The human genome is full of viruses
medium.com
medium.com
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?).
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.
It could be that old viral code has been repurposed long ago by evolution and serves a purpose.
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.
[0]: https://en.wikipedia.org/wiki/Transcription_factor#/media/Fi...
(In the course of reading about transcription factors, I came across something pretty neat that's related to all this about 3D structures: https://en.wikipedia.org/wiki/Transcription_factories)
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.
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.
See we know about computers pretty good. But about DNA we get ignorant.
> 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.
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?
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.
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.
"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.
This is what I believe happens with life.
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[0] - https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_Ref...
GGP here. This ^, and yes, not epigenetics.
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.
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.
https://www.thieme-connect.de/products/ejournals/abstract/10...
The busy beaver numbers are an interesting connection here.
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.
Seems like most of the focus has been on correcting single nucleotide errors. That’s more straightforward than trying to insert a new gene.
Append only immutable biotech
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.
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...)
(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.)
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...
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.
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-inter...
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.
https://www.newscientist.com/article/mg24532710-700-ancient-...
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.
If that appeals, I recommend Hannu Rajaniemi's Quantum Thief trilogy.
Literally, huh? In a word document?
- 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
from gevent import monkey
monkey.patch_all()
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.