Re: Junk DNA: A hypothesis

From: Larry Moran (lamoran_at_bioinfo.med.utoronto.ca)
Date: 01/24/05 

Date: Sun, 23 Jan 2005 22:55:01 -0500 (EST)

On Sun, 23 Jan 2005 15:18:35 -0500 (EST),
Tim Tyler <tim@tt1lock.org> wrote:
> Perplexed in Peoria <jimmenegay@sbcglobal.net> wrote or quoted:
>> "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:
>> > > jeffp <jeff@brilliantwebsites.com.au> wrote or quoted:
>
>> > >> Could it be that the junk DNA is a library of spare parts...a
>> > >> warehouse of previously resolved problems awaiting the next eon
>> > >> when its re-expression might be of value?
>> > >
>> > > [...]
>> > >
>> > >> Maybe this is something that has been raised and possibly even
>> > >> rejected before...but given that I've never seen it before, I
>> > >> thought I'd come to some people who would know. Any comments or
>> > >> references to pre-existing work?
>> > >
>> > > There are dozens of theories of possible "functions" of "junk"
>> > > DNA.
>> >
>> > Indeed there are. Let's see if any of them make sense ....
>> >
>> > > Junk DNA affects linkage - and the probability that genes are
>> > > split during meiosis - and if that probability is small it
>> > > can help some deleterious genes form selfish cartels.
>> >
>> > This one doesn't make any sense.
>>
>> Doesn't make sense to me either.
>
> Neither of you know what I mean?
>
> A hypothetical example:
>
> There are two alleles at different loci on the X chromosome
> that - when expressed together - act together to sterilise
> all male offspring.

You can't have two *alleles* at different loci. Alleles, by definition,
are variants of a single gene at a single locus.

What you mean is that there are two genes A and B at different loci.
Each gene has two alleles (e.g. A1, A2 and B1, B2). I think what you're
trying to say is that the combination A1 + B1 on a single chromosome
has some effect that isn't seen when the two alleles are on different
chromosomes. If that's what you're trying to say, please re-work your
example so that it makes sense.

Start with this genotype ....

                   A1 B1
                ------------------- X xhromosome

                   A2 B2
                ------------------- other X chromosome

or whatever combination you need to make your point.

When you get recombination you will end up with ......

                   A1 B2
                ------------------- X xhromosome

                   A2 B1
                ------------------- other X chromosome

You need to explain why these combinations have a different phenotype
and why it would be selectively advantageous to increase the frequency
at which they are shuffled.

Then you have to explain why there would be selection for increasing the
total amount of junk DNA in the entire genome rather than just moving
these genes to opposite ends of the X chromosome or to different
chromosomes. As an extra bonus, it would be nice if you could give an
example of any two *genes* that act like this.

The easiest way to minimize linkage disequilibrium is to put the two
genes on different chromosomes.

Larry Moran

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