Human DNA is >50% Virus DNA?!

Mr. Scott

Under the Amazing One's Wing
Mr. Scott
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This amazing New York Times article of 1/8/2007 is not just a superb summary of the history of the virus over the last 4 billion years, but also makes the astonishing claim that more than 50% of human DNA was in fact planted in our genome by viruses, and that has been a rich source of raw material for the mutations to create new genes, ergo, critical to the processes that evolved us!

...viruses have not only taken; they have also repaid us in ways we are just beginning to tally. “Viral elements are a large part of the genetic material of almost all organisms,” said Dr. Sharp, who won a Nobel Prize for elucidating details of our genetic code. Base for nucleic base, he said, “we humans are well over 50 percent viral.”

Scientists initially dismissed the viral elements in our chromosomes as so much tagalong “junk DNA.” But more recently some researchers have proposed that higher organisms have in fact co-opted viral genes and reworked them into the source code for major biological innovations, according to Luis P. Villarreal, director of the Center for Virus Research at the University of California, Irvine.

Some genes involved in the growth of the mammalian placenta, for example, have a distinctly viral character, as do genes underlying the recombinant powers of our adaptive immune system — precisely the part that helps us fight off viruses.
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linkola
 
I thought it was much more than 50%.

One thing to bear in mind is that most (>97%?) human DNA is inactive, in the sense that it doesn't code for proteins that are ever actually produced. It used to be thought of as junk with no function, but I think the view now is that it may play an important role in regulating which genes are active (for example by changing the shape of the DNA molecule).
 
So we're made from viruses?

Thank goodness they didn't invent vaccines for us. But I'd love to be able to have a vaccine to keep my Inlaws from visiting so often.
 
Paul said:
But remember, folks, mutation cannot increase the information content of a genome.
rolleyes.gif
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Oh but it does Paul, your own computer model shows how it occurs. But it is profoundly slow for anything other than a single selection condition targeting a single gene. You know it’s due to the Rcapacity affect.
rolleyes.gif
 
Kleinman said:
Oh but it does Paul, your own computer model shows how it occurs.
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Except that my own computer model does not include gene transfer from viruses. So I guess you're screwed.

~~ Paul
 
Kleinman said:
Oh but it does Paul, your own computer model shows how it occurs.
Paul said:
Except that my own computer model does not include gene transfer from viruses. So I guess you're screwed.
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I like the question Magic 9-Ball posted:
Magic 9-Ball said:
So we're made from viruses?
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The only thing screwed here is your theory of evolution by the mutation and selection sorting/optimization process. Your Rcapacity concept confirms it. You evolutionists keep working on the theory of evolution by viral genome transfers. Next time I treat a patient for shingles, I’ll tell them they are advancing evolutionarily.

Maybe you can explain this little problem in your hot off the press theory of evolution. How does a viral infection in a somatic cell get transferred to a germ cell?
 
Mr. Scott said:
This amazing New York Times article of 1/8/2007 is not just a superb summary of the history of the virus over the last 4 billion years, but also makes the astonishing claim that more than 50% of human DNA was in fact planted in our genome by viruses, and that has been a rich source of raw material for the mutations to create new genes, ergo, critical to the processes that evolved us!



linkola
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Not exactly a news flash.

Barbara McClintock won a Nobel for this in 1983.

The relationship between viral genomes and junk DNA was my PhD thesis in the mid-'90s.

I think the percentage is entirely unknown. It's also probable that they're including retrotransposons in this estimate, which are merely self-replicating DNA segments that cause repeater junk DNA like ALU. They have retrovirus properties, but probably evolved in isolation within the genome.

The other problem is that the directionality is not understood: did the viruses implant themselves into our genome, or did self-replicating parts of our genome escape as viruses?
 
Good god, Kleinman. Your "Evolution is bull" thoery doesn't cut it. That's already been well documented enough in many other posts. If you want to revive that discussion, please take it to the posts already in progress. We are all still waiting on your math, you know. You know, the math you said you could use to prove evolution is impossible.
 
Well, it would be strewn across the entire biological history of life. It's not like it all suddenly happened since Korg: 70,000 BC was walking around.

I remember being mildly disturbed upon realizing:

1. Being multicellular animals meant we were a specialized multi-cell colony. Just a fancy mat of bacteria.

2. That the mitochondria were almost certainly captured cells themselves that are now highly evolved as symbiotes. Even each cell isn't "you", per se.


In any case, I would submit virus infusion is still a distant second to sexual reproduction in scouring the gradient descent space of evolution, though it probably exceeds random mutation and stray cosmic rays or neutron strikes.
 
INRM said:
Okay I'm confused... cells created viruses?

INRM
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Pieces of DNA and RNA are transferred by a number of different mechanisms between organisms besides through sexual recombinations. I'm not sure one would just take a chunk of genome sequence and it would contain all the sequences needed to self replicate and spread to other organisms. My guess would be various sequences in the organisms' genome would be incorporated into an existing replicating framework.

In other words, genetic material is flowing all over the place. It flows in and out of organisms via a number of mechanisms. So it makes sense that certain genome segments which were likely to interact with specific organisms because they originated in those organisms could end up incorporated into viral replicators that then in turn used that organism's cellular machinery to replicate. The result would be a virus which was a sort of spawn from the organism initially but becomes an infectious virus operating externally.

This is, of course, entirely speculation on my part. In fact, I just now thought it up reading this thread. ;)


Some basic reading on lateral gene transfer:

Horizontal or lateral gene transfer

Lateral gene transfer and the nature of
bacterial innovation

Heat shock protein 60 sequence comparisons: Duplications, lateral transfer, and mitochondrial evolution

Microbial species 2: recombination
 
INRM said:
Okay I'm confused... cells created viruses?
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Not as a kingdom, but individual viruses could be new, containing host genome by accident instead of the original infection's genome. This is especially likely if there's retrotransposon dna floating around in the nucleus.
 
blutoski said:
Not as a kingdom, but individual viruses could be new, containing host genome by accident instead of the original infection's genome. This is especially likely if there's retrotransposon dna floating around in the nucleus.
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Originally, PERHAPS as a kingdom.

I believe it is likely that the virus came from a strand of naked DNA that escaped from a bacillus that was destroyed in some way, perhaps by over-replication of that bit of mutated DNA. Over time, further mutations brought forth the nucleocapsid and finally the proper virus. Of course conditions would have to be ideal, but there is deep time here.
 
Mr. Scott said:
How with this done before we had DNA sequencing?
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Just to add to bluto's post, DNA sequencing began in 1975 according to this summary. What changed and what I think has you confused was PCR lab technology and the science of bioinformatics (essentially computer programs that perform biology science data analysis) were more recent developments which have allowed an explosion in data analysis of genomes including sequencing entire genomes of a number of species.
 
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