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



Roberto, this post is exactly as clear as mud.

Dora

----- Original Message ----- From: "Roberto Takata" <rmtakata@gmail.com>
To: <dinosaur@usc.edu>
Sent: Friday, September 16, 2011 11:23 PM
Subject: Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)


Well, since you said: "now that we've gotten you to believe that it is
actually possible to have the DNA of the same protein coded two
different ways", I've got a bit confused.

It assumes that there was a time in which the mentioned 'you' thought
that it was not possible to have two (or more) different DNA sequences
coding for the same peptide sequences... Since it is not my case, I
was wondering if you (Dora Smith) have had make a misadressing.

The fact that you (Dora Smith) used the pronoun 'we' was of no help
here, since I was arguing with Erik Boehm; and I'm not recollecting
any message of your in this thread, except for the one addressed to
Mike Keesey.

Well, clarified that you was addressing to me. As implied from what
was said above the sentence: "now that we've gotten you to believe
that it is actually possible to have the DNA of the same protein coded
two different ways" is completely misguided. In any other way I would
not talk about "margin of error" since my first message about the
possibility of infer the DNA sequence from the coded peptide aa
sequence. And there will be no need of comparative sequence alignment.

So the answer to your first question: "how would you reconstruct what
was teh ancestral protein"? was given even before you asked it: by
comparison of the peptide sequences of the descendants. It is done not
only with protein sequences, but with morphological characters,
behaviour and a plethora of heritable characters.

Maximum likelihood - combined by other techniques - help us to manage
the probablity of alternative paths. If in a lineage the transition
mutation is more common than by chance, then that probability is taken
into account. No circular reasoning here.

[]s,

Roberto Takata

On Sat, Sep 17, 2011 at 12:57 AM, Dora Smith <villandra@austin.rr.com> wrote:
The person I was replying to. The person who argued about maximum
likelihood whatever would surely recognize himself.

Dora

----- Original Message ----- From: "Roberto Takata" <rmtakata@gmail.com>
To: <dinosaur@usc.edu>
Sent: Friday, September 16, 2011 7:35 PM
Subject: Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)


Pardon, by 'you' you mean me (Roberto Takata)?

[]s,

Roberto Takata

On Fri, Sep 16, 2011 at 9:30 PM, Dora Smith <villandra@austin.rr.com>
wrote:

I think the question was, now that we've gotten you to believe that it is actually possible to have the DNA of the same protein coded two different
ways, how would you reconstruct what was teh ancestral protein?

"Maximum likelihood" hardly does it - this is circular reasoning! The
question is, how would you arrive at which one is most likely?

Dora

----- Original Message ----- From: "Roberto Takata" <rmtakata@gmail.com>
To: <dinosaur@usc.edu>
Sent: Friday, September 16, 2011 1:33 PM
Subject: Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)


On Fri, Sep 16, 2011 at 2:54 PM, Erik Boehm <erikboehm07@yahoo.com>
wrote:

And when we find that extant organisms use more than 1 of the 4
possible
codon sequences to encode Serine at that position?

Align the sequences, put on a tree.

Lets take an example of humans and chips as the extant organisms.
In more than one case (such as hemoglobin), Humans and chimps have the
exact same amino acid sequence, but a slightly different DNA sequence
to
encode that protein.
Suppose we find a fossil ape that is just outside the Human-Chimp
clade.
Which DNA sequence do we use?

The reconstructed common ancestral one. We do it with humans - SNPs
and other intrapopulational variations are taken into account.

What if it is on the human branch, but very basal, do we assume in
every
case where there is ambiguity between humans and chimps that we use the
human version. Sure you could compare to gorillas, but what of the
cases
where the protein sequence is different (as the amino acid identity
with
them is not 100%). If we find consensus between the chimp and gorilla,
sequence, we conclude the chimp sequence is basal, but this basal
member of
the human branch.... we still don't know when to go with the human
encoding
for a particular aa, or the chimp encoding.>

We could use maximum likelihood, for example.

You simply cannot reconstruct the DNA sequence that made the amino acid
sequence with any certainty. You will be reduced to
arbitrary guessing.

"cannot with *any* certainty" is an exaggeration. It is made all the
time when the ancestral state is inferred from extant sequences.

Every single codon assignment is going to involve some level of
guessing
(unless it is methionine in a vertebrate).

It is true. Actually even when we find a methionine it will involve
some level of guessing. It is just that it will not be a random
guessing.

Even when consesnus sequences exist, you still find many variations
from
species to species (SNPs)....

Not only