Text 1315, 270 rader
Skriven 2005-01-03 15:01:00 av Tim Tyler (1:278/230)
Ärende: Re: The "fuel" of evoluti
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Perplexed in Peoria <jimmenegay@sbcglobal.net> wrote or quoted:
> "Tim Tyler" <tim@tt1lock.org> wrote in message
news:cr754q$dhl$1@darwin.ediacara.org...
> > Perplexed in Peoria <jimmenegay@sbcglobal.net> wrote or quoted:
> > > "Tim Tyler" <tim@tt1lock.org> wrote in message
news:cr460a$2hct$1@darwin.ediacara.org...

> > > > Here's a model where mutations occur with much greater biological
> > > > realism - where mutations occur in individuals with some fixed
> > > > probability - and individuals can have 0, 1 or more mutations
> > > > per generation.
> > >
> [snip discussion related to a bug in the model]
> > It makes little difference to the results:
> >
> > Asexual experiment
> > Deaths: 52950
> > -----
> > Sexual experiment
> > Deaths: 40855
> > -----
> >
> > > In your model, individuals accumulate mutations throughout their
> > > lifetime, and as soon as they accumulate enough mutations they die.
> > > This is true for both sexuals and asexuals, but sexuals have the
> > > chance of being born with too many mutations, whereas asexuals do
> > > not.  A truly bizarre model.
> >
> > Not at all.  That is the effect in the real world I was
> > attempting to to simulate.
> >
> > Sex combines deleterious mutations into a super-mutated individuals -
> > who then die.
> >
> > This is not a "bizarre" aspect of the model - it is the exact same
> > effect as the one in the real world which I was trying to simulate.
> 
> Yes, but the mutations that accumulate in your germ line
> and the mutations accumulating in your somatic cells (leading to
> senescence) are two separate issues.  Your model bizarrely
> combines them.  An esthetic judgement.  I can imagine a competing
> esthetics that say that your model *elegantly* combines them.

My model is of a single-celled organism - where the somatic line
*is* the germ line.

I made no attempt to model the soma/germ line split.  I /could/
do it - but it seems like added complexity without too much benefit.

> > > Especially since the defective sexuals get one "free" generation of
> > > reproduction before they have to face selection.
> >
> > I'm not sure what you mean here.
> > The sexual and asexual reproduction seems symmetrical in the model to me.
> 
> Another bug or "feature" of your model is that sexual organisms that
> are conceived with too many mutations to survive a round of selection
> will nonetheless still survive for one "generation" before selection
> removes them.  During this "free" generation, they have the same
> opportunity to reproduce as everyone else.  But, given that the average
> reproductive lifetime in your model is about 20 generations, I doubt
> that this makes much of a quantitative difference in the results.

I'm not too worried about heavily mutated individuals having a small
chance of reproduction.  Heavily mutated individuals probably often
have a small chance of reproduction in the real world as well - though
it is true that sometimes they will die before they are born.

> > > [regarding the claim that the model indicates sex removes deleterious
> > > mutations more efficiently]
> > > Not at all surprising, since dying asexuals always carry *exactly* 5
> > > mutations out of the gene pool, whereas dying sexuals carry 5 or
> > > more.
> >
> > Apologies for the bug :-X
> >
> > With the modification above, asexuals can carry many mutations out of
> > the population at any time.
> 
> Not really.  Fixing the bug has not fixed the problem.  You used to have
> about a 10% chance of picking up a single mutation in a generation and
> no chance of picking up more than one.  Now, with the bug fixed, you
> have a 10% chance of picking up one mutation, a 1% chance of picking
> up two mutations, a 0.1% chance of three, etc.

This mirrors the situation in the real world if the mutation rate 
is low.  I can bump up the mutation rate.  Here are the results for
10, 12 14 and 16 times the original mutation rate.  While 
small organisms can exhibit far lower error rates I reckon 
(10x) - an "average" of one mutation per generation - is fairly
realistic.

[final int mutation_attempts_per_generation = pop_size * 10;]

Asexual experiment
Deaths: 509818
-----
Sexual experiment
Deaths: 416943

[final int mutation_attempts_per_generation = pop_size * 12;]

Asexual experiment
Deaths: 608021
-----
Sexual experiment
Deaths: 506342

[final int mutation_attempts_per_generation = pop_size * 14;]

Asexual experiment
Deaths: 802038
-----
Sexual experiment
Deaths: 611156

[final int mutation_attempts_per_generation = pop_size * 16;]

Asexual experiment
Deaths: 966832
-----
Sexual experiment
Deaths: 996996

> > > I would be much happier if your model inserted all mutations at the
> > > time of birth, and if it permitted more than one new mutation to be
> > > inserted into an asexual newborn.
> >
> > It should have done the latter (and now does).
> >
> > I'm not sure about the former.  It seems less realistic to have mutations
> > occur only at birth.  In practice, old individuals have more mutated
> > offspring - and it seems useful to model that effect.
> 
> Useful in what sense? [...]

Greater realism: the more real world features the model reproduces,
the better.

> > > I agree that if you have a mutation count threshold, and the simulation
> > > cycle runs in the order [select -> recombine -> mutate -> select again],
> > > then you will have the effect you desire.  The reason is that when
> > > recombination operates on the post-selection population, it is operating
> > > on a population whose variance in mutations per individual has just been
> > > artificially lowered by the truncation selection.
> >
> > That isn't "artificial".  That's the effect in the real world I was
> > trying to model.
> 
> The artificial part is the sharp truncation. [...]

Agreed!  However, it /does/ clearly illustrate the circumstances under
which sex is favoured by mutation repair theories.

> > > It can't help but to increase the variance.  The effect is much smaller
> > > if the simulation cycle is [select -> mutate -> recombine -> select
> > > again].
> >
> > How is that different from what I am doing?
> 
> Well, you have multiple rounds of selection and mutation during the
> life of a sexual individual, but only one round of recombination.

Individuals can be parents of many offspring in their lifetime in
the model.  Do you mean something else?

> My point about the cycle order applies to non-overlapping generation
> models in which there is only one round of each per lifetime.

Less biologically-realistic models, you mean? ;-)

> > > And the effect disappears entirely if the selection threshold is
> > > reduced to a more realistic number of 1 mutation per individual.
> >
> > If *every* mutation is fatal, individuals would die as soon as they
> > are mutated - and sex would be combining totally unmutated individuals.
> >
> > That would indeed destroy the effect - but I fail to see how that is
> > more realisitic.
> 
> Actually, I probably erred in suggesting that you reduce the threshold
> to 1.  I should have suggested that you increase the mutation rate
> so that you don't "creep up" on the threshold.

Good.  Results above.

> You have to give the asexual individuals a chance for a significant 
> overshooting of the threshold, otherwise you are simply not being fair 
> to the sexuals.

*Some* populations do have error rates far below those in my model.
But I agree - and increased the mutation rate accordingly.

> > For example such a model fails if you can survive if you are deaf,
> > and survive if you are blind - but the combination of the two
> > defects effectively sterilises you.
> >
> > The /reason/ sex can be beneficial at cleansing deleterious mutations
> > from a population is that deleterious mutations can act togther
> > *synergetically*.  In other words, having mutation A and mutation B
> > can sometimes be a /lot/ worse than having either alone.  This is
> > what is sometimes known as "escalating damage" - e.g. see
> > Mark Ridley's Mendel's Demon, p. 117.  As Mark notes:
> > "sex only helps purge mutations if successive mutations do
> > escalating damage to the body" - p.123.  However there are some
> > good reasons to think that "escalating damage" really does
> > happen - at least some of the time.  One such reason has to do with
> > redundancy and backup systems - where single defects can be recovered
> > from and only *combinations* of defects are fatal.
> 
> Yes! I fully agree with the Ridley quote.  What he calls "escalating
> damage" is a prerequisite to any model attempting to justify sex
> as an error correction mechanism.  And while there is some empirical
> evidence in favor of "escalating damage", there is also some evidence
> against it.

Sometimes it happens, sometimes it doesn't.

> You certainly were not unfair in your choice of example.  Assume that
> a person who is both deaf and blind has fitness zero, while a person
> who is neither has a fitness of 1.  If blind people have fitness 0.7
> and deaf people have fitness 0.8, then that would be a case of escalating
> damage, and sex would be a technique for helping people to see and hear.

Yes.

> Certainly, in biochemistry, you see mechanisms which only work if
> every one of several genes is doing its job.  Each such mechanism is
> a case of "de-escalating damage" and thus an argument in favor of
> asexual reproduction as an error control mechanism!

I don't /think/ that is correct.  If such cirumstances were universal,
sex would not be favoured.  However, asexual reproduction would do no 
better at correcting errors.  Basically both the sexual and asexual
individuals would fail as soon as they encountered such a mutation.
 
Asexuality might spread in such a population by avoiding the costs of sex.

Since "deescalating damage" is rather irrelevant to the issue - and 
escalating damage favours sex - the issue boils down to how common 
escalating damage is.

> I'm not sure whether the most common situation is escalation or
> de-escalation.

Don't worry, nor is anyone ;-)

I /do/ however think that there are some cases of excalating
damage - and that those that exist will benefit from sex -
and promote its adoption.

> But it seems to me that proponents of the mutation
> elimination theory of sex have a tendency to assume
> that escalation is the norm, simply because they
> need that assumption in order to make their theory work!

Mark Ridley at least does a good job of spelling out the
consequences and significance of this modelling assumption.
-- 
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