> 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.
The article is rather fancifully written (and by a non-scientist) but as a professional genomicist, I can assure you that the human genome is full of viruses, the remnants of which are almost entirely non-functional, but are interesting in the way meteor craters are to geology.
Parent is saying that the vast majority of viral infections do not lead to permanent DNA changes (especially hereditary ones through the germline). However, over the course of history that tiny minority of cases has accumulated to form a sizable chunk of the human genome.
The quoted sentence from the article implies on the other hand that every viral infection leads to permanent DNA changes.
I haven't done enough research to have a personal opinion one way or the other, but you're not addressing the point of the comment you're replying to (unless you meant your comment to be more of a tangential commentary? That despite the error in the quoted part of the article the overall point of the article still holds?).
It's true that only retroviruses actually get into your genome, and that the bulk of viral-derived sequences in your genome are from distant ancestors, but the key argument of the article (that the human genome is full of viruses) is certainly true.
Presumably there are some effects to the large amount of non-functional DNA we carry around, has anybody looked in to this or thought about what would happen if we removed much of it (a sort of cleaning house gene editing for an experimental line of some species)
The article gives very clear idea, that "non-functional DNA" can become very functional after transposons spring into action(at birth, during illness, whatever the trigger), so writing it off as something that can be spring cleaned is too early.
As for clean house - what exactly is template here? Some humans have genes, that others don't have - DNA is not something, that has all the attributes of all humans with true/false values attached to them. Some humans have slanted eyes and have genes that are responsible for that look and others don't have such genes when they have no such feature and there are other genes responsible for their look. And this looks a sh!t job to sort out all "functional" genes of every human, as DNA of them is not going to be the same.
Editing out nonfunctional DNA looks like one of those ideas from 60s, when it was in fashion to remove appendix and make smaller stomach and they in the end paid with shorter lifespan.
You ever see a cryptic line of code with a comment next to it saying something to the effect of: "No idea what this does, but everything breaks if we delete it"?
It could be that old viral code has been repurposed long ago by evolution and serves a purpose.
I generally get annoyed at most analogies that compare DNA to code because they oversimplify a lot, but I really do like this particular DNA-code analogy.
My university molecular genetics course taught me that DNA is very complicated. Many of us know of the simplified model where an RNA polymerase, encouraged by some transcription factors, locates and binds to a promoter sequence, unwinds the strands, and constructs an RNA strand. However, DNA has a 3D structure. Histones can wind up DNA tightly enough to hide genes from transcription proteins, or they can unwind and expose DNA to encourage expression. Some transcription factors can bind to sequences several kilobases away from the target gene, cause that part of the DNA to fold onto itself, and ultimately bind to transcription proteins to encourage expression of the target gene.[0]
Extending your comment, it is entirely possible that bits and pieces of old viral code have accidentally led to weird things like this, and that many organisms now depend on this behavior.
Edit: I should also mention that, if it wasn't obvious, that viral DNA getting inserted into certain places can disrupt these complex interactions by increasing or decreasing the expression of a gene. For the cell/organism, this can be detrimental, benign, or perhaps beneficial.
I was worrying about this, specially your latest edit, when i mentioned cleaning up. We could limit to very new additions though just in case. I know that there's maybe no reason to think that this random additions are any worse than the random+selected pieces that were coding before, but just seems ugly somehow.
There is a cost in terms of energy required to replicate the genome. The cost is relatively small though and grows slowly within the population so it is subject to fairly weak selection. On the other hand deleting DNA is always quite a risky proposition.
As I remember it, it was stated in "The Selfish Gene" that the vast bulk of genetic code served only a single purpose: ensuring it itself was replicated. It had no known function for the organism, it simply was copied from generation to generation. The primary "goal" of any self-replicator. Since it didn't actively interfere with the genes that do have an affect on the construction of the structures the genes build around themselves to protect and propagate those genes, namely us and any other organisms, the genes would simply continue being copied along indefinitely.
Forgive my naive question, but if the host is not affected if that code is lost, then wouldn't you imagine that eventually all that code would be destroyed by random mutation? There's no selection.
The book really is a fantastic read. If you've any curiosity on the matter, I would suggest picking up a copy.
The premise is that it is not organisms, but genes themselves which are the primary target of evolution. All but the gene is mere trappings that surround their competitive replication. Those genes that manage to slide from generation to generation aren't doing nothing, they are those that are most successful at duplicating themselves into the next generation. If they do not hinder the organism in their duplication, there is no pressure for their removal.
The circadian rythm thing is so egregiously absurd that it's easy to overlook the other spectacular claim in that sentence. Some people could argue that viruses are alive, but that's far from the mainstream interpretation and to say that the statement is wading into some potentially really be controversial territory is an understatement.
Do you have any examples of retroviruses that cause the common cold? I did a quick search but couldn't find anything, but that sounds like something that would be really interesting to read up on - the classical retrovirus isn't necessarily something that can go away after a couple days of sniffles and I'm curious to know if there are long term consequences to colds caused by retroviruses.
The search results are probably flooded, if you need good info look for anything from before the resent outbreak.
Its on the wikipedia page for common cold, I think I got the factoid when I was searching google patents for coronavirus (might be interesting to check out as well) https://en.m.wikipedia.org/wiki/Common_cold#Viruses
I don't think coronavirus is an integrating retrovirus? It's an RNA virus for sure, but I haven't ever heard of it causing genome integration, and it would probably be a lot more dangerous (ability to cause cancer for instance) if it did?
The human body has around 40 trillion cells, and only DNA from one of gets passed on to each child. Considering how frequently that cell happened to be infected in human history the average person like has many individual cells with some new viral DNA. But, criticaly those changes are neither inherented by children or widespread across every cell.
In effect what’s being described is an interesting oddity rather than a significant effect on an individual level. Unless it happens to cause cancer, etc.
To pass a viral alteration of DNA to offspring, the retrovirus has to infect germline cells, which they usually don't - and in a way that produces a viable offspring, which is even rarer. That's not to say it doesn't happen over long enough time period - it clearly does.
Most retroviruses infect somatic cells, but occasional infection of germline cells (cells that produce eggs and sperm) can also occur. Rarely, retroviral integration may occur in a germline cell that goes on to develop into a viable organism. This organism will carry the inserted retroviral genome as an integral part of its own genome—an "endogenous" retrovirus (ERV) that may be inherited by its offspring as a novel allele.
This 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.
The 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.
Retroviruses spread by altering host cells' DNA, so I doubt it is really such an "incredibly rare" event for those infected by them, like e.g. HIV positive people.
There's also some stuff about circadian rythms in there that makes no sense - the main point of the article that our genome has viral dna in it is true and really cool, the details of the article are kind of fantasy though. If you're interested in learning more probably better to do your own research or read through the wiki or something rather than sift through this article which, while an admirable attempt by a non-scientist to explore an interesting phenomenon, is not a very successful attempt.
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.
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).
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/2012/3/120229-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.
> epigenetic markers .. You influence .. and pass on to .. grandchildren (as women..)
AFAICT, a woman significantly influences markers on the eggs (future grandchild) developing in her child (fetus/embrio) in her womb, but at the same time, she influences all the other cells (child). Some (even critical) processes are probably more influenced by the grandmother, but I wouldn't minimize the mother's effect.
> 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)
While I've heard this before, I never gave it much thought until just now. Is it fair to say that a child gets no DNA from her mother? Or in other words, each child is a mix of the DNA of their father and that of their maternal grandparents?
The half-DNA of eggs is selected as they divide from ancestor cells.
Eggs of a woman (baby/fetus) develop while in mother's womb, but they are more immediately inside the fetus, are formed from the cells of the fetus and are descendants of the same single cell zygote as (most) of the cells that form the woman's body.
Not sure what OP meant, but I wouldn’t say DNA is the machine. The ribosome is. But DNA is certainly much more than just code to build proteins. Or rather, it strongly interacts with its enviroment, so trying to understand its function in isolation will give you just the tip of an iceberg. In CS language, there is a lot of global state.
> 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.
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...
What GP is talking about is that information is never fully contained in a medium; it's encoded in the tuple (the medium, what reads the medium). E.g. take a JPG file. The picture in that file isn't fully contained in the bits that file consists of. Some of the information is contained in the JPG specification (and through it, in the JPG decoding library). You need both to get at the picture. Meanwhile, with a different decoding program, the same file can represent a piece of music. Or a text document.
"Gödel, Escher, Bach" goes into a detailed discussion about this.
On top of that, GP is talking about hardware that builds its own copies, possibly imperfect copies. That implies a lot of information relevant to the organism may not be directly visible in the DNA - it may sit within the replication machinery, and evolve there. It's kind of similar to the difference between machine code and microcode + actual traces in silicon.
A famous Turing Award Lecture by Ken Thompson, "Reflections on Trusting Trust", provides another example[0]. Consider a C compiler. How do you build one? From its C source code, using a different C compiler. Now imagine a malicious C compiler that a) injects a trojan into the compiled binary whenever it compiles, say, "login" program, and b) injects a trojan into the binary whenever it compiles another C compiler; that second trojan contains the code for injecting a) and b). You use that compiler to recompile the original C compiler, install it in a system - and from now on, not only "login" will be bugged, but you can't get a non-malicious compiler by recompiling the original one from source; the source contains no traces of the trojans, but they are there, in the binary of the compiler you're using, and they self-replicate.
> On top of that, GP is talking about hardware that builds its own copies, possibly imperfect copies. That implies a lot of information relevant to the organism may not be directly visible in the DNA - it may sit within the replication machinery, and evolve there.
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.
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.
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.
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.
> 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.
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.
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.)
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.
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.
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.
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...)
Since 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
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?
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.
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.
See 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.)
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.
I 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.
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.
“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.
Lynn 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.
Train 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.
I 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.
> 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.
Another 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.
> 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.
Evolution 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.
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.
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.