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.
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?
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.)
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.
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.
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.
> 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.
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.
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.
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.
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.
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.
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.
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.
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?
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)
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.
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.
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.
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.
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
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?
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!
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?
Humans aren’t symmetrical though.
This would more like zooming into one edge of a snowflake and then rotating it.
> 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.)
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.
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
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!
According to this article the image is computed and not really directly captured https://www.chemistryworld.com/news/explainer-what-is-cryo-e...
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.
This isn't fraud ... see the informative comments nearby.
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.
> 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...
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.
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.
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.
> 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.
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.
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.
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.
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?
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)
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.
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.
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.
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.
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.
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.
Interesting, hope that these discoveries can be used to fight those amoeba's which cause infections as well!
We have discovered a new giant DNA virus that may help us fight life-threatening amoebae was good enough.