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



Roberto Takata <rmtakata@gmail.com> wrote:

> Well, it seems that it would take longer to explain you why my
> assertion is a reasonable one..


And even then, I would not be convinced.  Your assertion is
unjustifiable.  There is just no way that because a chicken has CTT
encoding leucine in the second amino acid of this particular peptide
that we can say that _T. rex_ is also more likely to have CTT at the
equivalent position in its (unknown) DNA sequence.  BTW, the zebra
finch has proline here instead of leucine.  What does that tell you?


>>  Why do you assume that the choice of base in the chicken is ancestral?
>
> Excuse me. Where did I have assumed such a thing? I'm not assuming
> chicken sequence as ancestral.


Well, yes you are.  You reach this assumption in a roundabout fashion,
but it is exactly what your assumption boils down to.


> What I'm assuming is that chicken and
> T-rex sequences are homologous, are derived from a common ancestral.


The homology of the sequences is not really in doubt, since both
peptide sequences derive from the same part of alpha-2 collagen from
two animals.  You are not actually referring to 'homology' here, but
to 'sequence identity'.  You are making a huge leap of faith by
claiming that _T. rex_ probably has whatever codon the chicken has,
unless proven otherwise.


> Lets use parsimony for simplification.
>
> T-rex second codon must be: TTA, TTG, CTT, CTC, CTA or CTG for leucine.
>
> Since we have CTT for chicken, by parsimony, we infer that the T-rex
> and chicken common ancestral codon would have a C in the first
> position. So no additional evolutionary step is required. If ancestral
> was supposed to have T in the first position, an additional step of
> change from T->C in chicken will be required.


This is a complete misuse/abuse of parsimony.  You only have a sample
number of n=2 (chicken and the purported _T. rex_ sequence).


> Of course, comparing this just two sequences, using only parsimony -
> since the peptide sequences is identifical, we will endup assuming
> that the common ancestral will have the chicken sequence. We could do
> it, and assign a margin of error due to mutation fixation rate.
>
> Lets say that the mutation rate is constant over the time and along
> the sequence of, say, 1 SNPs per 100 mya. In this case, about 4 SNPs
> is expected.


You've lost me here.





Cheers

Tim