Michael Coyne (mcoyne at argo.net) wrote:
: Agschultz wrote:
: >
: > On October 6, 1995, Mary Kuhner writes,
: >
: > > In many organisms another substantial portion of the junk (DNA) consists
: > of
: > > thousands of copies of sequences which have the ability to duplicate
: > > themselves. These may or may not be useful in some way to the organism;
: > > they could survive even if they are not useful, as a sort of genetic
: > > parasite, because of that copying ability.
: Okay, now I'm confused. By what critera is DNA classified as "junk"? I would
: have assumed that junk DNA would imply DNA which, when examined at the sequence
: level, shows no evidence of a function.
Your confusion is understandable; there is no rigorous definition of
"junk" DNA. Nor is there any trivial way to prove that a segment
of DNA does not have biological function -- the label "junk DNA"
is as much (or more) an expression of our ignorance than a useful
definition.
: Even this is not enough of a
: definition, since many (most?) eucaryotic genes have exons,
: which are "useless"
Definition point: you have things backwards:
INtrons are INbetween the EXpressed EXons.
: bits of DNA (in as much as they don't code for anything) but still perform a
: vital function as "spacers", if you will. DNA which has the ability to
: duplicate itself (presumably unlinked to the replication of the chromosome)
: must therefore have some genes and therefore is not junk. How does this DNA
: duplicate itself (most DNA codes for proteins, which in turn do the work)? If
: these pieces of DNA excise themselves and form replicons which then
: re-integrate into the chromosome, they are behaving much like plasmids or
: viruses, and therefore probably were introduced to the genome by outside
: acquision. These pieces of DNA could be integrated viruses or plasmids, and
: could serve as a source of plasticity to the genome by adding a mechanism of
: introducing mutations.
Things frequently labeled as junk (not necessarily non-overlapping categories):
introns
dead retroviruses
pseudogenes (relics of genes with obvious defects)
transposons (retro- and DNA-based)
simple sequence repeats (e.g. (CAG)20 )
Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
robison at mito.harvard.edu
