----- "Dima Klenchin" <[EMAIL PROTECTED]> wrote: > > > But how do we establish phylogeny? - Based on simple similarity! > > > (Structural/morphological in early days and largely on sequence > > > identity today). It's clearly a circular logic: > > > >Hardly. Two sequences can be similar and non-homologous at all > >levels. Also, two similar proteins can be homologous at one level but > >not at another. It's also possible for two proteins that have no > >detectable similarity above random sequences to be homologous. Hence > >there is no circularity. > > Of course there is. Just how do you establish that the two are not > homologous? - By finding that they don't belong to the same branch. > And how do you decide what constitutes the same branch? - By looking > at how similar things are!
But you have not established that there is circularity. Logical circularity means that you assume (as an essential premise) one of your conclusions. What exactly is the argument you are criticizing, and what is the conclusion that is assumed? When we conclude that two proteins are homologous at some level, we have not assumed that they are homologous at that level. Rather, the conclusion of homology is an inference that uses similarity as relevant evidence. > > > Plus, presumably all living things trace their ancestry to the > > > primordial soup - so the presence or a lack of ancestry is just a > > > matter of how deeply one is willing to look. > > > >This is also wrong. Even if all organisms trace back to one common > >ancestor, that does not mean all proteins are homologous. New > >protein coding genes can and do arise independently, and hence they > >are not homologous to any other existing proteins. > > Just how do they arise independently? Would that be independent of DNA > sequence? And if not, then why can't shared ancestry of the DNA > sequence fully qualify for "homology"? Perhaps it could (although in some cases no), but still the new protein would not be homologous to any other protein *at the protein level*. > >You also ignore the levels of homology concept -- just because two > >proteins are homologous at one level does not mean they are > >homologous at others. For example, consider these three TIM barrel > >proteins: human IMPDH, hamster IMPDH, and chicken triose phosphate > >isomerase. They are all three homologous as TIM barrels. However, > >they are not all homologous as dehydrogenases -- only the human and > >hamster proteins are homologous as dehydrogenases. > > ... And all that is concluded based on sequence similarities [of other > proteins/DNAs] to construct phylogenetic tree. So, ultimately, > homology ~ similarity. This is a non sequitur. Yes, homology inference uses similarity as evidence, but that does not mean homology is equivalent to similarity. Two facile counterexamples to your claim: two proteins can be very similar yet non-homologous, and two very dissimilar proteins can be homologous. Homology is thus not equivalent to similarity. QED. > The "generic" concept of homology used to be used as a proof of > evolution. Today, things seem to be reversed and evolution is being > used to infer homology. A useful concept turned into a statement with > little or no utility. In fact quite the opposite is true. Before evolutionary theory, "homology" was a vacuous, mysterious concept with no utility. It was simply the descriptive observation that similar structures could have different functions. Now we know why that is the case. You have already pointed out that we have redefined homology (evolutionary homology is not the same as "generic", pre-evolutionary homology), and this fact proves that the logic is non-circular: we assume "generic homology" and conclude evolutionary homology. This could only be circular if the two concepts were identical, which you admit they are not. Your argument founders on an equivocation. Cheers, Douglas
