Re: Junk DNA: A hypothesis

From: Perplexed in Peoria (jimmenegay_at_sbcglobal.net)
Date: 01/24/05 

Date: Sun, 23 Jan 2005 22:55:04 -0500 (EST)

"Larry Moran" <lamoran@bioinfo.med.utoronto.ca> wrote in message news:ct10r4$80h$1@darwin.ediacara.org...
> On Sat, 22 Jan 2005 13:01:49 -0500 (EST),
> Perplexed in Peoria <jimmenegay@sbcglobal.net> wrote:
> > "Larry Moran" <lamoran@bioinfo.med.utoronto.ca> wrote in
> > message news:csrihj$1ddt$1@darwin.ediacara.org...
> >> On Thu, 20 Jan 2005 23:53:54 -0500 (EST),
> >> Tim Tyler <tim@tt1lock.org> wrote:
>
> [snip]
>
> >> > Another theory is that introns decrease the probability of
> >> > crossovers occurring in the middle of functional genes - and
> >> > turn meiosis into more of a proper shuffle - rather than
> >> > a shuffle that rips cards apart and glues them together again.
> >>
> >> This one is dead wrong.
> >
> > It was certainly stated badly. The theory, as I understand it,
> > is that introns are frequently placed so as to separate
> > functional domains of a protein. As such, they *increase*
> > the probability of a crossover between domains, and thus
> > promote "evolvability" by increasing the likelihood that a
> > recombination event will produce something that is both
> > novel and useful (since the domains were preserved).
> >
> > Of course, Larry would probably reject this theory, because
> > he rejects (correctly, I think) the idea that evolvability
> > is an aspect of organism-level fitness.
>
> I reject the possibility that evolvability is an aspect of
> organism-level fitness but I'm quite comforatble with the idea
> that there are other levels of evolution.
>
> However, I also reject this particular idea because it's wrong.
> Introns do not separate regions that encode functional domains.
> That's a nasty little fact that has a significant effect on the
> theory.
>
> > Nonetheless, the theory was proposed by a (Canadian) heavyweight
> > theorist.
>
> Walter Gilbert is just about the only remaining scientists who clings
> to this old idea. The exons = domains idea is also associated with
> Russell Doolittle at UCSD. Introns early (a related idea) was proposed
> by Gilbert and Ford Doolittle, who works in Canada. The refutation of
> both introns early and exons = domains was done mostly in the lab of
> Ford Doolittle. He disproved his own theory. (Actually, it was mostly
> his post-docs and graduate students.)

Thanks. I do tend to get the two Doolittle's confused. (Same with
the two Ridley's). In fact, I didn't realize that there WERE two
Doolittle's until I read Ford's paper disproving aspects of Russell's
theory. Somehow, though, I had formed the impression that Russell
worked at Dalhousie. Probably because I thought that "introns early"
and "exons = domains" were being promoted by the same Doolittle.

> > [snip]
> >
> >> > We know that some evolution takes the form of duplication and
> >> > modification. Rapid elimination of unnecessary non-functional
> >> > genes might significantly hamper this process.
> >>
> >> It might. But once again you are postulating selection for some future
> >> possibility. In this case you suggest that junk DNA has to be kept
> >> around because it might become useful in the future. How does an
> >> individual know that it needs to store excess DNA in its genome because
> >> theres' a small chance that one of its descendants might find a use for
> >> it at some time in the far distant future?
> >
> > I am uncomfortable with this blanket condemnation of any "advantage"
> > that might accrue from keeping something around that might become
> > useful in the future.
>
> Fine. Explain how it might work.

What? Right now in sbe? And lose my chance to publish in JTB
instead? ;-)

> > Of course, the mechanism of natural selection is not intentional. But
> > if the cost of keeping something around is low, things will tend to
> > be kept around.
>
> Agreed. Junk DNA could just be junk that's there by accident.

Agreed. And it could become a "frozen accident" if, as some other
poster has pointed out, it is difficult to remove because it's
removal in one organism of a species might interfere with that
innovator's ability to recombine with its more cautious conspecifics.

> > And if some of those things that are kept around do eventually prove
> > to be useful, then it will be the case that the organisms we see today
> > have been less tidy housekeepers that some of the organisms that have
> > gone extinct.
>
> In other words. There was no selective advantage for either keeping
> junk DNA or getting rid of it and there's no reason to propose that
> the junk DNA currently in our chromosomes is there for a reason.
> Is that a good summary of your poisition?

Do I see the existence of junk DNA as a problem crying out for a
solution? Absolutely not. Your hypothesis that "junk is junk" is
a satisfactory solution to THAT problem.

However, nature is inventive and opportunistic. If junk is not
a problem that nature had to solve, then it may, in some cases,
be an opportunity that nature has exploited.

> > And thus we see something that can be characterized as selection
> > in favor of sloppy housekeeping.
>
> I don't agree. The presence or absence of junk DNA is not due to
> selection.

But I think that you said earlier that the relative absense of junk
in microorganisms is due to selection. So your disagreement must
apply only to larger organisms.

In the case of metazoa, I think that there is some small selective
pressure to remove the junk (for efficiency's sake) with a stronger
countervailing pressure to retain it due to the issue that carrying
a different pattern of junk than the rest of your breeding population
may hurt your fertility (or that of your children). We have a
classic case of frequency dependent selection (with negative
heterosis.)

So, I would expect that the following slogan would summarize the
situation. "Junk got here by accident, but once it arrives, it
tends to be maintained by the reproductive processes of the species".

Hmmm. But note the similarity to THIS slogan: "Mutated genes got
here by accident, but once they appear they are reproduced without
further distortion by the replication processes of the organism".

Gee. All we need now is an empirical observation that not all
patterns of accidental junk are equally "useful" and a "selection"
process which tends to eliminate the "unuseful" patterns of junk.
And that is what Gilbert and the Doolittles thought they had
until Ford's graduate students spoiled the fun. The theory
was sound, but they just had the facts wrong. Oh well!

> If, at some point in the future, a species will survive
> because it accidently got rid of its junk DNA does that mean there
> is selection for good housekeeping?
>
> > It is a wierd kind of selection - many generations of tiny negative
> > selection pressure, followed by a few generations of strong positive
> > selection pressure, but it is selection nonetheless.
>
> No it isn't. The reason why it's a weird kind of selection is because
> it depends on some future event that you can't predict. Right now you
> have no idea whether organisms with small genomes will be lucky in
> the future or organisms with large genomes will be lucky. It makes no
> sense to say that junk DNA isn't junk because you *think* that some
> descendant in the future might just possibly acquire a mutation in
> that junk DNA.

No, I'm NOT saying that junk is retained today because it might be
useful in the future. I am saying that junk exists today because it
turned out to be useful in the past. Not much difference from my genes
for breathing oxygen. Nature did not have to see into the future
and predict that oxygen would still be around today in order to
provide me with those genes.

There IS a bit of a difference, though. ALL of my ancestors for the
last billion years benefited from those oxygen-breathing genes.
But very few of my ancestors benefited from the junk. Only a few
very innovative ancestors, scattered here and there through the
tree, benefited from the junk. Those fortunate few benefitted
enormously. In fact, due to inbreeding, those few individuals appear
in a very large fraction of the branches of my tree.

I'm sorry, I have to stand by my original statement:
"It is a weird kind of selection, but it is selection nonetheless."

> > And it is a pattern of selection that seems to "see" farther into
> > the future than some more steady and gradual form of positive
> > selection.
>
> No. It's wishful thinking on the part of some people who are
> philosophically uncomfortable with the idea that we have junk DNA.
> They make up stories so they can feel good about being an adaptionist.

I think that your theory regarding subconscious motivation has some
validity. I hope it doesn't apply to me. One reason why it may
not apply is that I enthusiastically agree with you that "MOST
"junk" REALLY IS junk".

[snip remainder]

Relevant Pages

  • Re: Junk Dna!
    ... No selection. ... Of course you could not possibly see introns in this light if you ... Tell me something, Collin. ... According to the present model of selection and evolution, "junk ...
    (talk.origins)
  • Re: Shall we get rid of our junk?
    ... > [If there is a selective explanation for 'junk DNA', ... > those species that can tolerate large amounts of junk DNA. ... > nature is "designed" by natural selection then junk DNA is a big ...
    (sci.bio.evolution)
  • 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: Shall we get rid of our junk?
    ... >> [If there is a selective explanation for 'junk DNA', ... >> those species that can tolerate large amounts of junk DNA. ... >> of evolution may not be due to natural selection. ...
    (sci.bio.evolution)
  • 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)