Virolution

There have been a number of interesting comments lately here at TSZ that referred to viruses.

Are viruses pre-biotic entities, and did they contribute to the origin of life?

Are viruses alive?

Do viruses evolve?

Are viruses an example of what evolution is capable of?

Did viruses contribute to the evolution of life?

Should be fodder for some discussion.

20 thoughts on “Virolution

  1. Virolution is the definitive guide to this amazing new field of research that has redefined the science of evolution and disease.

    Yet another “theory of evolution.”

  2. I am quite sure that our views on evolution would be very different had biologistsw studied genetics and natural selection before and not after most of them were convinced evolution had occurred.

    JBS Haldane

  3. Mung:
    Virolution is the definitive guide to this amazing new field of research that has redefined the science of evolution and disease.

    Yet another “theory of evolution.”

    Golly, I guess every time anyone learns anything new (or in more depth) about biology, we necessarily get a new theory. And I guess since we keep requiring a new theory every two weeks, we must not actually know anything at all.

    This has always been a problem with learning – the more we know, the more we realize we don’t know, and every answer sprouts several new questions. Quite clearly, the solution to this madness is to have a single explanation that applies to everything known and unknown, and cannot be tested (lest we learn something).

  4. The first surprise was the modest size of the human genome, at about 20,000 genes.

    Don’t know why anyone should be surprised by that. Hell, monkeys have 19,990 genes.

  5. Dear Flint, It’s ok if you don’t “get it.”

    If every discovery requires a new explanation then every discovery requires a new theory.

    It just happened, that’s all, leaves a lot to be desired. Don’t you agree?

  6. Mung,

    Well, there is also, “nature is just like that.”

    So if a frog can forego its lungs during embryonic development, and sidestep natural selection, well, so, nature has ways. Not a problem for the theory!

  7. phoodoo: So if a frog can forego its lungs during embryonic development, and sidestep natural selection, well, so, nature has ways. Not a problem for the theory!

    What theory?

  8. Whether viruses are “alive” or not is an argument that usual bogs down in conflcting definitions, and in the end it is not essential to decide it. But viruses definitely do evolve, and the field of evolutionary virology has been very active, particularly since the 1980s when viruses such as HIV were under intensive study with the DNA sequencing methods that had just become available.

    For virus phylogeny the methods used are very similar to those used in other organisms such as bacteria. So viruses make us explore some new methods, but do not massively revise our approaches to molecular evolution. Viruses did make possible collection of complete sequences before this could be done with bacteria or other organisms, simply because their genomes are smaller. They also let us make phylogenies with both present-day and fossil sequences, simply because evolution of RNA viruses such as HIV is very fast, so that those fossils were often available in someone’s freezer.

    A colleague of mine, Arno Motulsky, collected 300 blood samples from a hospital in Kinshasa in 1959. After he had used them for studying hemoglobin variants in Africa, he kept the samples frozen. By the 1990s they had been used to find the oldest-ever sample of HIV (one patient of the 300 apparently was infected).

  9. Joe Felsenstein,

    Viruses also allowed for creation of known real (not simulated) phylogenies with which to test phylogenetic methods. They work pretty well, it turns out. Joe can you recall any citations to the work? All I remember is that it was done in the Hillis lab.

  10. Joe Felsenstein:
    Whether viruses are “alive” or not is an argument that usual bogs down in conflcting definitions, and in the end it is not essential to decide it.But viruses definitely do evolve, and the field of evolutionary virology has been very active, particularly since the 1980s when viruses such as HIV were under intensive study with the DNA sequencing methods that had just become available.

    For virus phylogeny the methods used are very similar to those used in other organisms such as bacteria.So viruses make us explore some new methods, but do not massively revise our approaches to molecular evolution.Viruses did make possible collection of complete sequences before this could be done with bacteria or other organisms, simply because their genomes are smaller.They also let us make phylogenies with both present-day and fossil sequences, simply because evolution of RNA viruses such as HIV is very fast, so that those fossils were often available in someone’s freezer.

    A colleague of mine, Arno Motulsky, collected 300 blood samples from a hospital in Kinshasa in 1959.After he had used them for studying hemoglobin variants in Africa, he kept the samples frozen.By the 1990s they had been used to find the oldest-ever sample of HIV (one patient of the 300 apparently was infected).

    And everybody.
    Whoa. Do viruses evolve? HMMM
    If they are not living things then non living things evolve?!
    If they do then at what point are they given a new name in bioloy? I presume they have latin names. Is there a list of new viruses around that only evolved in the last 50 year?
    if selection affects them and there is a new result does iot mean they evolved? nO its just a new population of a segment of the old.
    I guess they might say a virus evolves because it made a new ability to resist a drug etc etc. Hmmm.
    It would mean its just using some existing trait and selecting on it.
    However much CHANGE a virus does it needs to be shown it could cross thresholds to actually be said to be evolving.
    Otherwise is trivial diversity within a type.
    People changed colours but people are not evolving or in different directions of evolution from the different colour populations.
    Evolutionism is not about mere change but about new traits that can turn a fish into a rhino.
    I don’t think mutations could ever turn a virus very much out of its basic type.
    In short they don’t evolve.
    The trivial change is not accurate sampling to describe them as evidence of evolution.

  11. Are viruses pre-biotic entities, and did they contribute to the origin of life?

    No, and no respectively.

    Are viruses alive?

    Yes and no, IMO

    Do viruses evolve?

    Yes

    Are viruses an example of what evolution is capable of?

    Yes. Are they an example of what The Designer is capable of?

    Did viruses contribute to the evolution of life?

    Continually, and in numerous ways, yes of course.

  12. Richardthughes:
    Are viruses pre-biotic entities, and did they contribute to the origin of life?
    No.

    Some would disagree with you there: The ancient Virus World and evolution of cells.
    Koonin EV, Senkevich TG, Dolja VV.

    Abstract
    BACKGROUND:
    Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.
    RESULTS:
    Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms. On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool. In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution. We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene. Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle. The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes. Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.
    CONCLUSION:
    The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes that went uninterrupted from the precellular stage of life’s evolution to this day. This concept is tightly linked to two key conjectures on evolution of cells: existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes, and origin of the eukaryotic cell by archaeo-bacterial fusion. The virus world concept and these models of major transitions in the evolution of cells provide complementary pieces of an emerging coherent picture of life’s history.

  13. Significant chunks of our genome are derived from historic viral infection. Some TEs themselves may have their origins in viruses – or vice versa for that matter. Some such elements make a protein coat, very like those of viruses, even though they never go ‘outside’.

    This is not massively helpful to Sal’s thesis that it-might-all-be-functional-you-never-know. It is certainly possible that Design arranged an infection for that very reason – to add function or sequence to the multi-layered fractal informatic integrome that modern science has discovered and Dan Graur hates [sic] … but not very likely.

  14. Rumraket,

    LGT between viruses during multiple infections can’t be ruled out.

    Let’s not forget that these are all protein coding differences, and hence everything coalesces through LUCA. There isn’t much reason to suppose LUCA was a virus, even if viral and cellular lineages don’t nest neatly subsequently.

  15. Are viruses pre-biotic entities, and did they contribute to the origin of life?

    I’ve gotten the impression, and Koonin sort of confirms this above, that there was a free-for-all of gene swapping in the pre-biotic world among indiscreet entities. Just as the sun, planets and asteroids coalesced out of the protoplanetary disk this prebiotic world coalesced into living cells and viruses more or less at the same time. But it seems to me theres no way to ever know this with any certainty and viruses could just as easily have arisen well after living cells formed

    Are viruses alive?

    No. Just as computer viruses aren’t computers. Below is the empirical formula for polio virus….enough said
    C332,652H492,388N98,245O131,196P7,501S2,340

  16. REW,

    I’ve gotten the impression, and Koonin sort of confirms this above, that there was a free-for-all of gene swapping in the pre-biotic world among indiscreet entities.

    It’s a view one hears from time to time – it was discussed recently on the Carl Woese thread – but I don’t think it has much going for it myeself. There are other ways to interpret the apparent ‘rampant HGT’ at the base of the ToL that people invoke in support of these ‘progenote’ ideas.

    In order to prosper, a gene needs to be attached to the consequences of its actions in some way.

  17. Allan Miller:
    Rumraket,

    LGT between viruses during multiple infections can’t be ruled out.

    Let’s not forget that these are all protein coding differences, and hence everything coalesces through LUCA. There isn’t much reason to suppose LUCA was a virus, even if viral and cellular lineages don’t nest neatly subsequently.

    I understand and I think koonin is sorta playing with the terminology by calling the very early replicator, non-cellular stage of life for a kind of “virus world”.

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