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

John Grehan jgrehan at sciencebuff.org
Sat Jun 27 14:20:32 CDT 2009


 
My comments inserted below. John Grehan

-----Original Message-----
From: mivie at montana.edu [mailto:mivie at montana.edu] 
" 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."

Perhaps by reading it morphologically.


"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."

If the apes cluster together then the chimpanzee-human hypothesis is
contradicted.

"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."

This is only a problem if the law of large numbers is applied.

"Once a character set is developed, it needs to be incorporated into the
next testing analysis, no matter what it is."  

And morphology may represent a test of molecular similarity.

"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)"

This application of the law of large numbers is moot if those large
numbers of molecular characters fail to represent apomorphic
similarities. 

"The constant carping about ear shape (or 4 other complex, questionably
homologous characters) vs millions of coden characters is just so
antiquated."

Just saying so does not make it so.

"The debate should be over better ways to evaluate the total set of data
available."

That is one option

"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."  

Why PAS. What's wrong with the Journal of Biogeography?

"It would be accompanied by huzzahs and press releases. " 

Well there were press releases etc. But no huzzahs.

"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!"

If that is in reference to me, in what way is the hominid origins paper
not a quality document?

"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."

Or it really focuses on a major, as yet unresolved question, can
morphological evidence falsify current interpretations of the genome
that rely on counting base matches?

John Grehan

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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