
Ancient Viruses Are Buried in Our DNA (2017) - bookofjoe
https://www.nytimes.com/2017/10/04/science/ancient-viruses-dna-genome.html
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memebox3f
Here's a thought. Perhaps viruses are picking up DNA from host organisms and
transmitting them to new hosts as they pass from one to the next. Viruses that
transmit advantageous DNA will survive in our genome. Viral DNA can be
particularly useful when it has an impact on the morphological development of
an organism, i.e. as it is developing from an embryo. If this is true it is
not surprising that we find a lot of activation of retro viruses during
embryonic development.

This also provides us a clue about how cancer develops. These retro viruses
are associated with the changing of form and function of the cell within which
they are contained, since they impact this within the development of the
embryo. When they are activated within adult cells they drive similar
functional changes. Which might be why many cancers, seem, to me, to look like
distinct entities, like the tissue has suddenly switched to a different
functional mode. It's not just one characteristic of the tissue that has
changed to make it dangerous, but a whole constellation of changes that
together seem to form a unified whole. I.e. we are looking at groups of
changes transported into the genome by a virus that has propagated because
those changes are advantageous to the host organism. These changes do not
suddenly arise within the body due selection pressures on the tissue, but are
activated and mediated by the virus.

This kind of cross species transportation of DNA, could well be analogous to
what we see at the microbial level, where horizontal gene transfer is an
important driver of evolution.

~~~
fifnir
> activation of retro viruses during embryonic development.

Citation on this? As far as I know (am writing a phd thesis on development++),
there's nothing like "virus activation". Viral elements (mostly transposons)
are big evolutionary players but are usually actively repressed by DNA
methylation (in eucaryots).

> Which might be why many cancers, seem, to me, to look like distinct
> entities, like the tissue has suddenly switched to a different functional
> mode.

I don't 100% understand your comments about viruses here, but related to this,
we don't need to imagine some virus orchestrating such a thing (besides, as
far as I know they are way too simple to drive complex eucaryot gene
regulation), but rather gene regulatory networks which if they get unbalanced
can lead to significant changes in morphology.

<edit> some spelling

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memebox3f
"The early embryo is a hotbed of activity for endogenous retroviruses, recent
studies have shown. To understand why embryonic cells make viral proteins,
scientists have run experiments to see what happens when viral genes are
silenced.

These experiments suggest that viral proteins help the embryo develop a
variety of tissues. "

From the op article.

I'm am not an expert in this at all, these are just my thoughts on the matter,
take them or leave them.

Regarding regulatory networks binding together elements so as to orchestrate
changes in morphology - I had not thought about this, of course you are
correct. Where you say that the viruses are too simple to drive sufficiently
complex changes to the regulatory networks, I would counter by saying that
chance mutations are sufficient to drive these changes.

~~~
fifnir
We have a LOT of "appropriated" viral code in our own DNA: "Reverse-
transcribed RNA molecules compose a significant portion of the human genome.
Many of these RNA molecules were retrovirus genomes either infecting germline
cells or having done so in a previous generation but retaining transcriptional
activity. This mechanism itself accounts for a quarter of the genomic sequence
information of mammals for which there is data."[1]

But that they are now part of us and when they are activated it's not some
virus waking up but parts of viruses that we have adapted into doing useful
things for out cells.

Viruses can cause significant changes in gene networks (for example
oncoviruses usually suppress tumor-suppressing proteins [2] which dramatically
affects things downstream), but the changes are not as holistic as I think you
are describing them.

Yes point mutations (and viruses) can derail neural networks and that can have
far-reaching consequences, but I think these things are accidental in both
cases and not some virus plan as I felt you were arguing.

[1]
[https://www.sciencedirect.com/science/article/pii/S136952741...](https://www.sciencedirect.com/science/article/pii/S1369527416300170)
[2]
[https://en.wikipedia.org/wiki/Oncovirus](https://en.wikipedia.org/wiki/Oncovirus)

~~~
memebox3f
You are probably right. You know far more than I, but I do have a knack for
seeing paradigm shifts coming. Take that as you will, I can't prove it, it's
just personal experience. Just try to remember, if this all unravels in favor
of my position, that you talked to some guy on the internet who saw it coming.
It's getting pretty annoying having called it ahead of time, and no one
remembering or caring that I said anything.

~~~
tomjakubowski
I'll bite: could you cite some instances of real paradigm shifts that you have
previously predicted in public?

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_bspline
Are ancient alien viruses buried in your DNA? Tonight on History Channel...

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magduf
That extra genetic code isn't ancient alien viruses. It's part of a message
from our forebearers, which has to be combined with genetic code from other
alien races in this quadrant.

There was a ST:TNG episode about this.

~~~
icanhackit
I vaguely remember this episode and want to rewatch it. Do you know what the
name or episode#/season it was?

~~~
magduf
[https://en.wikipedia.org/wiki/The_Chase_(Star_Trek:_The_Next...](https://en.wikipedia.org/wiki/The_Chase_\(Star_Trek:_The_Next_Generation\))

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kristiandupont
Legacy code.. It's everywhere!

~~~
amelius
Yeah and we're still using the same ancient language.

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ziyao_w
Haven't quite finished the article and know nothing about biology but sounds
similar to the novel Darwin's Radio
([https://en.wikipedia.org/wiki/Darwin%27s_Radio](https://en.wikipedia.org/wiki/Darwin%27s_Radio)).

Very interesting novel and unlike a lot of comments on the web I found it a
really engaging read.

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subcosmos
The endogenous retrovirus story is getting quite interesting, particularly in
dementia. Some of the top genes associated with brain atrophy appear to be
genes important for suppressing retroviral activity. See FUS and TDP43.

There is an increasing body of work in the literature showing that activation
of endogenous retroviruses occurs as cells become aged. In many cases, these
ancient viral elements in our genome can become activated by external
infections.

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jeletonskelly
There's an unbroken chain between everything current living thing and the
first living thing, so don't we share DNA with well... everything?

~~~
narag
_There 's an unbroken chain between everything current living thing and the
first living thing..._

I don't think that's an established fact at all. DNA is a very complex system
so it's reasonable to think that simpler systems predated it. Not that it
affects your reasoning at all, since every current living thing that we know
of does use DNA.

~~~
agumonkey
I do believe there's an abstract principle that we share with anything that
sustained its structure. Not a specific thing like a set of genes but the
underlying set of chaos-avoiding rules that makes living forms living forms.

~~~
asdff
These rules are the laws of thermodynamics.

~~~
agumonkey
I thought we were the optimized thermodynamics dual/dampener. Our system fight
to slow entropy.

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liftbigweights
Why not link to the book Virolution?

Why keep spamming nytimes?

[https://news.ycombinator.com/item?id=15416932](https://news.ycombinator.com/item?id=15416932)

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MKais
Maybe that's why we are evolving towards giving control to a new specie
(AI/Robots) that is not under the influence of our ancient code

Or maybe we already infected AI

