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protein folding

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  • protein folding

    A big step forward in creating future pandemics :
    So you can easily simulate the effect of mutations and recombinations in the
    computer without all that GOF-research and passaging.

    Apparently scientists are trying to hide this danger, but highlight the chances.
    It's these chances which are good for their research, their jobs, their careers,
    their funding.
    While the dangers are bad for them. Preventing possible future dangers
    is unpopular, non-rewarding.
    We've seen this in the discussion about
    Taubenberger's Spainflu publishing

    I've learned in those discussions, that scientists are biased, don't argue reasonably
    about the dangers. Things are being complicated and arguments found about
    some sub-problems,, but the overall logics is missing.

    Now, in the articles about deepminds yesterday's announcement, I didn't find any
    that even mentions the concern about using it for creating pandemics.
    I'm interested in expert panflu damage estimates
    my current links: ILI-charts:

  • #2
    gs I think that is a rather pessimistic take on a major advance. This is a promising step forward which could greatly speed drug design. Just getting the single protein structure at low cost and very quickly is an important first step which needs to be built on to develop the final biological form/function in vivo. Most proteins like flu HA or CoV spike are dimers or trimers of either one or multiple proteins and have many additional glycans which will effect their interactions. They also vary their conformation wildly dependent on environmental factors like the ph. All these need to be added to the model to be able to predict the biologically active form in vivo. Not all proteins can be crystalised so it will be particularly important if it works well on this group as their structure can not elucidated by X-ray crystallography. I do not see it changing the need for GOF anytime soon but will allow the sequence changes found in a GOF to be quickly visualised as structural changes giving important clues as to their mode of action.
    Last edited by JJackson; September 13, 2021, 07:20 AM.


    • gsgs
      gsgs commented
      Editing a comment
      I'm not questioning the "promising step" thing, the positive aspects
      and chances for research and useful applications.

      But I'm disappointed that noone talks about the associated dangers,
      we have no estimates. You think they are small ? Reference ?
      It is becoming common among researchers, that they are trying to hide the dangers.

      I do not see what additional measures could be taken from preventing
      this to be used for pandemic virus simulations.

      This seems like selling nukes for $1000 to everyone who wants them.

      I had enjoyed protein folding as a challenge for programmers and a chance for
      important algorithmical research. We had a protein-folding contest
      (not practiclly important) in our programming contest group, which I enjoyed.
      I only learned about pandemic viruses later, I didn't know about 1918 before 2004.
      I only learned about the magnitude of man-made-pandemics problem in 2011?
      before that I thought it was overblown by the Bush-bioterrorism hystery.
      I remember one key point was when monotreme showed these cheap
      DNA-synthesizers at ebay.

      I wonder whether you are qualified to estimate the risks from genetic computer simulations
      that this poses IMO or whether you just dismiss it as one of these conspiracies ?!

      I have no reference either, didn't see any paper or discussion about this yet.
      Just my momentary feeling from my experience with virus genetics evolution
      and computer algorithms.

    • JJackson
      JJackson commented
      Editing a comment
      gs I am not sure how you could quantify the risk which will increase with time. At present the barrier to using this technology is very high due to the extreme cost and sophistication of the hardware and software required but, like CRISPR-CAS will come down over time. I do not see cryo EM coming down but these are all tools which will make manipulation of biological molecules more controllable and understandable. Like many technological advances, like explosives and flight, they have associated risks but in general these are outweighed by the benefits. This is a problem for the future and I agree we need to start thinking about them now but not by stopping progress in the field as this has so many potential benefits. It would have been helpful, if a more mature technology, for this pandemic in rapid vaccine and therapeutics development. The good greatly outweighs the bad.

    • gsgs
      gsgs commented
      Editing a comment
      jjackson, you are not sure how I could quantify the risk, but you are doing
      just that by stating "The good greatly outweighs the bad".

      It's not the number of benefits but the magnitude.
      The ability to create multiple pandemics per year, per month
      would outweigh all the possible benefits that I can imagine.
      Well, except maybe the chance to manage them ;-)

      Expensive hardware and software ? Was that ever a problem in this sector ?
      Technology advances so quickly in computer-science and prices are going down.
      As a chess-player I had just observed this with deepmind's alpha-zero.

      And think at the longterm risk, not just the next decades.
      There will be virus-evolution computer emulation.
      It is possible and it will probably be done earlier or later.

      And they didn't talk about it in all the press-releases.