(Day 12 AM, Page 41 thru Day 12 AM, Page 55)
Q. And you studied a particular type of mutation, a
point mutation?
A. That's correct.
Q. And let me just ask you a few questions, and you
tell me if I'm fairly summarizing the results of your
computer simulation. What you're asking is, how long
will it take to get -- and please follow with me, I'm
trying to do this slowly and methodically -- two or more
specific mutations, in specific locations, in a specific
gene, in a specific population, if the function is not
able to be acted on by natural selection until all the
mutations are in place, if the only form of mutation is
point mutation, and the population of organisms is
asexual?
A. I would have to look at that statement closely
because there are so many different aspects to it that I
don't trust myself to sit here and listen to you say
that and form a correct judgment.
Q. Anything I said about that sound incorrect?
A. If you repeat it again, I'll try.
Q. I'd be happy to. Two or more specific mutations?
A. Actually, this dealt with one or more.
Q. One or more mutations?
A. Yes. If you notice, in figure -- if you notice
in figure 3, you look at the x axis, you notice that
there are data points there that start at one. So we
considered models where there were one, two, and more
mutations.
Q. Fair enough. In specific locations?
A. No, that's not correct. We assumed that there
were several locations in the gene that could undergo
these selectable mutations, but we did not designate
where they were.
Q. In the specific gene?
A. We were considering one gene, yes.
Q. In a specific population?
A. Yes.
Q. Okay. If the function is not able to be acted on
by natural selection until all mutations are in place?
A. Yes, that's what's meant by multiple amino acid
residue, multi-residue feature, yes.
Q. If the only form of mutation is point mutation?
A. Yes, that's a very common type of mutation, which
is probably half or more of the mutations that occur in
an organism.
Q. And if the population of organisms is asexual?
A. Yes, we did not -- actually, we did not confine
it just to asexuals, but we did not consider
recombination.
Q. Are prokaryotes an example of the kind of
organism that you were studying there?
A. Again, we weren't studying organisms, but, yeah,
they're a good example of what such a model has in mind.
Q. And to say this very colloquially, you conclude
that it will take a large population a long time to
evolve a particular function at disulfide bond, right?
A. A multi-residue feature. That's correct, that's
correct.
Q. And specifically --
A. I'm sorry.
Q. Go ahead.
A. Let me just finish. Depending on -- as we
emphasize in the paper, it depends on the population
size. And, of course, prokaryotes can oftentimes grow
to very large population sizes.
Q. And here the conclusion, the calculations you
concluded was that, if you had a population of 10 to the
9th power, that's a population of 1 billion?
A. That's correct.
Q. To produce a novel protein feature through the
kind of multiple point mutations you're talking about,
it would take 10 to the 8th generations, that's what it
says in the abstract, correct?
A. If, in fact, it was -- if, in fact, the
intermediate states were not selectable.
Q. Okay.
A. And if this is by gene duplication as well.
Q. Okay. So 10 to the 8th generation, that's 100
million generations?
A. That's correct.
Q. And yesterday, you explained about bacteria, that
10,000 generations would take about two years in the
laboratory, correct?
A. Yes.
Q. So 100 million generations, that would take about
20,000 years?
A. I'm sorry?
Q. 100 million generations, which is what you
calculated here, that would take about 20,000 years?
A. Okay, yes.
Q. And those are numbers based on your probability
calculations in this model, correct?
A. Yes.
Q. Now it would be true that, if you waited a little
longer, say, instead of 10 to 9th generations, 10 to the
10th generations, then it would mean that you wouldn't
need as big a population to get the function that you
are studying?
A. That's right. The more chances you have, the
more likely you are to develop a feature. And the
chances are affected by the number of organisms. So if
you have a smaller population time, and more
generations, that could be essentially equal to a larger
population size and fewer generations.
Q. So, as you said, so if we get more time, we need
less population to get to the same point, and if we had
more population, less time?
A. That's correct, yes.
Q. Now would you agree that this model has some
limitations?
A. Sure.
Q. And you, in fact, were quite candid in indicating
that in the paper?
A. That's correct.
Q. And if we could turn to, what I believe is, page
8 of the document. And if you look in the paragraph
that's actually continued from the previous page that
says, we strongly emphasize. And if you could --
A. I'm sorry. What page number is that?
Q. It's page 8 in the document. And it's up on the
screen as well.
A. Yes, okay. I've got it.
Q. Could you read into the record the text to the
end of the paragraph beginning with, we strongly
emphasize?
A. We strongly emphasize that results bearing on the
efficiency of this one pathway as a conduit for
Darwinian evolution say little or nothing about the
efficiency of other possible pathways. Thus, for
example, the present study that examines the evolution
of MR protein features by point mutation in duplicate
genes does not indicate whether evolution of such
features by other processes, such as recombination or
insertion/deletion mutations, would be more or less
efficient.
Q. So it doesn't include recombination, it doesn't
include insertion/deletion of the mutations?
A. That's correct.
Q. And those are understood as pathways for
Darwinian evolution?
A. They are potential pathways, yes.
Q. This study didn't involve transposition?
A. No, this focuses on a single gene.
Q. And transpositions are, they are a kind of
mutation, is that right?
A. Yes. They can be, yes.
Q. And so that means, this simulation didn't examine
a number of the mechanisms by which evolution actually
operates?
A. That is correct, yes.