Solving Alzheimers, Huntington, Prion diseases; Files150 and 151 of www.iw.net/~a_plutonium

Discussion in 'Health and medical' started by Archimedes Plut, Mar 12, 2004.

  1. I am massively revising my website of
    www.iw.net/~a_plutonium because it is written in a textbook
    fashion that it requires massive editing and deleting and
    adding onto about every 5 years. I have neglected this
    website for about 10 years and so I have a big job ahead of
    me. My other website of www.archimedesplutonium.com needs
    no periodic editing because it is structured as a archive
    that I merely collect the posts I post and enter or dump it
    into the website. Archiving does not require editing
    because it wants to save everything whether correct or
    riddled with error.

    Files 150 and 151 deal with Alzheimers Huntington and Prion
    disease. I was fortunate to have a running dialogue and
    conversation with at least 3 scientists from Berkeley and
    Cambridge Univ about these diseases starting with the year
    1997 and specifically these dates:

    Oct-Nov 1997 Dec 1998 Feb-Mar 1999 Jan 2004 anyone
    interested in that long history can view it at
    www.archimedesplutonium.com website

    I must have had over 2,000 posts to the internet in
    conversations with 3 or more scientists about these
    diseases. And my old practice of filling File150 and File151
    with many of those past posts. That practice must cease
    because my archived website handles all of those posts and
    no need to repeat those posts in this textbook website where
    I want to achieve understanding and clarity.

    So that means I have to toss out old posts from this website
    and to attempt to keep it current.

    Let me just remark on the history of Alzheimers, Huntington,
    and Prion. I dived into these 3 diseases back in October of
    1997 noting the analogy similarity of a ant disease in the
    tropics where a fungus infects an ant's brain and kills the
    ant. I could not escape the notice of a analogy between
    fungus ant disease and Prion disease. It then migrated theory-
    wise to thinking that Prion disease is the analogy to sickle
    cell anemia disease only with a deformed brain protein
    instead of red blood cells. It migrated into many other
    theories and hypothesis but then recently is news not of
    Prion disease with metal-ions from phosmet and magnetic
    manganese but news from Alzheimers in that the plaque
    buildup (much like prion buildup) is caused by a scissors
    that wrongly snips the APP protein into 2 segments wherein
    the one segment ends up being toxic Alzheimers plaques.

    So, is there a similar scissors mechanism or scissors-like
    mechanism that causes Prion disease?

    So I left the discussion of Alzheimers, Huntington, Prion
    just January of 2004 with the open issue of a Scissors
    mechanism for Alzheimers and whether Huntington and Prion
    also have a scissors mechanism and whether magnetic
    manganese is the metal ion culprit that causes Prion disease
    and whether Huntington and Alzheimers also have a metal-ion
    facilitator culprit.

    One of the issues I stressed and harped and harped on from
    1997 to present day is that the Nobel prize to Prusiner for
    his Prion theory was a prize that was a huge mistake and
    that it was perhaps 20 years too soon. To have given the
    Nobel to Prusiner was so premature, that the Nobel should
    have given a prize to any lead researcher of Alzheimers
    circa 1995 to 1997 and to have given a prize to any lead
    researcher for Huntington's disease circa 1995-1997. The
    reason the Nobel Committee never awarded Alzheimers or
    Huntington from 1990-2003 was because the mechanism for
    Alzheimers and Huntington are still not understood. Prion is
    not understand even to this very day, yet the Nobel
    Committee blustered and rammed ahead giving a prize out for
    Prion disease when it never should have. The Nobel to
    Prusiner is one of the worst Nobel awards ever given. The
    Nobel Committee in giving Prusiner the award were more
    rambunctious and impetuous than Mr. Bush wanting to invade
    Iraq in 2003. In fact, it can be argued that Mr. Bush had
    more grounds to invade Iraq than the Nobel Committee had
    grounds to award Mr. Prusiner the prize for his work on
    Prion disease. And it is ironic that Mr. Blix is from Sweden
    where the Nobel Committee is and that Mr. Blix is laying it
    straight as far as the groundless claims of Weapons of Mass
    Destruction.

    One other item I want to mention for Files 150 and 151 is
    that in that history of 1997 on Prion disease, is that I
    attacked the Prusiner Model on two grounds and it is these
    two grounds which convinced me back in 1995-March2004 that
    the Prusiner Model is a complete fake.

    (1) Thermodynamically it is impossible for a bad-prion-
    molecule to turn a good-prion-molecule into an identical
    copy. The energy equation does not give enough energy
    for a similar protein to alter a different protein into
    a identical copy. Just not enough energy.

    (2) If prion proteins really did what the Prusiner Model
    says then the lowest form of life is not the cell but
    proteins like prion-proteins because replication or
    reproduction is the main distinguishing characteristic
    of life. And the Prusiner Model is that a protein thence
    becomes the lowest form of life and makes the cell and
    DNA as excess baggage.

    On those two ground above convinced me that the Prusiner
    Model was a fake and that it is only a matter of time before
    the true mechanism of how Prion disease and how Huntington
    and Alzheimers work.

    Also I need to note that I suspect that Prion, Huntington
    and Alzheimers are different but that they are very much
    alike in several similarities. So that a mechanism of how
    each works may have a family resemblance. Such that if metal-
    ions plays a key role in Prion disease it is likely that metal-
    ions plays a role in Huntington and Alzheimers and likewise
    for the scissors mechanism in Alzheimers probably has a
    scissors mechanism to be found in Huntington and Prion.

    I believe these 3 diseases are related more than they are
    not related.

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies

    (www.iw.net/~a_plutonium) website of the science of AP under
    revision what used to be my old science website
    www.newphys.se/elektromagnum/physics/LudwigPlutonium from
    years 1993 to 2004
     
    Tags:


  2. Talkback

    Talkback Guest

    Archimedes Plutonium wrote:

    > I am massively revising my website of
    > www.iw.net/~a_plutonium because it is written in a
    > textbook fashion that it requires massive editing and
    > deleting and adding onto about every 5 years.

    Yeah, that should keep it current.

    I have neglected
    > this website for about 10 years and so I have a big job
    > ahead of me.

    Well at least the information is all up to date.

    > My other website of www.archimedesplutonium.com needs no
    > periodic editing because it is structured as a archive
    > that I merely collect the posts I post and enter or dump
    > it into the website.

    A trash can would be more appropriate.

    Archiving does
    > not require editing because it wants to save everything
    > whether correct or riddled with error.

    Good to know.
    >
    > Files 150 and 151 deal with Alzheimers Huntington and
    > Prion disease. I was fortunate to have a running dialogue
    > and conversation with at least 3 scientists from Berkeley
    > and Cambridge Univ about these diseases starting with the
    > year 1997 and specifically these dates:
    >
    >
    > Oct-Nov 1997 Dec 1998 Feb-Mar 1999 Jan 2004 anyone
    > interested in that long history can view it at
    > www.archimedesplutonium.com website
    >
    > I must have had over 2,000 posts to the internet in
    > conversations with 3 or more scientists about these
    > diseases.

    That's like 500 per scientist. I doubt that any
    knowledgeable person would humour you for this long.

    > I believe these 3 diseases are related more than they are
    > not related.

    Like a plane flies the same way a brick does not.
    >
    > Archimedes Plutonium whole entire Universe is just one big
    > atom where dots of the electron-dot-cloud are galaxies

    Depends on your perspective I suppose.
     
  3. Talkback

    Talkback Guest

    Archimedes Plutonium wrote:

    > I am massively revising my website of
    > www.iw.net/~a_plutonium because it is written in a
    > textbook fashion that it requires massive editing and
    > deleting and adding onto about every 5 years.

    Yeah, that should keep it current.

    I have neglected
    > this website for about 10 years and so I have a big job
    > ahead of me.

    Well at least the information is all up to date.

    > My other website of www.archimedesplutonium.com needs no
    > periodic editing because it is structured as a archive
    > that I merely collect the posts I post and enter or dump
    > it into the website.

    A trash can would be more appropriate.

    Archiving does
    > not require editing because it wants to save everything
    > whether correct or riddled with error.

    Good to know.
    >
    > Files 150 and 151 deal with Alzheimers Huntington and
    > Prion disease. I was fortunate to have a running dialogue
    > and conversation with at least 3 scientists from Berkeley
    > and Cambridge Univ about these diseases starting with the
    > year 1997 and specifically these dates:
    >
    >
    > Oct-Nov 1997 Dec 1998 Feb-Mar 1999 Jan 2004 anyone
    > interested in that long history can view it at
    > www.archimedesplutonium.com website
    >
    > I must have had over 2,000 posts to the internet in
    > conversations with 3 or more scientists about these
    > diseases.

    That's like 500 per scientist. I doubt that any
    knowledgeable person would humour you for this long.

    > I believe these 3 diseases are related more than they are
    > not related.

    Like a plane flies the same way a brick does not.
    >
    > Archimedes Plutonium whole entire Universe is just one big
    > atom where dots of the electron-dot-cloud are galaxies

    Depends on your perspective I suppose.
     
  4. Bob

    Bob Guest

    On 11 Mar 2004 12:49:20 -0800, [email protected] (Archimedes
    Plutonium) wrote:

    >
    >One of the issues I stressed and harped and harped on from
    >1997 to present day is that the Nobel prize to Prusiner for
    >his Prion theory was a prize that was a huge mistake and
    >that it was perhaps 20 years too soon.

    You diminish whatever merit the scientific arguments may
    have (and some are certainly worth discussion) by harping on
    the Nobel. None of us have anything to do with it, and the
    name calling is not constructive.

    (I think I am already on record as having predicted
    Prusiner's Nobel, but then being surprised how soon it
    came -- and even more surprised that he got it alone.
    But so what?)

    > To have given the Nobel to Prusiner was so premature,
    > that the Nobel should have given a prize to any lead
    > researcher of Alzheimers circa 1995 to 1997 and to have
    > given a prize to any lead researcher for Huntington's
    > disease circa 1995-1997.

    Well, I think the reason prion got it rather than those was
    the implication for "new life form". And he dominated the
    field unlike anyone in those, I think.

    >
    >One other item I want to mention for Files 150 and 151 is
    >that in that history of 1997 on Prion disease, is that I
    >attacked the Prusiner Model on two grounds and it is these
    >two grounds which convinced me back in 1995-March2004 that
    >the Prusiner Model is a complete fake.
    >
    >(1) Thermodynamically it is impossible for a bad-prion-
    > molecule to turn a good-prion-molecule into an
    > identical copy.

    Then apparently you do not understand the model. I have
    asked you about this before, but am still mystified what
    your concern is. To declare impossible what has been shown
    is not so helpful.

    >
    >(2) If prion proteins really did what the Prusiner Model
    > says then the lowest form of life is not the cell but
    > proteins like prion-proteins because replication or
    > reproduction is the main distinguishing characteristic
    > of life. And the Prusiner Model is that a protein
    > thence becomes the lowest form of life and makes the
    > cell and DNA as excess baggage.
    >

    Nonsense. The gene for the prion is a cellular gene.
    Proteins do not self-replicate, according to Prusiner or
    anyone else. Finding that the prion was encoded by a host
    gene was a key (_the_ key?) to allowing a non-viral (not
    containing nucleic acid) infectious agent to be accepted.

    >
    >Also I need to note that I suspect that Prion, Huntington
    >and Alzheimers are different but that they are very much
    >alike in several similarities.

    It is interesting how similarities have been accumulating.
    These similarities are all at the level of how an
    aggregating protein (or perhaps a precursor to the
    aggregating protein) causes neurodegeneration. But they are
    all clearly very different in how that protein arises.

    bob
     
  5. Bob <[email protected]> wrote in message news:<[email protected]>...
    > On 11 Mar 2004 12:49:20 -0800, [email protected]
    > (Archimedes Plutonium) wrote:
    >
    > >
    > >One of the issues I stressed and harped and harped on
    > >from 1997 to present day is that the Nobel prize to
    > >Prusiner for his Prion theory was a prize that was a huge
    > >mistake and that it was perhaps 20 years too soon.
    >
    > You diminish whatever merit the scientific arguments may
    > have (and some are certainly worth discussion) by harping
    > on the Nobel. None of us have anything to do with it, and
    > the name calling is not constructive.
    >

    True, but most people reading faintly have knowledge of the
    science and mostly interested in the human history aspect
    and it is that reason that I bring that into discussion. If
    you hear Alzheimers or Prion discussed in news, it
    invariably harps on the history.

    > (I think I am already on record as having predicted
    > Prusiner's Nobel, but then being surprised how soon it
    > came -- and even more surprised that he got it alone. But
    > so what?)
    >

    It holds back or retards progress in the field. And it can
    be sensed at this time in year 2004 where progress is very
    much being made in Alzheimers and in Parkinsons, but Prion
    disease is thwarted and denied the real progress it should
    be making. The Prusiner Model is a hurdle to progress in
    that field.

    >
    > > To have given the Nobel to Prusiner was so premature,
    > > that the Nobel should have given a prize to any lead
    > > researcher of Alzheimers circa 1995 to 1997 and to have
    > > given a prize to any lead researcher for Huntington's
    > > disease circa 1995-1997.
    >
    > Well, I think the reason prion got it rather than those
    > was the implication for "new life form". And he dominated
    > the field unlike anyone in those, I think.
    >

    Bob, what if. What if when Alzheimers was first seen in
    Germany in the early 20th century, what if Dr. Alzheimer had
    said that the brain plaque was caused by a deformed protein
    which when it comes in contact with a normal protein that it
    deforms the normal protein. And that the Nobel committee
    thence gives Dr. Alzheimers of Germany the prize in 1950.

    A Prusiner Model can be claimed to be how Alzheimers works.
    But every scientist in medicine knows that Alzheimers is not
    a disease where protein molecule A deforms protein molecule
    B into a copy of A.

    So the Nobel Committee does not award for "true accurate
    science" but instead awards more if a disease becomes
    epidemic as in England in the early 1990s and the epidemic
    social status forces the Swedes to award the person most
    prominent in that disease field.

    >
    >
    > >
    > >One other item I want to mention for Files 150 and 151 is
    > >that in that history of 1997 on Prion disease, is that I
    > >attacked the Prusiner Model on two grounds and it is
    > >these two grounds which convinced me back in 1995-
    > >March2004 that the Prusiner Model is a complete fake.
    > >
    > >(1) Thermodynamically it is impossible for a bad-prion-
    > > molecule to turn a good-prion-molecule into an
    > > identical copy.
    >
    > Then apparently you do not understand the model. I have
    > asked you about this before, but am still mystified what
    > your concern is. To declare impossible what has been shown
    > is not so helpful.
    >

    If you put a gallon of gasoline in your auto and asked to
    drive it from Berkeley to New England, it is
    thermodynamically impossible, for there just is not
    enough energy.

    It is impossible for a prion-bad-protein to deform a prion-normal-
    protein into an identical copy. I know, Bob, you and Colin
    have said years ago that the bad-prion protein garners
    energy from its surrounding environment to deform the
    normal prion but no-one is able to demonstrate such an
    energy pathway.

    In other words, bad-prion-proteins simply do not have enough
    energy within the molecule and outside the molecule of its
    environment to deform a normal-prion-protein.

    >
    > >
    > >(2) If prion proteins really did what the Prusiner Model
    > > says then the lowest form of life is not the cell but
    > > proteins like prion-proteins because replication or
    > > reproduction is the main distinguishing
    > > characteristic of life. And the Prusiner Model is
    > > that a protein thence becomes the lowest form of life
    > > and makes the cell and DNA as excess baggage.
    > >
    >
    > Nonsense. The gene for the prion is a cellular gene.
    > Proteins do not self-replicate, according to Prusiner or
    > anyone else. Finding that the prion was encoded by a host
    > gene was a key (_the_ key?) to allowing a non-viral (not
    > containing nucleic acid) infectious agent to be accepted.
    >
    >
    > >
    > >Also I need to note that I suspect that Prion, Huntington
    > >and Alzheimers are different but that they are very much
    > >alike in several similarities.
    >
    >
    > It is interesting how similarities have been accumulating.
    > These similarities are all at the level of how an
    > aggregating protein (or perhaps a precursor to the
    > aggregating protein) causes neurodegeneration. But they
    > are all clearly very different in how that protein arises.
    >
    >
    > bob

    It is interesting how Alzheimers is converging with Prion.
    Parkinsons is out of the picture but I am hoping that
    Parkinsons will also have similarities and be a member of
    what I call a Family of brain wasting diseases.

    Bob, back in 1997 when you first started discussing diseases
    with me, I never would have guessed that the convergence of
    Alzheimers with Prion would be so intense by year 2004 but
    it is shaping up that way.

    The scissors that snips the APP protein in Alzheimers
    disease snips the protein in two segments which is abnormal
    for the small segment becomes the plaque buildup. So if
    scissors snipping of proteins is the cause of Alzheimers,
    then it is highly likely that the cause of Prion disease is
    a rogue scissors.

    Now, how is a rogue scissors in Prion able to transfer by
    eating, while in Alzheimers, the rogue scissors is not
    transmitted through eating-- at least it is not known
    whether Alzheimers is transmittable through eating.

    Bob, your comment "new life form" is the heart of the
    argument against the Prusiner Model. RNA and DNA are life
    forms and their smallest particle is a virus which manages
    to use the energy of its environmental surroundings--the
    cell. So, Bob, back in the 1980s or 1990s, you should have
    asked yourself about the Prusiner Model that if he was
    correct then this prion protein particle would be a lower
    life form than even the RNA of the lowest virus. And Bob,
    you have been a scientist longer than I have, so did you
    ever ask yourself the reasonableness of whether a prion
    protein could ever be the Lowest form of life and usurp RNA
    as the lowest form of life. I suspect you never spent the
    time on that question, Bob, because if you had, you would
    never have endorsed the Prusiner Model to the extent you
    endorsed it.

    I am surprized also that Alzheimers is solving Prion disease
    whereas back in 1997, I would have bet that prion disease
    research would have solved prion disease itself and
    Alzheimers a disconnect. I do not know if there is a lesson
    or theme to be learned from this, even though prematurely.
    Whether the lesson is that when baffled by a disease, then
    the best avenue of attack is to find a Family Resemblance of
    Diseases and then be eclectic and use parts and pieces of
    one disease to guide oneself in the other disease.

    Bob, question: where is Colin from Cambridge England these
    days; I sort of miss his contributions, perhaps too busy.

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies

    (www.iw.net/~a_plutonium) website of the science of AP under
    revision what used to be my old science website
    www.newphys.se/elektromagnum/physics/LudwigPlutonium from
    years 1993 to 2004
     
  6. Bob <[email protected]> wrote in message news:<[email protected]>...
    > On 11 Mar 2004 12:49:20 -0800, [email protected]
    > (Archimedes Plutonium) wrote:
    >
    > >
    > >One of the issues I stressed and harped and harped on
    > >from 1997 to present day is that the Nobel prize to
    > >Prusiner for his Prion theory was a prize that was a huge
    > >mistake and that it was perhaps 20 years too soon.
    >
    > You diminish whatever merit the scientific arguments may
    > have (and some are certainly worth discussion) by harping
    > on the Nobel. None of us have anything to do with it, and
    > the name calling is not constructive.
    >

    True, but most people reading faintly have knowledge of the
    science and mostly interested in the human history aspect
    and it is that reason that I bring that into discussion. If
    you hear Alzheimers or Prion discussed in news, it
    invariably harps on the history.

    > (I think I am already on record as having predicted
    > Prusiner's Nobel, but then being surprised how soon it
    > came -- and even more surprised that he got it alone. But
    > so what?)
    >

    It holds back or retards progress in the field. And it can
    be sensed at this time in year 2004 where progress is very
    much being made in Alzheimers and in Parkinsons, but Prion
    disease is thwarted and denied the real progress it should
    be making. The Prusiner Model is a hurdle to progress in
    that field.

    >
    > > To have given the Nobel to Prusiner was so premature,
    > > that the Nobel should have given a prize to any lead
    > > researcher of Alzheimers circa 1995 to 1997 and to have
    > > given a prize to any lead researcher for Huntington's
    > > disease circa 1995-1997.
    >
    > Well, I think the reason prion got it rather than those
    > was the implication for "new life form". And he dominated
    > the field unlike anyone in those, I think.
    >

    Bob, what if. What if when Alzheimers was first seen in
    Germany in the early 20th century, what if Dr. Alzheimer had
    said that the brain plaque was caused by a deformed protein
    which when it comes in contact with a normal protein that it
    deforms the normal protein. And that the Nobel committee
    thence gives Dr. Alzheimers of Germany the prize in 1950.

    A Prusiner Model can be claimed to be how Alzheimers works.
    But every scientist in medicine knows that Alzheimers is not
    a disease where protein molecule A deforms protein molecule
    B into a copy of A.

    So the Nobel Committee does not award for "true accurate
    science" but instead awards more if a disease becomes
    epidemic as in England in the early 1990s and the epidemic
    social status forces the Swedes to award the person most
    prominent in that disease field.

    >
    >
    > >
    > >One other item I want to mention for Files 150 and 151 is
    > >that in that history of 1997 on Prion disease, is that I
    > >attacked the Prusiner Model on two grounds and it is
    > >these two grounds which convinced me back in 1995-
    > >March2004 that the Prusiner Model is a complete fake.
    > >
    > >(1) Thermodynamically it is impossible for a bad-prion-
    > > molecule to turn a good-prion-molecule into an
    > > identical copy.
    >
    > Then apparently you do not understand the model. I have
    > asked you about this before, but am still mystified what
    > your concern is. To declare impossible what has been shown
    > is not so helpful.
    >

    If you put a gallon of gasoline in your auto and asked to
    drive it from Berkeley to New England, it is
    thermodynamically impossible, for there just is not
    enough energy.

    It is impossible for a prion-bad-protein to deform a prion-normal-
    protein into an identical copy. I know, Bob, you and Colin
    have said years ago that the bad-prion protein garners
    energy from its surrounding environment to deform the
    normal prion but no-one is able to demonstrate such an
    energy pathway.

    In other words, bad-prion-proteins simply do not have enough
    energy within the molecule and outside the molecule of its
    environment to deform a normal-prion-protein.

    >
    > >
    > >(2) If prion proteins really did what the Prusiner Model
    > > says then the lowest form of life is not the cell but
    > > proteins like prion-proteins because replication or
    > > reproduction is the main distinguishing
    > > characteristic of life. And the Prusiner Model is
    > > that a protein thence becomes the lowest form of life
    > > and makes the cell and DNA as excess baggage.
    > >
    >
    > Nonsense. The gene for the prion is a cellular gene.
    > Proteins do not self-replicate, according to Prusiner or
    > anyone else. Finding that the prion was encoded by a host
    > gene was a key (_the_ key?) to allowing a non-viral (not
    > containing nucleic acid) infectious agent to be accepted.
    >
    >
    > >
    > >Also I need to note that I suspect that Prion, Huntington
    > >and Alzheimers are different but that they are very much
    > >alike in several similarities.
    >
    >
    > It is interesting how similarities have been accumulating.
    > These similarities are all at the level of how an
    > aggregating protein (or perhaps a precursor to the
    > aggregating protein) causes neurodegeneration. But they
    > are all clearly very different in how that protein arises.
    >
    >
    > bob

    It is interesting how Alzheimers is converging with Prion.
    Parkinsons is out of the picture but I am hoping that
    Parkinsons will also have similarities and be a member of
    what I call a Family of brain wasting diseases.

    Bob, back in 1997 when you first started discussing diseases
    with me, I never would have guessed that the convergence of
    Alzheimers with Prion would be so intense by year 2004 but
    it is shaping up that way.

    The scissors that snips the APP protein in Alzheimers
    disease snips the protein in two segments which is abnormal
    for the small segment becomes the plaque buildup. So if
    scissors snipping of proteins is the cause of Alzheimers,
    then it is highly likely that the cause of Prion disease is
    a rogue scissors.

    Now, how is a rogue scissors in Prion able to transfer by
    eating, while in Alzheimers, the rogue scissors is not
    transmitted through eating-- at least it is not known
    whether Alzheimers is transmittable through eating.

    Bob, your comment "new life form" is the heart of the
    argument against the Prusiner Model. RNA and DNA are life
    forms and their smallest particle is a virus which manages
    to use the energy of its environmental surroundings--the
    cell. So, Bob, back in the 1980s or 1990s, you should have
    asked yourself about the Prusiner Model that if he was
    correct then this prion protein particle would be a lower
    life form than even the RNA of the lowest virus. And Bob,
    you have been a scientist longer than I have, so did you
    ever ask yourself the reasonableness of whether a prion
    protein could ever be the Lowest form of life and usurp RNA
    as the lowest form of life. I suspect you never spent the
    time on that question, Bob, because if you had, you would
    never have endorsed the Prusiner Model to the extent you
    endorsed it.

    I am surprized also that Alzheimers is solving Prion disease
    whereas back in 1997, I would have bet that prion disease
    research would have solved prion disease itself and
    Alzheimers a disconnect. I do not know if there is a lesson
    or theme to be learned from this, even though prematurely.
    Whether the lesson is that when baffled by a disease, then
    the best avenue of attack is to find a Family Resemblance of
    Diseases and then be eclectic and use parts and pieces of
    one disease to guide oneself in the other disease.

    Bob, question: where is Colin from Cambridge England these
    days; I sort of miss his contributions, perhaps too busy.

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies

    (www.iw.net/~a_plutonium) website of the science of AP under
    revision what used to be my old science website
    www.newphys.se/elektromagnum/physics/LudwigPlutonium from
    years 1993 to 2004
     
  7. Bob <[email protected]> wrote in message news:<[email protected]>...
    > On 11 Mar 2004 12:49:20 -0800, [email protected]
    > (Archimedes Plutonium) wrote:
    >
    > >
    > >One of the issues I stressed and harped and harped on
    > >from 1997 to present day is that the Nobel prize to
    > >Prusiner for his Prion theory was a prize that was a huge
    > >mistake and that it was perhaps 20 years too soon.
    >
    > You diminish whatever merit the scientific arguments may
    > have (and some are certainly worth discussion) by harping
    > on the Nobel. None of us have anything to do with it, and
    > the name calling is not constructive.
    >

    True, but most people reading faintly have knowledge of the
    science and mostly interested in the human history aspect
    and it is that reason that I bring that into discussion. If
    you hear Alzheimers or Prion discussed in news, it
    invariably harps on the history.

    > (I think I am already on record as having predicted
    > Prusiner's Nobel, but then being surprised how soon it
    > came -- and even more surprised that he got it alone. But
    > so what?)
    >

    It holds back or retards progress in the field. And it can
    be sensed at this time in year 2004 where progress is very
    much being made in Alzheimers and in Parkinsons, but Prion
    disease is thwarted and denied the real progress it should
    be making. The Prusiner Model is a hurdle to progress in
    that field.

    >
    > > To have given the Nobel to Prusiner was so premature,
    > > that the Nobel should have given a prize to any lead
    > > researcher of Alzheimers circa 1995 to 1997 and to have
    > > given a prize to any lead researcher for Huntington's
    > > disease circa 1995-1997.
    >
    > Well, I think the reason prion got it rather than those
    > was the implication for "new life form". And he dominated
    > the field unlike anyone in those, I think.
    >

    Bob, what if. What if when Alzheimers was first seen in
    Germany in the early 20th century, what if Dr. Alzheimer had
    said that the brain plaque was caused by a deformed protein
    which when it comes in contact with a normal protein that it
    deforms the normal protein. And that the Nobel committee
    thence gives Dr. Alzheimers of Germany the prize in 1950.

    A Prusiner Model can be claimed to be how Alzheimers works.
    But every scientist in medicine knows that Alzheimers is not
    a disease where protein molecule A deforms protein molecule
    B into a copy of A.

    So the Nobel Committee does not award for "true accurate
    science" but instead awards more if a disease becomes
    epidemic as in England in the early 1990s and the epidemic
    social status forces the Swedes to award the person most
    prominent in that disease field.

    >
    >
    > >
    > >One other item I want to mention for Files 150 and 151 is
    > >that in that history of 1997 on Prion disease, is that I
    > >attacked the Prusiner Model on two grounds and it is
    > >these two grounds which convinced me back in 1995-
    > >March2004 that the Prusiner Model is a complete fake.
    > >
    > >(1) Thermodynamically it is impossible for a bad-prion-
    > > molecule to turn a good-prion-molecule into an
    > > identical copy.
    >
    > Then apparently you do not understand the model. I have
    > asked you about this before, but am still mystified what
    > your concern is. To declare impossible what has been shown
    > is not so helpful.
    >

    If you put a gallon of gasoline in your auto and asked to
    drive it from Berkeley to New England, it is
    thermodynamically impossible, for there just is not
    enough energy.

    It is impossible for a prion-bad-protein to deform a prion-normal-
    protein into an identical copy. I know, Bob, you and Colin
    have said years ago that the bad-prion protein garners
    energy from its surrounding environment to deform the
    normal prion but no-one is able to demonstrate such an
    energy pathway.

    In other words, bad-prion-proteins simply do not have enough
    energy within the molecule and outside the molecule of its
    environment to deform a normal-prion-protein.

    >
    > >
    > >(2) If prion proteins really did what the Prusiner Model
    > > says then the lowest form of life is not the cell but
    > > proteins like prion-proteins because replication or
    > > reproduction is the main distinguishing
    > > characteristic of life. And the Prusiner Model is
    > > that a protein thence becomes the lowest form of life
    > > and makes the cell and DNA as excess baggage.
    > >
    >
    > Nonsense. The gene for the prion is a cellular gene.
    > Proteins do not self-replicate, according to Prusiner or
    > anyone else. Finding that the prion was encoded by a host
    > gene was a key (_the_ key?) to allowing a non-viral (not
    > containing nucleic acid) infectious agent to be accepted.
    >
    >
    > >
    > >Also I need to note that I suspect that Prion, Huntington
    > >and Alzheimers are different but that they are very much
    > >alike in several similarities.
    >
    >
    > It is interesting how similarities have been accumulating.
    > These similarities are all at the level of how an
    > aggregating protein (or perhaps a precursor to the
    > aggregating protein) causes neurodegeneration. But they
    > are all clearly very different in how that protein arises.
    >
    >
    > bob

    It is interesting how Alzheimers is converging with Prion.
    Parkinsons is out of the picture but I am hoping that
    Parkinsons will also have similarities and be a member of
    what I call a Family of brain wasting diseases.

    Bob, back in 1997 when you first started discussing diseases
    with me, I never would have guessed that the convergence of
    Alzheimers with Prion would be so intense by year 2004 but
    it is shaping up that way.

    The scissors that snips the APP protein in Alzheimers
    disease snips the protein in two segments which is abnormal
    for the small segment becomes the plaque buildup. So if
    scissors snipping of proteins is the cause of Alzheimers,
    then it is highly likely that the cause of Prion disease is
    a rogue scissors.

    Now, how is a rogue scissors in Prion able to transfer by
    eating, while in Alzheimers, the rogue scissors is not
    transmitted through eating-- at least it is not known
    whether Alzheimers is transmittable through eating.

    Bob, your comment "new life form" is the heart of the
    argument against the Prusiner Model. RNA and DNA are life
    forms and their smallest particle is a virus which manages
    to use the energy of its environmental surroundings--the
    cell. So, Bob, back in the 1980s or 1990s, you should have
    asked yourself about the Prusiner Model that if he was
    correct then this prion protein particle would be a lower
    life form than even the RNA of the lowest virus. And Bob,
    you have been a scientist longer than I have, so did you
    ever ask yourself the reasonableness of whether a prion
    protein could ever be the Lowest form of life and usurp RNA
    as the lowest form of life. I suspect you never spent the
    time on that question, Bob, because if you had, you would
    never have endorsed the Prusiner Model to the extent you
    endorsed it.

    I am surprized also that Alzheimers is solving Prion disease
    whereas back in 1997, I would have bet that prion disease
    research would have solved prion disease itself and
    Alzheimers a disconnect. I do not know if there is a lesson
    or theme to be learned from this, even though prematurely.
    Whether the lesson is that when baffled by a disease, then
    the best avenue of attack is to find a Family Resemblance of
    Diseases and then be eclectic and use parts and pieces of
    one disease to guide oneself in the other disease.

    Bob, question: where is Colin from Cambridge England these
    days; I sort of miss his contributions, perhaps too busy.

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies

    (www.iw.net/~a_plutonium) website of the science of AP under
    revision what used to be my old science website
    www.newphys.se/elektromagnum/physics/LudwigPlutonium from
    years 1993 to 2004
     
  8. Wyrin

    Wyrin Guest

    "Archimedes Plutonium" <[email protected]> wrote in message
    news:[email protected]...
    > Bob <[email protected]> wrote in message
    news:<[email protected]>...
    > > On 11 Mar 2004 12:49:20 -0800, [email protected]
    > > (Archimedes Plutonium) wrote:
    > >
    > > >
    > > >One of the issues I stressed and harped and harped on
    > > >from 1997 to present day is that the Nobel prize to
    > > >Prusiner for his Prion theory was a prize that was a
    > > >huge mistake and that it was perhaps 20 years too soon.
    > >
    > > You diminish whatever merit the scientific arguments may
    > > have (and some are certainly worth discussion) by
    > > harping on the Nobel. None of us have anything to do
    > > with it, and the name calling is not constructive.
    > >
    >
    > True, but most people reading faintly have knowledge of
    > the science and mostly interested in the human history
    > aspect and it is that reason that I bring that into
    > discussion. If you hear Alzheimers or Prion discussed in
    > news, it invariably harps on the history.
    >
    >
    > > (I think I am already on record as having predicted
    > > Prusiner's Nobel, but then being surprised how soon it
    > > came -- and even more surprised that he got it alone.
    > > But so what?)
    > >
    >
    > It holds back or retards progress in the field. And it can
    > be sensed at this time in year 2004 where progress is very
    > much being made in Alzheimers and in Parkinsons, but Prion
    > disease is thwarted and denied the real progress it should
    > be making. The Prusiner Model is a hurdle to progress in
    > that field.
    >
    > >
    > > > To have given the Nobel to Prusiner was so premature,
    > > > that the Nobel should have given a prize to any lead
    > > > researcher of Alzheimers circa 1995 to 1997 and to
    > > > have given a prize to any lead researcher for
    > > > Huntington's disease circa 1995-1997.
    > >
    > > Well, I think the reason prion got it rather than those
    > > was the implication for "new life form". And he
    > > dominated the field unlike anyone in those, I think.
    > >
    >
    > Bob, what if. What if when Alzheimers was first seen in
    > Germany in the early 20th century, what if Dr. Alzheimer
    > had said that the brain plaque was caused by a deformed
    > protein which when it comes in contact with a normal
    > protein that it deforms the normal protein. And that the
    > Nobel committee thence gives Dr. Alzheimers of Germany the
    > prize in 1950.
    >
    > A Prusiner Model can be claimed to be how Alzheimers
    > works. But every scientist in medicine knows that
    > Alzheimers is not a disease where protein molecule A
    > deforms protein molecule B into a copy of A.
    >
    > So the Nobel Committee does not award for "true accurate
    > science" but instead awards more if a disease becomes
    > epidemic as in England in the early 1990s and the epidemic
    > social status forces the Swedes to award the person most
    > prominent in that disease field.
    >
    > >
    > >
    > > >
    > > >One other item I want to mention for Files 150 and 151
    > > >is that in that history of 1997 on Prion disease, is
    > > >that I attacked the Prusiner Model on two grounds and
    > > >it is these two grounds which convinced me back in 1995-
    > > >March2004 that the Prusiner Model is a complete fake.
    > > >
    > > >(1) Thermodynamically it is impossible for a bad-prion-
    > > > molecule to turn a good-prion-molecule into an
    > > > identical copy.
    > >
    > > Then apparently you do not understand the model. I have
    > > asked you about this before, but am still mystified what
    > > your concern is. To declare impossible what has been
    > > shown is not so helpful.
    > >
    >
    > If you put a gallon of gasoline in your auto and asked to
    > drive it from Berkeley to New England, it is
    > thermodynamically impossible, for there just is not
    > enough energy.
    >
    > It is impossible for a prion-bad-protein to deform a prion-normal-
    > protein into an identical copy. I know, Bob, you and Colin
    > have said years ago that the bad-prion protein garners
    > energy from its surrounding environment to deform the
    > normal prion but no-one is able to demonstrate such an
    > energy pathway.
    >
    > In other words, bad-prion-proteins simply do not have
    > enough energy within the molecule and outside the molecule
    > of its environment to deform a normal-prion-protein.

    I've tried this before but... AP, try looking at Pathologic
    conformations of prion proteins. (1998) Annu Rev Biochem 67
    p793-819 Also, I like to look at the serpin analogy http://-
    eagle.mmid.med.ualberta.ca/publications/JMB293p449.pdf

    AP, do you claim that crystallisation is thermodynamically
    impossible?

    Amyloid is just a great big Conga line of drunk proteins
    at a New years party, and the normal proteins just aint
    drunk enough to join in... yet. Until it hits midnight...
    An I know its not thermodynamically impossible to get
    drunk. Trust me
     
  9. "Wyrin" <[email protected]> wrote in message news:<[email protected]>...

    >
    > I've tried this before but... AP, try looking at
    > Pathologic conformations of prion proteins. (1998) Annu
    > Rev Biochem 67 p793-819 Also, I like to look at the serpin
    > analogy http://eagle.mmid.med.ualberta.ca/publications/JM-
    > B293p449.pdf
    >
    > AP, do you claim that crystallisation is thermodynamically
    > impossible?
    >
    > Amyloid is just a great big Conga line of drunk proteins
    > at a New years party, and the normal proteins just aint
    > drunk enough to join in... yet. Until it hits midnight...
    > An I know its not thermodynamically impossible to get
    > drunk. Trust me

    Crystallization is thermodynamically possible, and you know
    what Wyrin, thousands perhaps millions of chemists and their
    students have worked out enthalpies and entropies and
    whether the reaction will go and the rates of reaction. But
    why is it Wyrin that no-one ever worked out whether bad-
    prions react and change good prions. Is it because Mr.
    Prusiner is unable to do any such calculations? So why have
    you Wyrin not given any website that shows the entropy and
    enthalpies for prion reactions? Is it because they are
    nonexistant?

    Also a question Wyrin, in that you so heartily believe in
    the Prusiner Model. What would you assign a probability of
    correctness for a Prusiner Model when in the decade of the
    1980s and in the decade of the 1990s and even from the years
    2000 to March of 2004, it is still unknown and vastly
    unclear as to the role and function of normal-prions. In the
    past it was said that normal prions build or help build cell
    walls but as of March 2004 there is not a chemist or
    biologists in the entire world who is confident of what
    normal prions do or function as or their purpose. So, the
    question I have for you Wyrin, is what sort of probability
    would you assign for any scientist who claims to have a
    correct theory as to the mechanism and causes of a disease
    and to offer such a Model, yet still has no clue or firm
    clue or understanding of what the particle of his Model what
    that particles role or function or purpose was.

    Would you say Wyrin that the chances of any scientist
    finding a correct model for a disease wherein that scientist
    has little to no clue as to what the function or role of
    their main-element or main molecule of the disease (in this
    case normal-prions). Would you say that the chances of the
    Model being wrong is something about 99% with maybe a 1%
    chance that the Model is correct? Because that is where I
    would place the numbers.

    Any scientist in any field whether biology, medicine,
    chemistry, physics, if they do not know the role or function
    of their main issue under investigation, then any Model or
    theory constructed around that main issue is by all chances
    and probabilities going to be wrong.

    Analogy: suppose Sherlock Holmes or other famous detectives
    operated in the same manner that Mr. Prusiner operated to
    form his Model. Then Sherlock would be arresting people left
    and right without ever knowing whether anyone had been
    killed. We would have Sherlock Holmes stories where he goes
    out and looks for and hunts criminals yet no dead bodies.
    That is a similar analogy to Mr. Prusiner running out and
    running off concocting Models without ever knowing what
    Normal Prions function or role was.

    A good scientist knows that unless he fully knows and
    understands what normal and good Prions do and function,
    unless he knows that, his Models on prion disease are
    nothing but wild-speculation.

    Sorry if it sounds like I am picking on you Wyrin, but you
    deserve it with your scatterbrained tidbits above.

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies

    (www.iw.net/~a_plutonium) website of the science of AP under
    revision what used to be my old science website
    www.newphys.se/elektromagnum/physics/LudwigPlutonium from
    years 1993 to 2004
     
  10. Bob

    Bob Guest

    On 14 Mar 2004 23:30:17 -0800, [email protected] (Archimedes
    Plutonium) wrote:

    >> >
    >> >One other item I want to mention for Files 150 and 151
    >> >is that in that history of 1997 on Prion disease, is
    >> >that I attacked the Prusiner Model on two grounds and it
    >> >is these two grounds which convinced me back in 1995-
    >> >March2004 that the Prusiner Model is a complete fake.
    >> >
    >> >(1) Thermodynamically it is impossible for a bad-prion-
    >> > molecule to turn a good-prion-molecule into an
    >> > identical copy.
    >>
    >> Then apparently you do not understand the model. I have
    >> asked you about this before, but am still mystified what
    >> your concern is. To declare impossible what has been
    >> shown is not so helpful.
    >>
    >
    >If you put a gallon of gasoline in your auto and asked to
    >drive it from Berkeley to New England, it is
    >thermodynamically impossible, for there just is not
    >enough energy.

    agreed, but that is irrelevant.

    >
    >It is impossible for a prion-bad-protein to deform a prion-normal-
    >protein into an identical copy.

    You still have not answered the question. Why do you think
    that? Proteins fold and refold and adjust their folding all
    the time. This is basic protein chemistry. The total net
    energy of protein folding is very slight. Offhand I have no
    idea what the energetics of the proposed reaction is, but no
    one with the slightest understanding of proteins would think
    there is any problem with it.

    >
    >The scissors that snips the APP protein in Alzheimers
    >disease snips the protein in two segments which is abnormal
    >for the small segment becomes the plaque buildup. So if
    >scissors snipping of proteins is the cause of Alzheimers,
    >then it is highly likely that the cause of Prion disease is
    >a rogue scissors.

    The logic of that statement is zilch. In fact, it is known
    to be incorrect. There are many ways to make bad proteins.

    >
    >Bob, your comment "new life form" is the heart of the
    >argument against the Prusiner Model. RNA and DNA are life
    >forms and their smallest particle is a virus which manages
    >to use the energy of its environmental surroundings--the
    >cell. So, Bob, back in the 1980s or 1990s, you should have
    >asked yourself about the Prusiner Model that if he was
    >correct then this prion protein particle would be a lower
    >life form than even the RNA of the lowest virus. And Bob,
    >you have been a scientist longer than I have, so did you
    >ever ask yourself the reasonableness of whether a prion
    >protein could ever be the Lowest form of life and usurp RNA
    >as the lowest form of life. I suspect you never spent the
    >time on that question, Bob, because if you had, you would
    >never have endorsed the Prusiner Model to the extent you
    >endorsed it.

    What the prion model does is to show that the prion is not
    alive, any more than a virus is. Cells are the lowest form
    of life known. Viruses and prions use cells. The prion model
    resolved what had seemed to be a problem by showing how
    prions use cells. The prion is coded for by a cellular gene.
    Problem solved. (That we still may not agree on all the
    details of the prion transformation is not relevant to that
    basic issue. And how they cause disease has no relevance at
    all to the question of what a prion is.)

    >
    >I am surprized also that Alzheimers is solving Prion
    >disease whereas back in 1997, I would have bet that prion
    >disease research would have solved prion disease itself and
    >Alzheimers a disconnect. I do not know if there is a lesson
    >or theme to be learned from this, even though prematurely.
    >Whether the lesson is that when baffled by a disease, then
    >the best avenue of attack is to find a Family Resemblance
    >of Diseases and then be eclectic and use parts and pieces
    >of one disease to guide oneself in the other disease.

    well, that's progress.

    bob
     
  11. Bob <[email protected]> wrote in message news:<[email protected]>...
    > On 14 Mar 2004 23:30:17 -0800, [email protected]
    > (Archimedes Plutonium) wrote:

    > >
    > >It is impossible for a prion-bad-protein to deform a prion-normal-
    > >protein into an identical copy.
    >
    > You still have not answered the question. Why do you think
    > that? Proteins fold and refold and adjust their folding
    > all the time. This is basic protein chemistry. The total
    > net energy of protein folding is very slight. Offhand I
    > have no idea what the energetics of the proposed reaction
    > is, but no one with the slightest understanding of
    > proteins would think there is any problem with it.

    Would you not agree Bob that when two molecules collide and
    interact, that changes in one or both of the molecules is
    induced. That is normal collision and interaction. But would
    you not agree Bob that when a collision between protein
    molecules occurs and they interact and they go off as
    identical to one another, would you not agree that such was
    so implausible as to be unbelievable.

    It is what I said back in 1997, that unless you say the bad-
    prion molecule is a catalyst where a catalyst is unchanged
    at the end of the interaction. But that still makes the prion-
    catalyst unique amoung all other catalysts because the prion
    catalyst is the only 2 party catalyst and all other
    catalysts like platinum in the gasoline industry is a 3
    party catalyst.

    Bob, I agree proteins fold and refold and adjust their
    folding all the time, but your opinion of Prions as per the
    Prusiner Model is a superspecial sort of folding that no
    thermodynamical enthalpies or entropies can support.

    Toyota makes a car called Prius, sort of hybrid electric
    that gives more then 50 miles per gallon. Suppose cars were
    like protein collision and interaction. Suppose there was a
    Prion car out there and it collided and interacted with many
    other cars. Whenever a Prius collided or interacted with a
    GM or Ford or BMW or VW both are folded and misshapened
    after the event. But when a Prion collides and interacts
    with a Prius, both are undamaged and both drive off from the
    accident as brand new Prion cars-- totally unbelievable,
    forgive the expression, someone would say Twilight Zone
    science or X-files science.

    Protein folding in normal interactions is commonplace, but
    when 2 proteins collide and interact and leave the scene of
    the event as identical molecules, well, that needs special
    attention for it is against the rules of Thermodynamics and
    even the 2nd Law of Thermodynamics.

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies
     
  12. Bob <[email protected]> wrote in message news:<[email protected]>...
    > On 14 Mar 2004 23:30:17 -0800, [email protected]
    > (Archimedes Plutonium) wrote:

    > >
    > >It is impossible for a prion-bad-protein to deform a prion-normal-
    > >protein into an identical copy.
    >
    > You still have not answered the question. Why do you think
    > that? Proteins fold and refold and adjust their folding
    > all the time. This is basic protein chemistry. The total
    > net energy of protein folding is very slight. Offhand I
    > have no idea what the energetics of the proposed reaction
    > is, but no one with the slightest understanding of
    > proteins would think there is any problem with it.
    >

    Bob, I am rusty on calculating enthalpy and entropy for
    whether a reaction will go or not and the rate of reaction.
    I am please asking for you to calcalute those numbers for
    platinum and for gold. We all know that platinum is a
    catalyst but not a super catalyst that the Prusiner Model
    expects of a prion protein. Platinum is a normal catalyst in
    that it speeds up the rate of reaction and it ends up
    unchanged by the end of the reaction. In fact, there
    probably does not exist a supercatalyst for which this
    calculation I am asking of you Bob would demonstrate.

    We all know that platinum cannot change gold into more
    platinum, but please Bob work through the numbers and please
    give me a number for enthalpy and entropy that proves number
    wise that such a reaction is impossible.

    Working through the numbers Bob, it should be a huge
    negative energy to have to put into the reaction in order
    for Platinum to alter Gold atoms into making more Platinum
    Atoms. And, or, please work the reverse route of starting
    with Gold atoms and expecting them to change Platinum atoms
    into more gold atoms.

    Bob, I appreciate you constantly asking me to clarify why
    prions of the Prusiner Model are thermodynamically
    impossible. I keep answering that question. I keep telling
    you that if his model were correct implies Supercatalysts,
    implies chemistry of not just normal catalysts like platinum
    in the gasoline distilling industry but supercatalysts where
    platinum turns gold atoms into more platinum atoms. Chemical
    Reactions alter the molecules of shape and form-- this is
    normal. But it is not normal that molecule A when it bumps
    into molecule B and alters B into an identical copy, that is
    not normal. That is not allowed by thermodynamics and the
    Prusiner Model is just another way of saying SuperCatalysts
    exist when that is a falsehood.

    Bob, I am very rusty as it was over 30 years ago when at UC
    that I computed enthalpy and entropy and rates of chemical
    reactions. So please assist me. Please compute the numbers
    that shows that it is impossible for Platinum to convert
    Gold and vice versa. Show me the numbers that proves it is
    impossible in Chemistry for Platinum to convert gold into
    more platinum.

    Once those numbers are displayed, then it is easier to go
    the reaction of taking a Prion bad molecule and expecting it
    to convert a Prion good molecule into an identical copy.

    Yes, the flaw of the Prusiner Model is that it expects the
    world of science to have a Supercatalyst, but the world of
    science has no supercatalysts and these are impossible. A
    supercatalyst is more than a catalyst in that it is party to
    2 molecules whereas a normal-catalyst is party to at least 3
    molecules.

    Bob, I cannot find the numbers or work the numbers for prion
    proteins and it seems from your above reply that you cannot
    also. But you are more of a chemist than I will ever be, and
    thus you should be able to provide me with a number solution
    of enthalpy and entropy of a reaction between Platinum and
    Gold and why platinum cannot alter gold into an identical
    platinum copy and vice versa.

    ARchimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies
     
  13. Wyrin

    Wyrin Guest

    "Archimedes Plutonium" <[email protected]> wrote in message
    news:[email protected]...
    > "Wyrin" <[email protected]> wrote in message
    news:<[email protected]>...
    >
    > >
    > > I've tried this before but... AP, try looking at
    > > Pathologic conformations of prion proteins. (1998) Annu
    > > Rev Biochem 67 p793-819 Also, I like to look at the
    > > serpin analogy http://eagle.mmid.med.ualberta.ca/public-
    > > ations/JMB293p449.pdf
    > >
    > > AP, do you claim that crystallisation is
    > > thermodynamically impossible?
    > >
    > > Amyloid is just a great big Conga line of drunk proteins
    > > at a New years party, and the normal proteins just aint
    > > drunk enough to join in... yet. Until it hits
    > > midnight... An I know its not thermodynamically
    > > impossible to get drunk. Trust me
    >

    > Sorry if it sounds like I am picking on you Wyrin, but you
    > deserve it with your scatterbrained tidbits above.

    It didnt sound like you were picking on me - just that you
    were spouting a diatribe with little basis in fact. Those
    scatterbrained titbits - IF YOU ACTUALLY BOTHRERED TO READ
    THEM - would answer some of your questions

    > Crystallization is thermodynamically possible, and you
    > know what Wyrin, thousands perhaps millions of chemists
    > and their students have worked out enthalpies and
    > entropies and whether the reaction will go and the rates
    > of reaction. But why is it Wyrin that no-one ever worked
    > out whether bad-prions react and change good prions. Is it
    > because Mr. Prusiner is unable to do any such
    > calculations? So why have you Wyrin not given any website
    > that shows the entropy and enthalpies for prion reactions?
    > Is it because they are nonexistant?

    If you looked at the first reference I gave you, you would
    find some of the answer to this Pathologic conformations of
    prion proteins. (1998) Annu Rev Biochem 67 p793-819 http://-
    arjournals.annualreviews.org/doi/pdf/10.1146/annurev.bioche-
    m.67.1.793 Go to a local library and ask for this article,
    or purchase it online

    What do you think of the existance of prions in yeast?

    > Would you say Wyrin that the chances of any scientist
    > finding a correct model for a disease wherein that
    > scientist has little to no clue as to what the function or
    > role of their main-element or main molecule of the disease
    > (in this case normal-prions). Would you say that the
    > chances of the Model being wrong is something about 99%
    > with maybe a 1% chance that the Model is correct? Because
    > that is where I would place the numbers.

    What is the probability of correctness of the opinion of a
    person who is so inherently biased against Prusiner? He
    proposed a dogma-breaking theory and got a nobel prize for
    it. Ok, it might have been earlier than he deserved, but
    that doesnt invalidate the growing body of evidence that has
    been compiled to sugest his theory could be true

    > Analogy: suppose Sherlock Holmes or other famous
    > detectives operated in the same manner that Mr. Prusiner
    > operated to form his Model. Then Sherlock would be
    > arresting people left and right without ever knowing
    > whether anyone had been killed. We would have Sherlock
    > Holmes stories where he goes out and looks for and hunts
    > criminals yet no dead bodies. That is a similar analogy
    > to Mr. Prusiner running out and running off concocting
    > Models without ever knowing what Normal Prions function
    > or role was.

    Irrelevant

    >A good scientist knows that unless he fully knows and
    >understands what normal and good Prions do and function,
    >unless he knows that, his Models on prion disease are
    >nothing but wild-speculation.

    A good scientist basis his opinions on observations with as
    little speculation as possible. Here's a bit from my thesis
    where I try to put a balanced view on it. The first
    theories put forward to explain the observed infectivity
    and strain variation of prion diseases, such as scrapie in
    sheep and kuru in humans, suggested the existence of a
    parasite or 'slow virus' (Eklund and Hadlow, 1969; Hadlow,
    1995). However, the infectivity was resistant to
    decontamination by UV irradiation at 254 nm, which argued
    against the presence of a nucleic acid (Alper et al.,
    1967). Other properties of the agent included resistance to
    heat, including autoclaving at 120 °C, formalin treatment
    and ionising radiation (Gordon, 1946; Prusiner, 1998a). An
    'unconventional virus' was suggested but no actual details
    offered. No bacteria or virus has been found consistently
    associated with prion disease (Prusiner, 1998a). The term
    prion (from proteinaceous-infectious particle, lacking a
    nucleic acid) was put forward following evidence that
    procedures that modified or destroyed proteins could reduce
    scrapie infectivity (Griffith, 1967; Prusiner, 1982).
    Prusiner proposed, therefore, that the endogenous prion
    protein was the infectious agent, and a mutated PrP
    responsible for the inherited disease. This model has since
    been widely accepted, since it has been shown that PrP is
    the only factor that has been found to be associated with
    disease so far, and endogenous PrP is required for disease
    transmission (Bolton et al., 1982; Hope et al., 1986;
    Prusiner et al., 1993b).

    Nevertheless, some researchers still maintain that viral
    mechanisms are important in prion disease and to account for
    the observed strain variation, citing other viruses that are
    known to cause dementia and spongiform change in the brain,
    and that display resistance to classical decontamination
    techniques (Manuelidis, 1994a Manuelidis, 1995 #787).
    Furthermore, neither refolded PrPSc nor purified recombinant
    protein have yet been shown to be infective (Prusiner et
    al., 1993a; Manuelidis, 1994b). However, studies with yeast
    prions, and in vitro demonstration that resistance to prion
    infectivity correlates with the degree of homology between
    the host PrPC and exogenous PrPSc, are strong arguments in
    favour of the prion hypothesis (Bossers et al., 1997;
    Liebman, 2002).
     
  14. Steve Turner

    Steve Turner Guest

    On 15 Mar 2004 23:53:32 -0800, [email protected] (Archimedes
    Plutonium) wrote:

    >Would you not agree Bob that when two molecules collide and
    >interact, that changes in one or both of the molecules is
    >induced. That is normal collision and interaction. But
    >would you not agree Bob that when a collision between
    >protein molecules occurs and they interact and they go off
    >as identical to one another, would you not agree that such
    >was so implausible as to be unbelievable.

    ??? Why is this not believable?

    Steve Turner
     
  15. Steve Turner

    Steve Turner Guest

    On 16 Mar 2004 10:39:39 -0800, [email protected] (Archimedes
    Plutonium) wrote:

    >We all know that platinum cannot change gold into more
    >platinum, but please Bob work through the numbers and
    >please give me a number for enthalpy and entropy that
    >proves number wise that such a reaction is impossible.

    This is a nuclear transformation, not a chemical one.
    Chemical thermodynamics do not apply.

    Steve Turner
     
  16. "Wyrin" <[email protected]> wrote in message news:<[email protected]>...
    > "Archimedes Plutonium" <[email protected]> wrote in
    > message
    > news:[email protected]...
    > > "Wyrin" <[email protected]> wrote in message
    > news:<[email protected]>...
    > >
    > > >
    > > > I've tried this before but... AP, try looking at
    > > > Pathologic conformations of prion proteins. (1998)
    > > > Annu Rev Biochem 67 p793-819 Also, I like to look at
    > > > the serpin analogy http://eagle.mmid.med.ualberta.ca/-
    > > > publications/JMB293p449.pdf
    > > >
    > > > AP, do you claim that crystallisation is
    > > > thermodynamically impossible?
    > > >
    > > > Amyloid is just a great big Conga line of drunk
    > > > proteins at a New years party, and the normal proteins
    > > > just aint drunk enough to join in... yet. Until it
    > > > hits midnight... An I know its not thermodynamically
    > > > impossible to get drunk. Trust me
    > >
    >
    > > Sorry if it sounds like I am picking on you Wyrin, but
    > > you deserve it with your scatterbrained tidbits above.
    >
    > It didnt sound like you were picking on me - just that you
    > were spouting a diatribe with little basis in fact. Those
    > scatterbrained titbits - IF YOU ACTUALLY BOTHRERED TO READ
    > THEM - would answer some of your questions

    some files I cannot access for it interfers with my killfile
    such as pdf

    >
    > > Crystallization is thermodynamically possible, and you
    > > know what Wyrin, thousands perhaps millions of chemists
    > > and their students have worked out enthalpies and
    > > entropies and whether the reaction will go and the rates
    > > of reaction. But why is it Wyrin that no-one ever worked
    > > out whether bad-prions react and change good prions. Is
    > > it because Mr. Prusiner is unable to do any such
    > > calculations? So why have you Wyrin not given any
    > > website that shows the entropy and enthalpies for prion
    > > reactions? Is it because they are nonexistant?
    >
    > If you looked at the first reference I gave you, you would
    > find some of the answer to this Pathologic conformations
    > of prion proteins. (1998) Annu Rev Biochem 67 p793-819 ht-
    > tp://arjournals.annualreviews.org/doi/pdf/10.1146/annurev-
    > .biochem.67.1.793 Go to a local library and ask for this
    > article, or purchase it online
    >

    If you were scientifically objective about prion disease
    then you would not be in these newsgroups with the attitude
    of saying "you are wrong and here, I deposit for you sites
    in which to correct your misconceptions" Your trouble Wyrin
    is that you take some lofty high ground that you are the
    authority on prions and that you are here to correct
    everyone else. When you fact you are an incompetent in
    Prion science.

    > What do you think of the existance of prions in yeast?
    >

    If you had a gram of science objectivity, Wyrin, you would
    thence realize that since yeast which is chock full of prion
    proteins yet is utter harmless to animals, would indicate
    strongly that the Prusiner Model for prions is false. Why
    should prions in yeast never act like prions in animals,
    unless of course the Prusiner Model is a fake science model.
    But you, Wyrin, just does not have the science objectivity.

    > > Would you say Wyrin that the chances of any scientist
    > > finding a correct model for a disease wherein that
    > > scientist has little to no clue as to what the function
    > > or role of their main-element or main molecule of the
    > > disease (in this case normal-prions). Would you say that
    > > the chances of the Model being wrong is something about
    > > 99% with maybe a 1% chance that the Model is correct?
    > > Because that is where I would place the numbers.
    >
    > What is the probability of correctness of the opinion of a
    > person who is so inherently biased against Prusiner?

    No, I am both biased against Prusiner but also _able_ to be
    biased for Prusiner. But you, Wyrin, is incapable of being
    biased against Prusiner. Perhaps it is because you are part
    of the establishment with your job and career at stake. This
    is a common problem with most scientists in that they know a
    science theory is wrong but they cannot speak out against it
    because of their biweekly paycheck.

    > He proposed a dogma-breaking theory and got a nobel prize
    > for it. Ok, it might have been earlier than he deserved,
    > but that doesnt invalidate the growing body of evidence
    > that has been compiled to sugest his theory could be true
    >

    There is no growing body of evidence in support of Prusiner.
    There is evidence of variant types of bad prion proteins
    which disproves the Prusiner Model. How can that Model
    reconcile over 13 type flavors of bad prion proteins just
    for cows. And the growing evidence that a protein scissors
    is the cause of prion accumulation. That the scissors
    creates the bad prions. And the growing evidence that
    Alzheimers is very much like Prion disease and no-one
    expects the Prusiner Model to work for Alzheimers.

    > > Analogy: suppose Sherlock Holmes or other famous
    > > detectives operated in the same manner that Mr. Prusiner
    > > operated to form his Model. Then Sherlock would be
    > > arresting people left and right without ever knowing
    > > whether anyone had been killed. We would have Sherlock
    > > Holmes stories where he goes out and looks for and hunts
    > > criminals yet no dead bodies. That is a similar analogy
    > > to Mr. Prusiner running out and running off concocting
    > > Models without ever knowing what Normal Prions function
    > > or role was.
    >
    > Irrelevant
    >
    > >A good scientist knows that unless he fully knows and
    > >understands what normal and good Prions do and function,
    > >unless he knows that, his Models on prion disease are
    > >nothing but wild-speculation.
    >
    > A good scientist basis his opinions on observations with
    > as little speculation as possible. Here's a bit from my
    > thesis where I try to put a balanced view on it.

    You do not put a balanced view on this issue of Prion
    disease. It is your unbalance view of this entire issue that
    prevents you from making any progress.

    Example, you cannot even answer my question put to you. I
    asked you what you think is the likelihood of success of a
    science theory when the proponents of the theory have no
    clue or no firm basis of the purpose and design of what the
    prion protein molecule functions as? I asked you Wyrin, what
    is the chances of a theory about Prion disease of the
    Prusiner Model being correct when Mr. Prusiner never had a
    clear understanding of the role and function of the prion
    protein as of this very date?

    How likely is it for a Prion Disease Model to be correct
    when the authors of that model have little to no idea of
    what a prion protein does or functions or its purpose or its
    behaviour in the body.

    Wyrin, I said the probability is that of 99% wrong for the
    model and perhaps a low 1% that Mr. Prusiner guessed it
    correctly. For it would have to be a guess when a scientist
    constructs a Model around a disease but has little to no
    understanding of the protein function of prions.

    And funny how the Nobel Committee when it evaluated the
    giving of the award to Mr. Prusiner that not a single one of
    those Swedish scientist had a bell and light go off in their
    brains and said--- hey, how likely is it that the Prusiner
    Model is correct when Mr. Prusiner does not even know what
    the function of a prion protein molecule is, nor any other
    scientist of that time period.

    So, Wyrin, please answer my question: what is the likelihood
    that the Prusiner Model is correct when it was constructed
    without knowing or understanding of what a prion protein
    functions as within the body. I said the probability was 99%
    wrong and only a 1% chance that Mr. Prusiner had guessed it
    correctly.

    > The first theories put forward to explain the observed
    > infectivity and strain variation of prion diseases, such
    > as scrapie in sheep and kuru in humans, suggested the
    > existence of a parasite or 'slow virus' (Eklund and
    > Hadlow, 1969; Hadlow, 1995). However, the infectivity was
    > resistant to decontamination by UV irradiation at 254 nm,
    > which argued against the

    Tell me, did anyone ever think that Alzheimers was a virus
    led disease? Or that Parkinsons was a virus led disease?
    That is old history.

    But what Alzheimers and Parkinsons and Prion have in common
    is the cutting edge of science as far as prion disease is
    concerned. Don't keep bringing up Prusiner baloney because
    nothing of what Mr. Prusiner espoused in the 20th century is
    turning out correctly. Almost all of
    Mr. Prusiner's espousals of prion disease are turning out
    to be wrong.

    It is scissors that is the cause of Prion disease as it is
    scissors that is the cause of Alzheimers and Parkinsons. It
    maybe metal-ions such as magnetic manganese that corrupts
    the prion-scissors and that when meat is eaten from infected
    prion those prion-scissors or magnetic-manganese get lodged
    into the new victims brains.

    > presence of a nucleic acid (Alper et al., 1967). Other
    > properties of the agent included resistance to heat,
    > including autoclaving at 120 °C, formalin treatment and
    > ionising radiation (Gordon, 1946; Prusiner, 1998a). An
    > 'unconventional virus' was suggested but no actual details
    > offered. No bacteria or virus has been found consistently
    > associated with prion disease (Prusiner, 1998a). The term
    > prion (from proteinaceous-infectious particle, lacking a
    > nucleic acid) was put forward following evidence that
    > procedures that modified or destroyed proteins could
    > reduce scrapie infectivity (Griffith, 1967; Prusiner,
    > 1982). Prusiner proposed, therefore, that the endogenous
    > prion protein was the infectious agent, and a mutated PrP
    > responsible for the inherited disease. This model has
    > since been widely accepted, since it has been shown that
    > PrP is the only factor that has been found to be
    > associated with disease so far, and endogenous PrP is
    > required for disease transmission (Bolton et al., 1982;
    > Hope et al., 1986; Prusiner et al., 1993b).
    >
    > Nevertheless, some researchers still maintain that viral
    > mechanisms are important in prion disease and to account
    > for the observed strain variation, citing other viruses
    > that are known to cause dementia and spongiform change
    > in the brain, and that display resistance to classical
    > decontamination techniques (Manuelidis, 1994a
    > Manuelidis, 1995 #787). Furthermore, neither refolded
    > PrPSc nor purified recombinant protein have yet been
    > shown to be infective (Prusiner et al., 1993a;
    > Manuelidis, 1994b). However, studies with yeast prions,
    > and in vitro demonstration that resistance to prion
    > infectivity correlates with the degree of homology
    > between the host PrPC and exogenous PrPSc, are strong
    > arguments in favour of the prion hypothesis (Bossers et
    > al., 1997; Liebman, 2002).

    The Prusiner Model is equivalent to saying that the world
    has a supercatalyst. Platinum is a normal catalyst and used
    in the gasoline distilling industry. Where a normal catalyst
    like platinum speeds up the rate of reaction and is
    unchanged at the end and so platinum is party to at least 3
    molecules/atoms. If the Prusiner Model were correct then the
    world of chemistry has a Supercatalyst wherein it is party
    to only 2 molecules, not 3. And if platinum were a
    supercatalyst then it would be able to alter gold atoms into
    more platinum atoms.

    I don't expect you to understand any of the above paragraph
    Wyrin because your mind is so polluted in bias favor of the
    Prusiner Model that it is too much for you to handle.

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies
     
  17. acj

    acj Guest

    Steve Turner <[email protected]> writes:

    >On 16 Mar 2004 10:39:39 -0800, [email protected]
    >(Archimedes Plutonium) wrote:

    >>We all know that platinum cannot change gold into more
    >>platinum, but please Bob work through the numbers and
    >>please give me a number for enthalpy and entropy that
    >>proves number wise that such a reaction is impossible.

    >This is a nuclear transformation, not a chemical one.
    >Chemical thermodynamics do not apply.

    A better example would be if platinum catalyzed the
    conversion of, let's say, platinum chloride into platinum
    and chlorine. Start out with a beaker of pure platinum
    chloride, let's say one molecule decomposes spontaneouely,
    producing a Pt atom. This atom catalyzes a second molecule,
    resulting in 2 Pt atoms. Then you'd get 4, 8, 16 and I'd
    guess the result is it would appear to suddenly decompose.
     
  18. [email protected] wrote in message news:<[email protected]>...

    >
    > A better example would be if platinum catalyzed the
    > conversion of, let's say, platinum chloride into platinum
    > and chlorine. Start out with a beaker of pure platinum
    > chloride, let's say one molecule decomposes spontaneouely,
    > producing a Pt atom. This atom catalyzes a second
    > molecule, resulting in 2 Pt atoms. Then you'd get 4, 8, 16
    > and I'd guess the result is it would appear to suddenly
    > decompose.

    I probably did not use the best example with platinum
    catalyzing gold into more platinum. I am after the numbers
    and chemists would never compute these numbers because they
    automatically know that it is impossible for such reactions
    to go forth. But I want the numbers so as to "emphasize and
    show how impossible".

    I could restate the problem by asking for platinum and
    gold mix and what energy it takes for a platinum atom to
    steal away a electron from a gold atom to make another
    platinum atom.

    Or I could ask for the energies involved in a CO and CO2 mix
    where the CO converts CO2 into more CO.

    Or I could ask for the energies involved in ethylene-glycol
    to convert glycerol into more ethylene-glycol.

    I am keeping focused on the main issue-- Supercatalysts --
    that they do not exist because it takes too much energy for
    a molecule or atom that when it collides, it remains the
    same and yet still has energy coming from out of nowhere to
    convert other molecules into identical copies.

    Take any two molecules that are almost identical and compute
    the amount of energy required for one of those molecules to
    convert the other into an identical copy. I see it as
    impossible because the one molecule would be changed also
    and would not be the original itself, as well as the second
    being changed.

    Chemists never figure these energies because they never have
    a need to do so since they instinctively know that the
    reaction will never take place and that the energies are
    prohibitively large.

    But this is the only way to convince people who are enamored
    with the Prusiner Model that they are on false science
    grounds. If Prusiner were correct then the world has in
    existance at least one Supercatalyst-- bad-prions. But I am
    sure that Prusiner is utterly wrong and that the world has
    no supercatalyst. The closest the world has to chemical that
    in part acts like a supercatalyst is RNA and DNA in mitosis,
    but even there they are not catalysts.

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies
     
  19. Bob

    Bob Guest

    On 15 Mar 2004 23:53:32 -0800, [email protected] (Archimedes
    Plutonium) wrote:

    >Bob <[email protected]> wrote in message
    >news:<[email protected]>...
    >> On 14 Mar 2004 23:30:17 -0800, [email protected]
    >> (Archimedes Plutonium) wrote:
    >
    >> >
    >> >It is impossible for a prion-bad-protein to deform a prion-normal-
    >> >protein into an identical copy.
    >>
    >> You still have not answered the question. Why do you
    >> think that? Proteins fold and refold and adjust their
    >> folding all the time. This is basic protein chemistry.
    >> The total net energy of protein folding is very slight.
    >> Offhand I have no idea what the energetics of the
    >> proposed reaction is, but no one with the slightest
    >> understanding of proteins would think there is any
    >> problem with it.
    >
    >Would you not agree Bob that when two molecules collide and
    >interact, that changes in one or both of the molecules is
    >induced. That is normal collision and interaction. But
    >would you not agree Bob that when a collision between
    >protein molecules occurs and they interact and they go off
    >as identical to one another, would you not agree that such
    >was so implausible as to be unbelievable.

    No, would not agree. But it has no relevance anyway. That is
    not what happens. Prion A joins prion B, and takes the B
    conformation (loosely).

    >
    >It is what I said back in 1997, that unless you say the bad-
    >prion molecule is a catalyst where a catalyst is unchanged
    >at the end of the interaction. But that still makes the prion-
    >catalyst unique amoung all other catalysts because the
    >prion catalyst is the only 2 party catalyst and all other
    >catalysts like platinum in the gasoline industry is a 3
    >party catalyst.
    >

    I hope you are not getting hung up on the word catalyst.
    Prion conversion is probably not truly catalytic, since the
    "catalyst" ends up bound to the protein it changed.

    The point is that prion conversions have been amply
    demonstrated, and are within the normal behavior of
    proteins.

    Nothing you have said suggests that we are deceiving
    ourselves. I still await an argument why the conversion is
    impossible -- and there is a tremendous burden there, since
    it is well understood to occur and to be reasonable.

    If you want to argue that mammalian prions may have
    additional complexities (eg beyond yeast prions), fine. It
    is true that no one has yet demonstrated conversion to
    infective material in a cell-free system for a mammalian
    prion. But the prion basics are amply demonstrated, and
    there is no reason that the additional complexities cannot
    be accommodated within the current models. Time will tell.

    >Bob, I agree proteins fold and refold and adjust their
    >folding all the time, but your opinion of Prions as per the
    >Prusiner Model is a superspecial sort of folding that no
    >thermodynamical enthalpies or entropies can support.

    nope, not at all.

    >
    >Toyota makes a car called Prius, sort of hybrid electric
    >that gives more then 50 miles per gallon. Suppose cars were
    >like protein collision and interaction. Suppose there was a
    >Prion car out there and it collided and interacted with
    >many other cars. Whenever a Prius collided or interacted
    >with a GM or Ford or BMW or VW both are folded and
    >misshapened after the event. But when a Prion collides and
    >interacts with a Prius, both are undamaged and both drive
    >off from the accident as brand new Prion cars-- totally
    >unbelievable, forgive the expression, someone would say
    >Twilight Zone science or X-files science.

    cute, but irrelevant.

    Try driving a Prion!

    Your analogies really are not helping. In fact, they seem to
    be causing you to be misled.

    bob
     
  20. Bob <[email protected]> wrote in message news:<[email protected]>...
    > On 15 Mar 2004 23:53:32 -0800, [email protected]
    > (Archimedes Plutonium) wrote:
    (some snipping)
    > >
    > >Would you not agree Bob that when two molecules collide
    > >and interact, that changes in one or both of the
    > >molecules is induced. That is normal collision and
    > >interaction. But would you not agree Bob that when a
    > >collision between protein molecules occurs and they
    > >interact and they go off as identical to one another,
    > >would you not agree that such was so implausible as to be
    > >unbelievable.
    >
    >
    > No, would not agree. But it has no relevance anyway. That
    > is not what happens. Prion A joins prion B, and takes the
    > B conformation (loosely).
    >

    Are you saying that prion A and prion B after the collision
    and interaction are not identical when they disjoin and move
    off? And that only a *part* of prion A is identical to a
    *part* of prion B? So the identicalness is not the entire
    prion molecule but only a small surface area of each
    molecule? If so, that would help explain better the
    thermodynamical energies and also explain better various
    prion variety types in that only a small portion of the
    prion is identical or made identical.

    I had always thought of the Prusiner Model as identicalness
    for the entire molecule. Partial identicalness could have a
    ring of truth. I guess partial identicalness could be the
    conversion of helices to that of sheets, so that a bad prion
    converts a portion of a helix into a sheet geometry.

    But I need to know something. Bob, can you tell me of the
    most similar protein molecule that behaves in this manner
    and is not prions. Tell me if there are any bio-molecules
    that act and behave in the manner of bad prions. Are there
    any? Or are bad prions a unique case.

    >
    >
    > >
    > >It is what I said back in 1997, that unless you say the
    > >bad-prion molecule is a catalyst where a catalyst is
    > >unchanged at the end of the interaction. But that still
    > >makes the prion-catalyst unique amoung all other
    > >catalysts because the prion catalyst is the only 2 party
    > >catalyst and all other catalysts like platinum in the
    > >gasoline industry is a 3 party catalyst.
    > >
    >
    >
    > I hope you are not getting hung up on the word catalyst.
    > Prion conversion is probably not truly catalytic, since
    > the "catalyst" ends up bound to the protein it changed.
    >
    > The point is that prion conversions have been amply
    > demonstrated, and are within the normal behavior of
    > proteins.
    >
    > Nothing you have said suggests that we are deceiving
    > ourselves. I still await an argument why the conversion is
    > impossible -- and there is a tremendous burden there,
    > since it is well understood to occur and to be reasonable.
    >

    I could go along with a "partial conversion"

    >
    >
    > If you want to argue that mammalian prions may have
    > additional complexities (eg beyond yeast prions), fine. It
    > is true that no one has yet demonstrated conversion to
    > infective material in a cell-free system for a mammalian
    > prion. But the prion basics are amply demonstrated, and
    > there is no reason that the additional complexities cannot
    > be accommodated within the current models. Time will tell.
    >

    The best explanation to date why infective material in a cell-
    free system is a no-go is that the disease is caused by the
    protein scissors and you need cells to create the scissors,
    and thus the disease is not caused by prion converting other
    prion particles, but that the scissors is the culprit.

    Bob, I have asked Wyrin whether the alpha-synuclein in
    Parkinsons and whether the two proteins that accumulate
    in Alzheimers come in several varieties and types. Or do
    they come in one and only one brand or type? Would you
    happen to know?

    Also, I am trying to find out the most current state of
    knowledge as to the number of varieties or types of CJD and
    of Mad-Cow-Disease, and also of sheep scrapie. I vaguely
    remember 6 varieties for CJD and 13 for Mad Cow Disease.
    Bob, are you current on those numbers?

    Archimedes Plutonium whole entire Universe is just one big
    atom where dots of the electron-dot-cloud are galaxies
     
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