Cells Talk in a Language That Looks Like Viruses | Hacker News Reader

Cells Talk in a Language That Looks Like Viruses

quantamagazine.org

201 pointsomarkn40 comments

The idea that viruses are self-contained entities separate from the organisms they infect is an artifact of the human mind's power-saving system of modelling the world in terms of functional-decomposition. Viruses are non-living extraorganism messages crucial as a source of novelty in evolution.

Nevertheless, it would be nice to find cures for them.

It's as though the vesicles are email, and viruses are spam.

Previously on HN:

800 million viruses fall onto every square meter of Earth every day. They kill 20% of bacterial life every day. [0]

Video simulation of HIV infecting a cell and reproducing. [1]

[0] https://news.ycombinator.com/item?id=16839636

[1] https://news.ycombinator.com/item?id=16982396

Worse than spam. They're like that chain email all your relatives kept forwarding you about Bill Gates giving you a trip to Disney World if you sent it on to 10 other people.

Viruses are memes. Something that a cell hears, and then can't stop repeating.

If the messages between cells are e-mail, then viruses are computer viruses. The analogy is almost perfect - it's information that uses security holes to cause the host to produce and send copies of it.

And eventually the computer explodes, spreading email spam everywhere. Oh, wait.

Just realised 'viral meme' is a redundant phrase.

Vesicles are RPCs, and viruses are... Viruses. That's why informatics stole the word "virus".

We need other organisms to synthesize certain vital nutrients (not to mention free oxygen) for us. Does this mean that it is pointless to consider ourselves self-contained entities?

The 'inividualistic' feature of viruses is their genome, which is what gets replicated when they take over a cell, and which is subject to evolution itself, not just an agent in the evolution of 'true' organisms.

It's not an artifact of the human mind.

Organism's genes (and phenotype) that is transmitted sexually are easy to separate from viruses and bacteria. Of course there is some mixing, like retroviruses, but the distinction is not artificial.

viruses transmitted within species could be viewed as part of their host's genotype, regardless of whether their genomes are incorporated into the germ-line. When you catch a cold for instance, you have particles of another human's body inside you replicating

It’s an interesting point. Having no medical / bio knowledge, is argue that from a logical perspective it could easily go both ways. 1) we model them to talk because we do 2) we model them not to talk because we don’t recognize their form of talk.

The statement "There are fundamental differences between viruses and vesicles: Viruses can replicate and vesicles cannot" seems either paraphrased or dumbed down. Viruses can be replicated by cells, but they certainly cannot themselves replicate. And it's literally that kind of nitpicking that keeps science on track.

The distinction, I think, is the matter of where the genome resides. Viruses have their own genome; they need to hijack the mechanisms of cells to reproduce, but it is their genome that is being replicated and disseminated. For a vesicle, however, it seems that the genetic instructions for creating them are part of the cell's genome, and those instructions do not get copied into the vesicle (at least, not in a form that can get itself replicated) even in the case of vesicles containing some RNA.

I would think that even if there was a form of bacterial sex that involved using vesicles as the medium for exchanging genetic material, that would not necessarily be virus-like unless the genetic material being transferred was capable of promoting the creation of vesicles containing copies of itself by the receiving bacterium. I don't know if that case would be distinguishable from a virus.

I know, I was pointing out that the phrasing "viruses can replicate" is incorrect in every sense of that active verb "to replicated". They can be replicated, and there is a non-trivial difference between those two descriptions that matter to this scientific explanation.

Really? If you don't have anything to contribute to a discussion, please don't drum up noise. Splitting hairs over whether a virus replicates or is replicated is just spamming the forum!

I understand that with a wide enough audience, attention seekers will make some noise about some minutae they know that isn't relevant to the discussion. Don't be THAT guy.

There is a theory called viral eukaryogenesis and it's very much linked to meiosis.

> And it's literally that kind of nitpicking that keeps science on track.

I don't want to be nitpicking, but can you provide citations? How has nitpicking on popular science articles kept science on track?

Well, nitpicking on journal articles is how we do peer review. I'm not sure that needs a reference.

This is a popular science article, not a journal publication. This is also the first time I have heard of the peer review process being described as "nitpicking". Is this a new thing? Kind of hilarious! I want citations!

Would the word "meticulous" make you feel better?

I expect that is a better term. Nitpick implies unimportant, unnecessary finding of fault for the purpose of finding fault. Meticulous implies attention to detail and precision. They look the same after you submit your document for review.

Meticulous review of journal submissions is one thing. What the parent comment is doing is something entirely different. It is nitpicking on a statement in a popular science article that states that viruses replicate. Nitpicking on this is just showboating.

Does this explanation make you think better?

> And it's literally that kind of nitpicking that keeps science on track.

Yeah, no!!

>> And it's literally that kind of nitpicking that keeps science on track.

> Yeah, no!!

It looks like you are confusing the posts from two different people and repeating yourself. What you quoted was from TheRealPomax. I am a different person, and you already responded to that once.

> Does this explanation make you think better?

My thinking is perfectly fine, but thank you for your concern.

It has been a pleasure.

It's mindblowing that we can now directly image these vesicles https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448148/

We can in fact image them in multiple ways! Check out these super high resolution images of vesicles on a cell wall - the honeycomb bits are the vesicles' clathrin cages: https://taraskalab.nhlbi.nih.gov/media/

Apologies if I got this from HN, as I can’t remember the source, but the video halfway down this page shows the complexity of viral replication:

https://blogs.scientificamerican.com/observations/watch-the-...

The article hints at some of the same mechanisms for extracellular vesicles. If that’s the case then maybe they are more closely related than outwardly expressed in the copy.

I strongly recommend "A Planet of Viruses" by Carl Zimmer

http://www.press.uchicago.edu/ucp/books/book/chicago/P/bo222...

There are viruses that enter a host, merge with its DNA, replicate along with it for generations just like "normal" DNA. Eventually, it can "wake up", cut itself out of the host genes, and start replicating as a virus again.

Some of our DNA is apparently made out of viruses that did this and got stuck.

The model that emerges from consideration of recent discoveries is something like, bacteria and viruses form a single global organism that is the primary resident of this planet (by mass, by throughput, etc.)

I’m no biologist but this seems to blow a lot of things wide open.

Since these vesicles resemble viruses, is it possible for them to be a form of organism-to-organism communication? Accidental, or intentional?

Might there be pathogens that MITM vesicles en route? Rip them open and plant another message inside, and send them along?

> Might there be pathogens that MITM vesicles en route? Rip them open and plant another message inside, and send them along?

Seems like they do something effectively the same. Here's an excerpt from the article:

... retroviruses also drape a second layer over their protein shell by wrapping themselves in pieces of their host’s cell membrane. The host-derived membrane protects the virus from discovery by the immune system

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

One of the most important scarcely explored phenomena.

> More recently, however, scientists discovered that cells could package their molecular information in what are known as extracellular vesicles.

Seems like cells then need some type message-response mechanism. It could be that there's an incidental minmax game happening at a cellular level, leading to types of intelligence that we don't understand at all but maybe can be modeled.

I think this creates incredible disruption opportunities for drugs and healthcare if AI can augment the intelligence of a cell in the long term.

The article describes vesicles as a sort of language, I always thought of them as a cellular routing mechanism.

Whatever they are, I think they're super interesting. I named one of my routing libraries after a related organelle: https://github.com/jdonaldson/golgi

Similar for me, but they seem like a literal (network) packet than a routing algorithm/system.

Yeah, in my analogy a vesicle is a special kind of ADT-wrapped result, and the Golgi instance does the routing.

Also fwiw I dropped the name vesicle from API and docs because I didn't think anybody would understand the connection. Now I'm inclined to add it back in.

Wait, what? Are... are you God?

I've watched the original Ghostbusters, so yes.

Imagine how cool a story it would be if viruses were just a weapon developed by intelligent microscopic life. Relics of an ancient war who's history is written in the telomeres of our DNA in an encoding which we cannot decipher.

So... cancer is to tissue as viruses are to cell messaging?

This is obvious.

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