[Taxacom] SUSPECT: Re: Pongidae (was: orangutan outrage)

mivie at montana.edu mivie at montana.edu
Sat Jun 27 14:00:11 CDT 2009

Dear Richard,

I cannot find a single thing in your note to disagree with.  Even
different questions will have different sets of focus, and possibly use
the same data in different ways to best address them.  No matter what the
level of interest, there will not be any historical evidence remaining
(note: agreed that lots of stuff may have been overwritten and no longer
retained at all) that is not carried in the genomic code.  IF ( a huge IF
- put this in 72 point) we knew how to read this correctly, we could get
everything that is retrievable out of that genome, but we do not have a
clue how to really read it yet. So, we are stuck in a developing period
methodologically.  Look how much better we do now than in the first heady
days of PCR?  At least the apes cluster together now.

However, by focusing on morphological-is-better-than-molecular (or the
contrary) because it does not fit the 4 characters I like to use from
morphological data, it makes those of us still tied to morphological
characters (for whatever reason, choice, taxon, availability of material,
cash or whatever) look like ludites.  That is what bothers me.

Once a character set is developed, it needs to be incorporated into the
next testing analysis, no matter what it is.  I am not a complete total
evidence fan, but lean very heavily that way.  If lots of molecular data
already exist, they have to be used in any reasonable test of ongoing
hypotheses (unless  it is a test of the molecular method itself, when they
need to be removed for independence).  The constant carping about ear
shape (or 4 other complex, questionably homologous characters) vs millions
of coden characters is just so antiquated.  The debate should be over
better ways to evaluate the total set of data available.

If a robust test, meeting good scientific standards, of the hominid tree
was done that refuted the Homo-Pan pairing was conducted, it could be
published in the PAS.  It would be accompanied by huzzahs and press
releases.  We all love the overturning of orthodoxy, it is what we live
for as scientists. However, constant dithering about an alternative tree
on Taxacom by someone apparently incapable of producing such a quality
document (or else, where is it?) is enough to drive me to inpropriety!

We need to find a way to continue supporting both morphological-based
inquiry and exploration of retrieval of phylogenetic information from the
genome.  We have so far to go in both arenas, why make it one vs the
other?  The ongoing circular and pointless Pan-Pongo-Homo stuff just
degrades us all.

Michael Ivie

> Bravo, John. Good response.
> Much information about past selection of expressed traits or fixation of
> drifting traits will be there in the genome. Getting it out is the
> problem. Much history is overwritten in DNA. Slow-mutating sequences miss
> stuff. Extinct lineages have taken much with them into eraserhood.
> If we could identify proteomically developmental genes generating
> different expressed traits associated with selection in nature then match
> them with history accumulated by non-coding sequences, wouldn't that be
> nice? I think much is expected from QTL studies in this regard.
> I think a feature of misunderstanding on Taxacom are the different ideas
> different people have about exactly what it is that is evolving. A
> species? A population? An organism? A trait? An enzyme? A codon? Is ANY
> change the same as evolution, or is evolution associated with change and
> the fixation of certain expressed traits in a species that is then stable
> over long periods of time through maybe stabilizing selection (which is my
> take on it)? Should we vote? Or is this even more embarassing than our
> lack of agreement on something so basic? Look it up in the dictionary?
> BTW, strong expressions are stimulating, instructive, and worthwhile on
> Taxacom. I would hate to see anyone blackballed from this listserver for
> occasionally being robustly annoying. Truth is not necessarily captured by
> tippytoeing up behind it.
> _______________________
> Richard H. Zander
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166 U.S.A.
> richard.zander at mobot.org
> ________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu on behalf of John Grehan
> Sent: Sat 6/27/2009 11:42 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: SUSPECT: Re: [Taxacom] Pongidae (was: orangutan outrage)
> Michael,
> Thank you for taking the trouble to present in simple, first principles,
> your view of the situation. This is highly commendable. Naturally I have
> a counterpoint.
> First on heritable information. There has been quite a bit of debate
> over the nature of 'information' and its 'expression' (which implies
> preformationism). But going along with your argument I would say that I
> understand your statement and for the purposes of the phylogenetic
> hypothesis I have no need to contest it.
> Regarding the statement that "there is more information" in the genome
> than macromorphology - again that depends on the nature of information.
> But for my systematics evidence on the orangutan I have argued a
> cladistic application whereby the pertinent information is confined to
> those features that are unique, or nearly so, to the in-group that can
> be individually evaluated before analysis of competing evidence for
> relationships within the in group. In the absence of empirical evidence
> for base replacement this becomes problematic in molecular sequence
> analyses. Some admit this, but then argue the law of large numbers.
> As for "Therefore, all information available from morphology is
> THEORETICALLY available in the genome" I have no problem with that. The
> problem is identifying the morphological apomorphies in the DNA bases.
> Regarding" We all have our opinions on the techniques available at this
> time, and they are getting better all the time" don't confuse better
> techniques with better concepts. Better techniques applied to erroneous
> concepts = no improvement at all. One sees this in molecular clock
> theory.
> "We all have our opinions on the techniques available at this time, and
> they are getting better all the time" - I already said this.
> "So, please stop trying to debate the ridiculous" - I guess you are
> right -the molecular claims of immunity from falsification by morphology
> are ridiculous. But sometimes they need to be debated nevertheless as
> not all take this viewpoint.
> "And, just to set the record straight, I and many others still ridicule
> panbiogeography at every opportunity" Good for you. Confidence in your
> position is commendable. I would be interested to know how you explain
> away the success in panbiogeography of making novel geological
> predictions.
> "Lastly, I am amazed anyone cares about these 6 taxa" I'm kind of amazed
> too. If this were about some obscure ghost moths, for example, no one
> would give a damn. On the other hand, the hominid question forces issues
> into the open that are otherwise too easily ignored.
> Thanks for the vote of confidence. You can return to your cave now.
> John Grehan
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