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Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)

On Sat, Sep 17, 2011 at 12:39 PM, Dora Smith <villandra@austin.rr.com> wrote:
> Well, I think that the assumption that the least possible change occurred
> over time most parsimoniously implies that evolution itself does not occur.
> Dora Smith

If in a specific trait we do not observe change between descendants
than the most parsimonious assumption is that that trait haven't
change over time since the common ancestral. For example, the
functionally tridactly in T-rex and chicken would be regarded as a
unmodified shared condition.

It is not the same as 'evolution itself does not occur', since if we
observe differences in that specific trait, so we assume that
evolution occurred. Parsimony in this case will assume the fewer
possible steps - for example, T-rex possibly was flightless, chicken
even not a notable one is able to at least take short flight. By
parsimony, we assume that either the common ancestor was flightless
and flight capability evolved in the lineage that led to chicken only
once or the common ancestor was able to fly and the lineage that led
to T-rex lost the capacity only once. Assuming that flight skill
evolved and devolved several times in a lineage is not parsimonious.

Of course that it could change as more information is added. And, as
I've said before, the parsimony was used in the analysis for the sake
of simplification. As I've mentioned earlier, if we have sufficient
information, we could use, for example, maximum likelihood.


Roberto Takata

> ----- Original Message ----- From: "Tim Williams" <tijawi@gmail.com>
> To: <dinosaur@usc.edu>
> Sent: Saturday, September 17, 2011 12:38 AM
> Subject: Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)
>> Roberto Takata <rmtakata@gmail.com> wrote:
>>> You simply cut the part of the email message in which I actually
>>> showed how to make comparisons. So I will reproduce it:
>>> "That comparison allow us to have some improved knowledge about T-rex's
>>> DNA sequence. For example, the second codon first position in T-rex
>>> most probably was a C too (and not a T). Of course we cannot rule out
>>> the possibility of point mutation (either from T to C in chicken or C
>>> toT in T-rex).
>>> The sixth codon is more dramatic. The S aa could be coded by a TCN
>>> codon or by a AGY codon. In the chicken it is AGC codon. It would take
>>> at least two point mutations to convert a TCN into AGY and vice-versa.
>>> So, most probably T-rex had a AGY codon in that position."
>> Including your reasoning doesn't help your cause; your assertion is
>> still incorrect.  It would take too long to explain why.  But one
>> starting point is the assumption that the "T. rex" sequence is more
>> likely to adhere to whatever the chicken (or zebra finch) has, despite
>> the the bird and tyrannosaur lineages having diverged some time in the
>> Jurassic.  Why do you assume that the choice of base in the chicken is
>> ancestral?
>>> http://www.ncbi.nlm.nih.gov/protein/P0C2W4.1
>> OK, that sequence is indeed assigned to _T. rex_.  The "_T. rex_"
>> peptide sequence just happens to show 100% match to the chicken
>> peptide sequence....
>> Cheers
>> Tim