[HN Gopher] Ushikuvirus: Newly discovered virus may offer clues ...
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Ushikuvirus: Newly discovered virus may offer clues to the origin
of eukaryotes
Author : rustoo
Score : 126 points
Date : 2026-01-08 04:39 UTC (1 days ago)
(HTM) web link (www.tus.ac.jp)
(TXT) w3m dump (www.tus.ac.jp)
| Chance-Device wrote:
| Incidentally, anyone know what is going on with this image -
| "Cryo-EM map of a center slice of the ushikuvirus particle":
| https://journals.asm.org/cms/10.1128/jvi.01206-25/asset/1357...
|
| It's one quarter of an image flipped horizontally and then
| vertically, you can see the patterns.
|
| It's a bit odd to do that? Shouldn't it just be the original EM
| image?
| jiggawatts wrote:
| Rampant fraud in science papers has reached the point where
| hobbyists can point out obviously fake charts and graphics even
| in prestigious journals.
|
| Publish or perish needs to end.
| jibal wrote:
| This isn't fraud ... see the _informative_ comments nearby.
| RicoElectrico wrote:
| According to this article the image is computed and not really
| directly captured
| https://www.chemistryworld.com/news/explainer-what-is-cryo-e...
| observationist wrote:
| https://www.sciencedirect.com/science/article/pii/S104784772...
| - there are similar results in this paper, too.
|
| After a bit of digging - it looks like it's done to sharpen
| features as one of the standard steps in producing these
| images. Where there are rotational symmetries in the things
| they're looking at, they focus on the smallest unit, and then
| rotate accordingly. If you had a trilateral symmetry, or
| hexagonal structure, they'd rotate 3 or 6 times around the
| center.
|
| You're not getting a real image of the thing, but apparently
| it's got data from those other segments mixed in with the
| rotations, so you're getting a kind of idealized structure, to
| make the details being studied pop out, but if you have some
| sort of significant deviation, damage, or non symmetric feature
| it'll show up as well.
|
| It's called "imposed symmetry"
| https://discuss.cryosparc.com/t/what-is-actually-occuring-wh...
|
| Neat stuff, cool thing to catch!
| Terr_ wrote:
| So kind of like taking a picture of a human, and then taking
| each half, flipping along the midline, and blending to get an
| idealized Symmetrical Human?
| hnlmorg wrote:
| Humans aren't symmetrical though.
|
| This would more like zooming into one edge of a snowflake
| and then rotating it.
| Terr_ wrote:
| > Humans aren't symmetrical though.
|
| Perhaps you assumed a "radially" which wasn't part of my
| analogy? :p
|
| Land animals have a pretty consistent trend of exterior
| bilateral symmetry which is very noticeable. (Naturally,
| a completely normal Hunam such as myself cannot speak for
| how it may work in places other than my home planet
| Dirt.)
| hnlmorg wrote:
| I understood you meant bilateral symmetry. And yes, there
| are similarities, but we are not bilaterally symmetric.
| At least not to the extent where you can flip an image
| and have that look normal.
|
| Even faces look weird when flipped that way (there have
| been studies on this effect too). And that's before you
| get into the issue that it's common to have differently
| shaped breasts, different sized hands or feet. Ears
| shaped differently. Non-uniform teeth. And so on and so
| forth.
| yencabulator wrote:
| Only superficially.
|
| https://en.wikipedia.org/wiki/Axial_twist_theory
| Bjartr wrote:
| I think that might just be the original and it simply is
| symmetrical to that degree. I found a few more examples of
| "cryo-em center slices" and I've yet to find one that doesn't
| have really strong symmetry down to the small dot patterns.
|
| A different paper, this figure shows a number of cryo-em
| images, including a simulation, and they all show the same
| degree of pattern symmetry
| https://www.researchgate.net/figure/Central-sections-through...
|
| First figure in this third paper also shows symmetry of small
| patterns https://journals.asm.org/doi/10.1128/jvi.00990-22
| Chance-Device wrote:
| Thanks, those examples make it pretty clear.
|
| I still think it's super weird that it looks exactly like an
| EM image, but is generated. Anyway, good to know!
| possiblelion wrote:
| Interesting, hope that these discoveries can be used to fight
| those amoeba's which cause infections as well!
| embedding-shape wrote:
| I remember someone talking about "last universal common ancestor"
| at some point, the single "origin of the cells" or something. Is
| that the same as the "archaeal ancestor" they're referring to
| here? And is the "archaeal ancestor" the same as the "Primitive
| archael cell" mentioned in the last image in the article?
| (https://www.tus.ac.jp/en/mediarelations/20251219_9539_03.png)
| Tagbert wrote:
| From what I know - There are two sister groups, the Archae and
| Bacteria. Their ancestor would be LUCA. The first Archae would
| be the archaeal ancestor. There should be a first bacteria to
| match that.
|
| I believe that Eukaryotes then from Archae.
| adrian_b wrote:
| For now, it is still not certain whether Archaea is the
| sister group of all Bacteria, or only of one branch of
| Bacteria.
|
| There are some very important differences between Archaea and
| Bacteria, in membrane composition and in the nucleic acid
| replication and protein synthesis mechanisms, but there are
| several hypotheses about how these differences could have
| evolved and there is not enough evidence yet to be sure which
| of them is true, i.e. whether the distinctive membranes,
| ribosomes and certain enzymes of Archaea have never been like
| those of Bacteria, or they have evolved from those of
| Bacteria.
|
| The eukaryotes are hybrids, mainly between some Archaea and
| some bacteria (the ancestors of mitochondria). It is not
| completely certain whether the ancestor of the eukaryotes
| from Archaea belonged to a branch that was sister to all
| still existing Archaea or only of one branch of Archaea, but
| here the evidence makes it very likely that the ancestor of
| the eukaryotes belonged to an interior branch that was nested
| within the existing Archaea, i.e. it was sister to only one
| branch of the present Archaea.
|
| In the history of life, there have been many events of
| hybridization between very distant living beings, so the tree
| of evolution is only approximately a tree, while actually
| being a more general directed graph. A part of these events
| have been the results of symbiosis, the most frequent cases
| being of symbiosis with some phototrophic organism able to
| capture solar light or with some bacteria able to consume
| some unusual substance from the environment.
|
| Other such hybridization events have been with viruses, when
| the genes for some enzymes have been transferred permanently
| from viruses to their hosts and they have been retained,
| presumably for being better than the versions used by the
| hosts for the same function, previously. Even vertebrates and
| humans have a small fraction of their genome that originates
| from viruses.
| pfdietz wrote:
| I believe "archaeal cell" is referring to an Archaea, one of
| the three branches of life. All three branches derive from a
| more distant ancestor, LUCA. LUCA was undoubtedly preceded by
| other ancestors, but there is (by definition) nothing else
| branching from them that has survived.
| Terr_ wrote:
| I anticipate the definition will become increasingly
| subjective as we find biology-messiness inconsistent with our
| concepts of ancestry.
|
| For example, suppose horizontal gene transfer occurs from
| organism X to organism Y. Does that mean Y is now a branch of
| X?
|
| * Does it depend on _how much_ was transferred?
|
| * Does it matter only if the specific sequence was passed
| down? If so, how much mutation is too much mutation?
|
| * What if the same end-result occurred through a retrovirus
| instead of a plasmid. Is the virus an ancestor too?
|
| * What if the swap was simultaneous and bidirectional?
|
| * What about transitive links to organisms W, V, U that did
| the same?
|
| * Are mitochondria "us" yet? If so, are we the ancestors if
| they redevelop enough machinery to "escape"?
|
| etc.
| jibal wrote:
| The article discusses the (highly speculative) _hypothesis_
| that eukaryotes arose from a virus merging with an archaeal
| ancestor to form a nucleus. If the hypothesis is false (it is
| widely believed that eukaryotes arose from a joining of archaea
| and bacteria, not archaea and virii) then "an archaeal
| ancestor" doesn't even have a referent.
|
| The LUCA is the common ancestor of bacteria and archaea. That
| would have existed far earlier, as neither of those are
| eukaryotes.
| vintermann wrote:
| I'd like to take the opportunity to post this classic about
| the plural of virus:
|
| https://www.ofb.net/~jlm/virus.html
|
| More because it's funny than that it matters.
| jibal wrote:
| Yeah, I knew this but had a bout of brain flatus.
| gus_massa wrote:
| > _it is widely believed that eukaryotes arose from a joining
| of archaea and bacteria, not archaea and virii_
|
| IIUC the join with the bacteria is the explanation of the
| mitochondria (and later chloroplast). But it does not explain
| the nuclei that is weird too. Is it possible something like
| this? Archaeal + Virus = Pre-Eukaryote
| (extinct?) Pre-Eukaryote + Bacteria = Eukaryote
| (including animals, fungi and plants) Eukaryote + other
| Bacteria = Plants
|
| (Or swap the first two steps.)
| jibal wrote:
| > IIUC the join with the bacteria is the explanation of the
| mitochondria (and later chloroplast). But it does not
| explain the nuclei that is weird too.
|
| You're right ... my mistake.
| thangalin wrote:
| My brief, illustrated history of Microbial Mats (p.10) to
| Multicellular Eukaryotes (p.13) may be of interest:
|
| https://impacts.to/downloads/lowres/impacts.pdf
| BitwiseFool wrote:
| This is quite well made, thank you for sharing. I appreciate
| the relevance and knowledge section on each page's subject.
| avadodin wrote:
| We have discovered a new giant DNA virus that may help us fight
| life-threatening amoebae was good enough.
| adityaathalye wrote:
| Lends a whole other colour to that scene from The Matrix... Agent
| Smith monologuing at Morpheus bound to the chair.
|
| > Agent Smith: I'd like to share a revelation during my time
| here. It came to me when I tried to classify your species. I
| realized that you're not actually mammals. Every mammal on this
| planet instinctively develops a natural equilibrium with the
| surrounding environment but you humans do not. You move to an
| area and you multiply and multiply until every natural resource
| is consumed. The only way you can survive is to spread to another
| area. There is another organism on this planet that follows the
| same pattern. Do you know what it is? A virus.
|
| ref: "Smith Interrogates Morpheus Transcript"
| https://scottmanning.com/content/smith-interrogates-morpheus...
|
| ---
|
| Edit: Maybe it takes virulence to colonise the galaxy. A sobering
| thought.
| Erlangen wrote:
| > Every mammal on this planet instinctively develops a natural
| equilibrium with the surrounding environment but you humans do
| not.
|
| Though it's an interesting quote, I have to disagree. The
| reindeers on St. Matthew Island continued to multiply and
| depleted their food resources without any predators, until an
| extreme snow storms struck. They don't "instinctively" develops
| a natural equilibrium.
|
| https://www.adn.com/features/article/what-wiped-out-st-matth...
| kakacik wrote:
| Yeah 'instincts' are in real world just enough external
| pressure and death to keep the equilibrium going, whatever
| grisly happens behind the curtains.
|
| Hunters hunt as much as they can. Wolves regularly kill 10 or
| 20 sheep while eating one if they get the chance. Foxes do
| similar stuff with chickens. Nature is brutal and without
| empathy.
| cestith wrote:
| Housecats let outdoors often don't even eat what they hunt,
| because they have a steady supply of their favorite food in
| the house. They just hunt and kill because they are furry
| little murder machines. They really shouldn't be let
| outside unsupervised.
| embedding-shape wrote:
| > They really shouldn't be let outside unsupervised.
|
| Alternatively, get them a collar with a little bell, and
| let them try (and always fail) to hunt.
| cestith wrote:
| I guess the odd deaf squirrel wasn't likely to last long
| anyway. A bell could work to keep them from stalking.
| They can still run, leap, and ambush. It seems a bell
| should at least greatly mitigate the issue. I might say
| usually rather than always. To be fair, though,
| supervision won't stop them every time either.
| embedding-shape wrote:
| > They can still run, leap, and ambush.
|
| Whenever they do, there is a little _tingle_ _tingle_ ,
| whatever tiny little movement they're trying to do. They
| end up unable to catch anything basically, I literally
| never witnessed one of our cats catching anything growing
| up, nor them bringing any "gifts".
| close04 wrote:
| They don't develop this equilibrium "instinctively"
| (something exclusively inside them) but they do "naturally"
| (helped by the environment). Now the reindeer weren't really
| in their natural environment, they were put in very
| constrained, special conditions, with little flexibility,
| little time to adapt, and no ability to shape that
| environment. The environment forced them to adapt and lower
| the numbers, and eventually wiped them out with what was also
| probably a fluke. They were still 50% more individuals than
| when they arrived but no viable reproduction path ahead.
|
| This was an extreme example. Put humans on this type of
| island and you'll probably end up with them dying out just
| the same, despite our tendence to radically change the
| environment to survive. After all that's why the reindeer
| were there, so humans can survive absent a constant lifeline
| from civilization.
|
| Humans, and viruses to a degree, are much better at shaping
| their environment and adapting faster to what's thrown at
| them to compensate. The instinct is to change whatever
| possible of the surroundings to survive and thrive.
| perrygeo wrote:
| This. Mammals are (generally) K-selected species, meaning
| they invest heavily in raising their young. In the absence of
| natural pressures, mammals reproduce like crazy until they
| bump up against the environment's carrying capacity. Humans
| are not unique at all in our tendency to expand! It's just
| that we have opposable thumbs and language and tools to help
| us boost the carrying capacity.
| notarobot123 wrote:
| I never understood where the desire to "colonise the galaxy"
| comes from. Why is this a desirable goal? Compared to anywhere
| else we know about, Earth is an extremely unique utopia. A
| "better" planet would be measured in how Earth-like it is -
| perhaps bigger or with more/different exploitable resources.
|
| The only driver that I can really comprehend is the desire for
| freedom and autonomy in less populated spaces. The problem with
| this is that the human condition follows us everywhere. We'll
| recreate the same problems we have here everywhere we go. We
| can't run away from ourselves.
| DavidPiper wrote:
| I don't really think about this much, but your comment made
| me wonder:
|
| If we do find another earth-like planet within travel
| distance (impossible afaik but let's suspend disbelief for a
| moment), how do we determine whether it's worth colonising?
| And how to we measure it?
|
| "The resources on this planet will last 15.6B person-years
| which means if we send 5 million people there over time, we
| will have to prepare for their evacuation in ??? years"?
|
| Obviously totally moot if Earth's resources aren't going to
| last that long, but just had that thought bubble up.
| ZaoLahma wrote:
| Spread the risk and reduce the probability of extinction.
|
| We know for a fact that earth is doomed, on top of our own
| continuous efforts to kill ourselves off. No not recent
| climate change type of doomed, but the evolution of our sun
| is continuously pushing the habitable zone outwards. We might
| be able to deal with that particular annoyance by hiding
| underground when it becomes an emergency in half a billion
| years or so, but our utopia won't be as utopic anymore.
|
| Eventually however, the sun will balloon to a red giant at
| which point we better have a plan in place other than staying
| on this planet.
| SketchySeaBeast wrote:
| If we're thinking that far out we might as well all just
| lay down and wait for rain because there's no avoiding the
| heat death of the universe. Treating the sun dying out like
| it's a real concern that we need to address in the next 2,
| 200, 2,000, or 2,000,000 years is comical. Whatever is
| around to experience that won't be human as we know it.
| kakacik wrote:
| Mankind will either spread further or die, this is binary.
| How much spread we can achieve or how much is even possible
| (ie due to limit of speed of light) is another topic, but if
| we want even with c being the absolute limit we can colonize
| milky way in maybe 100 million years if we want... in theory.
| mr_mitm wrote:
| But for what? The beings that will have populated the milky
| way in 100 millionen years will not be humans anymore due
| to evolution. Some planets will be thousands of light years
| apart, meaningful communication will be impossible. Species
| will diverge. Why should I care about such a future?
| kakacik wrote:
| Some people, both men and women, like to see their
| specific genes propagating and thriving. Built in by
| evolution definitely. Most parents do understand this.
| SketchySeaBeast wrote:
| I get it, it's an irrational desire, but with the
| timespans we're talking the evolutionary distance is
| greater than that between us and whatever fuzzy things
| was scurrying under the feet of the T-Rex.
| krisoft wrote:
| > Why is this a desirable goal?
|
| It doesn't have to be a desirable goal to everyone.
|
| > The only driver that I can really comprehend is the desire
| for freedom and autonomy in less populated spaces.
|
| You got one of the big ones. But not the only one. Other is
| survival. Here on Earth we are all one bad infection outbreak
| away from ending human society as we know it. We have all of
| our eggs in one basket. Even if we would have a stable
| foothold on the moon and mars we would still be vulnerable to
| gamma-ray bursts and crazy despots with nuclear armed
| missiles.
|
| > We'll recreate the same problems we have here everywhere we
| go.
|
| We do. There are still benefits to the people who are "taming
| the frontier". And that is enough for it to happen. We also
| see that even though human condition follows us different
| places have a different feel to them. Some places we got some
| things better while others worse.
|
| > Compared to anywhere else we know about, Earth is an
| extremely unique utopia.
|
| To a certain extent. We can adapt the environments to us. And
| we can adapt ourselves to new environments.
|
| When I move to the arctic I leave my parasol at home and buy
| a coat. When I move to a gas giant I need to rethink more of
| my biology. Imagine if some of us can become a buoyant sail
| with manipulating appendages who feels as much home in the
| red dot of jupiter as a homid feels home on a dewy meadow. If
| we could I would for sure give it a go for a few hundred
| years, then come back and write a book about how it was.
|
| The fact that this is not easy is part of the lure of it.
| embedding-shape wrote:
| > The only driver that I can really comprehend is the desire
| for freedom and autonomy in less populated spaces
|
| Exploration and seeing what's beyond seems to be innate in
| some people, not so much in others. Personally, if someone
| gave me to the opportunity today to "Sit in this rocket and
| get launched out into infinity and report back what's out
| there", I'd probably do it, and I'm sure I wouldn't be the
| only one. Curiosity would be enough for me to go.
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(page generated 2026-01-09 23:01 UTC)