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

On Thu, Sep 22, 2011 at 8:39 PM, Tim Williams <tijawi@gmail.com> wrote:
> I think Dora Smith had a point when she said: "Well, I think that the
> assumption that the least possible change occurred over time most
> parsimoniously implies that evolution itself does not occur."

Nope. I've already answered that objection.

"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."

> Simply filling in the blanks in a _T. rex_ DNA sequence based on the chicken 
> sequence goes way further than parsimony.

Nope. It is just parsimony. Parsimony assumes the least evolutionary
changes as possible - least, not no evolution. And again, obviously,
we could develop a more complex model - one, for example, that take
into account neutral mutations that are fixed.

I've showed how it works well even for a chicken/croc comparison. The
technique gives the right answer to the first position in ambiguous
codon eight times in 14 cases.

>> It is not ignored. What is regarded is that, under parsimony, as few 
>> mutations as
>> possible is allowed (or we could use other parameters as codon usage bias,
>> transition/transversion rate and so on to build a more complex model).
> Yes, the model could be very complex indeed.  And yet, this model would still 
> be utterly
> useless.

Not really. As I've showed not only the technique could have practical
use but could be tested too.

> More _T. rex_ proteins (even assuming we have any now) would still be
> no help at all in reconstructing the exact DNA sequence.

I was not saying specifically T.rex protein - I've said dinosaur
proteins - but even more *T.rex* protein could help. Even more the
same *individual* T.rex could help.

Consider, for example, that a T.rex peptide sequence has a Ile in a
position. And other homologous T.rex peptide sequence has Lys in the
same position. Most probably the first peptide had a AUA codon and the
second had a AAA codon in the DNA sequences: other codon pairs would
require two or more steps to turn into each other.

> In these cases, I thought that the untranslated regions (UTRs) of the mRNA 
> were
> paramount.  Much more so than the part that is translated into protein.

Yes it has much importance. But it do not make the secondary and
tertiary mRNA structure unimportant.


Roberto Takata