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

Roberto Takata <rmtakata@gmail.com> wrote:

> 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.

Sorry, but this is complete nonsense.  The most recent common ancestor
of two bird species (*any* two bird species) was not ancestral to _T.
rex_.  This is important.  Refer to David's message regarding the
distinction between 'extrapolation' and 'interpolation'.

> For example, the
> functionally tridactly in T-rex and chicken would be regarded as a
> unmodified shared condition.

I don't know if you're referring to the manus or pes here.  Either
way, it probably doesn't matter, because I don't know what point
you're trying to make here.  _T. rex_ has a functionally didactyl
manus, and a functionally tridactyl pes (at least from a locomotory
perspective).  The manus of a chicken is absorbed into the wing
skeleton, and only digit (the alula) is 'free'; the pes is
functionally tetradactyl (chickens can perch).  In this context, the
"unmodified shared condition" would be functionally tridactyl for
manus and pes - neither of which is retained by the chicken.

> 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.

This analogy is completely inappropriate, because base positions in a
codon can change multiple times.  These changes may or may not lead to
changes in the identity of the codon, depending on which base position
changes.  I know you know this; which is why your comparison of codon
base changes to the origin of flight in theropods (which *occurred*
after the tyrannosaur line split from the bird line) is so odd.

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

Nope, it is just crap.

> Parsimony assumes the least evolutionary
> changes as possible - least, not no evolution.

In your example, this is a distinction without a difference.  For _T.
rex_ to have the same DNA sequence as a chicken requires no evolution
at all.

> 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.

Ummm... 8/14 not particularly impressive.  Especially considering it's
just the FIRST codon position.  What's your success rate for the third
position - the position that most readily reaches saturation.

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

You did not actually "show" it had "practical use" - you just
speculated that it could.

> 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.

When you say "homologous" are you referring to paralogous peptide
sequences?  Otherwise, what you said doesn't make any sense.  In fact,
it probably still doesn't make any sense, because if they are the same
protein/peptide, you've not explained why one peptide has Lys and the
other has Ile?

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

The most important determinants for expression are codon bias and
(above all) the sequence of the region upstream (promoters, enhancers,
and the like) of the open reading frame.