Ten Five reasons clumsy excuses to exclude viruses from the tree of life

I'm no biologist so I'm very baffled by this. What would be the purpose of deliberately excluding viruses from the tree of life? Then what? Where do we go from there? Are viruses supposed to be their own special category? Or is this an example of "write something really contentious so everyone disagrees with you and you can make a career for yourself"?

Abbie
Any update on the posting of the 'debate' video?

The "gene robbers" objection seems particularly weird. Imagine a Jurassic Park-type scenario in which a genome is synthesized by combining information from multiple species — extant, when convenient, and extinct, when you can get your hands on preserved cells. (Sure, it wouldn't be easy to make it all work together, but in the gedanken laboratory, all those difficulties can be avoided by judicious application of handwavase and polyunobtaniol.) Every protein-coding gene, every regulatory region, every LINE and SINE, every goddamn nucleotide in this organism would have been "robbed" from some other species. It's one big pile of horizontal gene transfer, but as Dr. F would say, it's alive.

Oh, and Biochem. Soc. Trans. is demanding a subscription. Bloody TwenCen mindset.

Chayanov-- People who are not virologists sometimes have very peculiar, very snobbish, views of viruses. Even ones who are biologists. Its like this paper was written by people who havent read anything about viruses since 1982, but are certain their ideas are extraordinarily clever.

Strider-- Its gonna be a bit. My friend is trying to edit 3.5 hours of video into YouTube-digestible chunks.

Blake-- Can you get this one? Mark Young has done some really cool shit with archaeal viruses, and what they have to say about viral evolution :) Shorter Mark Young: Viruses have been around since before the domains of life split. Funny enough, these authors didnt refer to him, as if they had never heard of his work...

viruses neither replicate nor evolve, they are evolved by cells.

WTF???

The first part is just special pleading. I could just as easily argue that eukaryotic cells aren't self-sufficient because they can't produce their own energy, but rather are parasitically dependent upon their mitochondrial hosts. (And yes, parasitism and symbiosis are part of the same continuum and any line separating them is arbitrary.) While we're at it, DNA doesn't replicate, it's replicated by special proteins. Etc, etc.

The second part is just plain stupid. If you're going to argue that viruses don't evolve but rather are evolved by cells, then NO organism evolves! We're all evolved by our environments! (It's called Natural Selection; look it up. [/snark])

[/rant]

Haha, <3

I'll try to grab both papers the next time I'm within range of an institutional subscription. (The surest way to turn any scientist into an Open Access evangelist is to lock them for a week in a place where their IP address is not recognized. . .)

Incidentally, given the current kerfuffle regarding the JREF's YouTube account, I've been suggesting that science people "diversify their portfolios" and start cross-posting to other video sites. We might as well make it harder for technical difficulties, flagbotting and bogus DMCA claims to knock science off the air. I know that the Boston Skeptics have started using Vimeo, which apparently has a 500 Mb-per-week upload limit.

Ok I'll have to repeat Chayanov's question since I also don't get it and I don't think you answered it fully - why does anyone care about whether viruses are officially on the ToL or not? And for that matter what's "officially" in this case anyways?

I assume it's not like if they get voted off the ToL then virologists need to be taken out of biology and stuffed in some closet with their own mini department right? :)

All I know is this: I ain't no kin to no virus!

Thanks for the post. Now that I see the actual arguments, I agree that for the most part they are stupid and irrelevant.

Unliving though viruses may be, still it is good to have stuff around that kills them -- heat, radiation, chemicals.

Coriolis-- Why should viruses be in the tree of life? Why should E. coli? Why should oak trees? Why should people? Because viruses are part of the Tree of Life is why they should be included! These authors are giving unconvincing 'reasons' for why viruses should be excluded, when there are reasons and ways to include them.

Like that textbook excerpt says, viruses are the most abundant life-form on this planet-- if they are to be excluded from the ToL, I want a damn good reason. These 'ten' are not it.

BaldApe-- I rearranged the order to group like 'reasons' with like, but what I typed in bold are their reasons. Of course they spend time explaining themselves, they didnt just say 'viruses arent alive' and move on, but I think you get the idea of the 'logic' that went into this paper from other excerpts...

Raoult and Forterre are the mimivirus masters from Marseilles they are almost a decade ahead of these guys who are Parisians .

The Parisian academics have to do a lot of work to catch up....

or

.....concoct some rickety framework for dismissing the work of the competition as 'unimportant'.

They are French.

Guess which option they chose.

French historians do this to each other all the time.

It occurs to me that if you replace 'virus' with sperm, all the same points (and their take-down) remain nearly unchanged. Not sure about using the word 'mitochondria' though..there's transfer between cell and mitochondria, but still linear organismally. Hmm...

I think Coriolis is asking why do these people care if viruses are included in the tree of life. What is the motivation for trying to exclude them?

"... one of the authors, who is a bacteria person or whatever ..."
Please, don't tar all of us "bacteria people" with the same brush. Viruses are organisms by any reasonable definition of the term, and in the worlds of "bacteria" (Eu- and Archae-) they are major drivers of evolution. Sure, their own evolution is complicated, but that's what makes 'em interesting.I would argue that a capsid alone does not a virus make, and genome organization is another useful tool in studying viral evolution -- and the root of my pet peeve about bacteriophage taxonomy, which doesn't acknowledge the relatedness of, for example, lambda and P22, because they are shaped differently!

ERV: I don't think you are being quite fair with Coriolis here. He/She was simply asking what practical consequences this has and who might make the determination. You say you want a "damn good reason" to exclude them, but the circular "Because viruses are part of the Tree of Life is why they should be included!" is hardly a reasonable answer to include them :-) Likewise, the shear abundance of an entity has little to do with it's qualifications. There are a lot of rocks on the planet, but I don't classify them as ToL material. Coleoptera are among the most abundant arthropods around, but that's not what makes them insects. You need more specifics (which I have no doubt that you can provide :-) .

To address the ToL question, you must define Life(TM) first, then list what qualities your virals have to meet these criteria. Obviously, a person's initial definition will influence their answer. For the record, I happen to agree with you and may go even further down the entity list before hesitating on the ToL question, but then I use a pretty loose "informationally" based definition.

Pdiff

I agree that viruses could be classified as alive. Pretty unconvincing arguement on your part also though.

Four fundamental programs separate life from pre-life forms: development, maintenance (energy consumption, self protection, etc), reproduction and death. Viruses have none of the above. But how the realm of pre-life had emerged?

"QUESTION: Are viruses alive? YES or NO"

Abbie - I see you gave pretty much the same answer as you did when Zimmer passed the question on to you.

I have to agree with you, more or less. Of the properties that are present with things we have no doubt are alive, viruses have several. That makes a Yes (exclusive) or No answer problematic.

Indications are that RNA can replicate itself, and that it can evolve. That right there pushes naked RNA toward the realm of living.

The main argument I have seen to classify viruses as non-living is that viruses can not replicate on their own, that they require the machinery of cells. I do like your logic concerning this reliance. I haven't come across it before, but I find it compelling. Most life relies on other life. We humans rely on other life, not just the plants and animals we eat but a host of symbiotes that we could not live without. I don't think anyone wants to claim humans are non-living based on that, so the argument about viruses is definitely weakened.

I'm confused by the argument that the polyphyletic nature of viruses is a reason to throw them off the tree of life. Warm-bloodedness is also a polyphyletic group. So is being winged. I don't think anyone wants to throw all the warm-blooded animals off the tree or throw off all the winged beings. Why would one think that viruses are substantially different in that regard?

So far as I can tell, we are faced with the issue of deciding where "living" begins and "non-living" ends. This is similar to determining where "red" ends and "violet" begins. We have this amazing spectrum between, so trying to classify everything between red and violet as either red or violet misses the point completely. We do not have red or violet, but something else entirely.

Concerning viruses evolving, is it possible that at least some viruses are descended from more bacteria-like organisms, shedding stuff that they can just take from other life?

I think the reason for wanting to vote viruses off the ToL is very similar to the motivation the IAU had for voting Pluto off the list of planets. In the end it's just a label, and people will continue to spend just as much time studying Pluto and other dwarf planets (and viruses) as they ever did. But folks are used to the idea of being able to count the planets on your fingers. Any reasonable definition that makes Pluto a planet winds up with our solar system ultimately having hundreds of planets, if not thousands, by the time we're done learning about the Kuiper Belt.

Similarly, if biologists don't draw the line at viruses, then who-the-heck knows what else we'll have to include in the coming years as we continue to learn about genetics, microbiology, and extremophiles.

Chayanov & Coriolis, maybe I can help, a little. I don't know how widespread it is, but I do know that to some people I've spoken with, their fear is that something "debatably-alive" like a virus is possibly viewable as a "link" between definitely unliving matter, and definitely living organisms, which may imply things they don't like, involving abiogenesis. Where's the divine "spark of life" added? Maybe...no such spark is needed....(Norman, co-ordinate!)

Metaphor: Viruses are one variety of mistletoe on the branches of the tree of life.

So some people with outdated notions of how life should be defined are uncomfortable with the implications of what viruses can potentially tell us about what life is? Does that about sum it up? I find that oddly fascinating, probably because I've never really thought about it before.

I think the reason for wanting to vote viruses off the ToL is very similar to the motivation the IAU had for voting Pluto off the list of planets.

First they came for Pluto, and I did nothing, for I was not a planetologist. Then they came for the viruses...

(article:) "it is hard to accept that the definition of an organism necessarily requires portions of another organism."

I don't know why it would be hard to accept organisms assimilating "portions" if you are going to accept symbiosis of whole organisms (what's the definition of a lichen? or a ruminant?) And sea slugs steal nematocysts from anemones, that seems like a portion.

They're just highly motivated nucleoprotein complexes.

Four fundamental programs separate life from pre-life forms: development, maintenance (energy consumption, self protection, etc), reproduction and death. Viruses have none of the above.

Um, actually they do. Viruses develop inside cells*, maintain themselves like a bacterial spore in the harsher environments, and die in order to reproduce inside another cell.
*Bacteria, et al. too.

Whitehead's comment about Western philosophy being a long footnote to Plato seems to apply. Why does an entity have to have an 'essential' form? What cosmic rules do we break if we fail to squeeze something into a convenient definition?

I think the break with essentialism one of the reasons why religiously-inclined thinkers (and others...) have difficulty with the idea of similarities or differences following a continuum. (Darwin's enunciation of common descent is the first Western instance of itI can think of. Anyone know of any predecessors?) It's so much easier to organise your world if you can wrap things into little packages and file them accordingly.

The tendency define things discretely says more about the human mind's talent for categorisation more than about the things (see? I'm doing it myself!) we perceive. But the theory has to folow the data, not vice versa.

Could the viruses have applied the functions of some primitive alimentary system to the task of getting integrated into their hosts?
Not sure this makes them more or less alive. My body reacts to a virus often with an fever, etc., as it would to other "alive" infectious agents. Good enough a reason as any to call the virus alive.

Yeah I think Phil got me right - I'm just wondering why anyone would be motivated to argue that viruses are or aren't "alive", other then for fun. I'm guessing Cicely is onto something with his/her answer - although it's hard to think that people would be getting published in nature over something that silly.

I read just this morning that HGT is a method that bacteria use to exchange genetic material. I wondered if the bacteria are wanting to get sick with the virus.
From the virus perspective it's a bit like saying people are a method houses use to exchange occupancy.
I'm more inclined to the idea that all parts of cells have evolved from things that originally developed without their containers

As mobius pointed out @21, viruses us the machinery of cells in order to replicate.
What the authors of the paper seem to be missing is that these mechanisms would be around before they evolved cells.

Abbie, please tell me you plan on writing a book one of these days. I'll volunteer to go through and put all the apostrophes in where they belong if that sweetens the pot for you.

Chayanov @ 28:

So some people with outdated notions of how life should be defined are uncomfortable with the implications of what viruses can potentially tell us about what life is? Does that about sum it up?

Well, yes, but also, they are uncomfortable with the implications of viruses' being included as "life", would potentially have for their religion-based viewpoint, and their religion's claim to be "the Truth, the Whole Truth, and Nothing But the Truth". It's something of a wedge; if you let the small end into their dogma.....

I don't think their reasons are reasons, but rationalizations. They wanted to "draw the line somewhere" for some unknown reason. Fine, but they needed to do that by definition, not rationalization. They should have left viri in the Tree of life (whatever weight that has) since they so obviously belong there, and created another "Tree of Cells" if they wanted to draw a line. That would be a nice easier to define tree. What purpose that would have I have no idea.

BTW... where do prions fit?

Well, yes, but also, they are uncomfortable with the implications of viruses' being included as "life", would potentially have for their religion-based viewpoint, and their religion's claim to be "the Truth, the Whole Truth, and Nothing But the Truth". It's something of a wedge; if you let the small end into their dogma.....

Hitchens is right. Religion poisons everything.

Great! Virologists dont think viruses are alive, so we dont need to include them in the Tree of Life!

That may be making the punishment fit the crime, but even if they're not necessarily the life of the party, it hardly seems fair to not include virologists in the Tree of Life...

Viruses just need to get laid.

I don't think viruses belong **on** the tree of life.

They belong woven through and around, emerging and diverging from, collapsing into, in threads and sheets traversing back and forth between, and creating a ghostlike cloud around all of the tree of life, appearing as if they were a dense thicket of wind-tattered spider-webs partially obscuring the trunk and branches.

Reality here is much cooler than a simple heirarchically-branching tree.

I'll tell you this much...the last time I had the flu, I felt like death warmed over. Maybe that's what they mean...

What about viroids - are they alive? Prions? Satellites (i.e. the subvirus kind)? Transposons?

Are most virologists in agreement concerning this question?
Is it possible to classify viruses in a third option -neither alive nor nonalive?

@46 sorry. NVM dumb question

I agree with lee. More like vines on and hanging from the tree, or Kudzu, completely consuming it.

BAllanJ,
I agree, sort of. The problem is that it is easy to come up with a particular definition that points towards a pre-determined outcome. If you insist that living things must have independent metabolism, the motivation for that insistence might very well be that you don't want to include viruses.

I love how you demonstrated the False Dichotomy. Can I use it? or a modified version?

I just want to point out that if they did the experiment in which they seed a completely sterile planet with bacteria, the bacteria would likely thrive (some would at least). But the first INTERESTING thing that would happen will surely be the appearance of new viruses!!
Parasitism is a fact of life, a simple consequence of the fact that freeloading is as much a living strategy as ducking it out with your surroundings to make a living. Life is the biggest game in town, and game theory applies.
Check out "tierra", the artificial life program. Seed it with a replicon and wait. Very early on, partial replicons that obligately leech on full ones appear and almost drive their parents to extinction, setting off a predator-prey type of dynamic between parasites and hosts, both evolving mechanisms against each other.
To say that viruses are not alive is like saying that a species of parasite that needs another species for its life cycle is not a real species because it's not independent.
This sounds like someone clinging to over-simplistic and obsolete conceptions of both "life" and "the tree of life".

Warm-bloodedness is also a polyphyletic group. So is being winged.

Incorrect. These groups can trace back to a single ancestor, which makes them monophyletic. They'd be polyphyletic if, for example, you found a bird nestled amongst the mammals in the Tree of Life ... but you don't, so they're not.

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.

Their case is a lot more convincing than the individual who wants to argue that viruses should be considered alive. A majority of bacteria are what you've called "self sufficient". As far as I know, not a single virus can claim that distinction.

And it goes beyond the "Well, if humans didn't eat plants and animals, they'd die out too!" The point is that for animals and bacteria, if you deny them a particular source for energy (which in turn leads to reproduction), they'll find another. If you deny the virus it's particular source of energy, it's done for. End of story. They are, in no way, independent on any level.

w00t! Three replies in a row! I'm retracting post #52 because I botched it, and need to rephrase.

For wingedness, it definitely depends on how you define "wing". Sure, you can lump bats into "wingedness" to create a polyphyletic group, but I doubt you'll see many biologists doing so, as they're analogous, not homologous structures. So Aves (birds/"true wings") is definitely a monophyletic group. Warm-bloodedness is polyphyletic (since reptiles insert themselves into the equation when searching for a common ancestor).

TomJoe, does this mean that pandas and wombats, both dependent on single species for their food if I recall correctly, are not alive?

NelC, panda's will eat other things if bamboo isn't available, and besides ... there are over 20 species of bamboo. Wombats as far as I can tell, do not have a diet that relies solely on a single species of plant.

Besides, even if you were correct, you've missed my point. It may be possible to find the exception in the animal kingdom, but it's just that ... the exception. For viruses, it's the norm ... they are (ALL OF THEM) not independent in any way/shape/form whatsoever.

For everyone's reading pleasure, an article originally printed in the the Scientific American on this subject by Luis P. Villarreal, Director of the Center for Virus Research, UC Irvine.

Similarly, neither cellular nor viral individual genes or proteins are by themselves alive. The enucleated cell is akin to the state of being brain-dead, in that it lacks a full critical complexity. A virus, too, fails to reach a critical complexity. So life itself is an emergent, complex state, but it is made from the same fundamental, physical building blocks that constitute a virus. Approached from this perspective, viruses, though not fully alive, may be thought of as being more than inert matter: they verge on life.

TomJoe-- Put an HIV-1 quasispecies in an area devoid of macrophages, and it will infect T-cells. Take out the T-cells, they infect astrocytes. It can even infect different cells from different species. Actually, HIV-1 is remarkably plastic in its potential host-cell rage.

If you put a panda in an environment devoid of bamboo species #1, it will eat bamboo species #2, right? Wipe out bamboo species #2, it will move on to bamboo species #3?

And while there are no self-sufficient virues, Ive yet to see a self-sufficient panda either.

I dont know what your point is.

snip Villarreal quote

Yes, thank you TomJoe, that what I already stated in the OP.

I also love Louis Villarreal. Would you like me to ask him whether he agrees with this Nature letter?

ERV,

And while there are no self-sufficient virsues, Ive yet to see a self-sufficient panda either.

So panda's don't make ATP on their own, they don't have cellular machinery of their own, they don't reproduce without the aid of another's cellular machinery? Oh wait ... they do! Ah yes, this comes down to the tired old argument that they need to eat (other things) to do all those things ... but, that's not the same as hijacking another species to achieve those ends, is it? And so we argue around and around.

As for Luis Villarreal, if you want to drag him into this discussion, by all means, feel free to do so. If he agrees with those who don't think viruses are "alive" ... w00t! If he doesn't, I doubt it's going to settle the issue once and for all. Heck, we argued the same thing in our advanced virology courses when I was back in graduate school, and I don't recall us coming to a consensus back then either. When it boils down to it, I don't think it's a matter of great import. Everyone I know knows viruses are important, and that they have played a major role in shaping the tree of life, regardless of whether they "deserve" a spot on it or not. But, since it seems to aggravate you so darn much, it's more fun to be the contrarian than admit such. ;)

This reminds me of the arguments - mostly back in the mist-wreathed past, early 1980's or so - that 'Cladistics' denied the existence of ancestors and therefore had nothing to do with evolution or (in another insane version) was inconsistent with evolution. Apparently there are still a few of these 'Pattern Cladists' around (e.g. in some corners of palaeontology). Could the motive for booting viruses off the ToL be something like, 'the ToL is made of clades, viruses are not a clade, therefore...'?

Hey, I never said it wasn't stupid. But like Abbie said, Viral phylogeny is hard.

Heck, what am I saying? Vertebrate phylogeny is hard enough in practice. Bacterial phylogeny is (at least conceptually) much worse, and viral phylogeny is brain-melting just to think about.

For wingedness, it definitely depends on how you define "wing". Sure, you can lump bats into "wingedness" to create a polyphyletic group, but I doubt you'll see many biologists doing so, as they're analogous, not homologous structures. So Aves (birds/"true wings") is definitely a monophyletic group.

What the heck? Of course both baths and insects are going to be lumped into the 'winged' category, making it polyphyletic. What else would you call those structures they have to fly? If you define a group by a feature A and then say that A in all groups have to be homologous of course you get a monophyletic group - but that was not what the poster you replied to meant when s/he said "winged".

YES and NO.

This is really a question of originality and functionality. It seems logical that RNA was the origin of life and that virii were the first expression of that life. Yes, all life is dependent, greatly or insignificantly, on all other life in some form, and also dependent on "non-living" things such as the sun, the earth, minerals.

I, being a scientist, do not myself believe in "life" at all. A continuum is a complex way of saying there is no good single definition. The dependencies of existence are obvious to any logical evaluation of reality. Whether or not we classify virii as "life" doesn't seem like a very interesting discussion to me. So what? Am I suppose to feel remorse when I transfect a cell culture, now? Sentience and sapience are of course "sacred", and that seems like the interesting argument to me. It seems to me that all bacteria are sentient in that they sense an environmental state, react to it, and that reaction has inherent memory (in the electrical/engineering sense), just as a neuron disturbed from its equilibrium alters protein expression to modify its connectedness to its environment: plasticity.

When looking at a cell membrane, it is not 'alive' but is critical to 'life'. Viruses are critical part of how the species on earth continue to evolve. Are they being utilized by cells, are virii utilizing cells? There's really no control, it's all just electrostatic interactions. We're trying to apply intent to the laws of Physics by declaring what is and is not "life". Does a cell membrane have a will? Does an endoplasmic reticulum have a will? Does a strand of DNA have a will? Then how can a bacterium have a will? Does one cell have a will, or two? "Will" is a philosophical construct to make discussion easy, but it has no real world materialist existence.

Virii are, therefore they are.

TomJoe: Bats clearly show that wingedness is not monophyletic. For warmbloodedness, consider Tuna.

Can't understand how the dumb authors got a Nature review !!! Viruses are at the boundary... it's like no-man's land... if at all they had to classify, then live is the more sensible option!! Blah!

Transformation of energy into a living matter needs a modus ssRNA, which creates a chain from simplest nucleotidal structures into dsDNA through eons, commenced in a primordial chemical soup producing bacterium, by their properties of being an antenna recepting information from the Cosmos how to shape about an organism capable to function in a given environment. Thus the most complex organism consists of "viruses" (RNA, DNA and bacteria - mitochondria), as structurally developed from viruses evolving into pro- and eurokaryotes, up to neurokaryotes, the latters the best suited colonies of viruses, as the humans are, which, being transformed from the energy into a matter, become capable to return into the Cosmos in an organized form and dominate the unorganized viruses, omnipresent over there. Hence capable of spreading across it the Cosmical Intelligence embeded into an Intelligent Homo Electronicus, the virusoidal colony. During the evolutionary path, from the simplest virus to Homo, does occur constant fight for primacy seen as invasion of viruses on any living creature and it will be lasting as long as Homos do not prevent such invasion on Earth and far beyond. So, viruses a part of the Tree of Life. Are Capsoided Life.

How come no one did comment on Czajkowski's explicitiveness regarding viruses as a part of the Tree of Life? Now he is elaborating more on the issue under the title PANAVIRA or PANVIRIA, as follows:

Dear Dave Talbott:
I do admire your Electric Universe conviction for electricity is the only force
keeping the Cosmos running and disseminating life across by means of
encapsulated DNA in viruses what I call PANVIRIA, again keeping the Cosmos
running for eons from one simple form evolutionary developed to as such
sophisticated one as a human is. Can you ever better elaborate the miraculous
relation of energy to matter, evident in nuclides of the Periodic Table of
Elements? Besides, many may speculate what electricity is, for no one knows what
it is.
Sincerely - me.

So, would any one combine these two comments in one and send it to Czajkowski directly at ?

CzAJKOWSKI'S address is:

Look for Wieslaw Czajkowski of San Diego at:

WdashinlowercaseCzajkowskiatyahoodotcom