'Obelisks': New class of life has been found in human digestive system (opens in new tab)

To the limits of where our understanding of how "entities" are connected to one another (homology). Yes, there's nothing like them. You could make an argument they are "viroid-like" and there's a deeper evolutionary connection between viroids/viruses/plasmids, but the information theory to formally establish such a connection is not sufficiently developed. It's a worthy scientific problem!

Is it common to find new viruses/viroids/biological agents? Well it certainly is starting to feel that way to me.

Largely we don't know. That's what makes them cool. This opens up a fairly large debate about where you draw the boundary of "life", "organisms", and "entities". It's a fun debate to have over a few beers since there is no objective correct answer.

My view is that Obelisks are more like Viruses or Viroids, or some kind of mobile genetic element. The key detail is that they appear to be strictly RNA elements (they don't have a DNA counterpart). So they're most likely using host RNA transcription machinery to make more copies of themselves, this is what viroids and satellite viruses like "Hepatitis Delta Virus" do.

What do they do? Well that's the right question. My guess is the kinds of things that bacteriophages do, Obelisks do too. Exploit cells to make more copies of themselves as selfish replicators.

How would they exist/maintain themselves without it's DNA counterpart?

Sure, in a redutionistic sense. In the same light "Hepatitis Delta Virus" is an RNA plasmid, yet it causes liver cancer in humans. I err on the side that the simplicity of the genetic system should not deceive us into thinking it's trivial. The next 12 months of discoveries is what makes this so exciting.

Probably. There’s a whole category of organisms that can’t cultured in a lab or effectively studied called microbial dark matter: https://en.m.wikipedia.org/wiki/Microbial_dark_matter

These kinds of DNA and RNA studies are the only ones that can realistically pick up evidence of these organisms outside of an extraordinarily lucky electron microscope slide.

Probably. This is a good illustration of just how hard it may be to conclusively find life on other worlds; we don’t even know what exists here on Earth yet.

I should certainly hope so.

Don't know. They're undetected =-)

There are preprints for all the papers [https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1], they're operationally the same.

How were they not noticed before? Well that's how science works. Someone eventually has to be the one to notice something is going on right?

I think it's a common fallacy that we, as a species, are not ignorant to the complexity of Nature. The hardest part is to see it.

No clear ideas. But I would not be surprised if a dozen labs have jumped at the chance of trying to figure it out. So wait a year and ask again.

Edit: Or better yet, try and figure it out for yourself. The tools to do this analysis are available to everyone.

Not that I know of, although this doesn't mean it isn't happening, it's something which has to be investigated in detail.

The classic phylogenetic classes are a fantastic model, but https://en.wikipedia.org/wiki/All_models_are_wrong :)

Phylogeny is the study by which things relate to one another. There is a divergence point at which point it becomes impossible to relate two sequences to one another. Obelisks, Zeta-Elements, Deltaviruses, viroids all veer towards their own divergence point into infinity, but their are higher-order genome organization traits which are consistent. We don't know if these traits are the same by origin, or the same by chance. Interestingly Ambiviruses also have this genome organization, but they have a protein which is de facto of an RNA virus.

My opinion is that these simple genome layouts (structured circular RNA elements with ribozymes) are like a cauldron of mixing simple genes, and when they come together just the right way, we see those lineages take off. Think of it as an ocean of ancient primordial RNA replicators, ready to fire off, and this process is ongoing even today.

Vanya thought that when you run them through the RNA folding software, it would give you these unusual straight rods which reminded him of Cleopatra's Needle (Obelisk, https://en.wikipedia.org/wiki/Cleopatra%27s_Needles). The name stuck around. Incidentally the name has some cool 2001: Space Odyssey monolith vibes to it, which I think has been fitting.

What have Obelisks ever done to you? Our first reaction shouldn't be to kill everything we don't understand :'(

Good pragmatic question though. It's not clear if any drugs up- or down-regulate Obelisk genome copy, you could re-investigate other drug-treatment studies to see if Obelisks incidentally present are altered and get an "accidental" study.

From a molecular perspective, the most likely compounds and methods would be those which work against viroid replication (i.e. RNA polymerase inhibitors, translational inhibitors, CRISPR,...). You just have to maintain a preferential toxicity to Obelisks over host cells.

That's exactly what they are though, some piece of garbage RNA cells are producing. A lot of things meet that definition if you think about it.

There are no RNA-based lifeforms. All known life is DNA based but uses RNA internally. The earliest common ancestor of all life was DNA based, LUCA https://en.wikipedia.org/wiki/Last_universal_common_ancestor

There is a hypothesis that once upon a time life passed though an RNA only stage without DNA and proteins. RNA world https://en.wikipedia.org/wiki/RNA_world

It's not OT at all. It depends on what you mean exactly by LLM, but we use them all the time. ESMFold2 was an LLM [https://www.science.org/doi/10.1126/science.ade2574] and was instrumental in advancing deep protein fold prediction in metagenomic space. Likewise AlphaFold2 it's direct application in creating FoldSeek for ultra-deep homology search. Both of these actually have radically improved our capacity to say Obelisks are _REALLY_ not like anything that's known.

Besides that I encourage all students to use ChatGPT for research, coding, copy editing, etc... I haven't encountered an LLM that can deal with difficult domain problems like we're facing, but I'd welcome the help. I'm for using all tools available, my main criticism with AI/LLM in general is the poor way in which uncertainty is reported.

Absolutely, reading Selfish Gene in high school set me on the path to this type of exploration. Genes, in the pure abstract sense, are the unit by which we interrogate understand evolutionary change. There's a large grey area about the boundaries of genes, but after a certain point, genes assemble into operational units larger than themselves, a genome. Obelisks are some of the simplest, most rudimentary genomes described thus far.

Everyday I get to do this kind of research, I'm grateful to be the one doing it.

And it's been replicated?

In case others don't get it:

https://asterix.com/en/portfolio/obelix/

We should not be so dogmatix in requiring scientific protocol - maybe there are some VitalStatistix we are not yet aware of.

Splendido.