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Poor reporting on reproducing virus

RobertBradbury writes "Google news is reporting on 60+ articles being published by the various news media under the heading of "Scientists create a virus that reproduces." Its complete ca-ca demonstrating a complete lack of biological knowledge. In the first place a larger virus, the polio virus, has previously been synthesized (so this isn't "new" news). In the second place the bacterial virus phi X (and almost all other viruses) is not capable of self-replication (or reproduction). To be capable of self-replication in a biological system one would require the genetic code for both a DNA or RNA polymerase and a ribosome (these are necessary to copy the DNA/RNA of the genome and produce the proteins essential for viral self-replication. No known gene sequences that I'm aware of would allow those requirements to fit into the 5000 base pairs of the phi X genome (its like trying to fit a very large set of machines into a very small box). My quick estimate is that it would require hundreds of thousands perhaps millions of base pairs to produce a self-replicating virus. Viruses are normally inherently dependent upon their host bacteria or cells for reproduction (they are parasites). So the news reports are fundamentally flawed and should be taken with a very large grain of salt."

9 Responses to “Poor reporting on reproducing virus”

  1. mhh5 Says:

    IF you're going to nitpick….

    You quote the articles saying "Scientists create a virus that reproduces." That is fairly accurate. They don't say "virus that self-replicates." If scientists had created a virus that did NOT reproduce, that would just be a protein shell with some random RNA segments. (which might not even classify as a virus?) So how exactly would you like journalists to phrase the headline? "Virus created that does not self-replicate but can reproduce given a suitable host"? Are you saying that the recent arrival of easily man-made viruses is not a cause for any concern? If so, why? Perhaps you should point out that equally harmful or even more dangerous viruses can be produced using more traditional means of breeding and selection. But the new twist in this story is that the ability to quickly develop novel viruses from scratch might be dangerous. Please justify why that is not the case.

  2. RobertBradbury Says:

    Re:IF you're going to nitpick….

    Ok, I'll agree that I'm picking at fine points. My justification is the public concern about self-replicating machines and as you point out some of the fine distinctions between "reproduce" and "self-replicate". The average individual is not going to make a distinction because for the average individual "reproduce" is equal to semi-self-replication.

    In answer to the questions… The proposed article title would be a step towards educating the public. The arrival of man-made viruses certainly is a point of concern (though the phi X virus is bacterial and of much less concern than the polio virus).

    Agreed, bioweapons development, especially in the Soviet Union, has shown that more traditional biological methods can produce very harmful variants. You are also precisely correct that as the methods to develop the viruses become faster and cheaper the knowledge is increasingly dangerous. I might argue that the current biotech situation is a trial run for what we are going to have to deal with with nanotech (if we survive long enough for it to develop). That is why I raised the point that article is inaccurate. The real nightmare arrives when someone produces an artificial virus that is capable of self-replication and is lethal to humans. It would be difficult but I can envision possible paths to do that.

    Robert

  3. qftconnor Says:

    Questions

    The real nightmare arrives when someone produces an artificial virus that is capable of self-replication and is lethal to humans.

    I'm a little – maybe more than a little – confused on this one. When you say "an artificial virus that is capable of self-replication", I take it you mean a virus whose genetic material (DNA, RNA, or, since it's an artificial virus, maybe something else) encodes a polymerase (or a suite of polymerases) and also the (many) genes need to make a ribosome. (1) Is that right? (2) Is the virus also supposed to pack copies of these polymerases and ribosomes (not just the genes) into its capsid? I don't think everything will fit without a humongous (that's a highly technical term for improbably large ;) ) capsid. If it doesn't, it still needs to co-opt cellular machinery to get started, so it's still not truly self-replicating. (3) The blurry picture I'm getting sounds like a cross between a virus and an obligate intracellular parasite – it's not a cell, but it's dependent on its host only for precursor molecules it needs (amino acids, nucleotides, ???) and does not need any host machinery. So, do you visualize it replicating in a cell-free solution containing the appropriate nutrients? (4) Why is this the real nightmare? How is this worse than an ordinary virus? (5) Since it has its own machinery, I would think that these enzymes would be good targets for drug development. Do you agree?

  4. Kadamose Says:

    Already been done

    The real nightmare arrives when someone produces an artificial virus that is capable of self-replication and is lethal to humans.

    It's already been done – both the AIDs virus and the Ebola virus are synthetic. From some of the material I have read, the AIDs virus' creation was was completely accidental and went awry – the creation of the Ebola virus, on the other hand, was completely intentional – but it, too, went askew. This is further proof that mankind is not yet responsible enough to use such knowledge.

  5. RobertBradbury Says:

    Re:Questions

    Good questions. First. Viruses consist of two and sometimes 3 components. You have to have the program (this is based on DNA or RNA), then you have to have a package into which the program is stuffed (a protein "capsid"), then in some cases you have a lipid coat around the protein coat in what are known as "enveloped" viruses. The envelope is stolen from human cells and serves to hide them from the immune system. So to be able to reproduce you have to be able to duplicate at least the genetic program and the protein components. Molecular biologists have been able to produce the components from a technical standpoint for at least a decade. Cost issues prevented this from being done frequently.

    The precise answer to (1) as I understand it is no. Most viruses steal the activity of normal cell DNA or RNA polymerase to make copies of their genetic code. There are however a few that carry the code for their own polymerases or in the case of HIV a reverse transcriptase (to translate RNA into DNA). The problem is that the more of the required mechanisms for reproduction that one wants to carry the larger the viral genome becomes, and therefore the larger the "package" becomes and the more visible to the immune system it becomes.

    Regarding (2) — almost always the virus only packages the genome material (DNA or RNA) into the capsid. At times a protein or two may be included to help viral infection/reproduction. The way to view a virus is as a "shell" — sometimes with some intelligence built within it.

    Regarding (3) — the way to look at almost all viruses is as an obligate intracellular parasite. It doesn't get to reproduce without many of the resources the cell provides — from nucleotides to enzymes (e.g. DNA polymerase).

    Yes, given the proper nutrients (and enzymes) self-replication of viruses is most likely possible. You are essentially providing a cell-like environment without the cell.

    Regarding (4) — It isn't worse than the problem of an ordinary environment except for the fact that one could devise a system to manufacture artificial virus in "industrial" quantities. Lookup what Aum Shinrikyo did with spraying Tokyo with Anthrax (not their chemical weapons efforts). If they had an artificial virus manufacturing capability things might have been much worse.

    Regarding (5) — the enzymes are good targets for drug development but one has the problem that if the virus is using the cell's normal enzymes and you block them you have a very harmful effect on the cell itself. So one has to target the proteins or enzymes that are specific to the virus and this is going to take a case by case effort. Fortunately efforts have and will continue to expand the rate of development in these areas. For example, a recent report suggested that there is some molecule in Green Tea that prevents the HIV virus from getting into cells. You can bet that there are several companies actively working on determining what that molecule is and developing an improved version that they can patent.

    Robert

  6. RobertBradbury Says:

    Re:Already been done

    I'm sorry Kadamose but your claims are completely unsupported. If you make a claim citing "some of the material I have read", then you have to cite the sources so people can determine whether or not they are reasonable. To the best of my knowledge (and you have to realize that I worked in biotech for more than a decade) your claims do not reflect the current understanding in molecular biology. For example — can you cite a complete history of precisely where the genes in the AIDs or Ebola virus came from? Do you have a knowledge of how difficult it is to evolve even a single gene? [For example there is a wealth of knowledge of how difficult it was for people to vary genes of the DNA polymerases required to accelerate the Human Genome Project. People have had to spend years on such efforts.] To imagine that we could have created a new virus from scratch is a fantasy of conspiracy fans.

    Though your point that it has "Already been done" is valid it is only valid with respect to the Polio virus and not with AIDs or Ebola. I believe that does not contrast significantly from the points I have previously made.

    Robert

  7. qftconnor Says:

    Re:Questions

    OK, I think I understand what you're saying now. I guess my hangup here was principally semantic. I wanted to distinguish between things that are truly self-replicating, in the sense that they have all of the machinery (enzymes) needed to make copies of themselves (call this "strong" self-replication, if you like), and things that merely are replicated (by host cell machinery). So yeast seem to me to be strong self-replicators, because they'll grow in a solution with just a few precursor molecules (no need to add enzymes), but ordinary viruses aren't, because they need to use ribosomes and other equipment provided by the host cell. There are I believe bacteria which are obligate intracellular parasites, but which are self-replicating in the strong sense. I don't know of any strong self-replicating virus; I thought you were proposing creating one.

    Incidentally, it occurs to me that since viruses self-assemble, as the number of components that need to go into the capsid increases, the greater the probability of something being left out by chance becomes. Hence the probability of producing defective viruses (duds) should increase with virus size, exerting a selective pressure to keep viruses small. I wonder if this is the case. This would operate in addition to your point about increased virus size increasing the probability of immune recognition.

  8. Kadamose Says:

    Re:Already been done

    Well, I guess you're right in a sense – the AIDs virus was not a virus built from the ground up. It's actually a mutation of 2 viruses – the Visna virus, and HTLV-1. (Human T-cell Leukemia Virus). Keep in mind, that these two virused were not spliced together – (which many proofs already discredit) -instead, they were tricked to 'pickyback' each other and replicate – this 'pickyback' feature is the same feature seen when taking over a T-cell host. Don't ask me how they did it, but they did.

    If you think I'm giving way too much credit to some scientists who have been dead for maybe over a decade now, you're wrong. Think about it for a moment – who wrote the textbooks that you, like everyone else, gained their knowledge on how these systems work? Though many people would like to believe that 'creating viruses' is something new, it's a misguided delusion, and there really isn't anything new under the sun.

    Do you honestly think that if someone created a virus that it would automatically spread to the news the next day? I don't think so – knowledge like this is only given on a need to know basis. That's how power and secrecy works. And no, I am not being paranoid – this is simply how the world works.

    I could even go on about how SARS was also made through man's tinkering, but I don't have any sources at the moment to back this claim up. I definitely believe that to be the case, however, and I am not easily persuaded, either.

    And believe it or not, more than 75% of the conspiracy theories out there are TRUE. And even those that aren't entirely true, have pieces of truth in them.

    Secrecy is such and ugly and stupid thing – if there was no secrecy, our technological (and pscyhcological) development would be light years ahead of what it is today.

  9. RobertBradbury Says:

    Re:Already been done

    Just because you claim it doesn't make it true. This page here points out flaws that are accepted by scientists with respect to the evolution of HIV from SIV. And where on Earth do you come up with a number like 75% of the conspiracy theories are true? Saying it does not "make it so". You have to do a robust analysis of the person who is making the claim.

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