Re: Cold water on micro-RNAs

In message <1183146025.092624.122580@xxxxxxxxxxxxxxxxxxxxxxxxxxx>, Vend <vend82@xxxxxxxxxxx> writes
On 29 Giu, 20:39, "Perplexed in Peoria" <jimmene...@xxxxxxxxxxxxx>
wrote:
<snip most>

I don't comment on the particular research you cited, but in general
the claim that most of our genome is junk strikes me as suspect.
There is a cost for replicating the genome, monotonically increasing
(perhaps linearly) with its length. Thus, if most of it was useless,
we would expect random deletions and natural selection to quickly
shrink it.

There are postulated, sequence-independent, uses for DNA. For example, it is argued that larger cells need more protein manufacture, and therefore more DNA transcription, requiring a larger nucleus to do all the RNA polymerisation, and that the easiest way of achieving a larger nucleus is to have more DNA. There's some statistical support for this idea, but I'm still skeptical. The direction of causation here is also ambiguous.

There are also possible explanations in terms of tuning the set of mutations that can occur.

However your prediction that mutation and selection would quickly dispose of junk DNA is not solidly based. One false assumption involved is that all junk DNA is passive.

In eukaryotes the cost of DNA replication is a relatively small part of the cell's energy and materials budget, compared to bacteria where the cost of DNA replication is significant and junk DNA is essentially absent.

Cellular organelles have much reduced genomes - not only mitochondria and plastids, but also nucleomorphs. Some microorganisms also have reduced genomes.

Because selection against junk DNA is weak, there is a balance between overall selection to eliminate junk DNA, and selection for bits of junk DNA which are good at getting themselves copied about the genome. Selection against inert junk isn't all that effective against active junk; perhaps there is instead an arms race between mobile genetic elements adapting to be copied more readily, and the rest of the genome evolving methods of stopping them being copied.


My guess is that most of the genome has some function, though possibly
only protein-coding, rna-coding and regulatory genes have a function
strictly dependant on the details of their nucleotide sequence.
Other parts of the genome could have a function dependent on their
size and coarse statistics and patterns.

Any theory on these lines has to explain the C-value paradox - the great variability in the amount of the size of the genomes of organisms. For example the cotton genus is though to be 5 to 10 million years old, but it has already evolved a greater than threefold variation in genome size; in fact some Australian diploid species have bigger genomes that the American tetraploid species.
--
alias Ernest Major

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Relevant Pages

  • Re: Non-Coding DNA preserved by genetic drift?
    ... > supersede natural selection as the dominant evolutionary force, ... > Junk DNA costs energy to duplicate and to carry around as part of each ... > were plotted against the species' total genome sizes. ... > population sizes, more genes, more junk DNA and longer-lived gene ...
    (sci.bio.evolution)
  • Re: Junk DNA: A hypothesis
    ... But once again you are postulating selection for some future ... >> individual know that it needs to store excess DNA in its genome because ... Junk DNA could just be junk that's there by accident. ... then it will be the case that the organisms we see today ...
    (sci.bio.evolution)
  • Re: Role of Junk DNA
    ... When researchers began mapping the genome, ... startled to find that humans have only 25,000 active genes. ... But researchers are now finding this junk DNA, ... by geneticists, may actually not be junk at all. ...
    (talk.origins)
  • Re: Junk DNA: A hypothesis
    ... I too dispute that modern organisms can select today for ... alleles that have no effect on their current fitness but which will ... My objection also applies at the level of the individual, the genome, ... the junk DNA. ...
    (sci.bio.evolution)
  • Re: Role of Junk DNA
    ... When researchers began mapping the genome, ... startled to find that humans have only 25,000 active genes. ... But researchers are now finding this junk DNA, ... by geneticists, may actually not be junk at all. ...
    (talk.origins)