Saturday, September 27, 2008

Botany Photo of the Day and the Oldest Living Organism

 
The oldest known organism on the planet is about 4,800 years old. Find out what that has to do with the Botany Photo of the Day.

It is often very hard to tell the difference between various species of pine. One of the distinguishing characteristics of this species (left) is that it has five needles per cluster. Other species have one, two, or three. I don't know if there is a species with four needles per cluster, or six.

Here's a question for all the adaptationists, is number of needles per fascicle an adaptation or is it just an allele that was fixed by accident? Is it an example of a morphological characteristic that is not an adaptaion?


17 comments :

  1. Larry,
    OT question. Which model are you using for this blog?

    ReplyDelete
  2. Larry: "Here's a question for all the adaptationists ..."

    Why direct this to adaptationist? If you are truly curious about the answer, wouldn't it be better to address it to those that study the biology of this plant in particular and the evolutionary biology of pine trees in general?

    BTW, exactly how does one make a strong case that some particular phenotypic feature is the result of genetic drift? (And can you do it *without* addressing all plausible selection explanations?)

    ReplyDelete
  3. mats asks,

    OT question. Which model are you using for this blog?

    I don't understand the question. Are you referring to blogger templates?

    ReplyDelete
  4. Yes, Larry, blogger templates. I wanted to use one that allows me to put the comments on the left side, just like you have.

    Thanks

    ReplyDelete
  5. Several Latin American pine species may have four needles per fascicle, but as a variant of species that usually have three or five. Four mexican pine species can have six or even more needles per fascicle, but usually have five.

    One pine species typically has four (P. quadrifolia), but it's believed to be a hybrid of a five-needle pine with P. monophylla.

    Anyway, as for the question of whether it's adaptive...I would have to say probably not. See "Ecology and Biogeography of Pinus", pg. 12. (It's on Google Books.)

    ReplyDelete
  6. Why direct this to adaptationist?

    Because adaptationists are BAD! THEY ARE EVIL! WE MUST KILL THEM(metaphorically speaking, bu exposing incocnsistencies in their arguments, and non-concordance with existing evidence)!

    ReplyDelete
  7. valhar2000 says,

    Because adaptationists are BAD! THEY ARE EVIL! WE MUST KILL THEM(metaphorically speaking, bu exposing incocnsistencies in their arguments, and non-concordance with existing evidence)!

    Actually, killing them comes later.

    Right now I just want to alert people to the fact that this kind of thinking exists. Most people don't even realize that they are making an unwarranted assumption that obstructs their ability to be open to non-adaptive explanations.

    Please don't give away the entire agenda. Remember, you were sworn to secrecy when you were inducted into the anti-adaptationist conspiracy.

    ReplyDelete
  8. "Here's a question for all the adaptationists, is number of needles per fascicle an adaptation or is it just an allele that was fixed by accident?"
    *rummages around for Token Adaptationist hat...ah here it is...*
    I don't know.
    Neither do you.
    I also don't know that this difference can be attributed to "an allele."
    Neither do you.
    I don't know any of the costs or benefits associated with different-numbered fascicles in different environments.
    Neither do you.
    In cases like this, assumptions of drift are just as unwarranted as assumptions of adaptation.
    I don't see how either of us gets any further in this without somebody doing a hell of a lot of work. I can't do it.
    Neither can you.

    ReplyDelete
  9. Sven DiMilo says,

    In cases like this, assumptions of drift are just as unwarranted as assumptions of adaptation.
    I don't see how either of us gets any further in this without somebody doing a hell of a lot of work. I can't do it.
    Neither can you.


    I agree.

    Next time you see someone making the assumption that all morphological differences are adaptive then I expect you to come down on them real hard.

    I expect you to remember this discussion and demand that they present evidence to support their assumption.

    Agreed?

    In case you've forgotten about those kind of adaptationists I suggest you read P-ter Accuses Me of Quote Mining.

    Here's what Richard Dawkins says,

    The adaptationism controversy is quite different. It is concerned with whether, given that we are dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. ... If a whole-organism biologist sees a genetically determined difference among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists.

    I assume you were a vocal critic of Richard Dawkins for saying this, right?

    ReplyDelete
  10. I contain multitudes (h/t Whitman).
    When I was a callow graduate student, an edited symposium volume came out called New Directions in Ecological Physiology (1987?), and we discussed it to death in a year-long weekly seminar. The gist of several of the chapters was your habitual point via Gould and Lewontin: that eco-physios had fallen into the trap of assuming that every detail of comparative biology deserved and required an explanation in terms of adaptation, but that this was surely unwarranted and that scientific rigor required that the hypothesis of adaptation be tested, not just assumed, etc. I know all that and of course I acknowledge that there are alternative mechanisms of phenotypic evolution that have to be considered as alternative hypotheses. I grant your intellectual point. That's what I was doing in my response above to your pine post. In principle, we agree.
    But I balance the intellectual principle (which I take very seriously, by the way; I would never refer in a scientific publication to some structure or function as an adaptation without evidentiary cause, and nor would my colleagues let me get away with it if I tried)--I balance the intellectual principle with a conviction, born of experience and specialized knowledge and shared with all of the many whole-organism biologists I know, that nevertheless adaptation is ubiquitous.
    I do comparative physiology of reptiles, and there are numerous crystal-clear patterns in physiology that closely parallel variation in habitat. These include true genetically based differences as well as others due to plasticity. The same is true in every other group of animals and plants (see Hochachka and Somero for the biochemical case). The predictive success of shamelessly adaptationist research programs like optimal foraging theory and life-history evolution is another strong line of evidence. What can I say? It's empirical.
    The stuff I read, write, review, measure, and teach for a living points to adaptation as a very strong signal among the noise of other, more random evolutionary processes. For a whole-organism biologist like me, Dawkins, and thousands of others, adaptation is simply a likely explanation, in a quasi-Bayesian sense, for phenotypic variation a priori.
    This is not some sort of ignorant assumption; we acknowledge that adaptation is an onerous concept (as G.C.Williams wrote 40+ years ago), and that a rigorous scientific claim of adaptation requires some hard-won data and analysis to support it. On the other hand, it is subjectively quite evident. And when the rigorous tests are pursued, adaptation is supported. *shrug*
    So no, I'm not critical of Dawkins's statements. I suspect he's right, that phenotypic variation is seldom selectively truely neutral. Of course I have no hard evidence to back such a sweeping generalization, and I'm perfectly willing to grant plausible exceptions. Is every single phenotypic trait an adaptation? No. Is selection perfect, is everything about organisms optimized? No, of course not. Is adaptation nevertheless a reasonable hypothesis? Yes, in nearly every case.

    ReplyDelete
  11. Sven DiMilo says,

    I balance the intellectual principle with a conviction, born of experience and specialized knowledge and shared with all of the many whole-organism biologists I know, that nevertheless adaptation is ubiquitous.

    And my conviction, born of experience and specialized knowledge is that many features of an organism are accidents of evolution and not adaptations. Just because your "conviction" disagrees with mine does not make you right. We need evidence.

    The predictive success of shamelessly adaptationist research programs like optimal foraging theory and life-history evolution is another strong line of evidence. What can I say? It's empirical.

    I think you need to be careful here. In many cases what happens is that scientists develop an adaptive explanation to account for some feature. Then, when that explanation has been shown to be adequate to account for the feature (making certain assumptions) they assume that the explanation must be correct.

    This is not "evidence." Let me give you an example. I could easily develop a Lamarckian explanation of some feature of snake physiology. It would be robust and it would account for all of the data. Does that make it correct?

    So, when you say that adaptation is a reasonable hypothesis in most cases, because time after time adaptation has been "proven," are you really being scientific? Are there really that many cases where adaptation has been scientifically proven? Or, is it more likely that adaptationists conclude that the explanation is "proven" whenever it is consistent with the data?

    That's what Gould & Lewontin argued. They claimed that adaptationists never consider non-adaptaionist explanations and that's why they are content to stop looking once they have an adaptationist explanation that is intellectually satisfying. This is what's wrong with the adaptationist program.

    On the other hand, it is subjectively quite evident. And when the rigorous tests are pursued, adaptation is supported. *shrug*

    Can you give me a couple of references from your own field where the adaptationist explanation has been "proven" and a non-adaptationist explanation ruled out?

    ReplyDelete
  12. predictive success of optimal foraging theory? C'mon

    More like "when it predicts, it predcits" kind of thing, haha

    Cause when it doesn't, it doesn't

    ReplyDelete
  13. It's pretty dishonest of you to keep putting the word "proven" in quotes as if I used it--I never did. Read my comment again. I am not willing to play the foil for your accustomed rhetoric against strawman adaptationists.

    My point, uncontroversial to pretty much everybody, is that adaptation is a clear inference from many many patterns in comparative biology. The proportions of nitrogenous waste excreted as ammonia, urea, and uric acid increase with terrestriality among turtles. Optimal temperatures for enzyme function correlate strongly to environmental temperatures in fishes and lizards. Minimum environmental temperatures are negatively correlated with maximal rates of energy expenditure for thermogenesis in small mammals and with insulation in large mammals. Salt-secreting glands are found in marine turtles (of three different families), not any others. Environmental drought frequency and the capacity to tolerate dehydration are correlated in mud turtles. Ad practically nauseum.

    Now, a hypothesis of adaptation makes the specific prediction that the functional capacities of animals should match their environments. Random phenotypic drift predicts random distribution of functional capacity among environments. The patterns are clearly concordant with the former hypothesis.

    I will freely admit that inferring (to say nothing of "proving") that any single feature of any single species or population is an adaptation is logically and logistically very difficult.

    As for references, I'll suggest, yet again, that you engage with Hochachka and Somero.

    ReplyDelete
  14. Sven, the problem is not the existence of adapation (which obviously exists), but the assumptio tat this is the result of a process of selection, that is, an accumuation of mutations that would not have occurred without selection (much like in artificla selection).

    In this sesnse, when you see and "optimized" behaviour, for instance, it is usually the case that it reflects behavioral plasticity (learining, for instance)

    Take your own example of reptilian urines. Are you even aware that you are talking about a trait that is phenotypically plastic? If you make a gator live in dry conditions, rather than water, it will switch from peeing ammonia to peeing uric acid. That adpative change is within the phenotypic plasticity, and does not require selection of any gene whatsoever.

    I know what you are thinking " the plasticity i the result of selection".But don't you even flinch a little when you infer a process of "selection for plasticity" that you actually have not observed? Do you even consider the possibility that palstcicty ca be inmmediate effect of physical factors, without a process of gene selection at its very origin?

    ReplyDelete
  15. Now, think experimentaly; you can select artifically for plasticity in the lab, but gues what? You cannot do that withotu exposing the individual organism to environmental moifictaor.
    In other words, you cannot "select for plastcicity" withotu the dreaded "environmentla modification fo the individula", a concept that has (erroneously) been considered "anathema" and "evolutionary irrelevant" according to classic neodarwinian doctrine.

    ReplyDelete
  16. Sven DiMilo says,

    It's pretty dishonest of you to keep putting the word "proven" in quotes as if I used it--I never did. Read my comment again. I am not willing to play the foil for your accustomed rhetoric against strawman adaptationists.

    I apologize. I realize that "proven" could be misconstrued. It wasn't my intent to put words in your mouth, I was simply looking for a word to describe your sense that many adaptive explanations have been empirically demonstrated.

    My point, uncontroversial to pretty much everybody, is that adaptation is a clear inference from many many patterns in comparative biology.

    Indeed, that's true and uncontroversial. What's controversial is when you take that inference and apply it to things that are much more ambiguous. In particular, I oppose those who claim that every visible phenotype is subject to selection.

    Now, a hypothesis of adaptation makes the specific prediction that the functional capacities of animals should match their environments. Random phenotypic drift predicts random distribution of functional capacity among environments. The patterns are clearly concordant with the former hypothesis.

    Not who's putting words in mouths? :-)

    Nobody denies that natural selection occurs. Nobody claims that everything is due to random genetic drift.

    What we're concerned about is whether some phenotypic difference between species are the result of selection or accident.

    I will freely admit that inferring (to say nothing of "proving") that any single feature of any single species or population is an adaptation is logically and logistically very difficult.

    My argument is that "inferring" adaptation in the absence of evidence is not only difficult but logically incorrect.

    ReplyDelete
  17. Here's an interesting paper on this subject from the viewpoint of animal-chauvinistic ecological physiology. I think I can agree with everything in here, and I'll bet you can too:
    http://compphys.bio.uci.edu/bennett/pubs/131.pdf

    ReplyDelete