[ExI] Tim May and DNA

[Stuart LaForge]

Quoting John Clark:

>  On Fri, Feb 8, 2019 at 12:31 PM Stuart LaForge <avant at sollegro.com> wrote:
>> If you look at what percentage of the human genome is conserved across 
>> different individuals, then it is only 20% of the genome.
>
> I don't know where you got that figure, with the exception of the  
> cheetah there is very little genetic diversity among humans compared  
> with other mammals, "All human beings are 99.9 percent identical in  
> their genetic makeup":
> https://www.genome.gov/19016904/faq-about-genetic-and-genomic-science/

Right, that conserved 20% is 99.9%  identical between individuals.  
That is what "conserved" means in this context. When I was in grad  
school, it was generally accepted that 80% was junk and 20% was  
conserved. I got 20% because 100% - 80% = 20%. The point is that the  
differences in the DNA between any two random randomly chosen  
individuals is likely to reside almost entirely in the junk portion of  
their DNA.

> And "about 60 percent of genes are conserved between fruit flies and humans"
> https://www.genome.gov/11509542/comparative-genomics-fact-sheet/
> But of course only about 1.5% of our genome encodes for genes, that  
> is to say encodes for proteins. 

Right again. 60% of the 1.5% of the human genome that encodes genes is  
identical to the whatever percentage of the fly genome encodes for  
genes. What are we disagreeing on here?

> http://blogs.discovermagazine.com/notrocketscience/2012/09/05/encode-the-rough-guide-to-the-human-genome/#.XF3Ey89KjUI  

This reference that you linked to upgrades my 20% figure to 25% based  
on the ENCODE project that I mentioned earlier. Although the original  
ENCODE study listed it as much higher at 80% being functional and only  
20% being junk. Since then several papers were written contesting the  
ENCODE study's claim. Why are you quibbling over percentages with me  
when the people actually doing the research can't agree? Every few  
months somebody comes up with a slightly different percentage based on  
their definition of "functional".

>> 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.
>
> If there is no selective pressure then they can't have a function,  
> and if they're full of mutations (and they are) then they would be  
> very poor backups.

They are not backups; they are more like scratch-paper to explore DNA  
sequence-space without penalty. Or you could think of them as a  
mutational buffer that absorbs mutations that would be otherwise  
harmful i.e. places where it is safe for the genetic recombination  
machinery to cut and paste DNA without damaging functional regions.

>> 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.
>
>> If can think of any experimental evidence or theoretical  
>> consideration that would lead me to conclude that very large parts  
>> of out genome is utterly worthless pure trash or even in some  
>> circumstances detrimental.

If there is no selective pressure, then they can't be "detrimental".  
They are neutral and DNA replication (as long as it is regulated) is  
relatively cheap. At worst they are like spandrels.

> Doctors want to transplant pig organs into humans but there is a  
> problem, in 25 different places in a pig's genome there are places  
> where retroviruses have inserted their genome into the pigs genome,  
> and that could be dangerous if  a organs like that were inside a  
> human. But about a year ago scientists used CRISPER gene editing to  
> get rid of those viral DNA segments and produced healthy pigs:
> https://www.sciencemag.org/news/2017/08/crispr-slices-virus-genes-out-pigs-will-it-make-organ-transplants-humans-safer?r3f_986=https://www.google.com/  

The pig endogenous retroviruses weren't harming the pig. As long as  
they do not harm their hosts, retroviruses and transposons can be  
agents of evolutionary change through horizontal gene transfer. If  
their presence aids survival, then they are selected for and if they  
are harmful, then they are selected against. If neither, then they are  
simply carried forward into the next generation with the rest of the  
genome, no harm no foul.

https://www.sciencedaily.com/releases/2014/12/141218141057.htm

Stuart LaForge