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.

Friday, November 07, 2008

Pittsburgh, part II

From now on I will report the slightly edited raw notes, since unfortunately I don't have time to sit down and write an essay-style report (the meeting is pretty intense, and I have to have lunches and dinners with colleagues, not to mention the occasional martini... :)

So, here are my impressions from one of this morning's sessions, on the concept of a Tree of Life (i.e., a universal tree-like phylogeny). Bill Martin (Dusseldorf) got things started by summarizing why many people now think that the history of life on earth cannot be drawn up as a simple branching tree, as Darwin did: prokaryotic lineages form extremely intricate network-like phylogenies, and since the earliest living organisms were prokaryotes, we are left with the base of the alleged tree that doesn't look like a tree at all.

Eric Baptiste (Paris) pointed out that if we are not looking at a tree of life we may not be able to come up with a coherent "natural classification" (meaning a hierarchical grouping of natural taxa) of all life on earth. The existence of a tree of life should not be an assumption in the image of which the data are molded in a Procrustean way, but rather one of several competing hypotheses to be tested against the data.

Yan Boucher (MIT) showed how mutation rates and rates of lateral gene transfer vary by orders of magnitude even within prokaryotes, which means not only that prokaryotes evolve differently from eukaryotes, but that in fact there is a variety of tempos and modes of evolution even within microorganisms. One of the consequences of this is that "species" are not a homogeneous category, but are probably generated by a variety of mechanisms.

Jeff Lawrence (Pittsburgh) elegantly explained how come prokaryotic phylogenetics still gives the appearance of trees even though there is rampant lateral gene transfer. The data show that gene transfer is not isomorphic, i.e. any given species of bacteria is not equally likely to receive genes from any other species. This leads to the formation of clusters that can be erroneously represented by tree-like phylogenies, even though the underlying evolutionary mechanism is not tree-generating. In turn this asymmetry of gene transfer is explained by the peculiarities of different groups of prokaryotes at the molecular structural level.

John Dupre` (Exeter) questioned the validity of the tree paradigm even for eukaryotes, pointing out that we now know of the occurrence of much interspecific hybridization not only among plants, but also vertebrates (for instance birds). Moreover, virus-mediated gene transfer seems to have been dramatically underestimated until now. Turns out that 10% of the human genome is made of functional retroviral sequences, and that about half (!!) of our genome is constituted of fragments of formerly active viruses. What makes this intriguing is that 25% of human gene promoters have sequence similarities to retroviruses, which means that retroviruses have actually significantly contributed to the functional evolution of the human genome.

Rob Wilson (Alberta) discussed the well known fact that bacteria pose an impossible challenge for the prevailing species concepts. His favorite alternative is what is known as a "homeostatic cluster view" of species (look it up, folks!). My favorite solution to this problem can be found here: Pigliucci, M. (2003). Species as family resemblance concepts: the (dis-)solution of the species problem? BioEssays 25: 596-602. At any rate, according to Wilson (and I agree), prokaryotic biology poses a problem for so-called "pattern monism," the idea that the same basic processes affect the evolution of all life forms. Hurrah for pluralism!

Marc Ereshefsky (Calgary) again hammered the point that prokaryotes defy the idea of a universal species concept. Microbiologists have long accepted that they need to be pragmatic about identifying different groups of bacteria, but have realized that there is no objective concept of species that applies to their organisms of choice (or have they simply given up because it's too hard to find one?).

Laura Franklin-Hall (NYU), unlike most speakers in this session, is a self-professed "tree apologist." She readily agrees that simple universal trees won't do the job, and she rejects even the idea of looking for a small number of selected genes that would identify a "core tree" of sorts across all living organisms (the reason is that then one has no justification for focusing on those specific genes, other than the fact that one wants to have a tree at all costs). However, she proposed the idea that perhaps we could identify sub-sets of local core trees, which can then be assembled in a larger whole and still give us a tree-like picture of how life evolved. 

Finally, Joel Velasco (Stanford) criticized the idea that we can derive "species trees" (as opposed to, say, gene trees). This is because species-level phylogenetics assumes a particular definition of species, and he nicely showed how different definitions, applied to the same data, will result in different trees. His solution is that trees should actually represent genealogies of organisms, not species. Organisms, of course, can have composite genetic histories, which means that organismal trees can then be thought of as consensus summaries of gene trees.

That's all for now, folks!


  1. I think there ought to be a moratorium on biologists with the Wilson surname. It would be hard enough with just EO and DS Wilsons being around but that is just a start. If anyone else with that surname wants to start a biology PhD they should have to change their surname first. Either that or someone should start a Wilson version of the Steve list in support of evolution.

  2. Of course they all have the same father- Tim Taylor's backyard neighbour on Home Improvement. It only remains to be seen how many Wilson's he fathered in his prolific youth, and- word has it- even more prolific middle age.

  3. Wow - great summary. But just a quick clarification. I (Joel Velasco) do not think that organism trees can be thought of as summaries of gene trees. Gene trees are important and organism trees are also important and these are not the same. But there is no useful third level the "species tree" (unless you just mean to reduce this to the history of organisms or to a summary of gene trees).

  4. Joel,

    thanks for the clarification, it was a very nice session!


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