Lucy in Newsweek

Fri Apr 2 10:24:33 CST 2004

I have to admit that I don't understand how you (John) pick what is good science
versus not good science, or what is personal opinion versus scientific consensus.
You admit that you don't understand how the algorithms work, but then reject
conclusions drawn by applying the algorithms.  You argue that phenetics does not
reveal phylogenetic relationships, but then base your claim for the human-orang
connection on overall similarity (more shared derived characters than human-chimp;
simply counting shared-derived characters is nothing more than using a Jaccard's
coefficient approach to the problem); you have to remember that shared-derived
characters are hypotheses and you don't know which ones they are until you have
placed the characters in a phylogenetic context; i.e., a character cannot be
designated a synapomorphy until a tree is specified).  You suggest that Rob is
basing his "claim" on "no information" when it is you who is rejecting the
relationships based on DNA because "DNA data may be in doubt."  Well, a great many
believe that the morphological data may be in doubt.  Let's face it John, you have
made your position clear ("It is my opinion that the DNA data
has more potential for being misleading...") and it appears that no argument that
can be put forth (at least right now) will change your mind.

Cheers,

Dick

John Grehan wrote:

> At 11:21 AM 4/2/2004 +1200, Rob Smissen wrote:
> >It seems to me that a phylogenetic hypothesis, like any other, should be
> >modified to accommodate all the available data, not just morphology or
> >molecules.
>
> I found the comments above and below by Rob to be interesting and useful -
> even where I may disagree.
>
> If all data are equal I would agree, but if not it would seem to me that
> there may be decisions to be made about whether or how different data are
> or are not integrated.
>
> >It is quite unscientific to simply prefer one or other as
> >more reliable or to haggle over methods of analysis.
>
> Contested evidence and methods seems to me to be the hallmark of science.
> This history of science is replete with the competition of ideas in the
> marketplace of science. It would seem to me that this topic is no
> different. The orangutan question definitely brings the morphology-DNA
> character question into sharp focus. The decision over the orangutan will
> have definitive conclusions for this question for the systematics of life
> in general.
>
> >It is the data (be
> >it morphology or DNA) that a phylogenetic hypothesis should explain.
> >Numerous explanations are available as to why either type of data can be
> >highly misleading in particular sorts of situations.
>
> With this I have absolutely no disagreement. Either source of data rests on
> various assumptions of informativeness. It is my opinion that the DNA data
> has more potential for being misleading as it seems to be phenetic - for
> all that it may be run through clustering algorithms used by cladists. On
> the other hand morphological characters can be of varying quality according
> to the level of documented comparisons made to establish their veracity (in
> most cases with hominid evolution this is extremely poor).
>
> > From even the very little mitochondrial DNA sequence data I've actually
> > looked at, it is
> >numbingly difficult to explain the similarities between humans and
> >chimpanzees (as compared other apes) by simple parallelism or
> >convergence.
>
> It's only numbingly difficult if one takes that to be the case. The
> alternative is to consider that overall similarity of DNA sequences really
> have little to do with the phylogenetic sequence. I have proposed that the
> only sequences that are relevant to such a sequence are those involved with
> the morphological synapomorphies (and if I understand my genetics well
> enough, the DNA representation of each synapomorphy may be scattered in
> different locations on DNA strands as they are brought together through RNA).
>
> >What other explanations are available? Lineage sorting?
> >Human-chimp introgression? Genetic engineering by extraterrestrial
> >aliens? Divine humour? Do they also explain similarities in nuclear
> >genomes?
>
> As above
>
> >On the other hand, what governs the evolution of the sorts of
> >morphological characters linking humans to Orang-utans - are some of
> >them based on quantitative variation under polygenic control and thus
> >likely to shift quickly back and forth under moderate selection?
>
> I've seen selection proposed to explain away some of the synapomorphies. So
> far this seems to be just a propaganda device, and it rests on the
> assumption that if a structure has a function, that function reflects a
> former selective process to establish said structure.
>
> >Personally, for my own group, I'm quite strident in rejecting
> >chloroplast DNA trees as representative of overall species relationships
> >because I can advance realistic explanations, based on the biology of
> >the organisms, for why they might be misleading.
>
> I would be interested in the citations, although I would note that what is
> a 'realistic' explanation for one person may not be realistic for another.
>
> >When it comes to ape
> >phylogeny, the molecularists might seem far fetched when they say
> >apparent synapomorphies shared by humans and orang-utans are the result
> >of convergence or parallelism, but so far I haven't seen ANY alternative
> >  explanation
>
> What literature have you read on the subject?
>
> >of the apparent molecular synapomorphies of humans and
> >chimps seriously advanced.
>
> So far I do not see the DNA being verified as synapomorphies at all. Agreed
> that I am not very familiar with the algorithms, but some of the analyses
> seem to just group taxa in the sequence of the taxa that share the most DNA
> sequences in common and sequentially add on from there the rest of the
> taxa. Nothing very cladistic in that. It seems to be more of a nearest
> neighbor joining technique that could be used in phenetics. I'm sure
> someone will correct my understanding on this and that will be welcome.
>
> >At least until then, I'll leave my money to a
> >chimp over an orang-utan. cheersRob
>
> It seems that this status quo choice is being made on the basis of no
> information (i.e. DNA data may be in doubt, but until something comes along
> that is convincing enough, this doubtful data will be accepted).
>
> John Grehan
>
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--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen