In article <badger.843783074 at phylo.life.uiuc.edu>,
Jonathan Badger <badger at phylo.life.uiuc.edu> wrote:
>lamoran at gpu.utcc.utoronto.ca (L.A. Moran) writes:
>>You raise a number of interesting problems but don't forget that many of
>>them also apply to those genes that seem to support Woese's Three Domain
>>Hypothesis. We should be skeptical of *all* current hypotheses concerning
>>the tree of life.
>>Yes, it is always worthwhile to be skeptical of all scientific
>theories. However, it is it also worthwhile to recognize that all data
>are not of equal significance.
I agree. Now, if we could only agree on which data was the most significant
then all our problems could be solved. (-:
> The fact that one can make gene trees
>showing any desired relationship is not particularly surprising nor
>informative in regard to organism trees.
Actually I find this very surprising. Why was it not a surprise to you?
> One of the reasons ribosomal
>RNA is a popular molecule for estimating phylogeny is that it
>minimizes many of the problems given above. This is not to suggest
>that *only* ribosomal RNA is good for phylogeny, but genes should be
>chosen with some amount of care to minimize these problems.
Many workers in the field have stated that nucleic acid sequences are much
less reliable that amino acid sequences. I agree with them. (There are
also other problems associated with the use of rRNAs.) It seems to me that
the use of ribosomal RNA sequences to reclassify bacteria willy-nilly
is bound to lead to an extraordinary amount of confusion later on. I can
think of no possible set of reasons that justifies using rRNA sequences in
preference to, say, HSP70 or GDH. Can you?
If you can't - and neither can Woese - then why is it that so many people
seem to believe that rRNA sequences give a more reliable picture of
species evolution? Isn't this simply uninformed bias due probably to
good promotion by certain proponents? It doesn't seem to be "science" by
any definition that I am familiar with.