11 ms·
The human genome is full of viruses
- throwaway2048 7y agoThere is also the theory that the eukaryote nucleus IS a virus https://en.wikipedia.org/wiki/Viral_eukaryogenesis https://en.wikipedia.org/wiki/Viral_eukaryogenesis
- EvanAnderson 7y agoNeato! Thanks for that rabbit-hole to explore.
- _bxg1 7y agoI'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.
- freepor 7y agoYou’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 7y agoBut in this case the program also creates the computer it runs on.
- mjg59 7y agoYou 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.
- c22 7y agoYou 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.
- TeMPOraL 7y agoSee https://news.ycombinator.com/item?id=22515015 https://news.ycombinator.com/item?id=22515015, in particular the "Reflections on Trusting Trust". You can bootstrap your target language from almost nothing by incrementally compiling more complex compilers, and all the intermediary complexity is stored in the compiler, not in the source code of the language you're trying to bootstrap. Notably, life did proceed like this - incrementally, from the first replicator. (Another way to look at it: a piece of code, be it DNA or a program written in a programming language, is just a bunch of symbols. You can't divine what these symbols mean from looking at the piece of code alone; you have to understand the mechanics of your compiler and your runtime. And these can evolve separately to the code you're looking at.)
- deleted 7y ago[deleted]
- Relys 7y agoWith a very complex CPU architecture and ISA (chemistry, laws of physics, protein folding, etc).
- 3pt14159 7y agoI 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 7y agoOr the converse of this, malicious DNA has been used to exploit sequencing computers. (https://dnasec.cs.washington.edu/ 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 7y agoThe 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...)
- bionhoward 7y agoSince protein folding is “solved,” you can make pathogen proteins with wildly different DNA to fool algorithms used to identify bioweapons. No bueno because baddies can order nasty germs printed cheap! There are no bug bounties for bio bugs
- inimino 7y ago> 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 https://en.m.wikipedia.org/wiki/Busy_beaver
- Ericson2314 7y agoModern 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.)
- dehrmann 7y ago> 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 7y agoI 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...
- rolph 7y agothe 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/10.1055/s-0029-1237423 https://www.thieme-connect.de/products/ejournals/abstract/10... https://sci-hub.se/10.1038/542406a https://sci-hub.se/10.1038/542406a
- ryankemper 7y agoFor those that aren't familiar, this principle is known as gene expression: https://en.wikipedia.org/wiki/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 7y agoMaybe 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.
- swiley 7y agoYou 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.
- refurb 7y agoYes, 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.
- neuronic 7y agoAnd I suspect that CRISPR and other tools will be far harder to use than expected by many, especially laymen. Simply due to the combinatorics involved when exchanging sequences in DNA, for example introduced by resulting new epigenetic dynamics.
- refurb 7y agoAgreed! Seems like most of the focus has been on correcting single nucleotide errors. That’s more straightforward than trying to insert a new gene.
- bionhoward 7y agoyou could add a new loop of DNA with a new gene, without an update to existing code. That might be easier than changing one letter Append only immutable biotech
- pergadad 7y agoJust 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.
- thaumasiotes 7y ago> 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 7y agoDomesticated and implanted, unable to survive outside the host, we're talking full H.R. Giger here.
- loufe 7y agoI 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/2012/3/120229-women-health-ovaries-eggs-reproduction-science/ https://www.nationalgeographic.com/news/2012/3/120229-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.
- taneq 7y agoDNA isn’t data, or even code. DNA is a machine that builds things.
- agumonkey 7y agoalso genes are influenced by a ton of context ecm, womb. if dna is code i'm still looking for eval semantics
- hinkley 7y agoMy 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.
- xg15 7y ago> 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. I believe this is the wrong way to think about this. From what I understand, DNA (plus epigenetics, etc) is more like a firmware that encodes the behaviour of a single cell. ("If this happens, build that protein"). Out of trillions of cells, each following its respective copy of that "program", plus all the interactions between the cells, plus physics and plus effects from the environment, a complex organism emerges. So, the complexity of the organism is the result of what is encoded in the DNA, but the DNA does not directly store it.
- dreamcompiler 7y agoYes, DNA is a programming language and ribosomes are the interpreter.
- tim333 7y agoThere 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 https://www.discovermagazine.com/mind/the-insanity-virus
- jdhn 7y agoWhat 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.
- vikramkr 7y agoI don't know if junk DNA was ever universally considered to be "junk" - it's been controversial terminology from the start which has proven to be justified with time as we learn more about what it does.
- webninja 7y agoFantastic article!!
- tim333 7y agoIt 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-for-multiple-sclerosis-clinical-trial https://www.fiercebiotech.com/biotech/geneuro-raises-eu17-5m...
- topaztee 7y agosuper interesting.
- abiogenesis 7y agoFascinating. It seems to be supporting a hypothesis I read a while ago (https://www.amazon.com/Next-Fifty-Years-Science-Twenty-first/dp/0375713425 https://www.amazon.com/Next-Fifty-Years-Science-Twenty-first...) on pathogens being a possible cause for depression.
- superkuh 7y agoMammals 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 7y agoOnce 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?
- GistNoesis 7y agoMonkey patching is not good engineering practice.
- jacob019 7y agofrom gevent import monkey monkey.patch_all() So good
- hirundo 7y ago“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.
- whoevercares 7y agoNow I’m more convinced Evolution might be driven by viruses
- ceejayoz 7y agoThey're certainly a source of selection pressure. One of many.
- vikramkr 7y agoEvolution is driven by a lot of things. It's driven by viruses by definition since of a virus integrates and makes a mutation to the germline, then that's a change which is evolution. And obviously bdosease is a major selective pressure driving evolution. And so so starvation, radiation, chemical mutation, errors in copying, heat, cold, literally everything that impacts survival and procreation drives evolution.
- deleted 7y ago[deleted]
- Papirola 7y agoFor sci-fi readers, I recommend Greg Bear's "Darwin's Radio" and the sequel "Darwin's Children".
- zed88 7y agoAnd they may awaken as well. https://www.newscientist.com/article/mg24532710-700-ancient-viruses-buried-in-our-dna-may-reawaken-and-cause-illness/ https://www.newscientist.com/article/mg24532710-700-ancient-...
- deleted 7y ago[deleted]
- crazygringo 7y ago> Even after recovering from an infection there will always be a piece of that virus encoded within your DNA. I did a little research and this appears to be almost completely false. This sentence makes it sound like every time you get a cold, your body's DNA is permanently altered. Which would be insane if true. The reality is that this insane outcome is incredibly rare, but nevertheless has happened enough times over all of human history that we have genetic code from viruses in our DNA, because a virus at some point managed to alter the DNA in a sperm or egg cell. But the quoted sentence is just not how infections work 99.99...+% of the time. The cold I got last month isn't in my DNA forever. It's very sloppy writing that appears to be aiming for sensationalism instead of accuracy.
- thombat 7y agoIf it was true then presumably we'd see the DNA of identical twins diverging with age (proxy for number of infections). Do we?
- ezoe 7y agoNot just twin, but your former self too.
- im3w1l 7y agoThis happens even from just spontaneous mutations. The body has many copies of DNA and they are not in sync with each other. Your cells diverge from your twins' cells, but also from each other.
- orestarod 7y agoThe DNA of every single cell in your body can have spontaneous mutations. But what is important for what you become in general is the DNA of your first cell that is rapidly multiplied to form your body. And what is important for what you leave on the next generation, is the DNA of your reproducing cells, which can too be individually altered, of course.
- ourlordcaffeine 7y agoIn addition, only retroviruses are capable of altering DNA in such a manner. The common cold is not a retrovirus.
- c-smile 7y agoAnd the most fascinated fact is that, despite of all these intruders and mutators, living organisms are damn stable and pretty effective devices.
- vikramkr 7y agoI mean, not that stable - the instability is kind of what allows evolution to happen. It's, well, it's good enough, stable enough, effective enough, and that's enough for life.
- dmd 7y ago> A biological virus (whether it is a true virus, an endogenous retrovirus, or a transposon) can literally lay dormant in a word document as a string of As, Ts, Cs, and Gs. Literally, huh? In a word document?
- Viliam1234 7y agoSure, that's why we get the usual advice: - wash your hands with soap as often as possible - do not touch your mouth, nose, or eyes when outside - always disable macros in word and excel
- knzhou 7y agoAnother fascinating fact is that about 20% of cancers are directly caused by viruses -- they push the cells they infect to be more cancer-like. The famous example is HPV, but there are many more.
- dreamcompiler 7y agoAnd some by bacteria. Helicobacter pylori for example
- fizixer 7y agoTrain of thought while reading title and comments: First: Genome cannot physically contain a bio-virus, so this must be genetic code, acting as a "computer virus" Second: Oh they're talking about viral genome embedded in human genome. Got it. Third: But wait, bio-virus genome embedded in human genome does not by-definition imply that there is something wrong with that human genome. It could just be an innocuous part of the viral genome. Fourth: Parts of human genome that could act as "computer virus" (i.e., be malicious to the human), and parts of human genome that come from a bio-virus may have some overlap. But you could have two other options too: (a) part of human genome that is malicious but not from a bio-viral source, (b) part of human genome that is from a bio-virus but is not malicious.
- mirimir 7y ago> In many ways, viruses are eerily reminiscent of the idea of ancient spells, which sit quietly as words in a book until someone utters the mystical syllables and unleashes the magic contained within. If that appeals, I recommend Hannu Rajaniemi's Quantum Thief trilogy.
- nwah1 7y agoLynn Margulis believed viruses often become symbionts, and speculated that diseases like syphilis and AIDS are so hard to cure because the viruses incorporate themselves into our genome. She also believed that the Eastern Bloc concept of symbiogenesis explains much of human evolution, and some of that is now accepted by the mainstream community. For instance, it is now believed that mitochondria were originally viruses that became symbionts. However, Margulis and many adherents of this view argue that essentially all of the organelles formed this way, and that symbionts play a vastly larger role in general. https://www.discovermagazine.com/the-sciences/discover-interview-lynn-margulis-says-shes-not-controversial-shes-right https://www.discovermagazine.com/the-sciences/discover-inter...
- redis_mlc 7y agoI used to work in genetics. We're not sure if the viruses are actually dormant or not. They may be the active ingredients for a lot of biological processes. In other words, viruses and junk DNA are probably essential parts of modern man. If you're squeamish, I suggest you just take what I said at face value, and move on with your life. If you're not, then you can google for some more info, but you won't like what you find. How sausage is made, and all that.
- dzink 7y agoA good example is the Arc virus. Research at some point proved that removing it from a creature’s genome, removed the creature’s memory. More: https://www.nih.gov/news-events/news-releases/memory-gene-goes-viral https://www.nih.gov/news-events/news-releases/memory-gene-go...
- tibbydudeza 7y agoWithout viruses we would not be here in our present state. The mammalian placenta uses ancient virus protein called syncytin to bond "other" to "own" and thus bypass the effect of the mother's immune system.