QUESTION: Do you like pie? YES or NO
ANSWER: Well, I like most kinds of pie. I dont really like cherry. Meat-pies are a big disappointment.
QUESTION: YES or NO!
ANSWER: Umm… I guess if you held a gun to my head, yes?
QUESTION: Great! Here is a nice greasy beefy meat pie! I know how much you like PIE!
ANSWER: … *blink*
QUESTION: Are viruses alive? YES or NO
ANSWER: Well, I think that ‘life’ is a continuum. Earth was once an RNA world, and has been growing and evolving since then, into ‘life’ as we know it today. To me, ‘life’ started with those RNA molecules. To say ‘No, real life started right THERE‘, and point to the evolution of cell-like bodies, or the acquisition of a ribosome-like structure, is kind of silly. Furthermore, considering the huge role viruses have played in the evolution of life on this planet, whether viruses fit some arbitrary definition of ‘alive’ is irrelevant as to whether they should be included in the Tree of Life. They must be included.
QUESTION: YES or NO!
ANSWER: Do viruses fit current idiomatic definitions of ‘alive’? No.
QUESTION: Great! Virologists dont think viruses are alive, so we dont need to include them in the Tree of Life!
ANSWER: … *blink*
I wish I could write a paper this childish and get it published in Nature:
1. Viruses are not alive
Futhermore, that viruses are not alive was officially acknowledged by the International Committee on Taxonomy of Viruses in 2000 and is still held by most virologists.
Their references for this statement are 1) a viral taxonomy conference 2) a textbook.
Discussions I have had on the topic ‘are viruses alive?’ have never included an ‘official acknoledgement’ that viruses are not alive, nor do I walk away with an impression that that opinion is ‘held by most virologists’, but maybe my scientific upbringing has been isolated. So I grabbed ‘Fields Virology’, THE virology reference off the shelf for a quick scan to see if I could find any definitive statements.
Page 1– Virtually all living organisms, when studied carefully, have viral parasites, and so these smallest of living entities exert significant forces on all life forms, including themselves.
Page 16– Viruses exist wherever life is found and are the most abundant life-form on the planet.
Page 24– Many have argued that viruses are not even living, although to a seasoned virologist, they exhibit a life as robust as any other creature.
Page 417 (*my* chapter, viral evolution)– Viruses lie in the border between living and non-living (a distinction that is intuitively clear but conceptually fuzzy), and are endowed with the potential to evolve at the highest rates among biological forms. Viruses lack an integrated metabolism, a fact that renders them totally dependent on cells. Yet, all life forms known to us are dependent on other life forms for long-term maintenance. The current studies on virus population structure and evolution offer the exciting possibility of learning about basic mechanisms of life in a highly transdisciplinary fashion, while developing new approaches to control viral disease.
From Principles of Virology:
Page 15– A virus is a very small, infectious, obligate intracellular (molecular) parasite.
‘Life’ is a continuum. Viruses fall on the continuum. Thats what virologists think.
These authors go on to justify their statement by saying that if we seeded a sterile planet with every known virus, nothing would happen. However if we seeded a sterile planet with all known bacteria, ‘life’ would continue. Thats nice. So seed the planet with all known obligate intracellular bacteria. Oh wait, nothing would happen. Seed this planet devoid of life of a male and female human. After a brief bout of cannibalism, nothing would happen. The authors strained analogy ‘proves’ nothing except that lots of bacteria are self-sufficient, or can team-up with other bacteria to get everything they need to survive. Fantastic.
2. Viruses are polyphyletic
3. There are no ancestral viral lineages
4. Viral lineages lack structural continuity
These three ‘reasons’ are the same reason: Viral phylogeny is hard.
Heres a tissue. And heres capsid. Go clean yourself up.
These authors response to Raoult and Forterre?
(In addition to viruses– ERV) Raoult and Forterre classify these genetic elements, including plasmids, transposons, viroids, virusoids and RNA satellites, as ‘orphan replicons’ that do not deserve the title of organisms but that could be included in the tree of life. However, if a tree of life contains elements that are not organisms, is it a tree of life or just a tree of genes from multiple origins?
Everything on this planet is connected. This includes viruses. This means they can, and should, be in the tree. Deal with it.
5. Distant hosts do not imply antiquity
I almost have no words for this ‘reason’. They set up one big damn straw-man to triumphantly knock down:
The fact that some viral lineages infect phylogenetically distant hosts is sometimes used as evidence for their ancient origin…
… Such host shifts could lead to false inferences of an ancient origin for widespread viral lineages if it is based only on the diversity of hosts, instead of on a careful phylogenetic analysis of viral and host markers to find the required evidence to prove co-evolution.
Well thanks for the phylogeny lesson, perfessurs! Duh? Cool recent paper on an ancient virus with a ‘distant’ host thats still related to other viruses for RAAAAAAAAAGE.
6. Cellular origins of metabolic genes
7. Cellular origin of translation genes
8. Viruses are gene robbers
9. Most horizontal gene transfer occurs from cells to viruses
Again, four ‘reasons’ that are really one. Viruses steal genes. What a mind blowing revelation. Especially from one of the authors, who is a bacteria person or whatever, who most surely knows that lots of pathogenic bacteria are ‘bad’ because they stole genes from viruses. But whatever. These statements mean nothing when deciding whether to include viruses in the ToL, except dont use genes that viruses stole to determine phylogeny. Use capsid. Like we already suggested.
10. Simplicity does not mean antiquity
Of course not. The viruses we see today are highly evolved creatures, just as we are. That doesnt negate the fact that we see every permutation of viral genome today (+ssRNA, -ssRNA, dsRNA, ssDNA, dsDNA, retroviruses, circular, linear), everything that you would expect to see at the beginning of life on this planet is still found in viruses. Because viruses have life-cycles that ‘more complex’ organisms on this planet do not use, they need weird proteins and enzymes that they could not have stolen from a host. The most logical conclusion, to me, is that they invented these proteins/enzymes billions of years ago. If they had to steal every ‘part’ they needed from developed organisms, they would not look like the viruses we have on this planet today.
Viruses are old. Sorry.
There is just so much stupid in this paper I dont have the patience to touch:
Even if we accept such an imperfect definition of life, viruses would still be excluded because of a fundamental peculiarity of viral existence that is often overlooked: viruses neither replicate nor evolve, they are evolved by cells. Even if some viruses encode their own polymerases, some of them error-prone, their expression and function require the cell machinery so that, in practice, viruses are evolved by cells — no cells, no viral evolution.
*FACEPALM!* If you dont feed people, we dont evolve either. We die. That doesnt mean we evolve because of food what the hell is these authors goddammed problem????
This whole article was baffling. I have no damn idea why this was in Nature.