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  1.  (8634.1)
    @John Skylar - I really dig this thread, and appreciate that you're taking the time to discuss Virology with us. It's rather eye-opening, and quite interesting, to say the least. Thank you.
  2.  (8634.2)
    Thanks so much, man. It's nice to share this stuff with so many people who look at a thing from so many different angles. I can't think about Virology a million different ways, and neither can you...but together, well...perspective is a great thing to have.

    And I don't know if y'all can get this paper because it's not open access, but I find it too fucking interesting not to mention, from the Journal of Virology, today. It's about the structure of one of the viruses that infects "extremophile" archaebacteria, which live in crazy inhospitable places. If we're to colonize other planets, we've a lot to learn from Archaebacteria and the viruses that infect them. This paper gives us the structure and stability of one such virus, which is a step in the right direction to understanding how such fragile, tiny things can survive in the harshest places.
  3.  (8634.3)
    Two updates for you, Whitechapel:

    One! I have heard some things about bees and colony collapse disorder. The big controversy was over whether bee colonies were dying because of a fungus or a virus. Today, PLoS ONE (normally kind of a junkpile journal, really) had an article answering the question: It's both! Apparently a fungus from genus Nosema and a virus from the family Iridoviridae ("Iridescent Viruses") work together to kill bee colonies. Now, perhaps, we can work to save the bees.

    ...also, I want to write some kind of story with a character named "Iridescent Virus."

    On another front, perhaps less significant, a question that I've been wondering about for two years was answered in today's PLoS Pathogens (not a junkpile). Retroviruses (like HIV) package two copies of their genomes, whereas other viruses package only one. No one knew why, but this paper suggests it helps the virus tell its genome apart from other RNAs inside the cell, and also helps the virus resist irradiation. So, clearly, retroviruses are ready to go with us into space.

    That question really bugged me for awhile, it's nice to see it answered.
    • CommentAuthorroadscum
    • CommentTimeOct 8th 2010
    John, thanks for the updates. Keep it up mate.
  4.  (8634.5)
    On closer inspection, and in light of this article, I'm going to say that CCD isn't necessarily a solved problem. It seems that there is a good reason that the article was in PLoS ONE, in light of a somewhat weak last figure and the fact that there is a controversy over the effect of pesticides on the bees.

    The numbers still suggest that iridovirus and Nosema in combination are involved in CCD. But that doesn't mean that susceptibility isn't caused by pesticide exposure.
    • CommentAuthorroadscum
    • CommentTimeOct 9th 2010
    An inconclusive article (Quote: the research does not "clearly define" whether the concurrent virus and fungus... is "a marker, a cause, or a consequence of CCD.") by a researcher funded by the manufacturer of a pesticide suspected of being implicated in the problem? I'll say it's not a solved problem.

    Reading through the article, it looks to me like Bayer are involved in a desperate attempt at some serious arse covering.
      CommentAuthorJohn Skylar
    • CommentTimeOct 11th 2010 edited
    Well, the news article is really sensationalist, to be fair. Scientists are a little more restrained, so I'll try and present why this is reason to doubt, not reject, the paper.

    For one, while the lead author (usually not the most experienced or notable scientist on the list) appears to have taken funding from Bayer at some point in the past, there is no evidence that any of the other authors (and there are 16 of them) had a conflict of interests. Furthermore, these people are at a variety of institutions, none of them affiliated with Bayer. So, don't believe everything journalists say. I'm not willing to reject this paper outright simply because one of its authors has a questionable connection in his past.

    Furthermore, the paper does pretty much get the smoking gun on the IIV/Nosema connection to CCD. The way that we assess if something is the causative agent of a disease is via a set of rules called Koch's Postulates. If they're satisfied, then we are willing to say that the disease is caused by the infectious agent in question.

    The paper appears to satisfy all four postulates, so it does seem to have found the cause. However, the satisfaction of postulate #3 is not demonstrated as independent of pesticide exposure. All they needed to do was test the bees for exposure to Bayer pesticides, show that there was none, and then include that as a supplementary figure. They probably didn't do that because they didn't want to pay the figure fees, and the reviewers didn't ask for it.

    I expect a paper from this group, sooner or later, that shows that bees that are totally naive to pesticides will still get CCD when exposed to IIV/Nosema. If that paper doesn't turn up, then you can start to suspect fishy things.

    And if any of the authors retracts their name from the paper, then you can really suspect fishy things.

    Until then it seems like the paper is okay, but that it could use a little bolstering and outside confirmation. I would not, however, say that the paper is invalidated.
  5.  (8634.8)
    Ah, the bee issue. I somewhat suspect that CCD is an excessively complicated thing. Still, this stuff seems to indicate progress, which is great.

    (This thread is lovely by the way, and much more interesting than pedagogy, which is what I am supposed to be doing)

    re: viruses as a form of communication gone horribly wrong... John, I talked to you over AIM about a few ideas on how to turn that into a plot, but unfortunately the only thing I can think of at present is using it as a backstory for a thing about superheroes/metas/mutans/what have you. Or possibly a virus as a vector for a beneficial mutation, something that evolved for species-wide survival (I know, I know, Evolution Does Not Work That Way). Or a way to explain psychics in a different sort of plot. It doesn't seem to be a plot-thing on its own, however.

    Interesting; in googling Mimiviruses I found out that apparently a mimivirus showed up in Rainbow's End as a form of mind control (according to Wikipedia); so not entirely a new idea, this plot kernel!

    So, now an actual question; re Mimiviruses - I've heard theories that mimiviruses are a proto-cell, a precursor to what we'd call Actual Life. What's the deal with this theory? And how legit do you personally think it is? ('You' here meaning 'y'all biologists in this here thread')
  6.  (8634.9)
    I was recently at a symposium, and I saw a poster that leads me to believe that this finding from March 2010 is going to be a somewhat big deal in the HIV field. I can't say more because I don't think this poster's contents are published yet, but keep your eyes peeled.

    tl;dr: Cannabinoids (like, say, THC) might interfere with the HIV life cycle.

    PLEASE NOTE: This is not specific medical advice, but mention of a curious finding. None of you are to go running around saying it's okay to have unprotected sex with everyone you meet if you smoke pot, because that is NOT TRUE. HIV is still a killer, and pot still has drawbacks (but so does alcohol).

    @Lucid Seraph

    We spoke about mimiviruses up top. I wouldn't call mimiviruses a proto-cell by any stretch, because they lack the protein expression machinery that is needed in order to replicate themselves. That machinery is only found in an actual cell, so mimiviruses could not preexist cells as they need them in order to replicate. There's not much of a chicken-egg problem with viruses and cells because we know that viruses are obligate parasites. No cell means no virus. However, mimiviruses might qualify as as proto-virus, a degenerate parasitic cell that gave rise to later viruses. That seems to be a strange idea, to me, since the diversity of viruses on the whole is so much greater than the diversity of mimiviruses. But it's possible. I just don't know how to test it to my satisfaction.
    • CommentTimeOct 14th 2010
    This whole thread is fascinating. It's a great place to start for the biopunk comic I am working on, but honestly, comic and narrative set aside, this stuff is just fascinating period.
    • CommentTimeOct 15th 2010
    Interesting stuff on retro-viruses there John Skylar. Thanks for posting it up!
      CommentAuthorJohn Skylar
    • CommentTimeOct 22nd 2010 edited
    (thanks @ smileyfish and Romeo)

    But also!

    Today, PLoS Pathogens is out, and it has an article entitled Social Media and Microbiology Education.

    It's written by Dr. Vincent Racaniello, who does the Virology Blog and the This Week in Virology podcast, both of which I've plugged on here before. Dr. Racaniello is a big inspiration for me, and I think that he's a scientist to watch because he is very driven about using new media and new venues to improve science education. The zeal and enthusiasm that he has for teaching the world about Virology in new ways reminds me of how bold Mr. Ellis can be in terms of finding new and interesting means to serve content to comics readers. It's good that there are people like this in fields that I like to follow.

    Anyway, it's not a technical article. It's Dr. Racaniello summarizing what he's learned from blogging, social networking, and podcasting in virology. I'm so glad to see this in print, and it's worth a read. I almost considered making a new thread for it but I didn't want to tempt an eely fate.

    In some ways, the article is a guide to open science. In other ways it's a guide to social media marketing, and not in the "I want to sell consulting services" douchebag way, but in the "I want to make the world a smarter place" way.
    • CommentTimeDec 14th 2010
    Forgive me for what may be a 101-level question, but:

    Can you folks point me to information regarding long-term effects of viral coexistence?
    The personal reason I ask is that I myself am infected with Cosackievirus, having had Hand-Foot-Mouth as a child. I've been observing some viral resurgence over the years (occasional deep blisters on hands).

    But beyond that, I am also interested in any possible link to psychological effects of long-term viral coexistence. I understand that recent research has shown, crudely, that it is possible for viruses to affect the behavior of the host in order to favor their reproduction. I am curious as to any research involving higher-order mammals and viruses such as the chicken pox virus or Cosackie.

    Long story short - with such long-dormant viruses, is there any evidence that those classes of viruses can have any effect on human behavior?
  7.  (8634.14)
    DISCLAIMER: I cannot give specific medical advice. Anything that I say is scientific analysis and does not consider the potential implications for medical treatment, because I'm not a medical doctor. If you want medical advice, talk to one of those.

    I'll say offhand that studies of viral persistence and host-virus equilibrium are not where they need to be to fully answer your question.

    Coxsackievirus is an ssRNA virus, so it falls into my realm of specialty, though as an enterovirus I'm slightly unfamiliar with some of its finer points. I will say that its ability to persist in fibroblasts and pancreatic cells is unusual among RNA viruses; most RNA viruses are bad at lasting in a host and are usually self-limiting.

    Notable exceptions are Measles virus, Nipah virus, and Hepatitis C virus. Unfortunately the symptoms of all of these in their persistent form are not good things to have, however, Coxsackie virus does not appear to have the same long-term prognosis. When it comes to ssRNA viruses that you could have a persistent infection from, it's better than the alternatives.

    And furthermore, there's some evidence that persistent viruses (namely HCMV and EBV) may actually help provoke a stronger immune response against other viruses, so I won't say that persistent infection is universally a bad thing. Chicken pox virus, also known as Varicella zoster, is a DNA virus related to HCMV and EBV. Its only known persistent issue is reactivation under stress to cause the disease known as shingles, which is neuronal but is not behavioral. It's not related to ssRNA viruses even a little.

    When it comes to potential effects on your behaviour or personality, I doubt that coxsackieviruses would be responsible. Unlike their cousin, Polio virus, Coxsackieviruses are very unlikely to infect the central nervous system, and when they do it is usually during initial infection and leads to encephalitis. I'm not ruling out some more complicated situation, but I think you really don't have to worry about that on a personal level.

    On a more general level, this is a pretty interesting question. My biggest question with respect to this is how Rabies virus can cause hosts to exhibit hydrophobia--literally fear of water--and whether or not this is helpful to the virus in some way.

    There are two long-term viral related psychological symptoms that I know of. One is the apparent correlation between maternal influenza virus infection (or cat ownership, incidentally, hinting at a toxoplasmosis relation as well, but we already know that's a neurotropic parasite) and later development of schizophrenia. And we're not even sure that's caused by influenza virus, nor is it a very strong correlation.

    The other is a long-term symptom of end-stage HIV infection, which is a horrible psychosis that some HIV patients develop...that's not the most common symptom in the universe, either.

    So tl;dr: no, there isn't much evidence that persistent RNA virus infection can have psychological symptoms, except for very specific viral infections (Rabies and HIV, specifically). Coxsackievirus has one disease associated with persistent infection, and that's diabetes. Talk to your doctor about that, but it's no guarantee that coxsackievirus infection leads to diabetes. If you're concerned about this as an intellectual question, then my answer should be enough. If you're concerned about it as a personal medical issue, please instead speak to a medical doctor as they will have a better idea about what causes certain symptoms, and whether or not it is a virus. I only know how viruses drive their symptoms; MDs know which causes, viruses or otherwise, drive the various combinations of symptoms that people can have. My knowledge is intentionally specialized and will therefore have many gaps with respect to what non-viral things might cause a given symptom.
    • CommentTimeDec 14th 2010
    Great stuff, and all caveats taken in the spirit they were given.
    I'd love to hear more in general on this topic, if folks feel like elaborating on such.
  8.  (8634.16)
    Just in case, you havent visited Warren Ellis's site. Article on first HIV infected patient to be cured. Although, the current cure sounds elaborate, expensive, unpredictable and hard on the patient.
  9.  (8634.17)
    This "cure" thing is kind of old news, really, since the publication showing his status of no virus and high CD4+ cells came out about a year ago.

    The big deal about this is that he's still cured now, so the scientists are willing to start using the word "cure." Great, but it's basically what we all expected when they showed he hadn't died.

    What's really going to be important will be to see if he doesn't get cancer from the treatment a few years down the line.

    At any rate, it's truly exciting research. Still, not going to help people in Africa with their HIV infections. At least not for many decades, at the pace of medical approval.
  10.  (8634.18)
    I don't know if you guys can see the actual paper (can't remember if Nature has a paywall or not), but here's the title:

    "Cocaine Analog Coupled to Disrupted Adenovirus: A Vaccine Strategy to Evoke High-titer Immunity Against Addictive Drugs"

    That's right. Using viruses with coupled small drugs to actually create an immune response against those drugs so they don't get the addict high anymore.

    There's been some work done already with anti-cocaine antibodies, but that only lasts about six months. This vaccine, based on a common virus, would provide protection from addiction for life.
    • CommentAuthorFan
    • CommentTimeMar 10th 2011
    > protection from addiction for life

    I don't know; maybe not. Don't people get addicted to lots of things simultaneously: you know, drink, cigarettes. drugs, gambling, etc.?

    Doesn't that imply, that it's not the particular substance, but that (those) people have a vulnerabiity to any kind of substance abuse: maybe poor impulse control, diminished incentives to be sober, maybe environmental, educational, and social/role-model factors too: who knows.
    • CommentTimeMar 10th 2011
    Two points there, Fan. First, you're confusing psychological and physiological addiction. You can get psychologically addicted to anything you like, but physiological addictiveness varies by substance.

    Second, the vaccine prevents not only addiction, but the drug's effect in the first place. You can't get high on cocaine once you've been inoculated. Sure, you might get addicted to sniffing powder, but that's significantly less bad for you. And remarkably unlikely.