Junk DNA

Ian A. York iayork at panix.com
Fri Apr 14 10:44:19 EST 2000


In article <38F72BFD.B993E32F at uoguelph.ca>,
Steve Scadding  <scadding at uoguelph.ca> wrote:
>
>Nature is extremely conservative and doesn't seem to carry forward much
>unnecessary baggage.  Remember the long lists of functionless vestigial
>organs that were generated in the latter part of the 19th century.  We
>now recognize that most of them have important functions.

I don't agree.  Nature *is* extremely conservative, and that's *why* we
carry forward so much unnecessary baggage.  I, for example, have hair on
my arms; that is almost certainly a functionless vestige of a furry
ancestor, not a finely-tuned sensory organ.  Starting with the assumption
that everything must be functional is what leads to the just-so stories
that armchair evolutionists put forth.

There are a great deal of evolutionary processes that happen without a
function, especially at the DNA level; the whole neutral mutation thing,
for example.

Similarly, there are a lot of things which are positively selected, which
are not intrinsically "functional".  Sexual selection, for example, is (at
least according to one major school of thought) based on intrinsically
meaningless criteria.

A lot of functions for "junk DNA" have been proposed.  The most recent
I've seen is that the physical size of DNA constrains the size of the
nucleus, and therefore the whole cell.  This argument claims that junk DNA
is there because it's the only way to make a big cell.  I find that a very
feeble argument, and it's typical of the arguments put forward for
functions--arguing in reverse, really.

A more convincing suggestion (at any rate, one I fund more convincing) is
that junk DNA is not merely junk, it's selfish DNA, parasitic DNA,
replicating itself with no benefit to to host.  That's very convincing for
the portion of junk DNA that carries reverse transcriptase motifs, for
example.  It doesn't necessarily explain everything.

A related argument was put forward in Science the other day (2000 Feb
11;287(5455):1060-2).  Here they note that DNA complexity is related to
the rate of DNA loss.  If you consider genome size (and amount of junk
DNA) as a balance between addition of new DNA, through reverse
transcription and gene duplication and polyploidy events and so on, and
DNA deletion, these guys suggest that the deciding factor is not addition
of new DNA, but removal of old; that is, even though there is pressure to
remove non-function DNA, the ability to do so varies widely, and
correlates with the presence of junk.  (They also present a couple of
indirect arguments that hint that junk really is junk, and
non-functional.)

Before I forget I want to comment on a couple of other questions from the
original post. The model organisms that have been sequenced so far don't
have nearly as much junk as human.  But that's because the genomes that
have been sequenced are from model organisms, selected for their
simplicity and compactness.  (Or are bacteria, which don't have much junk
anyway.)  In general, there's famously no correlation between an organisms
complexity and the size of its genome; this is known as "the C value
paradox".

The idea that adding junk will reduce the mutations that hit coding DNA is
wrong.  Making the genome longer will simply make more mutations; if you
make the genome ten times as long, there will be ten times as many
errors.  It doesn't help you that 9 of these errors hit junk; you still
have 1x the number of mutations hitting coding regions.

Ian 
-- 
    Ian York   (iayork at panix.com)  <http://www.panix.com/~iayork/>
    "-but as he was a York, I am rather inclined to suppose him a
     very respectable Man." -Jane Austen, The History of England




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