When I was an academic working in the bacterial virus (phage) field my lab used to find these viruses with no similarity to anything in the databases all the time. We would find virus after virus that had a totally unique genome. The only way we could identify the genes that encoded the structural proteins was to extract the virus proteins from purified viruses and get them mass speced.
The really amazing thing is if you looked at these viruses under an electron microscope they looked exactly like known viruses (most looked like a lambda phage [1]). There seems to almost an infinite number of ways of making viruses that look just like lambda.
The more I think about this, the more distressing this gets. I'd love to hear a little more about this.
Does this mean lambda phage form is some sort of biology's equivalent (or as close as it gets) of a universal constant, or rather — was the genes that encode the 'container' (apologies for my lack of correct terminology here) the same, and the viral payload different, or is it also the case that the 'container code' is also unique between these viruses?
>Does this mean lambda phage form is some sort of biology's equivalent (or as close as it gets) of a universal constant
Maybe this is somewhat true for bacterial viruses, but it's worth noting it's not universally true for phages. eg see [0]. And I can't think of any mammalian viruses that are lambda phage style lunar landers. Sometimes, virses are cyclinders [1] or some kind of roughly spherical geometric structure [2], although some are just kinda blob shaped [3] enveloped viruses (some viruses have an envelope-capsid-envelope structure).
Yes I think the “lambda” form is close to the most efficient structure that bacterial virus can take. The really interesting question is if this common form is a case of convergent evolution, or if the lack of similarity between all the viral genomes is due to the ancient origins of this virus.
One thing is certain and that is that we have barely scratched the surface of genetic diversity on this planet.
I don't doubt it. I would be willing to bet that that (unranked category) of "life" is one of the least cataloged. Plus, consider the variance in speed of lateral transfer and mutation.
> Viral novelty doesn’t surprise Elodie Ghedin of New York University, who looks for viruses in wastewater and in respiratory systems. More than 95% of the viruses in sewage data have “no matches to reference genomes [in databases],” she says. Like Abrahão, she says, “We seem to be discovering new viruses all the time.”
You don't know what you don't know, I guess. That also means there is an invaluable wealth of genetic knowledge out there that we haven't recorded yet. I can't wait to see what insights are revealed once we've catalogued that missing 95%.
As a species we've barely scraped the surface of understanding this earth. Consider: we haven't even scratched the crust of the planet. Not to mention the infinite space beyond.
This is sorta why it makes me even more mad that our species is more concerned about silly political arguments rather than investing large fractions of our GDP into Science, educating more scientists and unleashing them on the mysteries that the world has to offer.
Instead the greatest minds of our generation are now focused on selling ads. It feels so pointless.
> This is sorta why it makes me even more mad that our species is more concerned about silly political arguments rather than investing large fractions of our GDP into Science, educating more scientists and unleashing them on the mysteries that the world has to offer.
Science costs money and resources. Politics enables money creation and resource extraction. The capacity of our current society to do science is greater than in any society in history. That’s no accident. It’s the direct result of the environment created by our political decisions.
The Soviet Union is a great counter example. For a short time, it was at the forefront of science, thanks to the state directing resources to science. It was only due to the untimely death of the head of its space program, for example, that the Soviet Union didn’t beat the United States to the moon. But did the Soviet Union cure AIDS? Create the Internet? Create smartphones? No. It’s politics weren’t sustainable, and it collapsed, and in the long run, its capacity to do science turned out to be quite limited.
So maybe our “silly political arguments” serve a function after all?
The short book "A Planet of Viruses" includes this little fact and more, it's a good read for people who want an ELI5 introduction to what's known. My only change would be to have more pictures, but there's always the internet for that.
that's not just true for viruses, it's true for pretty much anything. we've barely scraped the surface in terms of sequencing microbes, fungi, plants, birds, fish, ..., not to even consider variation at the population (or god forbid, somatic cell) level.
Back in the day, you only knew about microorganisms and viruses that you knew how to grow. And that apparently excludes about 99.9% of stuff.
In Biology 101, I recall that we cloned bacteria from sewage, and then cloned a bacteriophage. But the instructors were very careful that we cloned E. coli :)
> Marine viruses, although microscopic and essentially unnoticed by scientists until recently, are the most abundant and diverse biological entities in the ocean. Viruses have an estimated abundance of 10^30 in the ocean.
Marine bacteriophages kill about 40% of all bacteria in the ocean every day.
(I don't know why you don't explode into viruses ten seconds after you enter the ocean, there must be a way that the maelstrom of evolution doesn't create monsters, eh? Or maybe we are playing Russian Roulette every time we go in the water?)
> (I don't know why you don't explode into viruses ten seconds after you enter the ocean, there must be a way that the maelstrom of evolution doesn't create monsters, eh? Or maybe we are playing Russian Roulette every time we go in the water?)
If humans start living in contact with the oceans for long enough we might! Viruses may seem magical but as with life, its statistics over the long run. There might be viruses with mutations that cause them to annihilate humans; but those mutants may just never have had the chance to come in contact with us and thus die off, or at least don't multiply.
I know "no recognizable genes" is in the title, but it's misleading. They're recognizable as genes, but never seen before:
> When the team sequenced its genome, none of its genes matched any scientists had come across before, the group reports on the bioRxiv preprint server.
These viruses seem to be as ancient as cellular life, and may preserve genes that did not become incorporated into the last common ancestor of living beings. That, or new protein families evolve even today.
> Some of Yaravirus’s genes look like those in a giant virus, but it’s still unclear how the two are related, Abrahão says. He and his colleagues are still investigating other aspects of the novel virus’s lifestyle.
I don't know enough about this stuff to comment coherently. Last I knew, it wasn't clear whether viruses were remnants of prebiotic stuff, or derived from cellular organisms, or some of each.
When I was a child I read a book of short stories, I think it may have been Ray Bradbury. Anyway a cosmonaut leaves earth at near-light speeds and returns what are a few months to him, I dont remember how many years had passed on earth. The world was covered in green goo and the only people left were Americans and Russians living in submarines and still trying to kill each other with biological warfare. I believe anyway, this was about 25 years ago. It made me very afraid of all arms races. Does anyone happen to know the name of the author/book/story?
The RNA-world hypothesis conjectures that life started via a chemical soup developing things similar to viroids.
These early RNA-based replicators would go on to become more complicated, first developing a protective barrier and then specialized organelles.
As a byproduct of that process, viruses developed which could interact with organelles (or just the soup inside a cell) to reproduce themselves without being part of the host "genetic code".
In approximate complexity order:
- self-replicating compound, in solution with precursors
- viroid
- virus
- bacteria
- archaea
- eukaryota
From that perspective, hiding viroids (or similar simple replicators) in comets and boosting them into other systems would be a relatively efficient way to "seed" life around the cosmos.
To me, viruses are simply the survival horde of random mutation and recombination of amino acids. Let it be long enough and a world of organic compounds would create something like viruses.
Technically it is a hypothesis which does not yet have a good experimental design that might prove or falsify it. And in that aspect it isn't "canon" so it isn't "reality." But it is far from being a preposterous idea, and there are labs that are working on various ideas on how one might prove or disprove it.
It's also possible it's attached to other parts of reality. Maybe this is thing that happens with great frequency in other parts of the universe/multiverse, even if it may not be what happened here.
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The really amazing thing is if you looked at these viruses under an electron microscope they looked exactly like known viruses (most looked like a lambda phage [1]). There seems to almost an infinite number of ways of making viruses that look just like lambda.
1. https://en.wikipedia.org/wiki/Lambda_phage
Does this mean lambda phage form is some sort of biology's equivalent (or as close as it gets) of a universal constant, or rather — was the genes that encode the 'container' (apologies for my lack of correct terminology here) the same, and the viral payload different, or is it also the case that the 'container code' is also unique between these viruses?
Maybe this is somewhat true for bacterial viruses, but it's worth noting it's not universally true for phages. eg see [0]. And I can't think of any mammalian viruses that are lambda phage style lunar landers. Sometimes, virses are cyclinders [1] or some kind of roughly spherical geometric structure [2], although some are just kinda blob shaped [3] enveloped viruses (some viruses have an envelope-capsid-envelope structure).
0. https://en.wikipedia.org/wiki/Phi_X_174 1. https://en.wikipedia.org/wiki/Tobacco_mosaic_virus 2. https://en.wikipedia.org/wiki/Mimivirus 3. https://en.wikipedia.org/wiki/Influenza
One thing is certain and that is that we have barely scratched the surface of genetic diversity on this planet.
> Viral novelty doesn’t surprise Elodie Ghedin of New York University, who looks for viruses in wastewater and in respiratory systems. More than 95% of the viruses in sewage data have “no matches to reference genomes [in databases],” she says. Like Abrahão, she says, “We seem to be discovering new viruses all the time.”
You don't know what you don't know, I guess. That also means there is an invaluable wealth of genetic knowledge out there that we haven't recorded yet. I can't wait to see what insights are revealed once we've catalogued that missing 95%.
This is sorta why it makes me even more mad that our species is more concerned about silly political arguments rather than investing large fractions of our GDP into Science, educating more scientists and unleashing them on the mysteries that the world has to offer.
Instead the greatest minds of our generation are now focused on selling ads. It feels so pointless.
Science costs money and resources. Politics enables money creation and resource extraction. The capacity of our current society to do science is greater than in any society in history. That’s no accident. It’s the direct result of the environment created by our political decisions.
The Soviet Union is a great counter example. For a short time, it was at the forefront of science, thanks to the state directing resources to science. It was only due to the untimely death of the head of its space program, for example, that the Soviet Union didn’t beat the United States to the moon. But did the Soviet Union cure AIDS? Create the Internet? Create smartphones? No. It’s politics weren’t sustainable, and it collapsed, and in the long run, its capacity to do science turned out to be quite limited.
So maybe our “silly political arguments” serve a function after all?
Don't forget the ones playing zero sum games, like high frequency trying.
And money gives you power. The greatest minds are focused on making money for themselves and someone else.
Ads make money unfortunately. Knowledge about our planet earth does not.
In Biology 101, I recall that we cloned bacteria from sewage, and then cloned a bacteriophage. But the instructors were very careful that we cloned E. coli :)
To be catalogued, whatever it is has to be noticed first. The world is much too big for that to happen to most things.
Seems like a fun field to go into if you want something named after yourself (and your family, and your friends, and your pet)
https://www.goodreads.com/book/show/10840041-a-planet-of-vir...
There are viruses that go into the hosts DNA, replicate along with it over generations, then wake up and start being viruses again!
The oceans are Grey Goo. https://en.wikipedia.org/wiki/Grey_goo https://en.wikipedia.org/wiki/Marine_bacteriophage
> Marine viruses, although microscopic and essentially unnoticed by scientists until recently, are the most abundant and diverse biological entities in the ocean. Viruses have an estimated abundance of 10^30 in the ocean.
Marine bacteriophages kill about 40% of all bacteria in the ocean every day.
(I don't know why you don't explode into viruses ten seconds after you enter the ocean, there must be a way that the maelstrom of evolution doesn't create monsters, eh? Or maybe we are playing Russian Roulette every time we go in the water?)
If humans start living in contact with the oceans for long enough we might! Viruses may seem magical but as with life, its statistics over the long run. There might be viruses with mutations that cause them to annihilate humans; but those mutants may just never have had the chance to come in contact with us and thus die off, or at least don't multiply.
Basically, none of our ancestors did. Or vice versa, mutatis mutandis, and so on.
> When the team sequenced its genome, none of its genes matched any scientists had come across before, the group reports on the bioRxiv preprint server.
https://www.biorxiv.org/content/10.1101/2020.01.28.923185v1....
> Some of Yaravirus’s genes look like those in a giant virus, but it’s still unclear how the two are related, Abrahão says. He and his colleagues are still investigating other aspects of the novel virus’s lifestyle.
I don't know enough about this stuff to comment coherently. Last I knew, it wasn't clear whether viruses were remnants of prebiotic stuff, or derived from cellular organisms, or some of each.
Aren't viruses dependent on hosts?
These early RNA-based replicators would go on to become more complicated, first developing a protective barrier and then specialized organelles.
As a byproduct of that process, viruses developed which could interact with organelles (or just the soup inside a cell) to reproduce themselves without being part of the host "genetic code".
In approximate complexity order:
- self-replicating compound, in solution with precursors
- viroid
- virus
- bacteria
- archaea
- eukaryota
From that perspective, hiding viroids (or similar simple replicators) in comets and boosting them into other systems would be a relatively efficient way to "seed" life around the cosmos.
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