[Taxacom] Pongidae (was: orangutan outrage)

John Grehan jgrehan at sciencebuff.org
Sat Jun 27 11:42:11 CDT 2009


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

-----Original Message-----
From: mivie at montana.edu [mailto:mivie at montana.edu] 
Sent: Saturday, June 27, 2009 12:09 PM
To: John Grehan
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Pongidae (was: orangutan outrage)

Clearly, this needs to be stated in simple, first principles for you,
John.

All heritable information passed between generations, including that
which results in multiple morphological expressions when interacting
with the environment, is passed via the genome, in its broad sense
(including nuclear and non-nuclear codes).  If you do not understand
this, well, we are wasting our time.

Therefore, all information available from morphology is THEORETICALLY
available in the genome.  At least this information is available to and
interpretable by, the developing embryo and immature, or it would not
develop the morphology it does.

The genome also includes many other groups of information, including the
biochemical codes (micromorphology?) and non-coding histories.  Any
evolutionary history retained by the organism at hand must be available
in the genome.

Therefore, there is more information in the genome than in
macromorphology.  Absolutely no question about whether or not molecular
data is more inclusive than morphology alone.

So, please stop trying to debate the ridiculous.

The real debate is whether an individual analysis technique can properly
interpret the data (molecular, morphological or biogeographic), not
whether the data themselves are better. In the case of a genome, that
horse has left the barn.  We all have our opinions on the techniques
available at this time, and they are getting better all the time, but
this argument forces morphologists like me to be embarrassed by silly
people who claim to be on the same side as me.

And, just to set the record straight, I and many others still ridicule
panbiogeography at every opportunity -- I did it this morning with some
students.  I wouldn't bother doing it in the literature, same as I would
not bother with other discredited ideas.  Not mentioning that barnacles
do not metamorphose into geese is not needed in a paper on barnacle
phylogeny in order for scientists and students to understand that
"ignoring" the theory is not avoiding a possibly valid concept.  Rubbish
is rubbish.

Lastly, I am amazed anyone cares about these 6 taxa (Homo, Pan X2,
Pongo, Gorrilla X2)enough to waste so much time on them.  There are far
more interesting questions in systematics.

I move that we all vote to support the idea that John's closest
non-human relative is an Orangutan. Maybe then he will declare victory
and drop it.

Michael Ivie

>
> What I see in the responses by Richard Zander and Ken Kinman is this 
> determination that the molecular evidence is really, really, right no 
> matter how it is contradicted by the morphological evidence. And by 
> hook or by crook they (or the molecular theorists) are going to find 
> an 'explanation' (excuse) to explain away the morphological anomaly. 
> The idea that bean counting of DNA bases is the essence of phylogeny 
> is now so entrenched that I doubt anyone who has walked out on this 
> plank will be able to back away (especially if they have claimed that 
> the chimpanzee theory is fact). Of course I have walked out on an even

> longer plank against popular opinion. But then only a few decades back

> panbiogeography was ridiculed out of hand, and while it is now just 
> generally ignored (standard scientific procedure by the majority - one

> technique that should be taught to students in science classes so they

> can recognize it in themselves or others), one can no longer get away 
> with ridicule.
>
> John Grehan
>
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth 
> Kinman
> Sent: Thursday, June 25, 2009 10:18 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] Pongidae (was: orangutan outrage)
>
> Richard Zander wrote:
>      If gorilla and pan were on a very short shared branch that did 
> not show up in molecular cladograms, then the paraphyletic group 
> homo-pongo would be the ancestor of gorilla-pan (mapping the traits 
> that characterize the taxa). Any evidence for a short molecular branch

> connecting gorilla and pan?
> ----------------------------------------------------
>  Dear All,
>       Richard Zander brings up a very important point.  The group 
> "Homo-Pongo" (and their extinct relatives) could very well have 
> paraphyletically given rise to a Gorilla-Pan clade.  If so, one might 
> regard gorillas as just overgrown chimps.  This would not surprise me 
> in the least.  And it would also mean that the morphological 
> similarities between humans and orangutans are retained plesiomorphies

> of the great apes that were subsequently lost in a Gorilla-Pan clade.
>       That is why I think a thorough evaluation of great ape genomes 
> is so important.  Whether the first such evaluation is "thorough" 
> enough to convince the vast majority of scientists remains to be seen.

> My own personal expectation is that it will support an African clade 
> (Gorilla, Pan, and Homo) with orangutans as an outgroup (sorry, John).

> However, I have no strong expectations whether Pan (chimps) will clade
exclusively
> with gorillas or with humans.  We shall see.   Until then, I see no
need
> to comment further.  And as I have pointed out several times, my 
> Family Pongidae will remain paraphyletic with respect to Family 
> Hominidae no matter what the results are.  The results will only 
> affect which genus of Pongidae that I will code as the sister group to
Hominidae.
>            --------Ken Kinman
>
>
>
>
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