[HN Gopher] The human genome is full of viruses
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The human genome is full of viruses
Author : olalonde
Score : 158 points
Date : 2020-03-07 17:37 UTC (5 hours ago)
(HTM) web link (medium.com)
(TXT) w3m dump (medium.com)
| hirundo wrote:
| "So powerful and ancient are viruses, that I would summarize
| their role in life as 'Ex Virus Omnia' (from virus everything)."
|
| We have met the enemy and he is us. Viruses may be both the
| gravest threat to our species and mothers and fathers of it. They
| are also, to a first approximation, the Red Queen, who must be
| obeyed. If we can disobey her, and distribute an effective
| vaccine in time to dent her latest royal tour, it will be an epic
| level up: the power to not consent to impregnation by horizontal
| gene transfer.
|
| It seems that we're not quite there yet.
| Papirola wrote:
| For sci-fi readers, I recommend Greg Bear's "Darwin's Radio" and
| the sequel "Darwin's Children".
| zed88 wrote:
| And they may awaken as well.
|
| https://www.newscientist.com/article/mg24532710-700-ancient-...
| GistNoesis wrote:
| Monkey patching is not good engineering practice.
| rubicon33 wrote:
| > And these endogenous retroviruses don't just sit silently in
| the genome -- their expression has been implicated in diseases
| like autoimmune disorders and breast cancer.
|
| I'm glad to see that more and more, people are waking up to the
| idea that viruses do far more than give you a runny nose and a
| cough.
|
| Those are just the symptoms of your body trying to repel the
| virus. The long-term effect of having new sequences of DNA in
| your genome, transcribed into proteins, is often unknown.
|
| I believe that as medicine advances and our understanding of
| viruses becomes more clear, we will discover that MANY of the
| disorders we don't currently have explanations for can be traced
| back to viral infections.
| throwaway2048 wrote:
| There is also the theory that the eukaryote nucleus IS a virus
|
| https://en.wikipedia.org/wiki/Viral_eukaryogenesis
| EvanAnderson wrote:
| Neato! Thanks for that rabbit-hole to explore.
| brundolf wrote:
| I've always thought of DNA as mere "data". "This goes here, that
| goes there", etc. And I've always wondered how such a relatively
| small amount of data could describe the massive complexity of a
| full-size organism.
|
| But this makes it sound like DNA is data the way Lisp is data: it
| can contain procedures and transformations and meta-statements
| about itself, and even mutate during the course of being
| interpreted. That would explain so much.
|
| The use of the term "virus" in software seems to be more apt than
| I'd thought.
| swiley wrote:
| You should read some of the genetic computing papers (I think
| the one on computing paths on a graph was posted here the other
| week.).
|
| My understanding is that DNA oligimers can interact with each
| other directly and perform what are essentially string
| operations. Like most systems that can perform string
| operations on themselves this appears to be capable of
| universal computation.
| agumonkey wrote:
| also genes are influenced by a ton of context ecm, womb. if dna
| is code i'm still looking for eval semantics
| Ericson2314 wrote:
| Modern cells are something first order like Harvard
| architecture. Crisper or RNA organisms you could maybe call von
| Neumann architecture. (rRNA actually containing vestigal tRNA
| and many coding sequences containing vestigial rRNA is very
| interesting.)
| freepor wrote:
| You've got half of it, but the other half is the existence of
| the cell to interpret the data. The DNA is like a Lisp program,
| but how much good would a Lisp program be without a computer to
| run it?
| UncleOxidant wrote:
| But in this case the program also creates the computer it
| runs on.
| Relys wrote:
| With a very complex CPU architecture and ISA (chemistry,
| laws of physics, protein folding, etc).
| mjg59 wrote:
| You can't bootstrap a cell from DNA - you need a
| functioning cell to start with. There's a lot of semantic
| data that's embodied in the existing set of proteins and
| other functional elements, and I don't think it's clear
| that the DNA of any moderately complex organism actually
| expresses that state.
| pishpash wrote:
| It probably doesn't, the cell is the totality of prior
| transformations leading up to it, most instructions of
| which may have been discarded because they're no longer
| needed or have never been saved in genetic material in
| the first place. If it did get encoded, then you would
| expect it to be used all the time, and you'd see cells
| come back to life once they're dead, but such an entropic
| feat has only happened once in the beginning within our
| lineage, and as far as we know, by chance.
| c22 wrote:
| You can't bootstrap a self-hosting compiler from a
| language you just made up either. You'll need to first
| write a compiler in another language then use it to
| compile the compiler you wrote in your new language. I
| think the compiler/program dichotomy is a more apt
| metaphor for cells and dna than the _computer_ /program
| one.
| refurb wrote:
| Yes, there are several layers of complexity that go beyond just
| the genetic sequence of a given gene.
|
| The sequence of the DNA also impacts thing like folding of DNA
| which impacts expression.
|
| And the intermediaries between the DNA and the protein (RNA),
| can also interact with the DNA itself to promote or retard
| expression.
|
| It's incredibly complex really.
| 3pt14159 wrote:
| I had a thought the other day. It's theoretically possible for
| a computer virus to lead to a biological virus. Corrupting the
| data of a computer responsible for manufacturing a vaccine, for
| example.
| taylorfinley wrote:
| Or the converse of this, malicious DNA has been used to
| exploit sequencing computers.
| (https://dnasec.cs.washington.edu/)
|
| I swear I heard Mikki Hypponen talk of a self-replicating
| version of this that exploited the sequencers to encode the
| exploit into other sequenced DNA, making this self-
| replicating, but I can't find a link.
| mattkrause wrote:
| The DNA-based attack was a little contrived.
|
| They deliberately introduced a vulnerability into a post-
| processing tool, then generated a DNA sequence that abused
| it. It's a creative idea but it would be fairly difficult
| find and use exploits in the wild. Sequencing has gotten a
| lot cheaper but it's still going to cost tens-to-thousands
| of dollars per attempt, so you can't do the genomic
| equivalent of packet stuffing on the cheap.
|
| (Nevertheless, it is true that a lot of biology-related
| code is not great but...)
| pergadad wrote:
| Just in case this is not known, human generic code is more than
| just DNA.
|
| Most important parts of what encodes us are:
|
| - DNA - epigenetic markers on the DNA which modulate which
| parts of the DNA are active. You influence these and pass them
| on to your children (as men) and grandchildren (as women, as
| girls are born with all egg cells they'll ever have) - cell
| organelles which copy the DNA, ensure the cell has food and
| lives, etc. These tend to be independent cells that were at
| some point captured by our own cells. So they have their own
| genetic code. These you only inherit from your mother (dad
| gives half the DNA with epigenetic markers, mom the other half
| (also with markers) and everything else.
|
| And of course much of what we are is shaped through gestation
| as well, I.e. the mother's body sends not just nutrients but
| also hormones etc that regulate gestation (and vice versa the
| child sends various messages to mom, up to even own cells in
| case of serious illness or accident or the mother).
|
| Fascinating stuff.
| loufe wrote:
| I found the egg claim interesting so I gave it a quick
| search: looks like there may be cases where these eggs can be
| replaced (https://www.nationalgeographic.com/news/2012/3/1202
| 29-women-...) but your claim does generally hold true. Wow!
| It gave me a weird feeling thinking that men would be
| procreating directly in a sense with their partner's mother.
| thaumasiotes wrote:
| > independent cells that were at some point captured by our
| own cells
|
| It makes a little more sense to think of them as
| "domesticated" rather than "captured".
| JulianMorrison wrote:
| Domesticated and implanted, unable to survive outside the
| host, we're talking full H.R. Giger here.
| inimino wrote:
| > how such a relatively small amount of data could describe the
| massive complexity of a full-size organism
|
| The busy beaver numbers are an interesting connection here.
|
| https://en.m.wikipedia.org/wiki/Busy_beaver
| dehrmann wrote:
| > I've always wondered how such a relatively small amount of
| data could describe the massive complexity of a full-size
| organism
|
| I'm not convinced it fully does. Remember that DNA is never in
| isolation; there's always a cell that's been replicated and
| passed down to offspring, so there's interplay between the
| hardware cell and software DNA.
|
| I also don't know much about biology and only took a high
| school class, so don't read into this beyond it being an idea.
| shijie wrote:
| I think what you're describing here is called "epigenetics,"
| or how different genes are expressed or not expressed due to
| environmental and other outside factors such as stress,
| etc...
| 01100011 wrote:
| I think the analogy would be something like:
|
| DNA is the code. Epigenetics are config options which can
| be saved to a file and passed on. The cell is the machine
| which interprets the DNA + config options.
|
| So there are three pieces, and I don't think OP was talking
| about epigenetics.
| rolph wrote:
| the big deal about epigenetics is that those [methylation
| and histone binding] are modifications that dont alter the
| sequence of the DNA but are also inherited by subsequent
| generations.
|
| https://www.thieme-
| connect.de/products/ejournals/abstract/10...
|
| https://sci-hub.se/10.1038/542406a
| ryankemper wrote:
| For those that aren't familiar, this principle is known as
| gene expression:
| https://en.wikipedia.org/wiki/Gene_expression
|
| To make an analogy to software, a common pattern is to have
| a monolithic repo with many different "personalities"
| (codepaths / configurations) that utilize different subsets
| of the monolith. DNA seems to work under a similar
| principle, a given cell will preferentially transcribe
| parts of the DNA based on epigenetic factors.
| enchiridion wrote:
| Maybe in a way. I think they are driving at an orthogonal
| argument. The DNA is more or less useless without cells. It
| seems like the machinery of the cell carries information
| about the whole of the organism in an abstract sense.
| pishpash wrote:
| The fact that you can make cells do completely different
| things by changing DNA though implies _most_ of the
| information is in the DNA. Sure you need machinery and
| environment, but that division is over all a more compact
| form of representation for the whole system the way that
| universal Turing machine and tapes are for the universe of
| interesting programs.
| hinkley wrote:
| My read on the situation is that the analogy for computer
| viruses holds if, in the process of getting and removing the
| virus, it creates lots of little memory leaks.
|
| They don't kill you, rarely do they help you, the rest of the
| time they are just a very subtle drag on an important resource.
| At some point when we understand these systems much much
| better, we might go so far as to try to surgically remove them,
| but we can't be absolutely sure there are no consequences.
|
| Turns out the rebooting (ie children) fixes the problem
| sometimes, but nowhere near all the time.
| superkuh wrote:
| Mammals could not and would not exist without the membrane fusion
| protein given to their ancestors by a retrovirus. This protein is
| _essential_ for forming the multiple nucleus cells that make up
| the placenta.
| campercoder wrote:
| Once a virus is inside our DNA... can it be removed?
|
| Also, lets say you want to get rid of your epstein barr virus
| that has invaded & now lives in every one of your cells... is it
| living in our cells, or is it just in our dna?
| tim333 wrote:
| There was an interesting article a while back on them playing a
| part in schizophrenia. "The Insanity Virus"
| https://www.discovermagazine.com/mind/the-insanity-virus
| webninja wrote:
| Fantastic article!!
| tim333 wrote:
| It is good isn't it. I just re-read it ten years after the
| original publication.
|
| I googled and Perron's start-up GeNeuro is still going,
| trying to fix MS with an antibody against HERV-W.
| https://www.fiercebiotech.com/biotech/geneuro-raises-
| eu17-5m...
| jdhn wrote:
| What a great read! I find it so crazy that after decades of
| thinking that there's all this "junk DNA" in us, it turns out
| that it may serve a purpose after all, even if that purpose is
| malicious.
| whoevercares wrote:
| Now I'm more convinced Evolution might be driven by viruses
| [deleted]
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