Re: Shall we get rid of our junk?


"Joe Felsenstein" <joe@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx> wrote in message news:dnsufn$14go$1@xxxxxxxxxxxxxxxxxxxxxx
> In article <dnphgl$2jh8$1@xxxxxxxxxxxxxxxxxxx>,
> Jim Kent <kent@xxxxxxxxxxxx> wrote:
> >In a broader sense the junk, though not needed at the *moment*
> >does serve a purpose. The system needs to be able to tolerate
> >a bunch of non-functional stuff so that it has the necessary freedom
> >to evolve new functions. Approximately half of the junk is the
> >relics of quasi-viral "selfish" DNA (transposons). The other half
> >is from portions of the genome being duplicated, and then one copy
> >of the duplication undergoing bit rot, since natural selection only
> >needs
> >to preserve one working copy. On rare occassions instead of
> >bit rot the second copy takes on a new function. If the duplicated
> >'junk' was deleted too quickly, there would be no opportunity for
> >new functions to evolve.
>
> Does that mean there is an individual selection explanation for the
> retention of the "junk"? Or must we necessarily invoke species
> selection if we explain it this way (the dying out of species if they
> get rid of too much of their "junk" and then need a new function)?

IIRC Tim Tyler and I have debated this issue in this group without
reaching closure. I argued that selection for junk retention does
require some kind of population-level selection. But the more I
puzzle over this question, the more convinced I become that the
usual models and categories of selection don't really apply.

It seems that there are three selective forces that must be
considered:

1. Presumably there is a small negative fitness effect on individuals
who carry a lot of junk because of the metabolic cost of replicating
the junk.

2. In a sexual population (and the question is meaningless if the
population is not sexual) there is presumably a negative fitness
effect on any individual who carries a different pattern of junk
than do his potential mates. This is because the chromosomes will
not be quite so homologous and this will interfere with recombination
and perhaps even with mitotic segregation.

This effect, if significant, makes it costly for an individual to
either gain or lose junk. If the population can be broken up into
inbreeding groups, there may be some selectable variation between
groups in the amount of junk carried, but there will also be a strong
tendency for the groups to become reproductively isolated and to
speciate.

3. Finally we are presuming that beneficial mutations arise more
frequently in high-junk individuals. But how do we model this?
Such a tendency, if it exists, is not an element of fitness for an
individual. Do these beneficial mutations come with an extra dose
of detrimental mutations as well, or does the magic only work for
good?

Maybe we should ignore the question of whether the junk leads to
benefit and simply try to model the notion that beneficial mutations,
however they arise, are frequently tightly linked to a batch of junk.
If this feature of linkage between junk and beneficial genes is
part of our model, and if junk is difficult to get rid of, then
we may see an increase in junk due to individual selection alone.

So much for the three forces. But we also have to consider various
mating systems. As a result of selective force #2, it would appear
that an increase (or decrease) in junk is most likely if the organism
is capable of hermaphroditic selfing or clonal reproduction, in addition
to normal two-parent sex. This allows new junk to drift to appreciable
frequencies in a subpopulation before having to face the issue of
mating back with the wild type.

My personal opinion: The presence of (and/or tolerance for) junk
played a big role in determining which microorganism species gave
rise to plants, animals, and fungi. But I have difficulty classifying
this "fact" about the biosphere's history as an instance of selection
at any level. Even if it is true that multicellular organisms can only
arise from a microorganism with lots of junk, that doesn't justify our
saying that that microorganism or its species was "more fit" or was
"favored by selection".




.

Relevant Pages

  • Re: Back in the good old days.
    ... a lot of that "95% junk" actually has a function. ... Put more succintly, certain random mutations are occasionally beneficial, and so subject to fixation by selection. ... Imagine you have a gene which (depending on which allele) turns ... But you want high fitness in your post-selection ...
    (talk.origins)
  • Re: Back in the good old days.
    ... lot of that "95% junk" actually has a function. ... certain random mutations (of which transposon ... to fixation by selection. ... Is the 'on' allele beneficial ...
    (talk.origins)
  • Re: Junk DNA: A hypothesis
    ... >> can help some deleterious genes form selfish cartels. ... But once again you are postulating selection for some future ... was that he was assuming that most junk consisted of pseudo-genes. ...
    (sci.bio.evolution)
  • Re: Back in the good old days.
    ... a lot of that "95% junk" actually has a function. ... Imagine you have a gene which (depending on which allele) turns ... But you want high fitness in your post-selection ... You have the group selection changing directions between generations, ...
    (talk.origins)
  • Re: Back in the good old days.
    ... lot of that "95% junk" actually has a function. ... serve a function for the organism that carries it. ... to fixation by selection. ... Is the 'on' allele beneficial ...
    (talk.origins)
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