
The human genome is full of viruses - olalonde
https://medium.com/medical-myths-and-models/the-human-genome-is-full-of-viruses-c18ba52ac195
======
crazygringo
> _Even after recovering from an infection there will always be a piece of
> that virus encoded within your DNA._

I did a little research and this appears to be _almost completely false_.

This sentence makes it sound like every time you get a cold, your body's DNA
is permanently altered. Which would be insane if true.

The reality is that this insane outcome is incredibly rare, but nevertheless
has happened enough times _over all of human history_ that we have genetic
code from viruses in our DNA, because a virus at some point managed to alter
the DNA in a sperm or egg cell.

But the quoted sentence is just _not_ how infections work 99.99...+% of the
time. The cold I got last month isn't in my DNA forever. It's very sloppy
writing that appears to be aiming for sensationalism instead of accuracy.

~~~
jhbadger
The article is rather fancifully written (and by a non-scientist) but as a
professional genomicist, I can assure you that the human genome _is_ full of
viruses, the remnants of which are almost entirely non-functional, but are
interesting in the way meteor craters are to geology.

Here is a review (nearly twenty years old from when the human genome was first
sequenced)
[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC138943/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC138943/)

~~~
sudoaza
Huh, can we remove those? isn't there a cost to have all those extra sequences
lying around?

~~~
Enginerrrd
You ever see a cryptic line of code with a comment next to it saying something
to the effect of: "No idea what this does, but everything breaks if we delete
it"?

It could be that old viral code has been repurposed long ago by evolution and
serves a purpose.

~~~
kibibyte
I generally get annoyed at most analogies that compare DNA to code because
they oversimplify a lot, but I really do like this particular DNA-code
analogy.

My university molecular genetics course taught me that DNA is very
complicated. Many of us know of the simplified model where an RNA polymerase,
encouraged by some transcription factors, locates and binds to a promoter
sequence, unwinds the strands, and constructs an RNA strand. However, DNA has
a 3D structure. Histones can wind up DNA tightly enough to hide genes from
transcription proteins, or they can unwind and expose DNA to encourage
expression. Some transcription factors can bind to sequences several kilobases
away from the target gene, cause that part of the DNA to fold onto itself, and
ultimately bind to transcription proteins to encourage expression of the
target gene.[0]

Extending your comment, it is entirely possible that bits and pieces of old
viral code have accidentally led to weird things like this, and that many
organisms now depend on this behavior.

[0]:
[https://en.wikipedia.org/wiki/Transcription_factor#/media/Fi...](https://en.wikipedia.org/wiki/Transcription_factor#/media/File:Transcription_Factors.svg)

(In the course of reading about transcription factors, I came across something
pretty neat that's related to all this about 3D structures:
[https://en.wikipedia.org/wiki/Transcription_factories](https://en.wikipedia.org/wiki/Transcription_factories))

Edit: I should also mention that, if it wasn't obvious, that viral DNA getting
inserted into certain places can disrupt these complex interactions by
increasing or decreasing the expression of a gene. For the cell/organism, this
can be detrimental, benign, or perhaps beneficial.

~~~
sudoaza
I was worrying about this, specially your latest edit, when i mentioned
cleaning up. We could limit to very new additions though just in case. I know
that there's maybe no reason to think that this random additions are any worse
than the random+selected pieces that were coding before, but just seems ugly
somehow.

------
_bxg1
I've always thought of DNA as mere "data". "This goes here, that goes there",
etc. And I've always wondered how such a relatively small amount of data could
describe the massive complexity of a full-size organism.

But this makes it sound like DNA is data the way Lisp is data: it can contain
procedures and transformations and meta-statements about itself, and even
mutate during the course of being interpreted. That would explain so much.

The use of the term "virus" in software seems to be more apt than I'd thought.

~~~
pergadad
Just in case this is not known, human generic code is more than just DNA.

Most important parts of what encodes us are:

\- DNA \- epigenetic markers on the DNA which modulate which parts of the DNA
are active. You influence these and pass them on to your children (as men) and
grandchildren (as women, as girls are born with all egg cells they'll ever
have) \- cell organelles which copy the DNA, ensure the cell has food and
lives, etc. These tend to be independent cells that were at some point
captured by our own cells. So they have their own genetic code. These you only
inherit from your mother (dad gives half the DNA with epigenetic markers, mom
the other half (also with markers) and everything else.

And of course much of what we are is shaped through gestation as well, I.e.
the mother's body sends not just nutrients but also hormones etc that regulate
gestation (and vice versa the child sends various messages to mom, up to even
own cells in case of serious illness or accident or the mother).

Fascinating stuff.

~~~
thaumasiotes
> independent cells that were at some point captured by our own cells

It makes a little more sense to think of them as "domesticated" rather than
"captured".

~~~
JulianMorrison
Domesticated and implanted, unable to survive outside the host, we're talking
full H.R. Giger here.

------
tim333
There was an interesting article a while back on them playing a part in
schizophrenia. "The Insanity Virus"
[https://www.discovermagazine.com/mind/the-insanity-
virus](https://www.discovermagazine.com/mind/the-insanity-virus)

~~~
jdhn
What a great read! I find it so crazy that after decades of thinking that
there's all this "junk DNA" in us, it turns out that it may serve a purpose
after all, even if that purpose is malicious.

~~~
vikramkr
I don't know if junk DNA was ever universally considered to be "junk" \- it's
been controversial terminology from the start which has proven to be justified
with time as we learn more about what it does.

------
superkuh
Mammals could not and would not exist without the membrane fusion protein
given to their ancestors by a retrovirus. This protein is _essential_ for
forming the multiple nucleus cells that make up the placenta.

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throwaway2048
There is also the theory that the eukaryote nucleus IS a virus

[https://en.wikipedia.org/wiki/Viral_eukaryogenesis](https://en.wikipedia.org/wiki/Viral_eukaryogenesis)

~~~
EvanAnderson
Neato! Thanks for that rabbit-hole to explore.

------
hirundo
“So powerful and ancient are viruses, that I would summarize their role in
life as ‘Ex Virus Omnia’ (from virus everything).”

We have met the enemy and he is us. Viruses may be both the gravest threat to
our species and mothers and fathers of it. They are also, to a first
approximation, the Red Queen, who must be obeyed. If we can disobey her, and
distribute an effective vaccine in time to dent her latest royal tour, it will
be an epic level up: the power to not consent to impregnation by horizontal
gene transfer.

It seems that we're not quite there yet.

------
dzink
A good example is the Arc virus. Research at some point proved that removing
it from a creature’s genome, removed the creature’s memory. More:
[https://www.nih.gov/news-events/news-releases/memory-gene-
go...](https://www.nih.gov/news-events/news-releases/memory-gene-goes-viral)

------
Papirola
For sci-fi readers, I recommend Greg Bear's "Darwin's Radio" and the sequel
"Darwin's Children".

------
nwah1
Lynn Margulis believed viruses often become symbionts, and speculated that
diseases like syphilis and AIDS are so hard to cure because the viruses
incorporate themselves into our genome.

She also believed that the Eastern Bloc concept of symbiogenesis explains much
of human evolution, and some of that is now accepted by the mainstream
community. For instance, it is now believed that mitochondria were originally
viruses that became symbionts.

However, Margulis and many adherents of this view argue that essentially _all_
of the organelles formed this way, and that symbionts play a vastly larger
role in general.

[https://www.discovermagazine.com/the-sciences/discover-
inter...](https://www.discovermagazine.com/the-sciences/discover-interview-
lynn-margulis-says-shes-not-controversial-shes-right)

------
fizixer
Train of thought while reading title and comments:

First: Genome cannot physically contain a bio-virus, so this must be genetic
code, acting as a "computer virus"

Second: Oh they're talking about viral genome embedded in human genome. Got
it.

Third: But wait, bio-virus genome embedded in human genome does not by-
definition imply that there is something wrong with that human genome. It
could just be an innocuous part of the viral genome.

Fourth: Parts of human genome that could act as "computer virus" (i.e., be
malicious to the human), and parts of human genome that come from a bio-virus
may have some overlap. But you could have two other options too: (a) part of
human genome that is malicious but not from a bio-viral source, (b) part of
human genome that is from a bio-virus but is not malicious.

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zed88
And they may awaken as well.

[https://www.newscientist.com/article/mg24532710-700-ancient-...](https://www.newscientist.com/article/mg24532710-700-ancient-
viruses-buried-in-our-dna-may-reawaken-and-cause-illness/)

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tibbydudeza
Without viruses we would not be here in our present state.

The mammalian placenta uses ancient virus protein called syncytin to bond
"other" to "own" and thus bypass the effect of the mother's immune system.

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redis_mlc
I used to work in genetics.

We're not sure if the viruses are actually dormant or not. They may be the
active ingredients for a lot of biological processes. In other words, viruses
and junk DNA are probably essential parts of modern man.

If you're squeamish, I suggest you just take what I said at face value, and
move on with your life.

If you're not, then you can google for some more info, but you won't like what
you find. How sausage is made, and all that.

------
c-smile
And the most fascinated fact is that, despite of all these intruders and
mutators, living organisms are damn stable and pretty effective devices.

~~~
vikramkr
I mean, not _that_ stable - the instability is kind of what allows evolution
to happen. It's, well, it's good enough, stable enough, effective enough, and
that's enough for life.

------
mirimir
> In many ways, viruses are eerily reminiscent of the idea of ancient spells,
> which sit quietly as words in a book until someone utters the mystical
> syllables and unleashes the magic contained within.

If that appeals, I recommend Hannu Rajaniemi's _Quantum Thief_ trilogy.

------
knzhou
Another fascinating fact is that about 20% of cancers are directly caused by
viruses -- they push the cells they infect to be more cancer-like. The famous
example is HPV, but there are many more.

~~~
dreamcompiler
And some by bacteria. Helicobacter pylori for example

------
dmd
> A biological virus (whether it is a true virus, an endogenous retrovirus, or
> a transposon) can literally lay dormant in a word document as a string of
> As, Ts, Cs, and Gs.

Literally, huh? In a word document?

~~~
Viliam1234
Sure, that's why we get the usual advice:

\- wash your hands with soap as often as possible

\- do not touch your mouth, nose, or eyes when outside

\- always disable macros in word and excel

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GistNoesis
Monkey patching is not good engineering practice.

~~~
jacob019

        from gevent import monkey
        monkey.patch_all()
    

So good

------
whoevercares
Now I’m more convinced Evolution might be driven by viruses

~~~
vikramkr
Evolution is driven by a lot of things. It's driven by viruses by definition
since of a virus integrates and makes a mutation to the germline, then that's
a change which is evolution. And obviously bdosease is a major selective
pressure driving evolution. And so so starvation, radiation, chemical
mutation, errors in copying, heat, cold, literally everything that impacts
survival and procreation drives evolution.

