The human genome is full of viruses • Hacker News Board

Re: The human genome is full of viruses

#81

Post by colechristensen » Sun, Mar 08, 2020, 3:41 AM UTC

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…

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)

Re: The human genome is full of viruses

#82

Post by sudoaza » Sun, Mar 08, 2020, 3:52 AM UTC

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…

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

Re: The human genome is full of viruses

#83

Post by mirimir » Sun, Mar 08, 2020, 4:14 AM UTC

> In many ways, viruses are eerily reminiscent of the idea of ancient spells, which sit quietly as words in a book until someone utters the mystical syllables and unleashes the magic contained within.

If that appeals, I recommend Hannu Rajaniemi's Quantum Thief trilogy.

Re: The human genome is full of viruses

#84

Post by bananamerica » Sun, Mar 08, 2020, 4:20 AM UTC

sudoaza wrote: post #82

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…

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

Re: The human genome is full of viruses

#85

Post by Enginerrrd » Sun, Mar 08, 2020, 4:27 AM UTC

sudoaza wrote: post #82

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…

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.

Re: The human genome is full of viruses

#86

Post by dehrmann » Sun, Mar 08, 2020, 4:31 AM UTC

TeMPOraL wrote: post #51

shijie wrote: post #15

Earlier quoted context omitted.

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...

What GP is talking about is that information is never fully contained in a medium; it's encoded in the tuple (the medium, what reads the medium). E.g. take a JPG file. The picture in that file isn't fully contained in the bits that file consists of. Some of the information is contained in the JPG specification (and through it, in the JPG decoding library). You need both to get at the picture. Meanwhile, with a differ…

> 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.

GGP here. This ^, and yes, not epigenetics.

Re: The human genome is full of viruses

#87

Post by narag » Sun, Mar 08, 2020, 4:32 AM UTC

sudoaza wrote: post #82

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…

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

Is there an equivalent to zero-filled memory?

Re: The human genome is full of viruses

#88

Post by tdy721 » Sun, Mar 08, 2020, 4:45 AM UTC

narag wrote: post #87

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?

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.

Re: The human genome is full of viruses

#89

Post by knome » Sun, Mar 08, 2020, 4:46 AM UTC

sudoaza wrote: post #82

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…

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

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.

Re: The human genome is full of viruses

#90

Post by nwah1 » Sun, Mar 08, 2020, 4:50 AM UTC

Lynn Margulis believed viruses often become symbionts, and speculated that diseases like syphilis and AIDS are so hard to cure because the viruses incorporate themselves into our genome.

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...