
Viruses are Largely Unrelated to Life on Earth. Where Do They Come From? - qqqqquinnnnn
https://demystifyingscience.com/blog/2020/3/20/originofviruses
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cowboysauce
It seems like the arguments made in the article would more readily support the
idea that viruses are spontaneously forming on Earth than in space. If viruses
are spontaneously forming on other planets or in interstellar space directly,
then they should be forming on the Earth as well. I think the Earth is more
likely for a number of reasons.

To start, viruses are generic material wrapped in proteins. The functionality
of proteins depends on their shapes and the environment strongly affects the
shape of a protein. Viruses that exist on Earth have proteins that are stable
on Earth. A virus that comes from a different environment would be liable to
fall apart on the Earth. RNA itself is pretty unstable by itself (hence why
cells use DNA), but there are plenty of viruses that use it as their genetic
material.

Infecting host cells is another matter. Viruses are generally pretty specific
with their host cells. They enter host cells by binding to specific proteins
on their surfaces. Once inside they take advantage of the specific cellular
machinery present. For example, the polio virus has a single strand of RNA
that codes for a single long polypeptide that is then sliced at specific point
by host enzymes to produce the final viral proteins. Some viral proteins act
to suppress the defenses of the cell and the immune system in general. An
alien virus would be insanely lucky to be able to infect local life at all,
let alone reproduce and spread. Unless life across the universe is incredibly
similar.

Given these thoughts, it seems like it would be more likely for viruses to
spontaneously form on Earth than another planet (or interstellar space).
Viruses forming on Earth would have the advantage of starting with organic
materials that already work with existing life. The Earth is generally
protected from harsh radiation and extreme temperatures. The most important
thing is that any forming viruses would have immediate (relative to crossing
space) contact with host cells to infect and evolve.

The only reason it wouldn't be happening on Earth is if the Earth is
completely unsuitable for it. Even if both are happening, the vast distances
and harsh nature of space should shift the equilibrium strongly towards native
viruses. But if the Earth is unsuitable for it then how are viruses able to
survive and reproduce on a planet that's so unsuitable for them?

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qqqqquinnnnn
I think it's a complexity problem. Someone downthread pointed out that there
are some viruses that are small - so small they consist of only two genes.

It's possible that the super simple minimalist viruses are spontaneously
produced and abundant in the universe. If all that's necessary is a strand of
nucelic acids and a repetitive peptide unit, then it's within the realm of
possibility that these would form simply because it's thermodynamically
favorable for them to fall together in some systems. Then, if they encounter a
living being, they're able to piggyback on it to multiply, mutate, and
recombine.

This could be further supported by the fact that viruses can coinfect cells
and effectively transfer genetic and protein material between each other.

By this model the simplest viruses are just products of chemistry that, when
exposed to life, gradually become more and more complex.

I guess the underlying point is that they could very well be forming on earth,
continuously. If they are, then that would explain the baffling, unending
diversity. They're just always forming new genetic material that gets iterated
on until it works well.

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ncmncm
To me the real question is whether any particular virus lineage evolved
independently, or started out as an organelle or other apparatus of a cell,
and got loose.

I doubt we will ever know, about most viruses, because they evolve so fast.
But it would be seriously cool to find a bacterium using them for
communication or as an extra-cellular library.

We already know about plasmids, of course, and there are plasmid viruses that
dispense with the protein wrapping. But do any bacteria communicate, or store
information in the environment, via non-viral genes wrapped in a viral protein
coat? Would we notice if they did?

We still would not know whether the bacteria co-opted a virus, or developed
the mechanism by itself. Indeed, it could be that the original developer of,
say, those mosquito-shaped phages was wiped out when they went rogue.

~~~
qqqqquinnnnn
this is a fascinating line of inquiry, and comes down to the methods of
detection being insufficiently fine-grain.

it's challenging to tell apart all of the pieces in a metagenomic sample
except through assembly. A "viral plasmid" like you describe would go
unnoticed simply because it would map to another sequence assembly.

there's indication of high copy-number plasmids in bacteria sometimes. not
sure if anyone has looked to see if any of those are kept in the outside of
the cell.

usually imaged cells are washed very well before imaging, otherwise background
is off the charts...

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blacksmith_tb
On the face of it that statement appears to be self-contradictory, given that
viruses use RNA or DNA, like all life on Earth?

~~~
magicsmoke
Agreed, some of the reasoning for extraterrestrial origins of viruses could
also be explained by terrestrial processes. For example, the fact that new
viruses are being added as quickly as old ones degrade and disappear doesn't
necessarily mean alien viruses, but could also be reservoirs of ancient
viruses being released into the environment or rapid mutation of existing
viruses. Viruses having an extraterrestrial origin implies either RNA is
spontaneously self-generating in the universe in large quantities, or somehow
getting carried over across interstellar space from an alien ecosystem, and
there's not a lot of evidence for either case. But given that viruses can
survive intact for long periods of time since they don't have to perform
biological processes (and maybe even longer underground away from degrading UV
light) and the vast diversity of life that has lived and gone extinct on this
planet, I'd be more inclined to think we're getting infected by Mammoth
diseases rather than Alien diseases.

This theory is less convincing when you consider that viruses don't seem to
share any common genetic ancestry with organisms living today, but they could
share genetic ancestry with extinct organisms that didn't leave leave any
living descendants with genetic mutation adding even more obfuscation to their
origins.

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cowboysauce
I don't think you'd even have to look at extinct life. There's so much life
that hasn't been categorized. You can basically take a soil sample from
anywhere in the world and find new microorganisms in it. Archea are a great
example of this. They're small, single celled organisms. They're best known as
being extremeophiles, but exist basically everywhere. But the majority of them
are difficult to culture and study. What's particularly interesting is that
viruses that infect archea are known to be very different from other viruses.

~~~
qqqqquinnnnn
So the crazy thing is that if you take a teaspoon of soil and sequence it for
bacterial information, almost all of that information is similar to what's
been found elsewhere. If you take that same teaspoon of soil and look for the
viral genetic information in there, it's wholly unique. They seem completely
unconnected to the rest of life, as far as nucleic acid signatures go.

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ajmarcic
Every time evidence leans the author towards "viruses might come from space",
I find myself leaning the other way.

My general view is that cellular life and viruses mutualistically co-evolved
from life-like junk at the very beginning. Cells provide the metabolisms
necessary to fight entropy. Viruses promote genetic diversity while acting as
a stress-test to ensure cells can survive their environments. This seems
separate from the trichotomy offered: \- Virus first \- Reductive virus \-
Escaped genes

"If viruses originate from the cells that they interact with, one would expect
there to be significant genetic overlap between the host and the parasite"

The generally small amount of genetic material in a virus is being used for
_viral_ reproduction. I assume most functions encoded in the genomes of cells
are useless and expensive for a virus to replicate. Hence, they'll drop out;
we'll be left with oddball viral genes for viruses to do virus things.

[clipped list of reasons] "All of these facts together suggest that viruses
are the raw material from which living creatures build their genetic material.
They’re like bricks in a building, ..." I think of viruses more as clipboards
(like copy-paste in your OS). Great for moving info around, but wholly
dependent on a cell metabolizing somewhere. Hardly building blocks.

"If that’s the case, it’s possible that the absolute simplest viruses, ones
who consist of genetic information encased in a capsid made from a single
repeating subunit, could be abiotic products of the cosmos. If that’s the
case, we would expect to still find viruses as you got further and further
away from the surface of the Earth."

Considering the density of viruses in the ocean (mentioned by the author), it
seems a simple gust of wind would be enough to cover the earth in viruses.

I believe extraterrestrial life is nearly certain and that viruses can survive
in space. I also think viruses depend on host cells to reproduce. A virus
would have to land in the primordial soup to be of any life-generating use. By
that point there would be enough lifelike junk for the virus to be an
unnecessary step in the recipe.

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LatteLazy
Some viruses have only 2 genes. One for a protease enzyme, one for their outer
shell. 2 genes. Isn't that incredible?

~~~
qqqqquinnnnn
It is! It's also why people are very much on the fence about them being alive.

~~~
LatteLazy
Yeah, i think I lean towards no on that too...

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nreece
Where in the article does it say that "Viruses are Largely Unrelated to Life
on Earth"?

~~~
qqqqquinnnnn
about 3/4 of the way down the page, just before the heading "Viruses all the
way down"

"Except you know what’s weird? Although the absolute diversity of prokaryotes
is widely held to be unknown and unknowable at any scale, most new genetic
information we find in bacteria is similar to genetic information we’ve seen
elsewhere. It’s a comforting reminder that, although large-grain diversity is
uncountably large, most genes in diverse bacteria have sequence-based
similarity. But when you sequence a sample of mixed viruses, most of that
genetic information has never been seen before, anywhere. "

