On 09/07/10 22:10, Jacob Keller wrote:
> In terms of "usefulness," I was actually thinking about cells learning how
> to make new proteins from other cells,
Which they do already by exchanging genes
>   or perhaps an immune system could use
> the info to make the right choice of starting materials.
The methods by which the immune system works have been at least 
partially elucidated, and are available for study.
>   Also, codon bias
> could be explained as resulting from the nature of the reverse translatase
> machinery.
1) Or, you could explain it as resulting from the nature of unicorns. 
You might understand that this would be an easier sell if you could 
first establish the existence of unicorns.
2) What is it about codon bias which you feel requires such an elaborate 
explanation?

>   Or an invader could copy the host's membrane proteins to evade
> detection.
They can do that now by
1) Stealing the host's genes
2) Stealing existing peptides and lipids and grafting them to their surface
> Ah, so many possibilities! And as I said before, considering that
> it would be so useful, and that the genius of macromolecular design observed
> in nature is apparently so unlimited, shouldn't it be out there somewhere?
"Design"? I think there are more appropriate descriptions for life as it 
has been observed. The complexity of life can be explained fairly well 
by Darwinian evolution, i.e. replication with variation coupled with 
selection. This works through modification of existing entities. The 
relatedness of many molecules and the theme of modification of 
pre-existing parts ought to be apparent to someone who has learned about 
replication and sources of genetic novelty, and spent any time studying 
protein structure.

The large barriers to the introduction of your reverse translation 
system have already been pointed out. Come up with a Darwinian sequence 
of how it could have developed gradually from existing systems and get 
back to us. For comparisons, Darwinian explanations for the development 
of ribosomal translation and the genetic code have been proferred. "I 
want it, therefore it should exist" doesn't cut it.
> Nobel prize to the one who finds it...
>
Certainly.
> NB It should not cross our minds, I don't think, that if it were there, it
> would have been found. Small RNA phenomena, for example, went undetected for
> years, despite their commonness and high importance.
>
Now that we have access to many complete genomes, if genes were being 
swapped by your reverse translatase system rather than horizontal gene 
transfer, the results should be readily apparent.

Cheers,

-- 
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                                David J. Schuller
                                modern man in a post-modern world
                                MacCHESS, Cornell University
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