Saturday, July 4, 2009

Viruses and Life

Recently it has come to my attention that viruses are really cool.

In terms of biomass (and numbers for that matter), they are by far a much more abundant organism on the earth then humans. They can infect essentially every living species from bacteria to plants to mammals, and can, in some cases, be notoriously hard to beat. In the oceans, viruses play important roles in geochemical cycles and carbon turnover. They kill approximately 20% of all microbial biomass every day, which has a major impact on nutrient and energy cycles.

This new found interest in viruses also is a result of the current projects I am working on. Viruses work by floating around in your system until they find a cell in your body that they are capable of latching on to. Once they`ve done this, they inject their DNA into the cell, and basically ``hijack`` the cell and use it to create more viruses. We can exploit this system in the lab. By taking out the genes in the virus that cause the cell to create new virus particles, and replacing them with genes who`s products we are interested in, we can use the virus as an efficient delivery system to insert new genes into cells. In my case, I have a plate of cells which I bombard with literally millions of virus particles. The virus particles will then dock on the cells (mouse embryonic cells in the case) and insert the gene for Cre recombinase , which will then act to cut out a different gene out of tGFP cellshe cell genome... though that part is a different story. You can just as easily have the virus inject green fluorescent  protein, which will cause the cells to glow a neon green in certain light.

Despite all this, there is still an ongoing debate as to whether or not viruses can be considered “alive”. I recently just read an article entitled “Ten reasons to exclude viruses from the tree of life” (Moreira, D. et al. Nat. Rev. Microbiol 7, 306-311 (2009).) which, as you can probably deduce, argued the negative. The main idea that this article was getting at was that essentially viruses can not reproduce, evolve or pretty much even survive unless it makes use of another cell.  They go as far as to say that if you were to take all of the world’s viruses and dump them onto a new, sterile planet, eventually they would all eventually die and decay. In contrast, they argue, if you were to do the same with all the different bacteria species on the Earth, it is likely that at least some of them would thrive.  The authors bring up a number of other points as well, such as the fact that it is impossible to trace a virus lineage back to a common ancestor (i.e. not a single gene is shared between all viruses) and that viruses only “steal” genes from cells, and do not develop them on their own.

While I can agree with most of the points that the authors make, I still feel unsatisfied accepting the view that viruses are not alive, and I think (for me at least) what it comes down to is the operational definition of life that is being used. This definition, which we all learned in grade 9 science class, basically sets down a check list of things that you need to be considered alive such as the ability to produce energy, waste, the ability to reproduce and adapt to surroundings… etc. This definition though, seems almost too stringent. To me, a much more fitting (though perhaps a too broad) definition would be this: life is the ability of a bit matter to actively work to persist its information throughout time. For example, how is it that the atoms that make up a virus “know” to seek out similar atoms and organize them into a similar form as itself before they fall apart? Where did this intrinsic “desire” to pass on this information come from? What makes some particular organization of matter more able to pass on this information while other random organizations just float around? To me this idea represents the very essence of what it means to be alive. You can even think of it on a larger scale. When we die, we lose the ability to maintain our organization of matter, and we decompose. During the time we are alive though, we take in atoms and molecules from our food and the air, and use those molecules as building blocks for our cells. When I think about it, it is a sobering thought. What would the world be like today if matter could not organize itself into reproducible forms? Probably pretty boring, I’d wager.


  1. Very cool.

    Where does the supposed RNA world self-replicating RNA fit in, then? It would be completely chemically defined, but capable of replicating its own information. If scientists can make a self-replicating RNA, would it be considered alive?

  2. I suppose I would argue it is alive, though only in the most limited sense. I can't recall offhand though... are there examples of completely synthetic self-replcating RNA? I guess if you really wanted to nit pick you could almost aruge that a radical reaction is alive as well using this definition. Perhaps this idea will need some revision...

  3. Not to my knowledge, but the thinking is that theoretically something had to exist once that eventually changed and gave rise to life as it is now. I'd say the actual creation of such a self-replicating molecule would hands-down get the Nobel. It would also stir up all sorts of bioethical issues.....

  4. not sure about self-replicating RNA, but i know they've made self-assembling nucleotides. it actually seemed like their experiment was pretty intuitive.

    steve i think that your definition of life is probably closer to reality, and i agree viruses are alive.

    for the last cuople of years ive been of the opinion that the term "life" is wildly overrated anyway. i really think its possible that one day in the future pretty much all fundamental biological processes will be boiled down to physics, and a lot of people are going to be upset.

  5. I think, like the tree of life, the "alive versus not-alive" concept is starting to fray really badly at the fringes. There certainly is a difference between myself and a chunk of granite (at least before the 12th beer) but more and more examples keep showing up that make the whole process of trying to set some definite threshold more and more difficult, and really not that meaningful anymore. Things are what they are.

  6. I think the line is going to get blurry no matter where you put it.

    For example where would the concept of memes fit into your definition? They would only be lacking in the material department.

    Another example, which i think is more fitting to this conversation is plant retro transposons. If you were to argue that viruses are alive then you would need to think hard about this group of transposable elements. They have high homology to animal retroviruses but always and only lack the sheathing proteins. They act in the same way viruses to but never leave the cell. So where would these (and all other TE's) go on our tree?

    Its a hard line to draw.

  7. @ Greg: The difference that I think most people would see between viruses and retro transposons is that on a superficial level, viruses seem more deliberate in their actions, whereas retrotransposons are just following the set of rules coded in to them. Realistically, this is what viruses are doing too, so its not a good argument. But then again, thats also what cells do...