Home » Darwinism, Intelligent Design » The tottering Tree of Life rots a little more …

The tottering Tree of Life rots a little more …

File:Tree of life SVG.svg

If you shut your eyes and believe hard, this is a tree/Ivica Letunic

Earlier today, we were discussing Massey University (New Zealand) evolutionary biologist’s attempt to jam non-Darwinian processes into Darwinism. Because, essentially, if Darwinism means what it has meant in the last 50 years (the Tree of Life), it is not true. So Darwinism must now incorporate material that Darwinists would otherwise reject, so that at least something about it can be true.

Friends write to say that we can expect many more articles like this in the near future, for example

a new Open Access article by Maureen O’Malley and Eugene Koonin:

This idea of treating tree branches as conjectural hypotheses is something that cladists enthusiastically introduced into phylogeny when Hennig’s systematics was translated linguistically and conceptually into a broader sphere of phylogenetic systematics. Cladists have tended to rely heavily on philosopher’s Karl Popper’s ideas of falsification (and corroboration), which has led to many oversimplifications of scientific practice. One major problem in this equation of hypothesis with falsifiable conjecture is that it is usually not the case that a hypothesis is abandoned or substituted when it is ‘falsified’. Much more commonly, the original hypothesis is modified to accommodate otherwise conflicting findings. This is what seems to have happened to the TOL hypothesis…” (p. 15; emphasis added)

- Here: Maureen A O’Malley, Eugene V Koonin, How stands the Tree of Life a century and a half after The Origin?
Biology Direct 2011, 6:32 doi:10.1186/1745-6150-6-32

In other words, if we take seriously the strong textbook claims that “such-and-such is predicted by Darwin’s hypothesis of universal common ancestry [Tree of Life],” we run the risk of concluding that the TOL is false, when the data fail to conform to the prediction. That is, we might think that the TOL is, well, just not true.

But that’s so … unDarwinian.

One bioinformatics guy puts it like this:

OK, I think the tree of life is obsolete. I have been spending a lot of time looking at horizontal gene transfer, reading about it, looking at it in genomes until my eyes water and my brain dessicates, occasionally blogging about it and soon to be publishing about it. Life is not a tree. To what extent it is not a tree it is debatable, but horizontal gene transfer is pervasive, if not rampant, in all kingdoms.

If that’s how information gets passed on, how does it originate? NOT via natural sleection acting on random mutation.

One wonders what landscape we’ll see when that Tree’s deadfall.

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10 Responses to The tottering Tree of Life rots a little more …

  1. Life is not a tree. To what extent it is not a tree it is debatable, but horizontal gene transfer is pervasive, if not rampant, in all kingdoms.

    “Indeed some of the most powerful evidence for Darwinian processes, as opposed to other kinds of processes, is that Darwinian process have limits, and those limits are exactly the limits we see in the nested hierarchies of living things – the almost total restriction of novelty to a single lineage, regardless of how useful that novelty might be in another.”

    – Elizabeth Liddle

  2. Horizontal transfer of DNA molecules is widespread in nature. Contrary to traditional theories, it is now well documented that all prokaryotes and many eukaryotes acquire novel genomic segments and biochemical functions from other, often unrelated cells rather than exclusively by vertical inheritance from progenitors. Such theories of exclusively vertical transmission were the basis of Darwin’s “tree of life” diagram at the end of Origin of Species.

  3. oops. That’s James A. Shapiro. Evolution. p. 91.

  4. That just means that it is more like a banyan tree than an oak tree.

  5. Yes Yes. But it also means that Elizabeth’s proposed falsification is meaningless and that what she describes as “some of the most powerful evidence for Darwinian processes” is in fact not so powerful. It may not even exist.

  6. From the article (which sums up their basic point):

    The comparative infrequency of HGT in the eukaryote part of the biological world means, however, that in this case the conceptual implications for the TOL might not be as drastic: the evolutionary histories of many eukaryotes appear to produce tree-like patterns (e.g., [27]). However, by definition, the TOL is supposed to be the tree of all life and all evolution, so it is conceptually and epistemically misleading to discount non-tree-like evolution when such processes occur in the majority of life-forms and history of life.

  7. No individual taxonomic barriers exist for horizontally transferred DNA…Thus, contemporary evolutionary theories have to incorporate horizontal transfer of multiple coding sequences from any realm of life as a basic mode of genome change.

    – James Shapiro

  8. 8
    Elizabeth Liddle

    Mung:

    You quote the quotee in the OP:

    Life is not a tree. To what extent it is not a tree it is debatable, but horizontal gene transfer is pervasive, if not rampant, in all kingdoms.

    And juxtapose my statment:

    “Indeed some of the most powerful evidence for Darwinian processes, as opposed to other kinds of processes, is that Darwinian process have limits, and those limits are exactly the limits we see in the nested hierarchies of living things – the almost total restriction of novelty to a single lineage, regardless of how useful that novelty might be in another.”

    – Elizabeth Liddle

    Yes indeed. Have you read The Relativity of Wrong, by Isaac Asimov?

    http://chem.tufts.edu/AnswersI.....fWrong.htm

    No, life is not exactly a tree, although the vast bulk of DNA encoded information is passed longitudinally, from generation to generation, rather than laterally, between generations.

    So life is well-represented by a tree. However, when it comes to bacteria, things are a little different, and when it comes to viruses, things are a little different, and even when it comes to sexual reproduction, there is lateral cross-over at the level of meiosis.

    So although a tree is an excellent metaphor, it is not perfect (as even Darwin anticipated when he talked about our common ancestor(s) being “few forms…or one”.

    But, as we all acknowledge freely, Darwin did not propose a mechanism for the variety from which “natural selection selects” to use a horrible tautology, or, to put it better, the variety that results in differential reproduction. Horizontal gene transfer is such a mechanism, but, ironically, messes up the tree of life a bit.

    But only a bit. Science proceeds iteratively, and often the exceptions “prove” (in the sense of test) the rule. Living things were seen to fall into a pattern of nested hierarchies that suggested common descent; Darwin suggested a mechanism by which such variety would result in speciation, given common descent; his theory required a mechanism for heritability and variety; DNA provided such a mechanism, including mutational mechanisms; additional mechanisms were found for variety, including horizontal gene transfer; this meant that the original explanandum had to be modified.

    It happens all the time in science.

    But it would be a huge mistake (read Asimov) to think that horizontal gene transfer blows evolutionary theory out of the water. It does no such thing. It merely makes us incrementally less wrong.

  9. Let us know when you have a testable theory Elizabeth.

  10. Is everyone here incapable of seeing the the diagram displayed in the form of a circle is entirely equivalent to one displayed as a “tree”?

    It’s really discouraging to think that math education has failed so miserably.

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