Viruses and the tree of life

19 March 2009

tree-of-life-with-genomeAre viruses living entities? I don’t believe so, but it’s an engaging question for debate. On a recent episode of “This Week in Virology” we concluded that it’s somewhat of a futile argument because everyone has their own view; perhaps our time is better spent studying viruses than discussing whether or not they are alive. The authors of ‘Ten reasons to exclude viruses from the tree of life’ cogently disagree:

We believe that considering viruses alive or not is not just a matter of opinion, contrary to a commonly held view, but rather is a matter of inference and logic starting from any given definition of life

Following is my distillation of why the authors believe that viruses are not alive, and why they do not represent ancient lineages of the tree of life.

1. Viruses are not alive
Throughout history there have been many definitions of life. Viruses do not meet the criteria for any of them.  They lack any form of energy, carbon metabolism, and cannot replicate or evolve. They are reproduced only within cells, and they also evolve within cells. Without cells, viruses are “inanimate complex organic matter”.

2. Viruses are polyphyletic
In a phylogenetic tree, the characteristics of members of taxa are inherited from previous ancestors. Viruses cannot be included in the tree of life because they do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. While cellular life has a single, common origin, viruses are polyphyletic – they have many evolutionary origins.

3. There are no ancestral viral lineages
No single gene has been identified that is shared by all viruses. There are common protein motifs in viral capsids, but these have likely come about through convergent evolution or horizontal gene transfer.

4. Because today’s viruses infect phylogenetically distant hosts doesn’t mean that they are ancient
It cannot be proven that early viruses appeared along with the first cells. The problem is that viruses move readily between diverse hosts. Consequently the ability of a virus to infect a particular species could lead to false conclusions about the ancient origin of viruses.

5. Viruses don’t have a structure derived from a common ancestor
Cells obtain membranes from other cells during cell division. According to this concept of ‘membrane heredity’, today’s cells have inherited membranes from the first cells that evolved, and provides evidence that cells are derived from a common ancestor. Viruses have no such inherited structure.

6. Viral metabolic genes originate from cells
Many viral genomes encode proteins involved in energy, carbon, and cellular metabolism. It has been argued that the presence of these genes indicates that viruses are ancestral to cells. Unfortunately, metabolic genes are not present in the ancestors of these viruses. This finding makes it difficult to argue that viruses predate cells.

7. Viral translation genes originate from cells
The mimivirus genome harbors genes encoding elements of the protein synthesis machinery. This observation has been interpreted to mean that viruses did not always rely on cells for translation. However, sequence analysis indicates that these genes are derived from cells by horizontal gene transfer.

8. Viruses steal genes from cells
Viral genomes encode many genes that have no homologues in cells. It has been suggested that viruses influence evolution of cells by donating new genes. Sequence analysis has failed to provide support for this hypothesis. Viruses are ‘gene robbers, not gene inventors and massive gene suppliers’.

9. Most gene transfer goes from viruses to cells
The movement of genes is mainly in the direction of cells to virus. Transfer in the reverse direction is minimal. Therefore viruses have not had a significant role in shaping the gene content of cells. This conclusion is paradoxical because viral genomes are the most abundant on earth.

10. Just because viruses are simple doesn’t mean that they are old
One view of evolution is that it is a process by which simple organisms become more complex. The simplicity of many viruses lead to their placement at the origin of life. This long-standing hypothesis ignores the fact that viral genomes are subject to selective pressure to maintain minimal size to ensure rapid replication rates. The authors conclude that viral simplicity is a consequence of parasitism, not antiquity.

Even though viruses are not living and should not be included in the tree of life, they play an important role in evolution of their cellular hosts by regulating population and biodiversity.

Are you convinced by these arguments? Post a comment and let us know whether you think viruses or living or not.

Moreira, D., & López-García, P. (2009). Ten reasons to exclude viruses from the tree of life Nature Reviews Microbiology, 7 (4), 306-311 DOI: 10.1038/nrmicro2108

  • http://hand-of-paper.insanejournal.com PaperHand

    I've never really understood the “are viruses alive or not?” debate. Life isn't a simple binary function. Whether you count viruses as alive or not depends on your definition of life, it seems to me. So, really, isn't the debate more “Is a definition of life that includes viruses useful or not?”? Framing the debate as “are viruses alive or not?” implies that there is an already-established definition of “life” allowing a debate over whether viruses fall in that established category.

  • http://arumanchan.blogspot.com/ Dave UH

    I thought that the line of reasoning was very cogently presented. I, as a supporter of viruses being alive and having a deep root in evolutionary history will have to rethink my previously held hypothesis, in light of recent discoveries. I believe that at this time there is not enough evidence to assert the view that viruses are remnants from the “RNA World”.

  • Pingback: discarded lies - hyperlinkopotamus

  • foop

    Seems to me that they can become alive in the right environments.

  • Pingback: Pages tagged "five ancestors"

  • Pingback: Are viruses alive? « MicrobiologyBytes

  • bill_mcculley

    Hello Dr. Racaniello,

    Great questions for discuss. I hope you don't mind laypersons (electrical engineers like myself) in asking a few questions I've been thinking about! One recommendation is perhaps a you can setup a general discussion area on this website for oddball questions like mine or others that aren't easily catagorized.

    This thread is about as broad as any other, so here are a couple of unconventional ideas I've had -

    1. Did you ever think, at a more primary fundamental level, perhaps proteins/amino acids themselves were the actual “intelligence” rather than DNA “driving the show”. Perhaps DNA is merely just a scoffolding which the amino acids decide to hang their hats. Perhaps there is something beyond the interaction between amino acids – beyond mere biochemstry? (Perhaps it sounds really strange)

    2. Did you ever wonder if, by the broad use of vaccines, we are exerting an artificial stress on the ecology of a virus, thereby essentially resulting in a stronger virus to be selected down the road? Sort of like the National forest park policy of preventing fires for for so many decades, thus creating conditions in which much larger, horrendous forest fires can now occur.

    Like I said, I'm interested about learning more. So I hope you don't mind my lack of exact terminology or my understanding in terms of the basic concepts of virology

    - Bill

  • http://www.virology.ws profvrr

    Hi Bill,

    Don't apologize for questions – here at virology blog there aren't any bad questions. We want to teach virology so all inquiries are welcome. In fact your questions are excellent.

    Having a discussion board is a great idea. I'll look into the software to run it. As for your questions:

    1. Chromosomes were known for many years to be composed of both protein and DNA, and scientists didn't know which was the genetic material. A key experiment was done in 1944 when Avery, McLeod and McCarty showed that DNA could induce a change in bacterial phenotype. In 1952 Hershey and Chase provided further support for DNA as genetic material, by showing that the DNA, and not protein, enters cells during a viral infection.

    2. Vaccines mimic (although not always perfectly) what happens in a natural infection – the production of immunity to the virus. This immune response clearly exerts selective pressure on the virus. A perfect example is the yearly antigenic change of influenza virus that is selected each year by population immunity. Some viruses, like poliovirus, are not antigenically variable and probably not subject to such selective forces.

  • Pingback: MicrobiologyBytes » Blog Archive » Are viruses alive?

  • jerryclatham28

    Viral translation genes originate from cells The mimivirus genome harbors genes encoding elements of the protein synthesis machinery. This observation has been interpreted to mean that viruses did not always rely on cells for translation. However, sequence analysis indicates that these genes are derived from cells by horizontal gene transfer.Viruses steal genes from cells Viral genomes encode many genes that have no homologues in cells. It has been suggested that viruses influence evolution of cells http://www.chase.com by donating new genes. Sequence analysis has failed to provide support for this hypothesis. Viruses are ‘gene robbers, not gene inventors and massive gene suppliers’.

  • Anonymous

    I do continue to have questions about point 4, and if anyone can assist in clarifying I would be much appreciated. The ODE is very serious about keeping the editorial control of the paper out of the publishers hands, but Steve Smith’s recommendation and (this is the point I need clarification on) proposed contract had language that separated editorial control of the paper chase.com from the publisher and, as far as I can tell, give the publisher a higher rank in business matters only.

  • Xelo

    I will agree that when outside a cell that the virion is not living or more aptly put dormant. However every organism is built to reproduce and pass on its genetic material from one generation to another. Once in side a host cell viruses reproduce and can use cellular energy to create more of themselves. Also they evolve, they respond to pressures from their biotic environment. Simply put, viruses evolve and reproduce, two characteristics that inanimate matter, should not posses.

  • Chelsea

    i was pondering about all of this and is it possible that the reason, in #9, “This conclusion is paradoxical because viral genomes are the most abundant on earth.” is because all life could have been created from different 'viruses'?

  • Chelsea

    my mother is greatly against vaccine use, and i have never once been vaccinated and have many health benefits due so..

    our race is so hideously fixated on saving EVERYONE that we do not take in account the future

    we are AFRAID of natural selection.

  • Chelsea

    YES YES YES!!!!!!!!!

  • http://sain-web.com Traveller

    This is quite impressive, I am pleased to read this post, keep posts like this coming, you totally rock!Cheers,Blog Review

  • Prophage

    Virses are living entities! They are obligate parasites which means that they need a host to replicate, otherwise they are dormant.

    They discovery of Sputnik- a virus that infects a virus also adds weight to this argument.

    Any genetic material capable of replicating can be considered “living”. It will only be a matter of time, loss of old dogma and a broader view of life sciences that will result in this idea becoming universal…

  • Pingback: ALVAC-HIV and AIDSVAX B/E

  • yoyo123a

    Your blog is nice,i like it.

    http://www.360huoyuan.com

  • tumblemark

    On the matter of virus monophylogeny, consider that their origin in the three kingdom tree of life has been established in the computational biology paper:

    Sun F-J, Caetano-Anolle´s G (2008) Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses. PLoS
    Comput Biol 4(3): e1000018. doi:10.1371/journal.pcbi.1000018

  • E.I.

    Yes, it is true that viruses do not fit into the cellular tree of life, but viruses are capable of forming phylogenetic trees of their own. These trees show relatedness among viruses of a particular domain (eukaryotic viruses, archaeal viruses, etc.) and do suggest a common viral ancestor. The fact that we know so little about viruses complicates these phylogenetic comparisons.

    As for the argument that viruses don't share a common structure… Viruses rapidly evolve; it's one of the major reasons for their tremendous success. This rapid evolution makes it difficult to say that viruses don't share things in common. We have little idea what the early earth was like, but it is obvious that conditions have changed since the origin of “life.” As viruses adapted to new hosts they altered their genetic makeup to make them better equipped for a certain host.

    The fact that there is not a common ancestor does not mean that it never existed. That is just illogical and completely unsupported. Cellular life leaves fossilized evidence. We are learning that viruses do as well, but it is much (MUCH) more difficult to collect this data (viruses are much smaller than cells).

  • ductub

    Prof. Racaniello,
    1. If your view is that viruses are not alive, are they dead? Or do you think they are neither alive or dead?
    2. If viruses are not alive, why some viral vaccines contain live viruses?
    3. Do you think that obligate intracellular bacteria are not alive either? They can't replicate without host cells, same as viruses.
    4. I disagree with the view that viruses cannot adapt and evolve, in fact as a professor of virology, you should know this better than anyone. If they can, they should be considered as a living thing, despite lacking the “organismic” structure and ability to metabolize. This is as opposed to inert structures, which can be considered as dead.
    Sincerely

  • ductub

    Prof. Racaniello,
    1. If your view is that viruses are not alive, are they dead? Or do you think they are neither alive or dead?
    2. If viruses are not alive, why some viral vaccines contain live viruses?
    3. Do you think that obligate intracellular bacteria are not alive either? They can't replicate without host cells, same as viruses.
    4. I disagree with the view that viruses cannot adapt and evolve, in fact as a professor of virology, you should know this better than anyone. If they can, they should be considered as a living thing, despite lacking the “organismic” structure and ability to metabolize. This is as opposed to inert structures, which can be considered as dead.
    Sincerely

  • Liz

    It is just plain scary that people like you, who have no clue about this stuff are making vaccines.

  • Chris Stacy

    Someone already answered you generally about proteins vs. DNA, but you ought to google these terms for more information on a tangent you would be interested in: “epigenetics” and “RNA world”. There are probably decent Wikipedia articles to get you started.

    Moreover,everything about DNA is subject to what is broadly called “regulation”. The story that DNA ultimately codes for proteins is an extraordinarily simplistic explanation. There is so much more to it, most of which we do not understand.

  • Dan, Tx

    I consider viruses to be alive, they have a genome, they use the genome to direct transcription, translation, and protein synthesis (except for viroids).  But even naked RNA strands of viroids are capable of replication in the correct environment (host cell).  What living organism can reproduce in the absence of nutrients? None. Viruses are no different, they require a very special set of nutrients. They are obligate parasites – many organisms are known that can not grow or replicate outside of their hosts, but can survive in a resting state. So, I see viruses as living. The flu is not cause by a toxin, it is caused by a pathogen that replicates and causes symptoms in its host.  Viruses probably have arisen many times as degenerated bits from other living forms and have been cobbled together from bits picked up along the way. So, they are very different from organisms that we think of in the tree (usually). However, over short periods of time populations clearly can evolve.  You seem hung up on the fact that the virus only is actively living when it inhabits a host cell. This is quite a prejudice.  Perhaps the earth could view us as viruses? After all, we don’t make our own planets, we just live off of ones that are already there.  Prions are the example of a non-living infectious agent.  I do draw the line at prions, because they do not possess a genome and are simply proteins that are unable to specify their own.

  • Ramsy

    I personally think that viruses are non-living and living, because of the fact that they sought of become alive when they enter a living cell. Another thing that boggles me is how do viruses know how to do their thing, how do they find a cell……?

  • Ifaithway

    how can you depend that virus is nonliving, when they say that when the virus attach in a living cell,the virus become living???

  • lunarlander

    Amen. You couldn’t have said it better. My sentiments exactly. Biological reality is fuzzy and humans like to stick things in dichotomous groups to understand them. Then they mistakenly assume that the groups are a property of reality itself and don’t see that the essence of what is being debated is only the arbitrary inclusion or exclusion of something based on a particular human construct. The real question, like you said is: What is your motivation for arbitrarily deciding to chop up reality as you did? For what functional reason should I be define something one way versus the many other ways in which it could be validly defined? Certain metaphors constructed by certain definitions may be more useful than others depending on context.
    What about organisms which were once freely reproducing and then became completely unable to replicate on their own without a host cell, like mitochondria and chloroplasts? Are my mitochondria alive? Are they as alive as my gut bacteria are? Are they part of my organism?- or are they an independent organism? Were they once an organism and now are not? Were they once alive and now are not? If not, exactly at what point in evolutionary history did they become “not an organism” or “not alive”? 
    What about our white blood cells which essentially move around and act just like amoebae but would not be considered an independent life form because they are a part of a larger organism? We could have a debate about all these things until the cows come home and there are no cut and dry answers to many of them but some of the debates are not very useful because they are only pointing out over and over again that neat boxes don’t map perfectly onto the seemingly endless continuum of biological reality. These debates highlight the awkward areas left over when trying to square the circle of reality so to speak; This exact type of debate can be had over what is an “organism”, “species”, “gene”, etc.? ad infinitum. I believe these debates can be fun, and can even be beneficial for refining classification and thinking about the world in different ways but they do nothing to change biological reality which ultimately defies this binary type of categorization we desperately attempt to apply to it. Metaphor is wonderfully useful for understanding natural phenomena but it should be recognized as such rather than an intrinsic property of reality itself.

  • Kupfernick

     Absolutely. The question is what is important, not the answer. The question helps frame the larger debate “What is life?” but in science we look for facts, not truths.
    “If it’s truth you’re looking for, Dr. Tyree’s philosophy class is right down the hall (Dr. Henry (Indiana) Jones, Jr.)”

  • haho

    For me it is irrelevant if viruses are alive or not; they have DNA and this mutates, they evolve so there can be drawn an evolutionary tree from the differences between their DNA. HIV viruses also continuously evolve and occur in different strains. It would be interesting to see the (many) evolutionary trees of viruses groups and any possible connections with the bacteria. Maybe viruses and their ancestors crossed the boundary of life many times in both directions and viruses might have bacterial ancestors?
    In any case, it might be assumed that viruses are as old as bacteria and have some 3 billion years of evolution behind them. However, since the DNA of viruses is very short and large parts of it will have evolved parallel to their host bacteria, the parts of the virus DNA from which an evolutionary tree can be constructed will probably be very limited.

  • cormac

    dead means they were at one point alive and no longer are. if something was never alive, its considered nonliving. live just means they’re contagious. and because something can adapt and evolve does not mean it is alive, that is one of many characteristics of life

  • Pingback: Viruses: Life’s Estranged Cousins? « Stranger Science

  • muskan

    hello

  • muskan

    kya kr rhe ho

  • muskan

    love

  • Pingback: How do creationists answer these questions: Are you an Ape? A Mammal? A Vertebrate? - Page 27 - Christian Forums

  • Arthfael

    I believe that several arguments against viruses being alive cited here are irrelevant, namely those of an evolutionary order. Being alive has nothing to do with how you came to be alive. May I remind you that we acquired a great part of our metabolism through horizontal gene transfer?
    As for lack of structure conservation, virus evolution is known to be faster (as should be expected) than that of other organisms. Simpler genomes, much higher populations, exposure to other genomes in the same compartment (cellular, other viruses), higher plasticity (esp. for RNA viruses). No surprise it’s difficult to see sequence or even structure conservation. Viruses may even have evolved independently several times and have converged to look superficially similar, just like algae have evolved independently several times (though in each case their photosynthesis was inherited directly or not from cyanobacteria).
    I believe that the question of being alive in the sense of life forms as we know them on earth comes back to the question of genetic information, a nucleic acid genome – or set of genes/nucleic acid sequences interpretable as information coding for at least a dissemination form – which have for a moment put their lot together and are attempting to perpetuate themselves. The means of replication/perpetuation are irrelevant, as long as the genome manages to perpetuate itself. For all genetic information, on earth, perpetuation appears to require a cellular life form, and viruses exist as cellular life forms – the so called viral factories in infected, usurped cells….