The biology hype of the week is the notion that viruses are alive. Well, the true answer to that is… maybe. But that’s not catchy enough for headlines, is it?
Let’s start, as usual, with the source. Nasir & Caetano-Anollés (2015) published a paper where they did a lot of computer sniffing in existing proteomics databases to find out that viruses express a few dozen unique protein folds and they share several hundred more with cells. In other words, some of the viral proteins are unique. Using this information and some neat math they managed to calculate an evolutionary tree, that is, they classified the viruses via genetic relatedness to themselves and living organisms. That’s the strictu sensu of the term “tree of life”. From this taxonomy exercise, the authors speculate about when and how viruses might have appeared. They concluded that viruses appeared as RNA chunks spat out of cells. To give you a little background, there are two main hypotheses about the origin of viruses: appeared before cells as free floating RNA, or they were pieces of RNA that have been kicked out of a living cell, so after the evolution of cells. All well and good, I’m not going to open that can of worms, which hypothesis is more supported from data and so on.
Now, and this is the contentious part, verbatim:
“Here, we put forth the bold conjecture of a universal tree of life (uToL) that describes the evolution of cellular and viral proteomes. […]. Thus, viruses should be considered “living” organisms that simply survive by means of an atypical reproduction method that requires infecting a cell” (p. 18).
It’s their opinion. Not a fact. Not – and this is important – a direct consequence of their awesome taxonomy exercise. For a formal definition, a conjecture is an opinion or conclusion formed on the basis of incomplete information (Oxford Dictionary).
Don’t get me wrong, I think this is a neat paper, and, frankly, I don’t have a horse in this race: I don’t care whether viruses are alive or not. But I do care to distinguish between fact and opinion, an intellectual exercise that seem to have eluded the science websites and science popularization zines and e-zines like EurekaAlert, IFLS, ScienceAlert, Gizmodo, Daily Mail, Wired, Popular Science, R & D Magazine, Laboratory Equipment, and many others, who ran titles saying “Viruses are alive” in just so many words. Note that even the authors themselves put the word “living” between quotes. Know the difference between opinion (that is, we think that because x makes y, maybe x is blue) and a scientific fact (x makes y, y makes z, therefore x must make z and we know that not only because it’s logical, but also because no other wretched letter wants to make z, believe us we tried, we made sure z is where we put it, because we put dye on it, we measured it, chopped it, looked at it with 5 different instruments, and we cannot make z without x though a poor grad student tried and tried in vain, we even modeled z, and yes, it is made by x, otherwise known as we eliminated all other testable bloody possibilities that we could think of. Unless q makes z in humans, but we can’t measure that. Or r makes z under Jovian gravity, but we didn’t get a grant for that…. get my drift what a scientific fact is?).
Now, rant is not over. The authors argue that viruses have a sort of metabolism and they replicate, so they meet the requirements for being classified as alive. For the sake of the argument, I can posit that either these two conditions are not enough for something to be considered alive, or we have then to conclude that cave crystals are also alive. Crystals only grow in the appropriate environment of a saturated solution and bits shattered off from them go into an inert mode waiting for appropriate conditions. Crystal growth can even be looked at as a sort of metabolism. So, if they are willing to characterize crystal growth as somewhere on the continuous scale of life, viruses can be there as well. Using their analogy, the living, metabolically active form for crystals is when they are growing in a saturated solution; and bits breaking off or the bulk waiting for solution conditions to change is just an atypical reproductive scheme. It even gets more interesting with some of the more modern more complicated crystal growth theories with preassembly into nanocrystals, editing or incorporating defects, etc. Ok, I’m getting tired and I made my point anyway. Rant over. Happy debating!
Reference: Nasir, A. & Caetano-Anollés, G. (25 September 2015). A phylogenomic data-driven exploration of viral origins and evolution. Science Advances, 1(8): 1-24. DOI: 10.1126/sciadv.1500527. Article | FREE PDF
by Neuronicus, 29 September 2015
The Science Portal 
There’s an emphasis on what you call `a sort of metabolism’, isn’t it (i.e. not only replication matters)? And that should make a difference to how far you locate viruses from paradigmatic life. I’m asking. I suspect that settling a borderline case type of dispute could almost never be more than conjecturing – what with scientific facts not being semantics facts (whatever the latter might be). It might turn out that uToL is a marginally better (measured by impact on research I guess) taxonomic machinery than what people regularly use nowadays. Shouts of ‘it’s alive’ are comparatively irrelevant.
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To be sure, to be sure! As I said, I have no contention with the paper, is nicely done, and you’re right, an uToL that includes viruses may prove to be not only a better taxonomic tool for researchers, but it may have real-life applications, in helping the discovery of new antivirals, for example. I was only ticked off about the shouts of ‘it’s alive’ – which I couldn’t agree with you more, they are irrelevant, – but they also distract from the really cool findings of the paper, including more evidence regarding the origin of viruses, focusing instead on an opinion which is not derived from the results. Moreover, the media shouts were stating that the paper has PROOF that viruses are alive, which I’m pretty sure even the authors would not claim.
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