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.

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/

That's different from what parent is saying.

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.

You said something completely unrelated to the parent's comment.

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.

Huh, can we remove those? isn't there a cost to have all those extra sequences lying around?

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.

[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.

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.

Of course, we’re on HN, someone will suggest a refactoring lol

As long as you have unit tests!

Any volunteers?

Use of this service constitutes acceptance of these terms.

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.

Is there an equivalent to zero-filled memory?

Sorta https://en.m.wikipedia.org/wiki/Non-coding_DNA

See we know about computers pretty good. But about DNA we get ignorant.

> Viruses [...]have circadian rhythms like all living things.

> 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 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.

In addition, only retroviruses are capable of altering DNA in such a manner.

The common cold is not a retrovirus.

Sometimes it is, it depends on the virus causing it.

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 author of this article is a philosopher promoting a book and not a scientist.

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.

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.

If it was true then presumably we'd see the DNA of identical twins diverging with age (proxy for number of infections). Do we?

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.

Not just twin, but your former self too.

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.

Mind linking some of the research? I've heard otherwise, but would be happy to read what you've read.

yes. that is completely false. now I'm doubting the whole article.

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.