Viruses are Largely Unrelated to Life on Earth. Where Do They Come From? | Hacker News Reader

Viruses are Largely Unrelated to Life on Earth. Where Do They Come From?

demystifyingscience.com

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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?

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.

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.

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...

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

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.

The last part of that is an interesting theory. Would you expect to see a lot of relatedness between different viruses if that were true?

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.

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.

If you sequence a virus and it has no genes that are found in any living organism, then it's hard to say that they're related... since all our definitions of relatedness come down to sequence similarity.

We haven't found nucleic acids, as such, in extraterrestrial environments, but we also haven't been looking very hard. Nucelobases, but nothing that seems to encode information. However, most conventional explanations for the origin of life include spontaneous formation of genetic information, driven by environmental conditions. If genetic information alone can be spontaneously formed, why couldn't the simplest viruses be generated by the same principle?

To play devils advocate, cells use RNA and DNA so an alien virus that uses a different type of genetic material would likely be unable to reproduce in cells that use such a strikingly different biochemistry. Detecting such viruses would be incredibly difficult especially since our biotech is focused on DNA and RNA.

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.

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

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

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

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

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. "

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