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Comment by jhbadger | Hacker News Reader

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/

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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.

https://www.discovermagazine.com/planet-earth/mammals-made-b...

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.

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