'Obelisks', a new class of life living inside humans

Obelisks eh? I wish this article had more on the dimensions of these little critters. Was hoping to read that they’re of 1:4:9 proportions, and thus the given name was a sort of hat tip…

Cue Zarathustra

yawnxyz• 1 year ago

This was a good thread on Obelisks: https://news.ycombinator.com/item?id=42547489

dang2• 1 year ago

Thanks! Macroexpanded:

'Obelisks': New class of life has been found in human digestive system - https://news.ycombinator.com/item?id=42547489 - Dec 2024 (134 comments)

'Obelisks': New Class of Life Has Been Found in the Human Digestive Sys - https://news.ycombinator.com/item?id=42498562 - Dec 2024 (1 comment)

New 'Obelisks' Class of Life Has Been Found in the Human Digestive System - https://news.ycombinator.com/item?id=39205052 - Jan 2024 (1 comment)

'Obelisks': New Class of Life Has Been Found in the Human Digestive System - https://news.ycombinator.com/item?id=39191349 - Jan 2024 (3 comments)

New Class of Life Has Been Found in the Human Digestive System - https://news.ycombinator.com/item?id=39174881 - Jan 2024 (2 comments)

fuzzfactor• 1 year ago

A never-before-seen class?

Seems like experts would need to consider any "inheritance" issues that might have been unexpected . . .

kens• 1 year ago

Although the title says "just discovered", obelisks were discovered a year ago. Obelisks are RNA elements inside bacteria inside humans. Here are some links for more information:

The publication in Cell: https://www.cell.com/cell/abstract/S0092-8674(24)01091-2

The preprint: https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1

An article about obelisks in Science: https://www.science.org/content/article/it-s-insane-new-viru...

An article in Derek Lowe's popular "In the Pipeline": https://www.science.org/content/blog-post/what-s-obelisk-any...

dang2• 1 year ago

Ok, we've taken out the 'just discovered' bit from the title above. Thanks!

ninalanyon• 1 year ago

The article makes it sound as though this is something only humans have. Which struck me as very odd.

But the paper in Cell says:

"• Found globally in diverse niches, obelisks also occur in human stool and oral microbiomes"

https://www.cell.com/cell/abstract/S0092-8674(24)01091-2

Much more reasonable.

adrian_b3• 1 year ago

Free preprint:

https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1

ahazred8ta• 1 year ago

They resemble a single stranded circular RNA plasmid, stuck together into a hairpin shape. Plant viroids are 250-450 bases long, while obelisks seem to be in the 1000-1200 range. https://en.wikipedia.org/wiki/Circular_RNA -- https://en.wikipedia.org/wiki/Hepatitis_D

enkid• 1 year ago

If viruses usually aren't considered alive, why would obelisk? I'm also curious how we know these are independent structures versus a by product of our own or our resident bacteria's cellular function. The mRNA seems unrelated to our own, but perhaps there's an unknown process that either generates new extracellular mRNA to create these protiens referenced in the article. Alternatively, could these be mRNA strands that escaped the cellular destruction process?

adrian_b3• 1 year ago

I do not agree with considering viruses as not alive.

A viral particle outside its host can be considered dead, in the sense that it is inert and it does not have any metabolism, but it is not definitively dead, as it will become alive again when entering a host. Alive in the sense that inside their host cells viruses observe the command "Crescite et multiplicamini" from the bible (grow and multiply), in the same way like any other living beings, even if they have to take control of various components of the host cell in order to do that.

I do not see any essential difference between a viral particle and a dormant seed or a bacterial or fungal spore or an encysted protozoan.

All such resistant forms of living beings have the purpose of remaining intact in environments where they cannot found the food or water or air that they need for a normal life. Viruses have the least demands from their environment, while the others may have greater requirements, e.g. the presence of small amounts of free oxygen and water in their environment, in order to not die permanently, but that is more like an imperfection in their current design, not an intrinsically necessary attribute.

Viruses cannot live without their hosts, but that is true for any obligate parasite. Humans can also not live independently, at least for now, but only together with many other living beings able to synthesize the substances that we cannot. Therefore it is hard to draw a line between alive and non alive based on the amount of dependencies on other living beings.

It certainly is more useful to include viruses in what is covered by the word "alive", because they are subjected to the same kind of evolution like the cellular living beings. Moreover in the same way like many kinds of cellular living beings have appeared by hybridization between cellular living beings with distinct genetic heritage, there are also plenty of cases where new species of cellular living beings have appeared by hybridization with viruses, i.e. by incorporating permanently in their genome some genetic material from a viral ancestor. This includes even humans (and all other vertebrates).

Therefore, if you draw a graph of the genetic relationships between cellular living beings, it is inextricably intermingled with the corresponding graph for viruses.

So I think that the most convenient way is to consider that the living beings are divided into cellular living beings and viruses.

Regardless of the word choice, biology must study both cellular living beings and viruses, anyway, because none of them can be understood in isolation from the others.

Myrmornis• 1 year ago

It's as the sibling post says: "alive vs not alive" and "same species vs different species" are just human concepts that we attempt to shoehorn biological reality into. There's nothing about biology itself that says that any given example should have a clear answer either way.

greazy• 1 year ago

As someone who works on viruses, we don't worry or care whether viruses are alive.

It's more of a philosophical question, and distilled down its really about whether viruses fit into a human centric view point of the world. We like to classify things into discrete groups. Biology is not discrete.

ProllyInfamous• 1 year ago

I'm about 3/4 done with The Demon in the Freezer (about: Level 4 labwork) and viruses seem very much willed-to-live...

paulddraper2• 1 year ago

Correct.

Viruses are traditionally “not life” because they don’t grow, convert nutrients to energy, or reproduce independently.

(Some smart commenter will point out something, but there is some difference. The complexity chasm between bacterium and virus is huge.)

But applying a colloquial definition, they can be.

adrian_b3• 1 year ago

Humans don't grow, convert nutrients to energy, or reproduce independently.

Humans need every day about 30 organic substances that they cannot synthesize, so these substances must be obtained from bacteria, plants and other animals.

Due to having internal reserves, a human will not die immediately when isolated from other living beings, but only after a month or even slightly more. A month of independent life is not enough to grow and reproduce.

However a virus that is encapsulated in its transmission form will also not die definitively immediately, but it can survive for many years independently of any other living beings, i.e. much more than a human can live independently.

There is a huge complexity chasm between any bacterial cell and a virus, but there is also a huge complexity chasm between a virus and any mineral or any chemical substance whose synthesis is known to be possible in abiotic conditions.

There is no doubt that cellular living beings and viruses are 2 very different kinds of things, but both are also very different from any non-alive things.

There are many characteristics common for cellular living beings and viruses, so normally one would need a single word for both of them, to avoid enumerating both of them whenever a sentence is true for both.

The most convenient is to call both of them as living. Those who do not include viruses between living beings utter extremely frequently sentences that are either incorrect or incomplete, because they are true for both cellular living beings and for viruses, but the authors mention only "living beings" with the meaning "cellular living beings", even if those sentences are equally true for viruses.

If you call viruses as non-living, then you must also say that humans and most animals have among their ancestors non-living entities, because our genome incorporates genes that have been obtained from viral ancestors.

The concept of viruses as "non-alive" has been an overcompensation for the previous belief that viruses might be living beings like any others. When it has been discovered than viruses are very different from cellular living beings there has been a fashion to call them non-alive, to demonstrate that one is up-to-date with scientific knowledge and one knows that viruses are very different from cellular beings in many features, even if they are alike in others.

Unfortunately this phenomenon has been very frequent in the history of scientific terminology. There are plenty of examples when after some people had discovered that some things are more different from other related things than previously believed, they gave a new name to their discovery, claiming complete distinctness from what was previously known, even if the correct point of view was midway, i.e. even if the new things were distinct enough to be classified as something different, they also shared enough characteristics with what was previously known to be better considered as just a new subclass of those things.

thebeardisred• 1 year ago

Does anyone else find it odd that we're getting virus news from the former android news aggregator "Boy Genius Report"?

'Obelisks', a new class of life living inside humans

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