'Obelisks': New class of life has been found in human digestive system
https://www.sciencealert.com/obelisks-entirely-new-class-of-life-has-been-found-in-the-human-digestive-systemBy unkeen at
ababaian | 22 comments | 3 days ago
This is now a peer-reviewed paper, published last month in Cell [https://www.cell.com/cell/fulltext/S0092-8674(24)01091-2].
Obelisks are part of a larger research program we're developing at the University of Toronto + collaborators, see also: Virus-Viroid Hybrids paper [https://www.nature.com/articles/s41467-023-38301-2] and the Zeta-Elements [https://www.nature.com/articles/s41586-021-04332-2].
Computational biology is driving a revolutionary expansion of our understanding of Earth's biodiversity. I believe Zeta-elements, Ambiviruses, and Obelisks are just the beginning. If you're interested, our "Laboratory for RNA-Based Lifeforms" (University of Toronto) is hiring passionate developers/post-docs/graduate students [https://www.rnalab.ca].
Edit: OK going to call it for now. I'll check in later today if there's any outstanding questions.
marojejian | 1 comment | 3 days ago
ababaian, does this truly mean no similarity to any other sequences, even virus/viroid?
That seems very exciting, since my understanding is that we see a lot of conservation within the known branches of life, and don't discover new ones often!
Though perhaps it's more common to find totally novel virus/viroids? How often do we find truly novel biological agents at the sequence level?
ababaian | 1 comment | 3 days ago
Is it common to find new viruses/viroids/biological agents? Well it certainly is starting to feel that way to me.
DoctorOetker | 1 comment | 3 days ago
The way it is phrased, insufficiently developed information theory is rather surprising. Did you mean to write that not enough genome data has been collected to formally establish a link, or are you actually stating that we have all the data but as a species have not sufficiently developed the mathematical subdiscipline of probability, information theory ?
I could follow the first, but the latter?
EDIT: I now believe you meant neither but more something along the lines of: we probably have plenty of data, and usual information theory should suffice, but we simply havent exhaustively applied the tools to collate the information and make the implicitly available data more explicitly manifest.
ababaian | 0 comments | 3 days ago
We know how to quantify homology, it just has not been applied to sufficient depth to the field of RNA/viroid evolution to resolve how much of an RNA element with extensive secondary structure, or ribozyme is evidence of a homology vs. convergence. And how could we resolve the two? It's easy with protein sequences, tricky with protein structures, but deep RNA evolution? That's a mystery.
Traubenfuchs | 1 comment | 3 days ago
We all understand cells/bacteria and their interaction with viruses: Viruses infect cells and make them into virus factoriesâŠ
What do obelisks do? Are they integrated / read by DNA machinery/organells into cells that then produce more obelisks?
Whatâs their life cycle?
How are they different from alread known viroids?
ababaian | 2 comments | 3 days ago
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.
brokensegue | 2 comments | 3 days ago
ababaian | 0 comments | 3 days ago
throwup238 | 0 comments | 3 days ago
bicx | 1 comment | 3 days ago
ababaian | 1 comment | 3 days ago
lukeschlather | 1 comment | 3 days ago
ababaian | 0 comments | 3 days ago
The second question is if it's parasitic, mutualistic, or neutral. If it's a parasite it should cause a fitness defect to the DNA organism's replication. As of yet I haven't seen evidence of this at the cellular level. But there is a strong argument that by depleting cells of nucleic acids (RNA) would have to be at least minimally parasitic. That is of course unless they confer some advantage to the cells with Obelisks. In which case, why don't all microbial cells have Obelisks. Importantly, the relationships between all the various Obelisks at least for now, is not lining up with microbial genome evolution. This would mean they are jumping from genome to genome.
Now you're in a late night pub discussion about where we should be drawing the boundaries of life.
trebligdivad | 1 comment | 3 days ago
ababaian | 1 comment | 3 days ago
trebligdivad | 1 comment | 3 days ago
richieartoul | 0 comments | 3 days ago
Iâm also not sure if DNA-seq data refers to the human host, or just all DNA they were able to sequence (which would include bacteria as well I guess?)
stainablesteel | 1 comment | 3 days ago
ababaian | 0 comments | 3 days ago
yawnxyz | 4 comments | 3 days ago
E.g. are there more "life" like obelisks and similar out there in genome samples?
throwup238 | 2 comments | 3 days ago
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.
hinkley | 0 comments | 3 days ago
https://www.wanderingspiritsglobal.com/whisky-fungus-baudoin...
It doesnât culture in agar. Unless you add alcohol to the Petri dish and then it does. Things like this are why I still have my fingers crossed that we will have one or more helicobacter pylori (the bacteria that causes 90% of ulcers) moments for intestinal ailments. These obelisks may turn out to be one of them, and understanding could lead to better treatments and prevention.
ababaian | 0 comments | 3 days ago
ceejayoz | 2 comments | 3 days ago
light_hue_1 | 1 comment | 3 days ago
ceejayoz | 1 comment | 3 days ago
https://science.nasa.gov/science-research/planetary-science/...
light_hue_1 | 1 comment | 3 days ago
ceejayoz | 0 comments | 3 days ago
aaroninsf | 1 comment | 3 days ago
Xvz Fgnayrl Ebovafba'f Nheben
nyokodo | 0 comments | 2 days ago
ababaian | 0 comments | 3 days ago
casenmgreen | 0 comments | 3 days ago
andrewflnr | 1 comment | 3 days ago
ababaian | 2 comments | 3 days ago
Edit: Or better yet, try and figure it out for yourself. The tools to do this analysis are available to everyone.
promptdaddy | 1 comment | 3 days ago
ababaian | 1 comment | 3 days ago
fudged71 | 0 comments | 3 days ago
1. "Are we looking at Obelisks the wrong way by trying to classify them within existing frameworks?"
Looking at the repository structure and tools developed (AlphaFold3.md, RNAfold.md, etc.), we're primarily using methods designed for known biological entities. The fact that specialized tools were needed suggests we might be forcing Obelisks into existing paradigms rather than understanding them on their own terms.
Perhaps instead of asking "what kind of virus is this?", we should ask "what kind of biological phenomenon are we observing?"
2. "What if Obelisks aren't entities but processes?"
The repository shows: - Complex regulatory elements - Stable host relationships - System-level effects - Consistent patterns across environments
This suggests we might be misconceptualizing Obelisks by thinking of them as discrete entities rather than as processes or systems that emerge from biological information flow.
3. "Are we asking the right questions about biological information?"
The unusual combination of: - Highly structured RNA elements - Complex regulatory patterns - Stable host relationships - Modular organization
Suggests we might need to fundamentally rethink how biological information is maintained and transmitted. Obelisks might represent a different paradigm of biological information organization.
4. "What if our concept of host and virus is too binary?"
The evidence shows: - Deep host integration - Stable relationships - Complex interactions - System-level effects
This suggests we might need to move beyond the binary host-virus paradigm toward understanding biological systems as networks of interacting information processes.
5. "Are we witnessing biology we don't yet have the framework to understand?"
The need for: - New detection methods - Specialized analysis tools - Novel classification systems - Complex structural analyses
Suggests we might be encountering biological phenomena that our current scientific frameworks aren't equipped to fully comprehend.
6. "What if Obelisks aren't unusual - what if our other classifications are too narrow?"
The widespread presence but previous lack of detection suggests: - Our detection methods might be biased - Current classifications might be too restrictive - We might be missing other similar phenomena - Our understanding of biological diversity might be too limited
7. "Should we be studying Obelisks' absence rather than their presence?"
The repository shows: - Consistent presence in some environments - Absence in others - Stable host relationships - System-level effects
Perhaps studying where and why Obelisks are absent could tell us more about their nature than studying where they're present.
8. "Are we confusing structure with function?"
The focus on: - Structural analyses - Sequence comparisons - Protein predictions - RNA folding
Might be causing us to miss the fundamental nature of what Obelisks do rather than what they are.
andrewflnr | 1 comment | 3 days ago
ababaian | 1 comment | 3 days ago
dotancohen | 1 comment | 3 days ago
ababaian | 3 comments | 3 days ago
andrewflnr | 0 comments | 2 days ago
Balgair | 0 comments | 3 days ago
dotancohen | 0 comments | 3 days ago
Maybe I will give this a crack. If I get anywhere I'll contact a local university to speak to a biologist.
Thank you.
kettleballroll | 0 comments | 3 days ago
bryan0 | 1 comment | 3 days ago
ababaian | 2 comments | 3 days ago
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.
layer8 | 0 comments | 3 days ago
DoctorOetker | 1 comment | 3 days ago
For example: https://www.selectadna.co.uk/dna-tagging-spray
One could easily fathom not just overt authorities but also covert authorities wishing to use similar technology.
Clearly an intelligence agency doesn't want the lower level police leaking detections of higher importance, so best to differentiate say DNA for cops and RNA for intelligence services, so that the pragmatic tools and workflows of police won't result in uncleared personnel figuring out things they aren't cleared for.
That wouldn't explain quasi biological statistics as opposed to white noise random sequences, which would suffice for tracking, but also would blow the cover as a man-made genome...
I.e. if RNA sprays had been reserved by some power bloc for intelligence service purposes (DNA sprays for usual law enforcement), then there is a clear incentive to have the secret pseudorandom sequences at least mimic plausible biology sequences, an adversary bloc detecting such a tracker might believe the sequence to be of biological origin, and intelligence associated academics would publish it: revealing both the detection by an adversary bloc and the academic's employment by intelligence circles...
SubiculumCode | 0 comments | 3 days ago
mmooss | 1 comment | 3 days ago
My poor understanding has been that there are cellular organisms / 'biota' (if those are the right terms - prokaryotes, eukaryotes, etc.) and viruses. Where do obelisks, Virus-Viroid Hybrids, Zeta-Elements, Ambiviruses all fit in that scheme, if they do at all? Or is there a new scheme?
And it is very cool for you to answer questions here. Remember us if you visit Sweden someday! :)
ababaian | 1 comment | 3 days ago
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.
mmooss | 0 comments | 3 days ago
> The classic phylogenetic classes are a fantastic model, but https://en.wikipedia.org/wiki/All_models_are_wrong :)
For the record, yes, I know. Unfortunately, we need models to organize the world in our limited brains, and the less intimate experience one has of something, the more simplified their model. This isn't my day job! :)
pseudosudoer | 1 comment | 3 days ago
ababaian | 0 comments | 3 days ago
zaptheimpaler | 0 comments | 3 days ago
RobotToaster | 1 comment | 3 days ago
ababaian | 1 comment | 3 days ago
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.
hinkley | 1 comment | 3 days ago
Some people carry staph on their skin their whole life and never end up with a lesion.
shwouchk | 0 comments | 3 days ago
kaycebasques | 0 comments | 2 days ago
Presumably you've got a lot of follow-up research to do. What are the most important research questions re: obelisks now?
adrian_b | 0 comments | 3 days ago
dj_gitmo | 1 comment | 3 days ago
ababaian | 1 comment | 3 days ago
brian-armstrong | 2 comments | 3 days ago
ababaian | 0 comments | 3 days ago
wbl | 1 comment | 3 days ago
LargoLasskhyfv | 0 comments | 3 days ago
alexwasserman | 0 comments | 2 days ago
ghostly_s | 1 comment | 3 days ago
ababaian | 0 comments | 3 days ago
Communitivity | 1 comment | 3 days ago
If I understand correctly, plants have RNA - would this mean new RNA-based lifeforms could also be found within plants?
light_hue_1 | 3 comments | 3 days ago
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
ababaian | 0 comments | 3 days ago
This podcast RadioLab with Carl Zimmer (11m) I think captures the essence of the idea near perfectly: https://radiolab.org/podcast/creation-translation
lolinder | 0 comments | 3 days ago
cyberax | 0 comments | 3 days ago
There are viruses that have entirely RNA-based lifecycle (even using RNA-dependent RNA polymerase). Our very favorite COVID virus is one of them.
endofreach | 1 comment | 3 days ago
ababaian | 0 comments | 3 days ago
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.
ucha | 1 comment | 3 days ago
ababaian | 1 comment | 3 days ago
mensetmanusman | 1 comment | 3 days ago
aaroninsf | 0 comments | 3 days ago
Hammerhead Self-Cleaving Ribozyme is quite a chunk of English.
Sxubas | 1 comment | 3 days ago
I am hopeful this discovery can lead to technology to improve people's life. Just thinking out loud, cancer treatments, orphan diseases treatment, prevent Alzheimer's progression, new vaccines.
Very long shots, but that's the beauty of unknowns. I'm highly jealous of scientists that will formulate and test hypothesis around this topic.
ababaian | 0 comments | 3 days ago
andybak | 1 comment | 3 days ago
I was confused at first. This isn't "Class" in the technical sense (i.e. the level between Phylum and Order)
digging | 0 comments | 3 days ago
treprinum | 0 comments | 3 days ago
readyplayernull | 0 comments | 3 days ago
So they have a higher chance of being re-created by random chemical processes at mostly any point in time and place in the universe. Omniterrestrial?
asymmetric | 4 comments | 3 days ago
moralestapia | 1 comment | 3 days ago
https://www.cell.com/cell/abstract/S0092-8674(24)01091-2
It truly is a new class of genomic elements.
kelseyfrog | 1 comment | 3 days ago
moralestapia | 1 comment | 3 days ago
They then expanded the search to millions of sequences, which are publicly available, and found ~30k different classes(!) of Obelisk elements. One could argue that the quality of each of these "experiments" may not be as good as IHMP, but still, the signal is more than sufficient to clearly demonstrate the existence and implied significance of these elements.
kelseyfrog | 6 comments | 3 days ago
dang | 1 comment | 3 days ago
https://news.ycombinator.com/newsguidelines.html
No doubt there are valid concerns but the value of comments formed by internet clichĂ©s and dismissive tropes is... lower than what we want here. When it comes with a tone of entitled aggressiveness, that's even worseâthat's enough to drive away the people who spend their lives working on a subject, and that would be the worst possible outcome for HN.
kelseyfrog | 0 comments | 3 days ago
throwway120385 | 1 comment | 3 days ago
I think you're trying to draw a comparison here between two things of completely different category, and I feel like you might not understand how different they are.
ababaian | 2 comments | 3 days ago
samus | 0 comments | 3 days ago
throwway120385 | 0 comments | 2 days ago
JoelMcCracken | 1 comment | 3 days ago
I think youâd be better served by trying to understand how psychological research has been done, why people go on about replication, what results are suspect from psych, and how they developed in the first place.
Bc it seems like youâre trying to justify the actions in psych world by other disciplines, but it just doesnât make sense.
kelseyfrog | 1 comment | 3 days ago
samus | 0 comments | 3 days ago
ababaian | 0 comments | 3 days ago
I am genuinely curious as to how best to present the evidence. What would you like to see to tame your skeptic?
gus_massa | 0 comments | 3 days ago
It's good to wait until replication and then 5 years to let the dust setle down.
But if the research group had group had a good past history, it's better to trust them while the other teams verify.
ababaian | 1 comment | 3 days ago
kelseyfrog | 3 comments | 3 days ago
I'm starting to realize that this may be a justification of their prejudice against these fields rather than a legitimate basis for dismissal.
JoelMcCracken | 2 comments | 3 days ago
The noticed it in multiple datasets.
What would replication look like here besides someone else looking at the dataset and agreeing that they also see the curiosities?
Or do you mean someone measuring a new fresh set of data and looking at it?
Asking for replication in this case is surprising, because seemingly the entire value is to prompt other research to go figure out whatâs going on with these things.
niam | 1 comment | 3 days ago
kelseyfrog | 0 comments | 3 days ago
Matticus_Rex | 0 comments | 3 days ago
So most findings in research psychology definitely need replication. But the idea that the existence of something is verifiably found across a bunch of different datasets doesn't need a new set of experiments to show -- you just check the data.
falseprofit | 0 comments | 3 days ago
The problem with psychology is that despite the fact that the subject matter is inherently more difficult to study, researchers are forced into the same publish-or-perish system as biologists and mathematicians. A higher degree of skepticism towards new studies might technically be prejudice, but itâs certainly justified.
robertlagrant | 3 comments | 3 days ago
readthenotes1 | 0 comments | 3 days ago
lifeisstillgood | 0 comments | 3 days ago
fecal_henge | 0 comments | 3 days ago
tokai | 0 comments | 3 days ago
martin82 | 0 comments | 3 days ago
Not that it matters at all.
dbcooper | 2 comments | 3 days ago
magicalhippo | 0 comments | 3 days ago
[1]: https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1
Thoreandan | 0 comments | 3 days ago
husamia | 0 comments | 2 days ago
kylehotchkiss | 1 comment | 3 days ago
Do these have a known utility or is it possible some junk DNA is involved with their encoding?
joe_the_user | 0 comments | 3 days ago
Notably, I think the "viruses first" theory for the origin life has gained force. This says that first came protein/DNA soup, then came viruses and only then came cellular organisms.
And if you want something that doesn't "piggyback", you'd have to wait for photosynthesizing plants and that's several steps further in evolution (in my layman's understanding of current theory).