You know when professors say something thats really obvious, but they say it in such a way that suddenly the universe makes sense, and your head explodes?

I had one of those moments yesterday while listening to a professors presentation on a nifty herpes virus, cytomegalovirus (CMV is like EBV— pretty much everyone has been infected, but it doesnt hurt you unless youre immunocompromised).

Now in contrast to my elegant, streamlined retroviruses, herpes viruses are friggen monsterous. HIV-1 is about 10,000 base-pairs long (single stranded RNA), with nine genes, while CMV is 235,000 base-pairs long (double stranded DNA) with hundreds of genes. Both viruses have the same ultimate needs (basically, a ribosome from the host cell), but DNA viruses can afford to carry around lots of bells and whistles, including virally encoded mimics of our proteins.

One example would be CMVs ‘UL146‘– a viral protein that looks and acts exactly like one of our chemokines, CXCL1. Basically this mimic of CXCL1 turns an infected cell into a gingerbread house. All these nice, fresh, yummy immune cells trot right up the CXCL1 chemokine gradient to the infected cell, only to get infected themselves (ie, THE CAEK IS A LIE!!!).

That is so cool.

But this is when my head exploded:

Prof: Weve been co-evolving with these guys (herpes viruses) for millions of years. They know our immune system better than we do.


When we look at cells, they dont look like this. They dont look like a bright technicolor world of teeny machines chugging away. We dont ‘see’ shit. Thats why incredibly important facets of our inner biology can go undetected for years and years and years.. until someone says “Hey, wait a minute… ” and does the right experiments to ‘see’ what we cant literally see.

We are continually surprised when new molecular machinery, millions of years old, jumps out of the closet screaming “BOOOOO!!! BWAHAHAHAHA!!!”

But then we feel like idiots because viruses dont appear to be as shocked as we are… CMV using a sneaky chemokine is not ‘new’. It knew about the biochemistry of chemokines before we did. Hell, we only discovered chemokines because of viruses.

Just like we discovered tetherin because of viruses.

Viruses know us better than we know ourselves.

EARGGGGHHP! **head explodes again**


  1. #1 Torbj�rn Larsson, OM
    June 24, 2008

    I like the idea that evolution is a close analogue of a learning system, in fact so close that it makes sense to say that the whole populations genome learn “how to survive” as I think Dawkins put it in his article on the Information Challenge (from ID to him).

    But this goes both ways – we, our genome, knows them as much as they know us. Co-evolution, remember?

    (Okay, perhaps we are slow learners compared to the speed freak capabilities of the HIV quasispecies genome. Then again we have a large house with recipes. And matching capabilities in the adaptive immune system.)

    What scares me isn’t when viruses molecular machinery screams out loud. What scares me is then our own molecular machinery goes on a rampage. An adaptive immune system that doesn’t always recognize “self”, or worse launches suicidal attacks on invaders, who ordered that?

    But at least I have something screaming back to that buggerman of a virus. Bwa ha ha!

  2. #2 mikel
    June 24, 2008

    The most important cellular processes have been discovered with viruses. Why? because the virus must economize in the information that it carries, so if a virus messes with a process, that means that it is important for the cell.

  3. #3 Doubting Foo
    June 24, 2008

    I have a stooped question…if doctors use a virus to cure someone of cancer (I think I read that somewhere) could that virus magically become an ERV and protect that person’s subsequent offspring?

    Sorry if that sounds completely ridiculous…I know computer viruses, not people viruses.

  4. #4 The Chemist
    June 24, 2008

    Aw man, I wish my head would explode!

    It is amazing how much we take our ignorance for granted though. In many ways, we can’t even suspect what we don’t know.

  5. #5 mcmillan
    June 24, 2008

    Doubting Foo –

    It probably wouldn’t be passed on. The virus are used to get DNA into the cells of the body, but only certain cells are responsible for the DNA that gets passed on to the kids. So even though the virus could get integrated into the patients body and possibly treat cancer, unless it also integrates into the germ cells that make egg and sperm cells this change wouldn’t be passed on.

    Hope that helps some, don’t worry about asking questions like that. We all had to learn it from somewhere.

  6. #6 Murray
    June 24, 2008

    Weve been co-evolving with these guys (herpes viruses) for millions of years.

    Right. So, why would we need toxic drugs to kill them?

  7. #7 efrique
    June 24, 2008

    Ceiling Virus Iz Watching You

  8. #8 Kathy
    June 25, 2008

    I just wanted to drop you a line to thank you. I’ve been lurking for a while.

    I just took a class in Virology this past Winter, and just fell into…well, perhaps “love” is a bit strong, but I’ve definitely developed a fondness for them.

    Thank you for your blog, and I’ll go back to lurking quietly. 🙂

  9. #9 Bob O'H
    June 25, 2008

    Viruses know us better than we know ourselves.

    Well, I’m sorry. If they don’t publish, it’s not our fault.

  10. #10 Stephen Wells
    June 25, 2008

    @Murray: antelope have been co-evolving with cheetahs for quite some time too.

    To Abbie: bonus points for gratuitous reference to fictitious nature of promised cake.

  11. #11 Felstatsu
    June 25, 2008

    Aww, don’t go back into lurking Kathy, I’m in the entirely wrong field for this information, yet I’m here, posting what I can because I enjoy the reading and the conversations that happen based on what ERV posts. It’s more fun when there’s more people to talk to.

    Oh, and efrique, basement virus iz watching u bak.

  12. #12 Felstatsu
    June 25, 2008

    Sorry, double-post if someone else isn’t faster than me, kinda forgot what I was going to say about the article. Too intent on the basement virus I guess.

    Anyways, while not head explosion inducing for me, this is really cool information. Due to my field it was kind of expected that viruses know more about us than we do, since in my field, dealing with hackers and computer virus related things it becomes obvious that the invader has to know more about some aspect of the system more than the person running it to not get caught.

    For example, many common anti-virus programs don’t normally run a full scan unless the end user changes a lot of settings. A person who knows their way around the anti-virus software can write a virus that will stay out of the way of places that unchanged AV software will look, it will be caught by any end user who does set up a real full system scan though. Next option is by knowing more about the way files are scanned, a virus that doesn’t set off any triggers while the file is being scanned will not be caught by any AV program the hacker is able to do this for until the AV definitions are updated to find what this virus is doing to hide. Then the virus has to evolve again to get around the better AV software, AV software evolves, going on until one side gives up I’d guess. Not likely going to happen at any rate.

    Good read though, I just don’t have to clean up head explodie pieces from my desk.

  13. #13 Jim
    June 25, 2008

    “The most important cellular processes have been discovered with viruses. Why? because the virus must economize in the information that it carries, so if a virus messes with a process, that means that it is important for the cell.”

    This was a “head exploding” revelation for myself and lead to me choosing my current thesis adviser (we use poliovirus to look a a variety of cellular processes). Never thought I would find myself predominantly becoming a cell biologist in a virology department.

  14. #14 Felstatsu
    June 25, 2008

    I suppose I forgot to mention that another thing about computer viruses in the line that takes information of yours (such as credit card information from online banking) and the line that causes your comp to be a bot. One of their best ways of avoiding detection is to keep your machine from getting anything else and for them to keep everything important working well. While biological viruses target important things because the virus needs them usually for consumption to reproduce them self, computer viruses target important things for protection so they can reproduce them self. A little different, but in the end both rely on actions related to important things in the host to continue the virus’s survival.

    Almost enough to let me understand why ID people talk about designed complexity, but sadly for them, I still think it’s utter crap. I just understand their reasoning a bit better without believing it any more than before, maybe even less.

  15. #15 efrique
    June 25, 2008

    Hi Abbie… did you see this:

  16. #16 Ben Teague
    June 26, 2008

    My biggest head-exploding moment came during my brief, doomed career as a grad student. This would have been about the year they invented the inclined plane.

    While analyzing some hideously difficult problem in orbital dynamics, the professor broke off and said in a musing voice, “You know, there aren’t any physics problems in the universe, just in physics class.”

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