Ancient Viruses Buried in DNA | Hacker News Reader

Ancient Viruses Buried in DNA

nytimes.com

84 pointsgrzm33 comments

Credit H.G. Wells:

> By the toll of a billion deaths man has bought his birthright of the earth, and it is his against all comers; it would still be his were the Martians ten times as mighty as they are. For neither do men live nor die in vain.

Other species have chalked up a lot more deaths than that.

But they don’t write about it

Read 'Darwin's Radio' by Greg Bear.

First heard of this from Frank Ryans book Virolution. It explains a lot of what had been termed junk DNA previously.

Excellent book. It made the subject so readily accessible to the layman.

And yet it doesn't shy away from the details. One of the main things I took away was how symbiosis could be the driving force behind evolution instead of purely the traditional competitive based changes.

I've not heard of that book before but will have to check it out. Did it happen to mention any of the experimental research done showing that removal of 'junk DNA' makes organisms (microorganisms anyway) less capable of adapting to environmental change? As I remember it, some researchers took a bacteria (probably e. coli, that's usually the easiest to do this sort of thing with but I'm not certain) and separated out two populations. In one they let it be, and in the other they stripped out all 'junk' DNA that didn't play a role in protein synthesis. Then they introduced harsh conditions to both (I think something like high acidity or low availability of food or something like that) and while the 'junky' population adapted relatively quickly, the 'pure' population quickly died off and wasn't able to gain beneficial mutations quickly enough to survive.

I'm not sure if junk DNA was covered directly in the book. It may of been a radio interview about the book where I heard junk DNA discussed. From what I remember a large portion of say our DNA was not understood so was considered junk but old viruses assimilated into our DNA could make up as much as 40% of us. The assimilated DNA could then act like a defence so removing it would be bad.

And there is another line of thought.

Bacteria's pay dearly for each extra bit of DNA they carry, since the energy cost of DNA replication is linear with respect to the length.

Bacteria's with less DNA can replicate more quickly and thus outcompete other bacterias.

The fact that after so many generations they still carry that "junk" which they pay for suggests it really is useful in one way or another.

No, most of the viral junk DNA is just repeating copies of non-coding regions (Alu and other repeats). This is an example of an actual coding gene from a virus, which is much more rare and sporadic.

So can genes transfer between species via viruses? Is that why our features are similar to pigs?

Inter-specicies bacteria DNA transfer can happen, which is freaky.

https://en.wikipedia.org/wiki/Horizontal_gene_transfer

Eugene M McCarthy came up with a different hypothesis for that, which is quite humorous but not obviously false.

As has been answered before, we know for a fact that gene transfer exists between species, we just do not know for sure how it happens (as it is certainly a very rare event). Potential candidates are extracellular RNAs, intracellular bacteria as vehicle and last but not least transfer via virusses.

On the other hand, our features are not particular similar to pigs, its just that pigs are similar sized mamalian omnivors (ergo similar inner organs) and can be bred well.

I suspect a close examination of the pig's genome would also be a remarkably multifaceted demonstration of the DNA evidence for evolution.

Two minute introduction: life is largely built out of proteins, which are chains of amino acids (small organic molecules) which "fold" into interesting shapes and interact with each other in interesting ways. Our DNA is a set of blueprints for making a suite of proteins that builds us.

One of the curiosities in our DNA is that multiple sequences can code for the same amino acid in a protein. It doesn't matter how it's coded in your DNA, the protein still functions the same way. So one piece of evidence in favor of evolution is that most organisms share a common DNA sequence for common proteins, even though there are potentially millions (or more!) of different sequences which would code for the same protein.

So if humans and pigs have evolved any of the same proteins since they diverged millions of years ago, you should also expect them to be coded for in "more different" ways than if they were evolved in a common ancestor.

(You wouldn't expect the coding for the proteins to be completely different, since they probably evolved from a protein shared by the common ancestors.)

Thank you for that explanation!

Similarity is more easily explained with convergent evolution: https://en.wikipedia.org/wiki/Convergent_evolution

I thought these foreign viruses become part of our DNA which we pass down from generation to generation.

It isn't buried in our dna rather inserted into it and become part of our dna.

I read a previous article years ago that argued certain traits (mental illness, risk-taking, etc.) could be the result of viruses that successfully joined the human genome via the reproductive organs.

This area of study could end up pretty interesting.

I don’t think it makes a difference though if the genetic changes happen via happenstance (cosmic radiation, etc) or via infiltration due to viruses, etc, does it? Isn’t it all one and the same to evolution?

Yep. A DNA sequence is a DNA sequence. Once it has successfully installed itself into your genome it doesn't matter where it came from. There's no revision control in DNA.

I don't think it is the same. Virus DNA has the purpose of making more Virus, it has function and structure, not just overwriting with randomness.

Was the hypothesis only argued for negative traits? I don't see any particular reason why traits we find distasteful today, and only those, are blamed on ancient viruses.

The article mentions both. While random mutations are more likely to be negative than positive, selection pressure means that older changes are more likely to be neutral or positive if they remain.

Acquisition of the RAG proteins responsible for generating the diversity of your immune system's B and T cell repertoire (allowing you to develop defenses to microbes you have never seen before) may be the result of a herpes virus inserting itself into germ line cells of our ancestors (likely sea lamprey or sea urchin).

In short, without viruses we wouldn't be able to defend ourselves against viruses (and other pathogens).

Source: http://journals.plos.org/plosone/article?id=10.1371/journal....

PDF: https://www.pdf-archive.com/2017/10/06/journal-pone-0005778/

They probably play a part in Schizophrenia http://discovermagazine.com/2010/jun/03-the-insanity-virus

DNA is the world's oldest blockchain

DNA is the opposite of immutable

Does your DNA change day to day?

Your DNA is like a datacenter with a billion nodes that all start out with the same content in DRAM. Although error correction can compensate for most bit flips, at this scale you still get a really low mean time between failures, leading to differing memory contents over time.

According to Wikipedia, "In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day."

There are mechanisms to repair this damage, but they don't always work. Sometimes the result is cancer.

An excerpt from my genetics professor:

"Even in the absence of mutagens, an average gene will mutate about once in a million generations. ~10^16 cell divisions occur in a typical life span so somewhere in cells that are part of you each of your genes has mutated 10^10 times (hence cancer)."

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