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RE: Mice given bat-like forelimbs through gene switch

David Marjanovic wrote:

>> Most prokaryote (bacteria + archaea) taxonomy is quantitative, and based
>> on the degree of similarity (sequence homology) of the 16S rRNA gene.
> So there are still molecular biologists who call similarity "homology"...
> no, people. No. That's not what homology means.

Then fill me in.   What does 'homologous' mean?  If all 16S rRNA genes have a 
shared ancestry (and they do), why are they not homologous?   

>> Prokaryote taxonomy does follow a clade system to some degree.
>> Classification is based on the sequence homology of the 16S rRNA genes.
> So it's phenetic, not cladistic. Is that what you want to say?

No.  Phenetics is based on overall morphological similarity, which doesn't work 
for prokaryotes (at least not for higher-level classification) where external 
physical characteristics are a poor indicator of shared ancestry (as assessed 
by 16S rRNA sequence identity).  Physical characteristics are encoded by genes, 
and genes are prone to rampant lateral gene transfer.  Cladistics would also 
not apply, for the same reason. 

Phenetics works to a certain degree for medical diagnostic purposes - but only 
if you stretch the definition of phenetics to include biochemical reactions.  
But this only applies to a very narrow band of bacterial species.

>> Aside from that, the concept of 'clade' doesn't really hold for bacteria
>> and archaea, given the propensity of interspecific gene transfer.
> Oh, lateral gene transfer doesn't make the concept inapplicable. It merely
> complicates the issue: clades are no longer either nested or mutually
> exclusive.

The phylogeny of archaea and bacteria is based principally on the 16S rRNA 
gene.  Using the phylogeny of the 16S rRNA gene as the basis for prokaryote 
classification (and life in general) is neither phenetic or cladistic.   This 
applies to any molecule-based phylogeny.

> Even the PhyloCode deals with this: Note 2.1.3
> http://www.ohiou.edu/phylocode/art1-3.html, Article 16
> http://www.ohiou.edu/phylocode/art16.html... hey, wait. I thought there was
> a statement that lateral gene transfer does not constitute hybridization?

My reading of 2.1.3 (and the PhyloCode in general) is that it applies at the 
organismal level, not at the gene level.  To be honest, I don't know to what 
extent PhyloCode could (or does already) apply to the classification of 
bacteria and archaea.  



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