Monday, March 17, 2008

My virus boyfriend-- A love that cannot be

Me: "OMG! My boyfriend published another paper!!"

Bossman: "Ugh. Do you have any idea how old he is?"

Me: "Our love, it is forbidden."
My virus boyfriend Patrick Forterre is still fighting the good fight for viruses:
Redefining Viruses: Lessons from Mimivirus
Why the hell arent the most abundant creatures on the planet included in the tree of life??

Viruses arent just wads of selfish genes. They are an organism. They contribute massively to the evolution of 'life' on this planet.

We arent slack-jawed TARD Creationists pointing at a Panda Bear slurring "Dat der is a BEAR kiiiind." We use genetics to establish phylogenetic trees, ergo, who is related to whom. Why do we point to viruses and drool "It aint ALIVE! It caint go in deh tree!"

It doesnt make any sense. Like having a ribosome imparts an organism with a 'soul' that allows it to be considered 'alive' and included in Earths evolutionary tree of life.

But that is the stickler for including viruses in the tree. Usually its the ribosomal sequence thats used to compare amoebas to oak trees. And viruses dont have them. Viruses really dont have anything in common with cells (so much for the "But viruses r just de-evolved CELLS!!" hypothesis) so how can we attach them to the Tree?

Forterre suggests that we just use the protein that all viruses have in common, capsid, to create a mirror tree. Like a reflection in a graveyard pond, a Tree of Undead Viruses.


Its a start. But I do not like. I dont see the viral world evolving like a mirror Tree of Life with viruses evolving with their hosts in an alternate dimension. I see The Tree of Life and the Tree of Undead Viruses hopelessly intertwined-- in the same dimension-- we can detect where we got protein A and protein B from viruses and where bactereophages stole protein C and protein D from their hosts or one another. I dont think Forterre would suggest that the trees are isolated, as it appeared in a diagram in this paper, but that is going to be the outcome if you compare Ribosomal Encoding Organisms to Capsid Encoding Organisms.


It is a start :)


Seabhag said...

Why not something like the DNA molecule itself? Use the 3' Backbone to represent the 'normal' tree of life, and the 5' (or the other way around) to represent the "Undead Tree of Viruses".

Yeah, it's got a lot of issues, I'll leave those with the evolutionary biologists, and geneticists; but it might work. Plus it's got that whole 3D intertwined idea that you were suggesting.

Rob said...

While it's true that viruses contribute massively to the evolution of life, so does magnesium. We are full of ERVs, some of them are inactive while others are somewhat actively transcribed. And of course we have made use of some viral genes, like syncytin. So are we viruses? To me this is a grey area that does not necessarily benefit from a further revision of the definition of 'life' it just shows how concepts break apart at the boundaries.

Anonymous said...

You know, often I have to go read to understand the gist of one of your posts, or a comment, because I have zero formal education beyond H.S. But the exuberance you have for viruses, which I share, makes it worth the effort. Thanks for taking the time to write your blog. It is much appreciated.

kezdro said...

I wonder whether, in a tree, they should be considered separate from the organisms at all. How are plasmids treated, and bacteria based on them? I would think, given the way they work, the two should be treated fairly similarly. They both become part of the host's genome, becoming an integral part of that organism, only really different in that they are often passed horizontally rather than vertically (well, the active viruses), and that their code is not always present in all cells (but then, red blood cells don't have that much host DNA either).

Something like a tree of life for horizontal transfers (plasmids and virii), linked to a tree of life for vertical transfer (the classic one). Be a devil to figure out though - unlike the verticals, the horizontals can jump around a fair bit..

I think that made sense. I know what I mean..

Anonymous said...

I'm learning biology and I wonder why viruses are not considered living. Not having cells (TeH CeLL Theory) is to me kinda like Creationists dwelling endlessly about "kinds"

Anyway, good luck on your forbidden luve.


Bayesian Bouffant, FCD said...

Viruses aren't just wads of selfish genes. They are an organism.

Not unless the definition of "organism" has shifted since I went to school.

Mark said...

Is there a tree of viruses? I mean, did they all evolve from a single common ancestor? I remember hearing somewhere that viruses are genetically more similar to the organisms they infect than with each other; with the inference that every once in a while, a cell generates one, unrelated to any previous virus.

William Wallace said...

This is getting surreal. Virus boyfriend?

And the questions are getting tough....what's that I hear?

Ah, crickets chirping.

minusRusty said...

I thought that viruses were represented by that mossy-colored hue covering The Tree...

Torbjörn said...

I believe I see your point, Forterre wants to equalize the domains, but digs himself a hole instead. I don't see any progress over the idea of a consistent evolutionary genetic definition of organism instead of based on cellular traits.

This paper may not get to the point Forterre wants to make, but is perhaps more along the lines of Doolittles genealogies of genes. Using a global constraint analysis on tRNA evolution (and in accompanying and confirming papers on proteins) they manage to include viruses, establish domains & lineage relationships & epochs, and possibly root the studied tree:

In a process that reconstructs history from molecular sequence and structure and at the same time forces molecules belonging to lineages into groups, we tested alternative hypotheses of origin and established when major organismal lineages appeared in evolution. Remarkably, timelines showed that Archaea was the most ancient lineage on earth and that viruses originated early in the archaeal lineage. Our findings unroot the universal tree of life, and, for the first time, provide evidence for an evolutionary origin of viruses.

But as I understand it they observe that genomic diversity makes virus origins still compatible with just about any hypotheses out there, such as the ancient viral world. Maybe viral lovers have to embrace the differences. :-P But I believe they can claim that viruses are old, very old, and that the identifiable domain was involved at the root of the evolutionary bush.

Torbjörn said...

Oh, and of course Forterre can now claim that no analysis of early evolution would be complete without viruses. So he got his wish!

Btw, even if the heading and the summary figure capitalizes the putative domain as "Viruses", it isn't really named in the text.

I'm curious, has anyone rushed to claim the name yet, and what is it/should it be? "Viruses", or "Viria" analogous to "Bacteria"? Or something else altogether, as "virus" is latin for "poison", while "bakterion" at least is greek for "small staff"?

Can ERV infect us with her wisdom here?

-DG said...

I haven't yet read all of the Constraints paper that was mentioned, just skimmed through it, but I shuddered in horror a lot just reading the abstract. Forcing things into monophyletic groups when they wouldn't go?

That's not very kosher.

Count me among the people who want to include Viruses among the living, I don't see why they aren't. And there is more then just ribosomal RNA analysis in terms of reconstructing the tree of life. The problem is that there probably isn't a good set of common genes to try and connect Viruses to the other three Domains of Archea, Eubacteria, and Eukaryotes. We have enough trouble as it is resolving the relationship among those three and there are still divisions as to whether the Three Domain Hypothesis is really that great of an idea.

I think that the view will slowly come around that viruses are life, whether we are able to practically determine their relationship to the rest of the tree may prove problematic. And indeed they may not actually tie to that tree in the conventional sense. It all depends on what our ideas about the early stages of life are like.

-DG said...

I should add that if early life was this sort of huge population of cells/proto-cells with LGT being the dominant form of gene transfer driving evolution it may be difficult, if not impossible, to ever resolve the base of the Tree.

kezdro said...

-dg: we may be able to do so to the same degree as Proto-Indo-European though

Unsympathetic reader said...

mark: "I mean, did they all evolve from a single common ancestor?"

I doubt they could be 'rooted' and I'm unconvinced they share a common ancestor. Different types could have "budded off" at different times from very distinct sources and mechanisms.

I do consider them 'life': They are forms that follow evolutionary steps and have autonomous existences at some stage in their life cycles. One thing they lack which sets them apart from traditionally defined 'life' is active metabolic compartments.

Torbjörn said...

Uh, oh. My posting never made it before the laptop crashed. I repost FWIW:

@ -DG:

Thanks for the reply!

I shuddered in horror a lot just reading the abstract. Forcing things into monophyletic groups when they wouldn't go? That's not very kosher.

I suspected as much. If constraint analysis is unfamiliar, it will be contentious.

AFAIU constraint analysis makes it possible to pick out weak support for theories among all available ones. An analogy to coding theory is to pick up signals buried in noise, which is actually possible.

If this is coherent with monophyletic groups when the constraints are lifted and especially before that I dunno of course. As a layman you hope that all phylogenetic analysis is tested afterwards. If not else, so by looking for consistency when adding data over species/molecules.

Also thanks for the remainder of the reply. I believe I could follow it.

-DG said...

@ - Torbjörn

No problem, I'm relatively familiar with constraints analysis and I understand the reasoning behind it, but it is definitely something that will set phylogenetics people on edge. One problem isn't the constraints analysis itself but we actually don't expect tRNA's to form monophyletic groups for biological reasons from what I understand as well.

Torbjörn said...

- DG, thanks again.

It snows outside, and an interesting paper seems to be less interesting at the moment. Figures.

Salamander said...

I'm sorry to have to inform you that Patrick Forterre is *MY* boyfriend. So are Christian de Duve and Graham E. Budd. Hands off! ;-)

Anonymous said...

Mark asked if viruses all evolved from a single common ancestor. My angle is structural biology, and in a nutshell there are very strong structural similarities in capsid proteins that seem to sort them into several groups that may represent ancient lineages of protein fold and thus common ancestry. One is the double-beta-barrel fold of the adenovirus "hexon" protein, solved crystallographically (so it must be true!) and subsequently seen in atomic models of bacteriophage (PRD1) and archaeal virus (STIV) capsid proteins, thus connecting viruses from the three domains of life. Another is as yet less well supported by structural evidence, but what there is suggests that the tailed bacteriophages (~95% of the viruses on the planet - now that's a serious amount of viruses!) and herpesviruses are related, and the representative fold is that of bacteriophage HK97 capsid protein. Despite striking structural similarities (by which I mean the way the capsid proteins are folded) within each group, any similarity between amino acid sequences of the virus capsid proteins is often undetectable. Because the similarities cross boundaries between eukaryotic, prokaryotic and archaeal hosts, the lineages would be very old. Given the time-span, and rapid turn-over of virus populations, there has been enormous opportunity for exploring sequence variation, but apparently the capsid protein fold must remain roughly fixed for virus capsids to function. Nonetheless, the same basic fold is sufficiently flexible to build capsids of quite different size and complexity. I fear I have gone on rather too long, but its really interesting - really!

-DG said...

And not surprising, it is well known that structural similarity is preserved much much longer then sequence similarity is. Most protein folds are relatively robust to changes in sequence. Although sometimes it only takes one change to completely trash some major structural features.