Australopithecus and orangutans

[Jason de Koning]

Herb,

> First let me say that my statement, "What kind of argument is…," was 
> unnecessary on my part. Your argument was clear and reasonable, and 
> accepted by many. I should like to blame my response on having lived 
> through the taxonomic wars where reasoned and well thought out and 
> argued evolutionary narratives were called Just-So Stories, and 
> sarcasm was wielded as often as logic. It was hard to be civil. That 
> said I still disagree with your argument and your response to my 
> criticism.

Thanks, I appreciate that.  It can be hard to maintain civility when we 
all carry such baggage, so I fully understand.

> A hypothesis is accepted not because there is a lot of support for it 
> but because it has greater explanatory power than any of the competing 
> hypotheses. ... At the risk of sounding sarcastic, support for a 
> hypothesis may give a sense of comfort or confidence but that's about 
> all it is, a good feeling. Science doesn't choose by the majority > vote.

I don't disagree with your comments on parsimony and congruence, but 
your philosophical comments mystified me a little.  Support for a 
hypothesis makes you feel good?  Well I guess so, but in experimental 
science, tests of predictions and the resulting information about 
support for your hypotheses (be you Bayesian or otherwise) are the 
currency of progress.  You can't have support without greater 
explanatory power--these seem the same to me.

> Further I reject both your statements that seemed to imply I am one 
> that "…argued …that molecular data contains no historical signal…." 
> and "…chooses to ignore molecular data out of principle…." I certainly 
> believe that molecular data do contain historical information. I'm 
> just not sure what that information is. I hold the position proposed 
> by Gould and others that evolution is hierarchical, operating 
> independently at each the species, organism, and genetic levels. So I 
> am not certain that uncovering evolutionary patterns at the molecular 
> level (historical signals) will reveal patterns at the species level, 
> the level which is most interesting to morphological cladists.

First, I did not mean to insinuate anything about your specific 
beliefs.  My comments were mostly meant for those who seem to want to 
fully disregard molecular evidence out of hand, believing that it is 
invalid, untrustworthy, or tainted in a way that other discrete-trait 
character data is not.   I think that your comments above are 
completely reasonable.  In fact, Gould's commentary on hierarchical 
selection ("Gulliver's further travels.." in Proc Roy Soc Lond) is one 
of my favorite opinion pieces on the 'objects of selection' debate in 
recent memory.

> I don't think it's stretching it to view molecular evolution of 
> conserved sequence as decoupled from the evolution of the organism. 
> After all conserved sequences are selected because it is thought they 
> are not influenced by selection at the level of the organism. This 
> means there may be more than one historical signal. It's analogous to 
> trying to figure out the phylogeny of the host from the phylogeny of a 
> parasite when the two can, and often do, have different tree 
> topologies. The fact that they may be congruent in some cases doesn't 
> help unless you know the answer ahead of time.

I completely agree that neutral molecular evolution is decoupled from 
organismal evolution, but that is the point exactly.  If a molecular 
sequence is not influenced by selection, then mutations randomly 
diffuse through populations (vertically) to fixation, and fixed 
differences thereby carry a signal which, by definition reflects only 
history and not selection.

Cheers,
- Jason