A DNA ‘parasite’ may have fragmented our genes
quantamagazine.org
quantamagazine.org
It's likely parasites can alter our genetic expression and behavior today as well like rabies and toxoplasmosis(cats often have it). Rabies causing the fear of water is truly mind bending, how does it do that?!
Toxoplasma infection is classically associated with the frequency of schizophrenia, suicide attempts or "road rage". https://pubmed.ncbi.nlm.nih.gov/31980266/#:~:text=Toxoplasma....
Rabies:As the disease progresses, the person may experience delirium, abnormal behavior, hallucinations, hydrophobia (fear of water), and insomnia. https://www.cdc.gov/rabies/symptoms/index.html#:~:text=As%20....
And the craziest thing is, the cordyceps fungus doesn't actually infiltrate the ant's brain! Autopsies found the fungus spreads all over the ant's body, but not its brain!
But yeah, fungus directly controlling ant muscles, while it's brain is helpless is quite terrifying. Also terrifying is the raise of fungus infections in humans recorded in hospitals in India and UK in the recent years. If they do adapt to living in a warm human body we will have a major problem - fungus are killing more trees, bugs and reptiles than viruses and bacteria combined, the air in our cities is full of their spores.
It doesn't.
> Rabies:As the disease progresses, the person may experience delirium, abnormal behavior, hallucinations, hydrophobia (fear of water)
This is a weird mistake for the CDC to make. The etymological meaning of "hydrophobia" is "fear of water". But the English word is completely disconnected from that; it just means "rabies". Because of this, the disambiguation page for "Hydrophobia" on wikipedia links to rabies as well as to "aquaphobia", an actual fear of water which had to be named badly because the name "hydrophobia" was already taken.
Rabies was named "hydrophobia" because rabies patients will generally refuse water when it's offered to them. They do that because rabies makes it difficult to swallow, not because they're afraid of the water.
I don't really know how to find the answer to that question, though.
† I guess if it were a really literal translation of the Western term, it'd be 蜜尿病.
it's both! it's neither! oh, and it's also the runtime!
The best you get to shutting off (without permanent cell death) would be the computer equivalent of hibernation. All the proteins and RNA are still there just waiting for the signal to activate again.
Life doesn’t reboot as you say, it is split off from other organisms whether seed, sperm, rhizome or any other method it’s just cells dividing and spitting off other cells.
Mind boggling to me.
Why expect that the universe wouldn't subsequently continue to let it happen, again and again?
It's possible our origin was from a community of ancestral organisms, but at some point all terrestrial life that we have discovered so far intermixed enough to create an effective universal common ancestor that we all appear to branch from.
There is some evidence that things like the genetic code, the choice of RNA/DNA nucleotides, and the set of the 20 aminoacids aren't really random. That would not rule out life arising multiple times, but the likelihood that it merged with other lineages would be even higher.
Short summary: https://www.science.org/content/blog-post/why-these-amino-ac... . A more in-depth paper: https://www.sciencedirect.com/science/article/abs/pii/S03781...
I think over the span of billions of years, evolution tends to converge too much for the trees to remain very distinct from each other.
Some of this has been solved by literally allowing the microbes to sit in culture for a year or so in order to either wake up from hibernation, or adapt to the culture composition.
> see if the universal metabolic molecules like, for example, the hydrogen carriers NAD+/NADP+/NADPH, are truly universal.
For anything that's based on DNA or RNA we now do direct sequencing of environmental samples. From this direct sequencing we can pull out individual genes and pathways.
> I think over the span of billions of years, evolution tends to converge too much for the trees to remain very distinct from each other.
We've got over 20 recognized genetic codes already from existing life. These are highly similar, but this probably points to similar origins instead of convergence.
This is supposing that certain parts of the periodic table are more hospitable to biochemistry than others (i.e. that we don't have transition-metal-based life forms that just operate too slowly for us to notice, or some other orthogonal sort of way to be alive).
We are survivors(!) from a long-dead process. And have become far more than that process could have ever imagined, if it could have imagined.
We are Tron!
Fungal spores[0][1] come to mind.
[0] https://en.wikipedia.org/wiki/Spore#Fungi
[1] https://space.stackexchange.com/questions/37268/can-mushroom...
https://www.livescience.com/58309-how-tardigrades-survive-dr...
Ie, in the DNA => RNA => Protein cycle, viruses are a loop from Protein => DNA or Protein => RNA. Introners are a loop from RNA => DNA.
* DNA => RNA => Protein
* RNA => Protein
* RNA => DNA => RNA => Protein
As far as I know, there is no method to do Protein => DNA or Protein => RNA at the celular level.
It would be very surprising. RNA and DNA are quite similar and have similar encoding, so RNA <==> DNA is a 1 to 1 translation.
The translation to RNA to proteins is not 1 to 1, and the translations table is quite arbitrary, so untranslating at the celular level looks extremely difficult.
More like infecting compiler so every application build using it will include virus, including building compilers that will add virus code to their output and propagate it.
https://www.smithsonianmag.com/science-nature/virus-genes-hu...
This is a follow-up talk to his talk: 'DNA: The Code of Life' https://www.youtube.com/watch?v=EcGM_cNzQmE
“We are but a raft of genes in an ocean of retrotransposons”
A little hyperbolic, but dang there are a lot
Original paper: https://www.pnas.org/doi/10.1073/pnas.2209766119
> "Birth of new spliceosomal introns in fungi by multiplication of introner-like elements (2012)"
https://pubmed.ncbi.nlm.nih.gov/22658596/
These are postulated to be relatively rare events, so catching one in the act would be difficult:
> "However, dating of multiplication events showed that they degenerate in sequence and length within 100,000 years to eventually become indistinguishable from RSIs. We suggest that ILEs not only account for intron gains in six fungi but also in ancestral eukaryotes to give rise to most RSIs by a yet unknown multiplication mechanism." [ILE's being closely related intron sequences, RSIs being the regular jumbled-up types]
This is the gene equivalent of a filesystem: the DNA fragments are like disk blocks. The interposing sections are file metadata. The shearing mechanism is the filesystem reconstructing a stream from the lower layer blocks. There's probably some redundancy and error correction in there too.
It needs a filesystem for the same reason they were invented for computers: to provide an impedance match between the upper layer semantics (a stream of pairs describing a protein) and the lower layer storage (blocks). Using block structured storage is more flexible in terms of being able to insert in the middle of a file, etc etc.
I think there is a lot for both fields to learn by studying knowledge from each. Bioinformatics seems to be on that track.
Maybe you're right in some way, but also consider whether using the nomenclature and ideas used to described processes of DNA repair, transcription, and translation in biology to describe electronic computation works well. If it does work well, then maybe the reverse would also work well. If it leaves much to be desired, then consider the possibility that computer science ideas may be too specific to electronic or mechanical computation.
ps: I absolutely do not put computing above other fields though. I just wish for some pragmatic polymathism sometimes.
Why would that be true? It is a cool analogy but implying that it is the reason requires much more.
Justification is needed.
But it’s like trying to explain how atoms work using a solar system analogy. It might help with the really easy stuff, maybe? (orbitals) But sticking with it makes going any deeper pretty confusing.
I've never seen DNA as close to a filesystem, and our current best bet on introns functions are they are used to create alternative splicing products from the same DNA chunk. I cannot identify this function in a filesystem, where you can obtain two or three different valid files from the same data just by skipping some blocks.
Metadata is everywhere... histone modifications, glycosylation, etc..
The analogy doesn't go very far, however.
A woodworker could make a better analogy: DNA is like a box of leftover wood. You can chose the "exons" and build a closet with them, a different sort would make a table.
My point is we CS shouldn't feel pity for the biologist not being able to draw analogies with our field. You don't need an analogy when you are already the best at understanding the system directly.
I like to explain ML to biologists as an analogy with neurons, but it only can go so far. As soon as you need to teach the details things are no longer so similar. The reverse is also true: you can explain a neuron to a CS as a ML neuron, but when you need to explain neurotransmisors in detail, the analogy doesn't work anymore.
I'm not arguing at all that the analogy is a poor fit. Just that there are several instances of that kind of technique in CS. See also: Compression algorithms that include backpointers, so that medium-sized repeated runs (like common parts of filenames or fileheaders) can be represented by saying "The next 8 bytes are the same as the 8 bytes 32 bytes ago".
Introns are not for space saving or for efficiency. They provide variability. Is like ZFS could give you slightly different files from what you initially save. E.g. you store feral_cat.jpg spanning a number of blocks, and then just skipping blocks you can get back: feral_cat.jpg, persian_cat.jpg, egyptian_cat.jpg, russian_cat.jpg, alien_cat.jpg, tabby_cat.jpg... You never store "persian_cat.jpg" and try to save some genome space reusing blocks. persian_cat.jpg is just a possible useful image that appears magically from the original feral_cat.jpg.
I'm sorry, but this is just not a reasonable analogy. DNA sequences are not like computer files. The reason that they're distinct modules in these sequences is due to the need for evolution to be feasible. And also for the basic reason that the sequences are linear and so modules tend to appear in these linear sequences. But there also tremendous nonlinearities as well. Things at very long distances can be importantly related to each other.
The introns are not metadata. There are regions that can be removed selectively and in combinations to cause diversity in the produced proteins. That diversity is advantageous because it allows a single DNA sequence to present many different proteins that are typically related, but can be very different structurally. This splicing capability has evolved apparently from entities that can be seen as endogenous viruses or DNA parasites that have the ability to insert and splice themselves out of DNA and RNA sequences. In many confusing words, that's what the article or pointing at is talking about.
The introns do provide a kind of redundancy, but only in the sense that there are areas that can be modified with minimal effect on cellular function, at least relative to modification of the exons, which directly correspond in a one to one way with proteins.
There is error correction. It's called homologous chromosomes. Everyone talks about there being one genome, but in most complex forms of life, you have more than one copy per cell, usually two, and often more. These multiple copies, in addition to allowing for recombination and sexual reproduction, provide templates on which errors which arise during life can be corrected. However, there are no error correcting codes.
If you'd like to learn more about the actual details of these systems, I strongly suggest an undergraduate molecular biology textbook. The best one in existence is called the Molecular Biology of the Cell.
There are indeed many similarities between computing systems and biological systems, but the analogies you are making don't appear to be clear. Read a book like this, deeply and slowly, and it might change your life. At very least, it'll mean that the world you live in is much less mysterious and much more exciting.
But they also change the 3D conformation of the DNA itself, which changes access by transcription factors, etc.
There are some weird case, where the same txt file has two cat pictures, and sometimes instead of removing the two cats, the system removes also the texts between the cats.
Shout out to this book. Not only has the most amazing imagery, but you can learn a lot just by skimming the book, because of how well organized it is.
[1] One of my favorites is that the bases of ADN are translated in groups of 3 to amino acids, so the code reads like
AAABBBCCCDDDEEEFFF
-JJJKKKLLLMMMNNN--
--PPPQQQRRRSSSTTT-
As a non-CS person I find this explanation opaque.