"Steve Schaffner"  wrote in message
>
> I didn't hear any gasps, and I was in the audience.
>
I would have gasped, though I didn't attend.

This is exactly the sort of thing that makes science so exciting. We think
we have more or less understood how genes relate to the phenotype, and then
some totally unexpected data comes up.
>
> The speaker did mention that many were also conserved
> relative to chicken, but not to Fugu.
>
Fugu (pufferfish) have an unusually small genome, which might explain this.

> Random possible explanations that occurred to me (assuming the
> conclusion that they're conserved is robust):
> 1) They are not functionally important regions conserved by
> selection, but extreme cold spots of mutation.
>
Don't like this one, as then you would expect a hierarchy of perfectly
conserved, slightly degraded, and severely degraded conserved sequences.
>
> 2) They are functionally important but only in the context of their
> immediately surrounding sequence, e.g. that they easily form
> secondary structures that stop replication.
>
So they are selfish DNA killers? This is certainly a possibility. Another
possibility is that they are the viruses themselves, and are capable of
horizontal transfer.
>
> 3) They are functionally important with modest selection
> coefficients (e.g. the study would not have been able to observe
> 1% effects).  This possibility would seem to require that many
> conserved regions perform a single function, so that knocking
> out many has the same modest effect as knocking out one.
>
The problem here is that we are expected to believe that the gene has a
modest selection coefficient, but changing more than a few bases (how good
is the homology?) destroys it totally, and that the sequence has been
conserved since the mammal / bird split. I don't like that at all.
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