chloroplast and other genes (was Lucy in Newsweek)

[Ken Kinman]

Brian,
    I totally agree, and my comments on characterizing "molecular data as phenetic and unreliable" were certainly not directed at you.  They were directed mainly at John Grehan who continues to downplay the importance of molecular data.  And John may think my use of words like "balance" are somewhat political in nature, but to me it is just common sense.  I look at it this way------just as it is prudent to diversify a stock portfolio, it is likewise prudent for biologists to diversify their data portfolios.  The portfolio for an orangutan-man clade is not balanced if it has no molecular component.  Likewise the Pan-Homo portfolio needs more morphology added to it.  John embraces the latter, but seems reluctant to admit to the former as well.

     To answer Don's question, I also rely heavily on "gut feeling", even when it runs counter to what appears to be lots of evidence.  A prime example is my "gut feeling" that bivalves evolved first, and that they evolved into radulate molluscs (NOT the other way around).  When I offered evidence in favor of my viewpoint, many malacologists seemed to think I was just engaging in unscientific storytelling.  I guess only time will tell if my gut feelings about that one are right or not.  I always liked Darwin's quote about speculation being good for science (and that includes the orangutan-man hypothesis if more evidence can be found for it).
             ------ Cheers,
                         Ken Kinman

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I am not sure whether anyone said "reject ALL molecular data as phenetic and unreliable". Its just a case of how we tend to interpret the sequence data. We tend to accept that when two genes share 90% sequence similarity they are "closer" together than the third gene which shares 80% sequence similarity with the other two. By applying "parsimony of logic" we would tend to exclude the fact that the higher degree of similarity arose due to effects such as parallelism, gene transfer, or perhaps even other effects which we consider not be the "logical" - thus "overall similarity" (i.e. phenetic influence) plays a subtle underlying role. Cladistic analysis would then build on that concept. This might also influence what Don Colless calls "gut feeling". Certainly my earlier e-mail which includes reference to a "phenetic" approach was not meant to imply that this makes molecular data unreliable AT ALL. The "unreliability" reputation of a phenetic approach has come via the misunderstanding that phenetic = phenotypic. In the early days of the 16S rRNA cataloging the opinion was expressed that simple Sab values (i.e. measures of overall similatiry) were phenetic, to which the counter argument was that there were "phylogenetic" (but were they using cladistic analysis!?). Under certain circumstances phenetic approaches will also reflect evolution accurately and my impression is that some of the discrepancies bewteen molecular and moprhological data arise simply because one accepts that a "greater degree of genetic similarity" reflects a closer degree of evolutionary relatedness. My impression is that some 10 years ago we were given the impression that once complete genomes were available we would have all the answers. This reminds me of approaches in the early 1960s, where the goal was to obtain a sufficiently broad spectrum of data which would give a "relibale result". Even in the case of sequence data we are now moving into a period of selecting the "correct" data set and weighting, which seems to me to be something we went through with the phenotypic data some decades ago. Brian