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  • charliefarber 8:23 am on November 19, 2015 Permalink | Reply  


    I’m a 3rd year undergraduate interested in pursuing graduate studies in viral ecology. Are there any active online communities I could participate in to learn more about the field?

  • hannah little 7:58 pm on July 20, 2014 Permalink | Reply
    Tags: phage   

    Are phage alive?

    • Bob Blasdel 12:50 pm on July 24, 2014 Permalink | Reply

      This is an often surprisingly philosophical question that everyone seems to have their own idiosyncratic answer to.

      The question of what makes a thing ‘alive’ to begin with is tricky enough though typical answers tend to concentrate around a few key points,

      *Autopoiesis, or the ability of an entity to write itself, to self replicate producing new independent organisms.
      *Homoeostasis, the active maintenance of a constant internal physical environment conducive to the maintenance of other life functions – such as consistent pH, temperature or salinity.
      *Organization, being structurally composed into units such as cells.
      *Metabolism, possessing a scheme of enzymes capable of transforming chemical compounds into molecules needed for the maintenance of other life functions as well as harness external energy sources to power it.
      *Growth, the ability for populations of the thing being described to expand.
      *Adaptation, the ability for those populations to evolve through natural selection towards fitness in their current as well as new environments. and finally,
      *Stimulus response, the ability to internally respond to changes in the external environment.

      At first blush it becomes easy to see why most everyone waffles and hedges when asked this deceptively complex question about viruses in general, especially the larger ones like this meet some of the criteria easily, others with a little bit of hedging, while others just get confusing. The most common solution to the inadequacy of an alive/not-alive dichotomy for describing viruses that I’ve seen from people who study the viruses of microbes has been to make a distinction between ‘living things’ and ‘organisms’ before creating an idiosyncratic definition for each term so as to assign both terms to cellular life and only one of the two to viruses. However, my solution requires a small philosophical leap that I first heard described by Dr. Patrick Forterre at the first Viruses of Microbes conference in Paris in 2010.

      If you were going to count the number of frogs in a pond, and somehow had access to technology that would let you, would you include the millions of eggs released from each fertilized egg sack as frogs in your final number? What about the tadpoles? Similarly, if you were going to count all of the viruses on earth, would you count the inert dead viral particles or the vital and germinating virally infected cells? What I’m trying to get at is that, while historically we’ve thought of a virus as a viral particle that infects cells, it might make a lot more sense to think of viruses as the actively infected cells that produce viral particles. Indeed, once you shift your perspective enough, viruses – and particularly the viruses of microbes – seem a lot more alive with a lot less need for definitional dissembling.

      Viruses, when thought of in this way, author their own reproduction in unambiguous autopoiesis, they just use the brush of their hosts to do it with in a way not so unlike other intracellular obligate parasites. They actively maintain homeostasis, and generally for internal environments fundamentally different from the one their hosts formerly maintained. Both the actively infected cell and viral particles are organized into discrete units. The viruses of microbes often maintain an energy store of ATP through fundamentally different mechanisms than their host uses, while all but the smallest demolish their host’s metabolisms – replacing it with their own viral metabolisms. They are capable of a speed of both exponential growth and evolution unmatched by even the fastest forms of cellular life and they respond to external stimuli in their own unique ways. While their viral particles might only fit these distinctions in pedantic meaningless ways, like fire or transposons would, I would argue that the infected cells they produce are indeed very much an independent organism. They certainly don’t encode for all of central metabolism on their own, but then again neither do we as humans, as we leave much of it to our gut symbiotes.

      However, the two biggest problems with my process for simply saying yes to this question are the two parts of the viral life cycle where the virus would then be pretty unambiguously at least mostly dead, the viral particle and lysogeny. The way in which dormant viral particles become mostly dead can still be thought of as analogous to the way endospore forming Firmicutes will generate a tough and metabolically inert structure out of their guts when times are rough in order to spring back to life later, which is to say, slightly alive. More troubling for my definition though are temperate phages and retroviruses that turn off their host lethal genes upon infection and meld with their host, becoming a composite creature known as a lysogen. A virus that is currently in this stage of its life cycle, known as a prophage or provirus, isn’t really its own entity at all lacking all of the characteristics of life with exception of a response to stimuli in some prophages. However, a provirus already isn’t a virus any more if it can’t generate a productive active infection, and so I think we should refrain from calling it ‘the virus’ in opposition to the infection it can produce, in the same way that we would refrain from calling an egg or a tadpole ‘the frog’, even if they are still viruses.

      Thus I would say that yes, at least many phage are indeed alive, at least when defined in what I feel to be the most meaningful way.

      Liked by 1 person

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