-one correspondence has weakened in its explanatory power and is being replaced by more complex yet more realistic models of developmental biology (“evodevo”). To me, this is very interesting because it is an example of science swimming upstream against parsimony … it turns out that the simplest explanation (a Cartesian gene-trait correspondence) is not correct, and a more subtle, nuanced, and complex set of relationships involving hierarchical effects and emergent properties is correct. As a firm disbeliever in the “Law of Parsimony” as it is usually applied, I like this.

Genomics replaces simple conceptions of the genotype. We have a more holistic understanding of the genome, we understand evolutionary scenarios involving whole genome duplication and other less drastic yet still genome-level evolutionary changes, and so on. Here I think we are conflating methods (genomics as a method) and evolutionary process (genome duplication) a bit, but Scott’s point is simple and well taken: Go back a couple of decades and try to imagine what we could be doing with genetics in 2008, and you couldn’t.

With respect to ‘speciation’ … the diversification of forms, the diversity of life, the disparity produced by evolutionary process … again, the same theme. Scott pointed out that we know of approximately 1.7 million species, but estimates suggest there may exist somewhere between 10 and 100 million species. Go back twenty years or so and you would have seen field biologists starting to confront this reality, especially in certain habitats, almost with a sense of disbelief. I remember hearing from a colleague just back from visiting an Amazonian research site … a fogging sample was taken from a large area of rainforest canopy in a previously uninvestigated area to see what percentage of the insect species (which would fall out of the canopy because of the “fog” ….) would be new species. Five or ten percent would be really cool.

So they fogged the canopy, about a thousand species were represented in what came out of the canopy, and the researchers did not recognize any of them. Probably a few had been described before, but if so, not many. Totally blew their minds. And I’m not exaggerating by more than one order of magnitude (hey, it was a long time ago).

Finally, Scott talked about his own field: He’s a bird phylogeny guy, and he noted, really, two different things. One is that now, compared to a couple/few decades ago, phylogenies are often seen in connection with evolutionary biology research projects … so much research is now couched in phylogenetic terms, and this is new.

This is incredibly important. Not only do we increasingly pay attention to phylogenetic context, but methods of study involving the phylogenetic structure of the data are now routinely applied.

Also, the scope of phylogenetic studies has changed dramatically. Scott published his first bird phylogeny a few years back (I don’t think he said exactly when) with something like 10 birds on one phylogenetic tree. That was actually pretty impressive at the time. Recently, he co-authored a paper with over 800 species on the tree. Effectively two orders of magnitude more, and that is not uncommon. If this trend continues, the birds may cause the trees to collapse!

I remember being at a AAAS meeting where Sibly and Alquist gave one of their papers on bird phylogeny. This was not when they first started out with this business of using DNA to assess relationships, but they had applied some new methodologies and had a “complete” tree for birds … complete in the sense that all major bird groups were represented. People were pretty excited, it was like a tipping point in the history of science because for the first time a whole symposium at a major meeting was all about phylogeny of birds. Another symposium at the same meeting addressed human evolution and DNA phylogeny. But it still was fewer than about 100 birds. Most of the arguing and fighting (and there was quite a bit) was about mutation rates.

Today, phylogenies are routinely used, massive phylogenetic analyses continue to reveal important features of evolutionary pattern and process, and our methods of analysis are very sophisticated.

We’re all still fightin’ about mutation rates, though.


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Comments

  1. #1 Freddie G.
    June 20, 2008

    I was thoroughly impressed with the workshop for teachers today. We had excellent presenters and many new ideas were suggested. One that I personally liked was an interactive website that helped students understand cladistics. It is great for high school biology students, but may be a little tougher for the younger students. Here’s the link to the site (I don’t know how to insert this so I hope cut and paste will work):
    http://www.ucmp.berkeley.edu/education/explorations/tours/Trex/index.html

  2. #2 Colugo
    June 21, 2008

    Four approaches/areas that have become increasingly mainstream in the last couple of decades:

    1) importance of lateral transfer of functional genes via germline retroviruses and other mechanisms

    2) multilevel selection – not just group and species selection, but somatic selection and other levels – combined with view of history of life as major transitions

    3) heritable epigenetic change

    4) plasticity and evolution – developmental plasticity as the leading edge of evolution: Balwinism, genetic assimilation, genetic facilitation

  3. #3 C. David Parsons
    June 21, 2008

    THERE IS A NEW DISCIPLINE:

    The Quest for Right, a series of 7 textbooks created for the public schools, represents the ultimate marriage between an in-depth knowledge of biblical phenomena and natural and physical sciences. The several volumes have accomplished that which, heretofore, was deemed impossible: to level the playing field between those who desire a return to physical science in the classroom and those who embrace the theory of evolution. The Quest for Right turns the tide by providing an authoritative and enlightening scientific explanation of natural phenomena which will ultimately dethrone the unprofitable Darwinian view.

    The backbone of Darwinism is not biological evolution per se, but electronic interpretation, the tenet that all physical, chemical, and biological processes result from a change in the electron structure of the atom which, in turn, may be deciphered through the orderly application of mathematics, as outlined in quantum mechanics. A few of the supporting theories are: degrading stars, neutron stars, black holes, extraterrestrial water, antimatter, the absolute dating systems, and the big bang, the explosion of a singularity infinitely smaller than the dot of an �i� from which space, time, and the massive stellar bodies supposedly sprang into being.

    The philosophy rejects any divine intervention. Therefore, let the philosophy of Darwinism be judged on these specifics: electron interpretation and quantum mechanics. Conversely, the view that God is both responsible for and rules all the phenomena of the universe will stand or fall when the facts are applied. The view will not hinge on faith alone, but will be tested by the weightier principle of verifiable truths � the new discipline.

    The Quest for Right is not only better at explaining natural phenomena, but also may be verified through testing. As a consequence, the material in the several volumes will not violate the so-called constitutional separation of church and state. Physical science, the old science of cause and effect, will have a long-term sustainability, replacing irresponsible doctrines based on whim. Teachers and students will rejoice in the simplicity of earthly phenomena when entertained by the new discipline.

  4. #4 llewelly
    June 21, 2008

    As a firm disbeliever in the “Law of Parsimony” as it is usually applied, I like this.

    The ‘law of parsimony’ is not useful for its accuracy. It is useful because it greatly simplifies discussion and analysis of models, and design of experiments – thus allowing scientists to move gently from simple models to complex models. It’s like using stairs instead of trying to do the ultimate high-jump.

  5. #5 themadlolscientist
    June 21, 2008

    Flunk off, Parsons, you trolling tardbot.

    Let the ignoring begin.

  6. #6 Mike O'Risal
    June 21, 2008

    …Recently, he co-authored a paper with over 800 species on the tree. Effectively two orders of magnitude more, and that is not uncommon. If this trend continues, the birds may cause the trees to collapse!

    If anything’s going to collapse the trees, it’ll probably be fungi. AFTOL2 is in its nascency now. 30,000 fungal species are known, but estimates as to the true number of species in the kingdom range up to 1.5 million. New ones are being discovered at an amazing rate in some unusual places (see Meredith Blackwell’s work on yeasts from Coleoptera for a good example).

    Anyhow, if you happen to bump into David Hibbett at the conference, ask him about AFTOL. There are several such projects going on, including one for the Coleoptera. I have an inordinate fondness for beetle phylogeny, you know.

  7. #7 Mike Haubrich, FCD
    June 21, 2008

    I just read an article yesterday in Science News about how the study of SNP’s illustrates that reductionism across populations leads to misleading analysis, and that ever larger samples of the genome are needed to illustrate their relationship to genetic disease in the population. Researchers are having to develop new statistics in order to obtain meaningful results.

    I am not sure how that relates to phylogenetic mapping, but it does dovetail nicely with your statement that “the genotype-phenotype one-to-one correspondence has weakened in its explanatory power…”

  8. #8 Greg Laden
    June 21, 2008

    Mike, did you blog that? Is there a paper out there on this? Sounds interesting.

    llewelly: Partly true, I’m sure. But it would be important to understand this linguistically. “Parsimony” is a word that refers to a concept and we can understand how the concept is operationalized by how people use it. And generally, people … scientists … are equating parsimony with truthiness.

    I like you way of describing it, but I have a somewhat different way :

    The parsimonious (simplest) explanation is the explanation that will be wrong in the smallest number of ways, compared to other explanations.

    And thusly, science marches on.

  9. #9 Laelaps
    June 21, 2008

    I’m biased by my own interests, of course, but I find the recent collaborations between paleontologists and geneticists and developmental biologists to be a big step forward, too. When G.G. Simpson wrote Tempo and Mode in Evolution paleontologists and geneticists didn’t seem very interested in each other’s work, but I’ve seen this start to change. There are more books about the fossil record that talk about changes in development (like Major Transitions in Vertebrate Evolution) and some molecular studies have provided hypotheses that were later confirmed by fossil evidence. (Specifically I’m thinking of the date of the last common ancestor between chimpanzees and humans and the notion that whales evolved from artiodactyls. Neil Shubin’s work with Tiktaallik also has married techniques from different fields.)

    Anyway, the talk sounds interesting and I’m definitely glad that there are some big changes happening in evolutionary biology.

  10. #10 Mike O'Risal
    June 21, 2008

    About AFTOL, you mean? I haven’t blogged on it; I wasn’t around for the first phase and the second hasn’t started yet (and I don’t know whether or not I’ll be working on it directly, although some of the work I do on polyporoid fungi might end up in there; remains to be seen).

    Check out the linked page, though. It’ll take you to all of the resultant publications, people involved, etc. It’s some foundational work that’s gone a long way toward clarifying fungal phylogeny. That’s largely what my lab works on, by the way. I’m researching the origins of fungal dependency in Tenebrionidae and Polyporales, Hymenochaetales, etc. myself.

    A really good paper to check out regarding AFTOL is:

    Lutzoni, F., F. Kauff, C. J. Cox, D. McLaughlin, G. Celio, B. Dentinger, M. Padamsee, D. Hibbett, T. Y. James, E. Baloch, M. Grube, V. Reeb, V. Hofstetter, C. Schoch, A. E. Arnold, J. Miadlikowska, J. Spatafora, D. Johnson, S.Hambleton, M. Crockett, R. Shoemaker, G.-H. Sung, R. Lücking, T. Lumbsch, K. O’Donnell, M. Binder, P. Diederich, D. Ertz, C. Gueidan, K. Hansen, R. C. Harris, K. Hosaka, Y.-W. Lim, B. Matheny, H. Nishida, D. Pfister, J. Rogers, A. Rossman, I. Schmitt, H. Sipman, J. Stone, J. Sugiyama, R. Yahr, R. Vilgalys. 2004. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany 91: 1446-1480.

  11. #11 Mike Haubrich, FCD
    June 21, 2008

    Greg – I haven’t yet blogged it. I am far behind because of “The Hard Luck Truck.” I do have the link to the article by Regina Nuzzo in Science News:

    Nabbing Suspicious Snips. (Warning, slow server response time.)

    I’m going to have to read it a few times before blogging it, because it is a little advanced for my level of formal science training (none.)

  12. #12 Mike Haubrich, FCD
    June 21, 2008

    Hey, after posting my response I realized that you may have been referring to Mike O’Risal’s comment. Avoidance of such confusion is part of the reason I agreed to name my son “Bing.”

  13. #13 Greg Laden
    June 21, 2008

    No, Mike I was talking about your.

  14. #14 Mike O'Risal
    June 21, 2008

    Actually, Mike H., after rereading Greg’s comment, I think he was replying to you, not me.

    There’s too many Mike’s around! Compounding it even more, I’m a mad mycologist, but of course there’s also Mike the Mad Biologist. I may have to change my name to something more exotic…

  15. #15 Greg Laden
    June 21, 2008

    OOps… My comment about “did you post that” was to Mike H.

    Thanks for the link, Mike O!

  16. #16 JimV
    June 21, 2008

    The ‘law of parsimony’ is not useful for its accuracy. It is useful because it greatly simplifies discussion and analysis of models, and design of experiments – thus allowing scientists to move gently from simple models to complex models. It’s like using stairs instead of trying to do the ultimate high-jump.
    Posted by: llewelly | June 21, 2008 1:17

    I wanted to say something in support of Occam’s Razor while not exactly disagreeing with our host, but this says it much better than I could. Thanks.

  17. #17 Greg Laden
    June 21, 2008

    It is not really a matter of being against or for Parsimony/’Occam’s Razor’ … My assertion is that it is used in a particular way (regardless of how all us smart people THINK it should be used) very commonly. In the last 48 hours at this conference I’ve seen it used twice, both exactly the same way…

    Given two hypotheses that are before us, determine that one is simpler and pick that one as more likely true … in other words, reject a hypothesis (the one you did NOT pick) because the other hypothesis has fewer steps.

    This can lead us to shun explanation s that are complex even when dealing with phenomena that are complex. This could help explain (in part) the bankruptcy of the reductionist shool of thought.

    Yet, the principle has value. But again, I personally would prefer to think of it as stated above.

  18. #18 windy
    June 22, 2008

    I just read an article yesterday in Science News about how the study of SNP’s illustrates that reductionism across populations leads to misleading analysis […]
    I am not sure how that relates to phylogenetic mapping, but it does dovetail nicely with your statement that “the genotype-phenotype one-to-one correspondence has weakened in its explanatory power…”

    Actually, no it doesn’t. Focusing on individuals, not populations, helps the researchers to zoom in on the right SNPs. The “suspicious snips” article is neutral on the question of how strong the SNP-disease correspondence is. (Towards the end it says: “And there’s still a nagging question: After you’ve bagged your gene, what do you do?”)

    “One genotype – one phenotype” is an easy strawman to bash on, but saying that evolutionary biologists have been attached to it until fairly recently is strange. Norms of reaction (first named 99 years ago!) have been textbook fare for over half a century. “Phenotypic plasticity” is getting on in years as well. What evolutionary geneticist in the last couple of decades has been unaware of these concepts?

  19. #19 Not Uri Geller
    June 22, 2008

    The one-gene : one-phenotype “falsehood” is not a lack of understanding of phenotypic plasticity. It is exactly what it says it is, a belief in one gene linked to one phenotype and visa versa. Which is a falsehood.

  20. #20 windy
    June 22, 2008

    The one-gene : one-phenotype “falsehood” is not a lack of understanding of phenotypic plasticity.

    Of course it is; if someone knows that phenotypic plasticity happens, they cannot at the same time claim that a genotype always results in the same phenotype. Rather obvious when you think about it.

  21. #21 John B
    June 22, 2008

    Comment 1 Freddie G

    I have been using the “What did T-Rex” taste like with 7th grade students the last couple of years.

    The changes for biology and what to teach (certainly not maintained well in our CA state standards) at times seems daunting task.

    Another idea I have recently been introduced to is that of “slab pull” and gravity as the main “force” driving plates.

    My point being that the diverse evidence from different fields for evolution is important to share with younger students and as teachers we have the greatest job in the world trying to keep somewhat abrest of portions of it.

  22. #22 Greg Laden
    June 22, 2008

    Windy … yea, but, I think a different issue is being addressed here. Try this on:

    There are NO traits (phenotype) which can be explained by the operation of a single gene, in any system on Earth.

    I hear good things about the T Rex thing.

  23. #23 Freddie G
    June 22, 2008

    John B,
    It is good to know that the T Rex program works for 7th grade students. Do you let them go through the folders on their own or do you provide something for them to fill out as they go?

  24. #24 windy
    June 23, 2008

    There are NO traits (phenotype) which can be explained by the operation of a single gene, in any system on Earth.

    Since there are no organisms with only a single gene in their genome, that’s rather obvious. And “single gene” is yet another issue. Even if someone holds the “one genotype one phenotype” view, which I doubt anyone does, they can still think that each trait is affected by several genes.

  25. #25 Pete Dunkelberg
    June 23, 2008

    Buzzwordiness

    Genomics replaces simple conceptions of the genotype. We have a more holistic understanding of the genome, ….

    … Greg adds in comments:
    This can lead us to shun explanation s that are complex even when dealing with phenomena that are complex. This could help explain (in part) the bankruptcy of the reductionist shool of thought.

    ===

    huh? so far as I can tell, the same scientific methods are in use and working well.

  26. #26 Andrew
    June 23, 2008

    Pete: How old are you?

Current ye@r *