<< This brings up the second problem -- from which the signal-to-noise problem
really stems -- which is that of extinction.  Even if we've sampled the
genomes of every living thing on Earth, we know with certainty that we're
missing a substantial amount of data from extinct organisms.   >>


This may not always be the case.
Here's why - IF as I have suggested, every
adaptive step is some type of better energy
moderation or evolved form of energy moderation
 - then we know the driving force
to begin life and the driving force
in changing life etc.
In its most basic form IMO its energy in/waste out.

Now match that with the environment that
that extinct species lived in.

Once we learn life is not as random as we think
(one can't have a random chemical system built
on a cyclical non random heat cycle environment) then
we will have more clues than we do now IMO.
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