Humans are at least 8% virus

By Razib Khan | October 30, 2012 6:25 pm

In the comments below there is a lot of talk about the worry of transferring gene X from organism 1 to organism 2, where the two organisms are very far apart on the tree of life. I’m a little sanguine about this, but that’s because there is already much of this going on through natural processes.

Carl Zimmer for example points out that 8 percent of the human genome seems to derive from endogenous retroviruses (the post draws on material from his book A Planet of Viruses). This is probably a low bound number, as he notes in the comments. Additionally, this isn’t just limited to viruses. See: Horizontal gene transfer between bacteria and animals.

I think on of the chasms between geneticists and the public is that a lot of things that seem creepy and strange to the public are part & parcel of the geneticist’s professional toolkit. For example, to my knowledge no transgenic mice have turned into the Brain. I have friends that order weird mouse varieties, and then do weirder things to them, every week.

CATEGORIZED UNDER: Genomics
MORE ABOUT: Viruses
  • chad

    As I pointed out in the last topic, geneticists make use of Agrobacterium Tumafaciens which survives by infecting plants, inserting a stretch of DNA containing several virulence genes into the plant causing it to develop tumors and produce unique amino acids that the bacterial utilizes.

    Of course the ultimate form of genetic engineering was the endosymbiosis of mitochondria and chloroplasts. As part of that ongoing evolution, mitochondrial/chloroplast DNA continues to migrate and be inserted into the nuclear genomes.

    Nature is a far more radical engineer compared to humanity, yet opponents of GMOs believe there is an intrinsic “goodness” to the sorts of natural hybrizations that radically recombines entire genomes of divergent species, as in the case of the Rutabaga, but are scared of sticking one bacterial gene with known effects into a plant.

  • jose

    Pinky:
    Cerebro, que vamos a hacer esta noche?

    Cerebro:
    Lo mismo que hacemos todas las noches, Pinky, ¡tratar de conquistar al mundo!

    Son Pinky y Cerebro, Son Pinky y Cerebro
    Uno es un genio
    El otro no es tan cuerdo
    De laboratorio son
    Con genes insertados
    Son Pinky Son Pinky y Cerebro,
    bro, bro, bro, bro, bro, bro, bro … NARF!

  • ac

    I think it’s probably best that the public not really understand; where I work, we have a viral core where we can order viruses to be custom-made for us. It’s really handy! But it’s probably best that we don’t freak the public out.

  • T

    When I first found out about virus DNA in the human genome I was surprised but it didn’t change my worldview. When I found out about this http://en.wikipedia.org/wiki/Polydnavirus my mind was blown and I realized that pretty much anything is possible.

  • Hemo_jr

    So the average person alive today has much more virus DNA in their genome than Neanderthal and Denisonian DNA combined.

  • zmil

    The two sets are not necessarily mutually exclusive.

  • Sandgroper

    #5 – Denisovan. Do you mind? We of the Denisovan Liberation Front who are in touch with our inner Denisovan have feelings, you know.

  • DK

    That a large portion of our genome is various defective mobile elements that accumulated over millions and millions years of evolution does not mean that a chance that therapeutic virus inserts into and inactivates an essential gene is zero. Vast majority of retroviral insertions into ORFs will be disrupting. Exons are ~ 1%, so risk is on the order of 1%. 1/10th of those can reasonably be expected to have “serious” consequences, so overall risk is about 0.1%.

  • http://www.rishon-rishon.com David Boxenhorn

    Do we know of any human genes that have appeared out of “nowhere” – i.e. don’t have cognates in other hominids, or even other primates?

  • Geoff

    You’re right, I have not seen any transgenic mice become the Brain. I have seen a lot of Pinky’s, though!!

  • Riordan

    Yes, nature undoubtedly can be just as “creative” as many of our current GMOs. But the deeper details between them can matter, significantly perhaps gigantically. To use your example of retrovirus in our genome, I would compare it with the fish tomato again……

    First, where would they have come from? I don’t dare to pretend to know, but I’m sure there is a very high likelihood they originated from nearby organisms if not species directly related to us (i.e. proto chimps, perhaps rodents, other mammals etc.) or the general environment/habitat our ancestors were living in (soil, water). Those retroviruses coming from perhaps a hundred miles away or so are less likey, but still eminently possible. Those from thousands of miles away but in the same continent/geographical range is probably not very likely, but who knows. On the other hand, those retroviruses from say, the deep sea trenches or perhaps in underground caverns a mile deep we can probably safely rule out. Probably. This contrasts with certain examples of current GMOs such as the fish tomato, where something from the deep sea was cloned into something inland many, many distances away which would have been almost impossible even allowing for generous circumstances in the past. We now have the power to “bridge” certain species from areas where they once would have never conceivably met.

    Second, the way the virus gets disseminated to us matters. How many intermediate organisms it goes through will impact its subsequent influence on our ancestors. Short distances, probably goes directly from the vector to us. Longer distances, more intermediates. At each intermediate another complex interplay comes in, where it has to go under various selection mechanisms and eventually reach equilibrium with its host in order to spread to its eventual target. More importantly, its passage through intermediates would also be eventually calibrated with the variuos ecosystems during its passage. It goes without saying whatever genetic payload the virus brought in the final destination will have been altered in the process. Not so much with those antifreeze proteins from the fish, which can be cloned altered into a tomato plant, with no natural selection mechanisms in play nor any consideration of its final role in the ecosystem. The switch is so sudden and unchanged that the rest of organisms in the environment would not have time to adjust to it.

    Third, time scale. Many of the retroviruses got into our genome through long stretches of time, tens and hundreds of thousands of years, if not millions. Perhaps some of the faster ones got through in a matter of few centuries, one can speculate. But within a period of 15-20 years? That is highly doubtful. This contrasts with our current technology, which allows us to potentially leapfrog such time scale so that new genes can be integrated into targeted species within 4-5 years of research, and then spread through unprecedented scale in the next 8-10 years. Even the most powerful viruses of the past would envy that scale and speed, not to mention being unable to remotely match that record.

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    #11, are you a biologist? your comment frankly reads like bullshit to me, but i’m not a virologist (a lot of the phylogenetic stuff sounds like bullshit, and i’m more qualified to judge that).

  • http://www.rishon-rishon.com David Boxenhorn

    Riordan’s comment sounds, to me, like a long way of saying that a large (huge!) quantitative difference = qualitative difference.

  • Gil

    @11 doesn’t conventional argriculture skip all those steps, too, though? Instead of one gene ending up in an unlikely place, we have a whole species worth of genes in the ‘uncalibrated’ environment.

  • chad

    #11

    When you boil your post down to what it really is saying:

    “Its better to get a virus from a closely related species…something like HIV…than to stick a gene from fish into a Tomato even though that fish gene will have no harm.”

    Your reasoning for this has nothing to do with real effects, but is premised on two factors that are assumed to be inherently good:

    1) Changes that take a long time are better than changes that are quick
    2) The more closely related on the phylogenetic tree, the better it is.

    Both are bad assumptions.

  • Riordan

    #12. Razib,

    Not professionally, though I did receive my undergrad degree in cell and molecular bio. I’m a current pharmacy school student going through some training in public health and infectious diseases as an empahsis. So no, I guess not. However, those things I’ve mentioned, largely point #2 in my post, are the basic stuff that was emphasized to me during both undergrad and grad school courses I’ve took. But I have no doubts they are not at the same level of PhD level courses in virology or evolutionary genomics. Reegarding aspects of phlyogeny, I’ve took a look at my post and while the factors of time scale and geographical distance can be relevant to phylogeny, I’m a bit lost as to where my post strayed into that territory outright . I’m sure it’s far from perfect, but can you say briefly which parts you find objectionable?

    #13. David,

    Because of the complex nature between “quantitative” and “qualitative” comparisons, I do not dare to venture into that specific debate. What I was trying to get was that no matter the specific nature of those differences between natural genetic “engineering” such as genomic retroviruses, and current if not future GMOs by humans, the scale and degree can be quite vast in certain factors that bares consideration.

    15. Chad,

    I….. really do not understand how your ascribing a values judgment onto my post which I did not even try to imply. I do have my personal preferences, but in my post I never ventured to say that natural genetic engineering is preferable to human ones, at all. At least, that’s I labored hard not to do. I was simply pointing that though natural and human “GMOs” can be surprisingly similar, in certain important aspects they really do differ, and with our current progress with technology, it can very much be a Brave New World that previous events of natural history would have a hard (if not impossible) time trying to replicate.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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