[ExI] Tim May and DNA

[Stuart LaForge]

Quoting John Clark:

> True, but there is reason to think much of the genome really is  
> nothing but parasitical junk at least from our point of view; after  
> all the entire point of Evolution is to get genes duplicated and our  
> phenotype, aka our bodies, are just a means to that end. And the  
> fact that some very commonplace looking creatures can have a huge  
> genome gives support to the idea that there must be a lot of junk in  
> genomes.
> The human genome has about 3 billion base pairs but a
> Mexican salamander called a Axolotl has 32 billion base pairs, the  
> marbled lungfish has 130 billion base pairs, and a humdrum looking  
> Japanese flowering plant called Paris japonica has 150 base pairs,  
> 50 times the size of the human genome. It's hard to believe that  
> little bush or the body of a  lungfish is inherently more complex  
> than a human even if its genome is.

Yes, the C-value enigma still does not have a widely accepted  
solution. Even two related species in the same genus can differ wildly  
in the amount of DNA they have. Much of the controversy stems from the  
nuances of what constitutes "function" in biology.

If you look at what percentage of the human genome is conserved across  
different individuals, then it is only 20% of the genome. One can  
safely assume that that 20% encodes vital functions that have been  
selected for as being necessary for survival and the other 80%, aside  
from the tiny fraction which accounts for phenotypic differences  
between individuals, could be thought of as parasitical junk.

On the other hand, studies like the ENCODE project have found that if  
one defines function as binding to proteins found in the nucleus or  
being chemically modified, then 80% is functional and only 20%  
completely lacks a function.

So much depends on how you define function but in the end, one does  
have a lot of extra DNA lying around in eukaryotic cells. Some  
important caveats however to the notion of junk DNA is that redundancy  
and mutation are the engines of evolutionary adaptation. The so called  
junk DNA varies widely between individuals because there is no  
selective pressure to conserve those sequences and so those sequences  
are free to silently mutate. Similarly if you have a redundant copy of  
a necessary gene, you can safely modify the copy without disrupting  
the function of the original.

So perhaps junk DNA is what a programmer would call a "sandbox" where  
nature is free to experiment and innovate without disrupting crucial  
functions. I guess I am ok with the term junk DNA as long as one  
distinguishes between junk and trash. Trash is stuff you throw out  
while junk is stuff you keep because you hope to find a use for it  
someday.

Stuart LaForge