Re: [asa] Re: "junk" DNA

Some good information on the history of the term Junk DNA (and its
evolution) can be found here:

http://genomicron.blogspot.com/2007/06/function-non-function-some-function.html

The origin of the term was found in pseudogenes

<quote>In 1972, Susumu Ohno coined the term "junk DNA". The idea did
not come from throwing his hands up and saying "we don't know what it
does so let's just assume it is useless and call it junk". He
developed the idea based on knowledge about a mechanism by which
non-coding DNA accumulates: the duplication and inactivation of genes.
"Junk DNA," as formulated by Ohno, referred to what we now call
pseudogenes, which are non-functional from a protein-coding standpoint
by definition. Nevertheless, a long list of possible functions for
non-coding DNA continued to be proposed in the scientific
literature.</quote>

And its conclusions

<quote>
To summarize,

    * Since the first discussions about DNA amount there have been
scientists who argued that most non-coding DNA is functional, others
who focused on mechanisms that could lead to more DNA in the absence
of function, and yet others who took a position somewhere in the
middle. This is still the situation now.
    * Lots of mechanisms are known that can increase the amount of DNA
in a genome: gene duplication and pseudogenization, duplicative
transposition, replication slippage, unequal crossing-over,
aneuploidy, and polyploidy. By themselves, these could lead to
increases in DNA content independent of benefits for the organism, or
even despite small detrimental impacts, which is why non-function is a
reasonable null hypothesis.
    * Evidence currently available suggests that about 5% of the human
genome is functional. The least conservative guesses put the possible
total at about 20%. The human genome is mid-sized for an animal, which
means that most likely a smaller percentage than this is functional in
other genomes. None of the discoveries suggest that all (or even more
than a minor percentage) of non-coding DNA is functional, and the
corollary is that there is indirect evidence that most of it is not.
    * Identification of function is done by evolutionary biologists
and genome researchers using an explicit evolutionary framework. One
of the best indications of function that we have for non-coding DNA is
to find parts of it conserved among species. This suggests that
changes to the sequence have been selected against over long stretches
of time because those regions play a significant role. Obviously you
can not talk about evolutionarily conserved DNA without evolutionary
change.
    * Examples of transposable elements acquiring function represent
co-option. This is the same phenomenon that is involved in the
evolution of complex features like eyes and flagella. In particular,
co-option of TEs appears to have happened in the evolution of the
vertebrate immune system. Again, this makes no sense in the absence of
an evolutionary scenario.
    * Most transposable elements do not appear to be functional at the
organism level. In humans, most are inactive molecular fossils. Some
are active, however, and can cause all manner of diseases through
their insertions. To repeat: some transposons are functional, some are
clearly deleterious, and most probably remain more or less neutral.
    * Any suggestions that all non-coding DNA is functional must
explain why an onion needs five times more of it than you do. So far,
none of the proposed unilateral functions has done this. It therefore
remains most reasonable to take a pluralistic approach in which only
some non-coding elements are functional for organisms.
</quote>

A very good article. Please remind me what ID has contributed to our
knowledge of 'junk DNA'?

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Received on Fri Jun 15 12:24:41 2007