• Politics of life

    From Edward Montague@21:1/5 to All on Tue Jul 7 00:02:47 2020
    Sometimes I wonder if our health is a political pawn .

    Consider, for instance, the implications of an effective treatment
    for cancer. Might this be perceived in various circles as a diminishing of the nuclear deterrent.
    A strategic advantage if one group had this whilst another didn't.

    At the very personal level, which many of us seldom approach,
    politics and the machinations of those who have a contrary agenda
    to your well being are the last things you want to confront.

    Few might be aware of this; some decades ago the WHO were
    promoting measures to curb the world's population.
    A disaster, especially for the worlds unacknowledged minorities.

    Now imagine an individual from this minority, how difficult is it
    going to be to aspire to life extension in the sense that we're considering this.

    Anyway a bit of reality and a bit of paranoia.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to sciw...@gmail.com on Sat Aug 29 19:22:40 2020
    On Tuesday, July 7, 2020 at 7:02:49 PM UTC+12, sciw...@gmail.com wrote:
    Sometimes I wonder if our health is a political pawn .

    Consider, for instance, the implications of an effective treatment
    for cancer. Might this be perceived in various circles as a diminishing of the nuclear deterrent.
    A strategic advantage if one group had this whilst another didn't.

    At the very personal level, which many of us seldom approach,
    politics and the machinations of those who have a contrary agenda
    to your well being are the last things you want to confront.

    Few might be aware of this; some decades ago the WHO were
    promoting measures to curb the world's population.
    A disaster, especially for the worlds unacknowledged minorities.

    Now imagine an individual from this minority, how difficult is it
    going to be to aspire to life extension in the sense that we're considering this.

    Anyway a bit of reality and a bit of paranoia.

    This does seem to be related.

    Today I was watching flying videos on youtube.
    I was interested in the instrumentation in today's aircraft, mostly computerized.
    The pilot relies upon these to chart a safe course through weather, his journey, aircraft parameters.
    This is all necessary for a safe flight, autopilot is .available once the correct circumstances have
    been establihed.

    If only genomics,, protein assembly, drug discovery was presented in a similarly comprehensible
    and interactive manner, especially considering that lives depend upon this too.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to sciw...@gmail.com on Sun Dec 20 14:50:58 2020
    Concerning Alphafold 2.

    This is considered an advance in protein folding prediction
    by many.

    https://www.nature.com/articles/d41586-020-03348-4


    Some however say that the intervening steps in the
    folding need to be made apparent, in an accurate manner.

    From https://geneonline.news/en/2020/12/11/spotlight-alphafold-maybe-this-centurys-biggest-breakthrough-in-computational-biology/

    "The predicted structure from AlphaFold2 is a snapshot of the protein’s conformation, much like a crystal structure and not dynamic modeling of
    the protein folding."


    The latter is usually the domain of the standard computational
    molecular dynamics.


    Understanding an intervening configuration of the Covid 19 virus
    spike was crucial in the development of a vaccine.

    https://pubs.acs.org/doi/10.1021/acs.jpcb.0c03716#


    Computational Molecular Dynamics continues to be limited by the
    available hardware, especially when modelling large molecular
    complexes.

    https://par.nsf.gov/servlets/purl/10100859

    All of this initially appears to be a software issue, whereby
    we merge different approaches and cross reference the results,
    or train a larger system that utilizes different modules.

    The code for Alphafold 2 is yet to be made publicly available.




    General Reference

    Folding
    https://www.hpcwire.com/2020/10/14/how-foldinghome-identified-and-visualized-sars-cov-2s-weak-spots/
    https://www.nature.com/articles/s41401-020-0485-4


    https://towardsdatascience.com/alphafold-2-explained-a-semi-deep-dive-fa7618c1a7f6
    http://occamstypewriter.org/scurry/2020/12/02/no-deepmind-has-not-solved-protein-folding/

    CMD
    https://ieeexplore.ieee.org/document/6375578
    https://iopscience.iop.org/article/10.1088/1742-6596/180/1/012028/pdf
    https://www.hpcwire.com/2020/07/15/heffte-highly-efficient-fft-for-exascale/

    Folding
    https://www.blopig.com/blog/2020/12/casp14-what-google-deepminds-alphafold-2-really-achieved-and-what-it-means-for-protein-folding-biology-and-bioinformatics/
    https://www.skynettoday.com/briefs/alphafold2












    On Sunday, August 30, 2020 at 2:22:41 PM UTC+12, sciw...@gmail.com wrote:
    On Tuesday, July 7, 2020 at 7:02:49 PM UTC+12, sciw...@gmail.com wrote:
    Sometimes I wonder if our health is a political pawn .

    Consider, for instance, the implications of an effective treatment
    for cancer. Might this be perceived in various circles as a diminishing of the nuclear deterrent.
    A strategic advantage if one group had this whilst another didn't.

    At the very personal level, which many of us seldom approach,
    politics and the machinations of those who have a contrary agenda
    to your well being are the last things you want to confront.

    Few might be aware of this; some decades ago the WHO were
    promoting measures to curb the world's population.
    A disaster, especially for the worlds unacknowledged minorities.

    Now imagine an individual from this minority, how difficult is it
    going to be to aspire to life extension in the sense that we're considering this.

    Anyway a bit of reality and a bit of paranoia.
    This does seem to be related.

    Today I was watching flying videos on youtube.
    I was interested in the instrumentation in today's aircraft, mostly computerized.
    The pilot relies upon these to chart a safe course through weather, his journey, aircraft parameters.
    This is all necessary for a safe flight, autopilot is .available once the correct circumstances have
    been establihed.

    If only genomics,, protein assembly, drug discovery was presented in a similarly comprehensible
    and interactive manner, especially considering that lives depend upon this too.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to sciw...@gmail.com on Thu Jan 28 23:50:30 2021
    On Monday, December 21, 2020 at 11:51:01 AM UTC+13, sciw...@gmail.com wrote:
    Concerning Alphafold 2.

    This is considered an advance in protein folding prediction
    by many.

    https://www.nature.com/articles/d41586-020-03348-4


    Some however say that the intervening steps in the
    folding need to be made apparent, in an accurate manner.

    From https://geneonline.news/en/2020/12/11/spotlight-alphafold-maybe-this-centurys-biggest-breakthrough-in-computational-biology/

    "The predicted structure from AlphaFold2 is a snapshot of the protein’s conformation, much like a crystal structure and not dynamic modeling of
    the protein folding."


    The latter is usually the domain of the standard computational
    molecular dynamics.


    Understanding an intervening configuration of the Covid 19 virus
    spike was crucial in the development of a vaccine.

    https://pubs.acs.org/doi/10.1021/acs.jpcb.0c03716#


    Computational Molecular Dynamics continues to be limited by the
    available hardware, especially when modelling large molecular
    complexes.

    https://par.nsf.gov/servlets/purl/10100859

    All of this initially appears to be a software issue, whereby
    we merge different approaches and cross reference the results,
    or train a larger system that utilizes different modules.

    The code for Alphafold 2 is yet to be made publicly available.




    General Reference

    Folding https://www.hpcwire.com/2020/10/14/how-foldinghome-identified-and-visualized-sars-cov-2s-weak-spots/
    https://www.nature.com/articles/s41401-020-0485-4


    https://towardsdatascience.com/alphafold-2-explained-a-semi-deep-dive-fa7618c1a7f6
    http://occamstypewriter.org/scurry/2020/12/02/no-deepmind-has-not-solved-protein-folding/

    CMD
    https://ieeexplore.ieee.org/document/6375578 https://iopscience.iop.org/article/10.1088/1742-6596/180/1/012028/pdf https://www.hpcwire.com/2020/07/15/heffte-highly-efficient-fft-for-exascale/

    Folding https://www.blopig.com/blog/2020/12/casp14-what-google-deepminds-alphafold-2-really-achieved-and-what-it-means-for-protein-folding-biology-and-bioinformatics/
    https://www.skynettoday.com/briefs/alphafold2
    On Sunday, August 30, 2020 at 2:22:41 PM UTC+12, sciw...@gmail.com wrote:
    On Tuesday, July 7, 2020 at 7:02:49 PM UTC+12, sciw...@gmail.com wrote:
    Sometimes I wonder if our health is a political pawn .

    Consider, for instance, the implications of an effective treatment
    for cancer. Might this be perceived in various circles as a diminishing of the nuclear deterrent.
    A strategic advantage if one group had this whilst another didn't.

    At the very personal level, which many of us seldom approach,
    politics and the machinations of those who have a contrary agenda
    to your well being are the last things you want to confront.

    Few might be aware of this; some decades ago the WHO were
    promoting measures to curb the world's population.
    A disaster, especially for the worlds unacknowledged minorities.

    Now imagine an individual from this minority, how difficult is it
    going to be to aspire to life extension in the sense that we're considering this.

    Anyway a bit of reality and a bit of paranoia.
    This does seem to be related.

    Today I was watching flying videos on youtube.
    I was interested in the instrumentation in today's aircraft, mostly computerized.
    The pilot relies upon these to chart a safe course through weather, his journey, aircraft parameters.
    This is all necessary for a safe flight, autopilot is .available once the correct circumstances have
    been established.

    If only genomics,, protein assembly, drug discovery was presented in a similarly comprehensible
    and interactive manner, especially considering that lives depend upon this too.

    Jan 29 2021

    Yet to be substantiated .

    https://cen.acs.org/physical-chemistry/protein-folding/DeepMind-AI-predicts-protein-structures/98/web/2020/12

    https://scitechdaily.com/major-scientific-advance-deepmind-ai-alphafold-solves-50-year-old-grand-challenge-of-protein-structure-prediction/

    from https://www.newscientist.com/article/2261156-deepminds-ai-biologist-can-decipher-secrets-of-the-machinery-of-life/

    "
    Lupas thinks for the next few years researchers will still need to do
    some experimental work to check shape predictions, but will
    eventually be able to rely on computation alone.
    This will make a huge difference, he says, but the real revolution
    will come from being able to use computers to predict how proteins
    interact with other molecules.
    "

    from
    https://youtu.be/ShQgQbnX-Ko?list=PL3lZhmfYpIKuPyW945016C78YmictCOTK&t=4

    Distinguished Speaker Seminar Series, episode 1: The revolution
    in protein structure prediction .

    " lipid protein and other complicated interactions considered
    ameanable to the techniques used in alphafold 2 "


    Read more:

    https://www.newscientist.com/article/2261156-deepminds-ai-biologist-can-decipher-secrets-of-the-machinery-of-life/#ixzz6kumrx8ER




    Another consideration, utilize what nature has developed.

    https://www.eb.tuebingen.mpg.de/protein-evolution/

    Watch the video.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to All on Tue Feb 23 20:08:54 2021
    Using a neural network to identify regulatory activity of
    the genome .


    https://www.sciencedaily.com/releases/2021/02/210218151102.htm https://github.com/kundajelab/bpnet/

    Pypi package

    https://pypi.org/project/bpnet/ ?
    https://pypi.org/project/bpnet-lite/

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to All on Tue Apr 13 14:23:58 2021
    Of note

    Exosomes

    pubmed.ncbi.nlm.nih.gov/32759948

    There are other factors that are known and have yet to be
    addressed.

    The late Joshua Lederberg, former president of the New York Academy of Sciences, and Nobel
    recipient, was well aware of Exosomes; many decades ago.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to sciw...@gmail.com on Sat Apr 17 19:31:18 2021
    On Wednesday, April 14, 2021 at 9:23:59 AM UTC+12, sciw...@gmail.com wrote:
    Of note

    Exosomes

    pubmed.ncbi.nlm.nih.gov/32759948

    There are other factors that are known and have yet to be
    addressed.

    The late Joshua Lederberg, former president of the New York Academy of Sciences, and Nobel
    recipient, was well aware of Exosomes; many decades ago.

    These Exosomes can be separate from the normal genetic material of the cell, yet interact with the DNA, and most likely RNA, of the cell.
    From the link presented you're able to determine that Exosomes can also be encapsulated.

    Some Exosomes have a circular DNA structure and undergo rapid mutation, promoting further
    cancerous growth; just as well someones seeking an assay and remedy.

    Exosomes are different than Exomes .
    Exomes are related to the Exons of the cells natural DNA.

    Joshua Lederberg was also interested in Proteomics; I have a brochure from NYAS on the topic, that they published when they and Joshua were beginning this project.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to All on Sat Apr 17 19:48:42 2021
    On Sunday, April 18, 2021 at 2:31:19 PM UTC+12, sciw...@gmail.com wrote:


    Exosomes
    pubmed.ncbi.nlm.nih.gov/32759948

    Another link on a similar topic,

    https://www.the-scientist.com/features/cancer-may-be-driven-by-dna-outside-of-chromosomes-68590

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to All on Fri Apr 23 06:18:52 2021
    Examining immune response, in the lab, before applying therapy.


    https://www.researchgate.net/publication/323528075_In_vitro_immunotherapy_potency_assays_using_real-time_cell_analysis

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to All on Mon May 3 15:35:21 2021
    I'm attempting to piece together how drug discovery happens.
    This is by no means comprehensive, or necessarily precise; at this time.

    target drug

    configuration
    determined
    by x-ray diffraction,
    cyro-em and/or
    protein folding
    software.
    __________________
    protein <-- docking ----- ligand, possibly a protein too. | repeat
    | |
    | <-------------------------

    energy , some measure of goodness of fit,
    nowadays also determined through software .

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to All on Sun May 9 00:01:27 2021
    Attachment ?

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From sciwiseg@gmail.com@21:1/5 to All on Sun May 9 20:42:09 2021
    An edited version, to make everything more comprehensible.

    Target molecule, usually a protein .

    Configuration determined by x-ray diffraction, cyro-em and/or protein
    folding software.

    Large databases exist for the known molecules.

    --------

    Drug

    Ligand, possibly a protein too.

    Very large databases exist for the known molecules.
    Using known drugs we're also able to use other information, like the toxicity to humans.

    --------

    Docking, where we determine how well the drug binds to the target protein.
    The energy released during docking is one measure of goodness of fit,
    nowadays also determined through software .

    The docking evaluation might be repeated numerous times, the structure of
    the drug being tweaked every so often. Also different drugs are likely to be evaluated.

    -----------

    Vaccines utilizing mRNA also require information from this methodology, especially the sequence of events involved in protein folding.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)