> 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?).
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 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.
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?
> 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...
> 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.
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?
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.
Readit News
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.
Here is a review (nearly twenty years old from when the human genome was first sequenced) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC138943/
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?).
> circadian adj. of, relating to, or showing rhythmic behaviour with a period of 24 hours; especially of a biological process
No, they don't.
And the rest of the paragraph is equally goofy.
The common cold is not a retrovirus.
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.
From wikipedia-
https://en.wikipedia.org/wiki/Endogenous_retrovirus
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.
Deleted Comment
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.
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.
It makes a little more sense to think of them as "domesticated" rather than "captured".
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.
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?
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.
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The busy beaver numbers are an interesting connection here.
https://en.m.wikipedia.org/wiki/Busy_beaver
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.
Simply due to the combinatorics involved when exchanging sequences in DNA, for example introduced by resulting new epigenetic dynamics.
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.
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.
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 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.
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...
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https://en.wikipedia.org/wiki/Viral_eukaryogenesis
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.