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The human genome is full of viruses

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Re: The human genome is full of viruses

#91

Post by dwohnitmok »

jhbadger wrote: post #74
crazygringo wrote: post #44

> 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 ov…

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?).

Re: The human genome is full of viruses

#92

Post by markdown »

pergadad wrote: post #25
_bxg1 wrote: post #3

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 wo…

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 an…

> 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?

Re: The human genome is full of viruses

#93

Post by [deleted] »

crazygringo wrote: post #44

> 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 ov…

[deleted]

Re: The human genome is full of viruses

#94

Post by kibibyte »

Enginerrrd wrote: post #85
sudoaza wrote: post #82

Earlier quoted context omitted.

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.

Re: The human genome is full of viruses

#95

Post by quickthrower2 »

bananamerica wrote: post #84
sudoaza wrote: post #82

Earlier quoted context omitted.

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

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

As long as you have unit tests!

Re: The human genome is full of viruses

#96

Post by redis_mlc »

I used to work in genetics.

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.

Re: The human genome is full of viruses

#97

Post by quickthrower2 »

jhrmnn wrote: post #65
bouncycastle wrote: post #61

Earlier quoted context omitted.

So, DNA is the compiled executable?

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.

It’s a complex lisp macro then?

Re: The human genome is full of viruses

#98

Post by jhbadger »

dwohnitmok wrote: post #91
jhbadger wrote: post #74

Earlier quoted context omitted.

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 per…

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.

Re: The human genome is full of viruses

#100

Post by svaigsq »

colechristensen wrote: post #81
jhbadger wrote: post #74

Earlier quoted context omitted.

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…

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.

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