[Taxacom] SINES, LINES and chromosonal rearrangements

[John Grehan]

Comments inserted below.

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth Kinman
Sent: Sunday, May 08, 2011 11:31 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] SINES, LINES and chromosonal rearrangements

> Hi John,
>     Yeah, I latch onto whatever new technology can offer, and if it
> proves even more reliable all the better.  

It's a tricky thing to equate a technological advance with a conceptual
advance. And whether it is more reliable is another matter.

> But it's simplistic and
> misleading of you to characterize it as totally abandoning the old and
> leap-frogging to ONLY the new.   

I don't think I am misrepresenting anything. Molecular theorists have
indeed jumped from one molecular method to another as they come to
recognize that their original 'solutions" are indeed problematic (e.g.
DNA hybridization is now accepted even by molecular theorists to be a
phenetic analysis even though it was once proclaimed as the key to
resolving phylogeny.


>      Likewise, it would simplistic of me to say that newer
> morphological data (made possible by electron-microscopes) totally
> leap-frogged over all previous morphological observations.  However,
> like molecular data, the newer morphological data is often extremely
> important.   

But in morphology no one is saying that a form of morphology not seen
before makes the previous morphological data redundant.

>      The point is that you can have misleading (homoplastic) data
> whether it is molecular or morphological.  This is especially true of
> the simplest of molecular data (single base changes) and even some
> simple morphologies (possesion of two eyes, which has evolved
> independently in many metazoans), or fins for swimming (many amniotes
> reverted back to swimming in the ocean with arms evolving back to
> fin-like appendages---various Mesozoic reptiles, penguins, and
> cetaceans). 

Yes, in principle I would agree that one could have misleading evidence
in morphology or molecular data, but one does not know which is which
until a final result is accepted (e.g. 'tree').

>       I don't think your orangutan-hominid morphological data is as
> broadly simplistic as possession of two eyes or even possession of
fins
> for ocean swimming, but I still think it is homoplastic in the sense
> that many morphologies can be developmentally related (even from just
> one change in a development gene) in ways that we are only beginning
to
> understand.

This is just speculation. But given that argument one might say that the
fossil record is pretty much phylogenetically meaningless - it could all
me misleading due to homoplasy. A fossil primate, for example, could in
reality be something else entirely.

>     So that is why I will tend to trust whole genomes (properly
> analyzed) over most morphological data.  It's not leap-froggjing to
the
> new and totally ignoring the older data, but just following the newer
> data (molecular or morphological) where it overturns the older data
> which turned out to be homoplastic.  

You are welcome to trust whatever you like (and in this case no doubt
most share your belief. The orangutan evidence is also genomic in that
it represents hereditary information (which DNA bases alone do not).

> Some of the older morphology
> continues to hold up (such as possession of a nucleus in eukaryotes),
> but morphology has its pitfalls (and I suspect an orangutan-hominid
> clade is one of them).  

Well of course I would say that DNA analysis has its pitfalls too and
the chimpanzee-human clade is one of them.

> Whole genomes (and especially the development
> genes) are where the answers will be most often found, and then new
> (often overlooked) morphologies will be found that are congruent with
> them.  It is working fairly well for angiosperms, so I have no doubt
it
> will work for the apes as well. 

No doubt it work's "fairly well" for animals too. But what does "fairly
well" really mean? How does one know something works "fairly well" or
well at all?

The genome is often characterized as the whole of "hereditary
information" When one looks at DNA bases one sees molecules, not
'information'

John Grehan

      
          -------------Ken Kinman      
----------------------------------------------------------

John Grehan wrote:
       It was interesting to see ken now latch onto particular kinds of
molecular data being more 'reliable'. That's a shift from "molecular
data=DNA) being more reliable than morphogenetic data. The history of
molecular approaches has witnessed a continual leap frog as each
molecular evidence was first touted as the refutation of morphogenetics,
and then as its own inherent faults come to light the molecular
theorists jump onto the next 'breakthrough' technique - SINE's etc being
among the latest) and denounce the former 'proofs' as inadequate, but
that will not finally be solved by the new technology. 



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