In the latest "Nature" (3 Sept 98, pp17-18, V395) Diethard Tautz writes a piece on the difficulties – and possible pitfalls – of interpreting homologies, which will be of interest to many list members.
"Homology: Similarity in structure of an organ or a molecule, reflecting a common evolutionary origin…"
Coined in 1854 by Owen, the term did not at first have a phylogentic significance, but refered to the type of thinking which led to such similarity series as: fish – flying fish – aquatic birds – birds – bats – flying squirrels – tetrapods – monkeys – man.
. . . not now believed as a lineage, but as DT says: "On the other hand, we do not know the true answer on the phylogentic descent of tetrapods, as homology concepts tend to fail when it comes to tracing evolutionary novelties." How dare he ! ;-)
He stresses that homologues at the molecular level are just as confusing, but says that with biotechnology companies getting involved, ". . . it will eventually be investors and shareholders who have to be convinced that invoking homology is valid". At last! People for whom the right answer is vital will start to get involved! But is the average shareholder more subtle than Chris Brochu?
"Taking phylogenetic continuity alone as the prime criterion for homology causes the problem of circularity, because phylogenies are themselves deduced from homologous characters. . ." circularity again – as mentioned in http://www.cmnh.org/fun/dinosaur-archive/1998Mar/msg00013.html . I think this is a different circular argument – so now there’s two. "This of course can be avoided by using . . . DNA sequences. But even in well established phylogenies, it often emerges that independent evolution of similar characters (convergence) must have occurred. There could therefore be dormant genes or ‘latent homologies’ that are not expressed in a stem species, but that have been regained after further speciation and give the erroneus impression of convergence." This is the mechanism sometimes used to account for the "mosaic" distribution of characters amongst Archie – Troodon – droms. for example.
In illustration of his next point he says: "In tetrapods, digits 3 and 4 are the first to develop and are also the ones that are most stable against perturbations. In [newts and salamanders] the same seems to be the case for digits 1 and 2. So if 3 and 4 are homologous to 1 and 2, digit 3 would be equivalent to digit 5 in [other] tetrapods and digits 4 and 5 in [newts etc] would be novel structures. . . . Closer study of developmental characteristics and comparative analysis of Hox gene _expression_ seem to confirm this view." I’m surprised – but the chick digits thing always was going to have a surprising solution one way or another – not that I’m saying this is the solution.
He ends with: "Homology, then, is an idealised principle that works under idealised conditions, but such conditions almost never apply. This is reminiscent of the concept of the Hardy-Weinberg equilibrium in population gentics. It exists only under idealised conditions, but it is the tracing of the reasons for deviation from these conditions that is central to understanding the evolution of populations. Could one apply a similar thinking to homology?" Clearly he doesn’t think the most "scientific" way of taking homologies is raw.
In the first paragraph he said: "But although the concept lies at the heart of much of biology, it has become increasingly elusive. Has [homology] therefore become a word ripe for burning, as J Maynard Smith remarked . . .?" (But without it, what other tool are we left with? . . . as J Jackson remarked.)
One lesson is clear however – homologies are a minefield, and we will usually be wrong if we approach them simplistically – and mechanically.
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You will all by now have forgotten (if you ever noticed) that no reply from me appeared in response to Mickey’s last criticism of my choice of content. This was because my rather fulsome post started with ‘Review’ (as incidentally did my attempted post "Sci. Am – past" back in Feb); the list processing program regards this as a special word and it chucked the whole thing out, thus saving Mickey the trouble of having to decide whether to chuck me out.
(I also let Tom Holtz have the last word in our last exchange, both on the list and subsequently off-list, but this as usual signified weariness with his rhetoric rather than agreement on my part!)
John V Jackson