Re: Junk DNA: A hypothesis

From: Tim Tyler (tim_at_tt1lock.org)
Date: 01/25/05 

Date: Tue, 25 Jan 2005 00:23:02 -0500 (EST)

Larry Moran <lamoran@bioinfo.med.utoronto.ca> wrote or quoted:
> On Sun, 23 Jan 2005 22:54:59 -0500 (EST),
> Tim Tyler <tim@tt1lock.org> wrote:
> > Larry Moran <lamoran@bioinfo.med.utoronto.ca> wrote or quoted:
> >> Tim Tyler <tim@tt1lock.org> wrote:

> >> > It seems to me that a useful approach would be deliberately excising
> >> > the "junk" DNA from small organisms and seeing how they fare over an
> >> > extended period in comparison with wild-types.
> >>
> >> That's a difficult experiment. However, we can examine very
> >> closely related species, like frogs and some plants, that
> >> differ by several- fold in the amount of DNA they have.
> >> The amount of DNA doesn't seem matter. How do you explain that?
> >
> > Most likely selective forces acting on junk DNA are weak.
>
> In other words, the evidence suggests that junk DNA is really junk?

Selective forces being weak and them not being responsible for adaptations
is not the same thing. What qualifies as selection which is so weak
as to be ineffectual depends on the effective population size - and
in large populations, even very weak selective forces can have
dramatic long-term effects.

> >> >> This seems to be mostly computer scientists discussing biology. I
> >> >> didn't see anything there that's worth remembering. Perhaps you could
> >> >> summarize their very best argument for the selective advantage of
> >> >> excess genomic DNA?
> >> >
> >> > I don't know if I'm competent to judge that.
> >>
> >> Then why did you post a summary of this nonsense?
> >
> > That's a leading question - on the same lines as
> > "have you stopped beating your wife yet" :-|
> >
> > What I posted was not nonsense - so your question's
> > premise is mistaken.
>
> It looked like mostly nonsense to me. I think it's quite legitimate to
> ask why you would post it if you didn't believe it.

I don't believe *anything* I post. Indeed, I don't have any beliefs:
all my opinions are subject to occasional review.

> >> Tell me about the "neutral net" theory. It looks like techno-babble
> >> to me but I assume you see something that I don't. Why do you think
> >> it's a "good" hypothesis?
> >
> > The "neutral network" theory deals with the question of how systems
> > can escape from local maxima.

[snip A brief description of what neutral networks are]

> > - http://chat.carleton.ca/~tcstewar/papers/extrema.html
> >
> > Neutral networks are areas where many mutations are nearly
> > neutral - and much variation can exist without being
> > selected against.
> >
> > Introns and junk DNA can both create neutral networks. In both
> > cases do so mainly by facilitating the action of mutations
> > involving repositioning start/stop codons. If genes are
> > jammed next to each other, there's reduced scope for such
> > mutations to do anything interesting. If there's space
> > at each end of an allele and it is broken in the middle,
> > such mutations have more room to provide interesting
> > variation.
>
> Let's see if I understand the neutral network theory ....
>
> An organism will accumulate and maintain ten times more DNA in its
> genome than it requires because there's a chance that one of its 30,000
> genes might, at some unpredictable time in the future, acquire a mutation
> in its stop codon that leads to a longer polypeptide.
>
> This excess DNA will persist for thousands of generations in hundreds
> of species without any obvious benefit but we can't call it junk because,
> who knows, some of it might possibly become useful in the future. Is that a
> good summary of how the neutral network theory challenges the concept of
> junk DNA?

That seems rather rhetorical ;-)

To start with, I'm *only* attempting to identify the selective forces
that favour not eliminating junk DNA. I wouldn't claim that any
particular theory is /so/ effective that it outweighs all junk DNA's
costs. I haven't attempted to quantify all the effects involved -
and I don't think all their respective strengths are known.

I *do* think evolvability is important. It is important in the
short term primarily because of pathogens. Junk DNA may well
make a positive contribution to evolvability - and that may
contribute significantly to hindering mechanisms that eliminate
it from arising.

Selection can eliminate junk DNA quickly enough when it needs to:

``Furthermore, the present lack of significant amounts of nucleomorph
  secondary DNA confirms that selection can readily eliminate functionless
  nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA.''

 - http://calorierestriction.org/pmid/?n=10902541 

-- 
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Relevant Pages

  • Re: Junk DNA: A hypothesis
    ... > explanation for junk DNA? ... Most likely selective forces acting on junk DNA are weak. ... great number of mutations, which do not affect the fitness ... Neutral networks are areas where many mutations are nearly ...
    (sci.bio.evolution)
  • Re: Junk DNA: A hypothesis
    ... >> explanation for junk DNA? ... > great number of mutations, which do not affect the fitness ... > Neutral networks are areas where many mutations are nearly ... Let's see if I understand the neutral network theory ...
    (sci.bio.evolution)
  • Re: Junk DNA: A hypothesis
    ... Likely negative selective forces ... Junk DNA has a metabolic cost. ... such as disease-restance genes. ... Junk DNA can act as a sponge for intracellular mutagens ...
    (sci.bio.evolution)
  • Re: Primes in DNA (was: Definition Challenge)
    ... this is not really about mutations. ... The alleged "junk DNA" is not necessarily junk. ... generation of bacteria had a pump to remove excess sulfur. ... I meant "simple" repeats, like TTTTAAAATTTTAAAA. ...
    (talk.origins)
  • Re: Get your New Junk here!
    ... On the one hand organisms "wish" to reduce the number of detrimental mutations, which means that there is pressure to improve DNA proof-reading and repair, to the point where the cost of the mutations equals the cost of the proofreading and repair mechanisms. ... On the other hand organisms "wish" to increase the number of beneficial mutations, and in particular "wish" there to be sufficient beneficial mutations to track environmental changes, or keep up in intraspecific or interspecific arms races. ... If say, transposon activity, has a different ratio for these categories from say, point mutations, then increasing the amount of transposon activity (and hence junk DNA) might be beneficial. ...
    (talk.origins)