Prion disease is really a fungus transposon disease 
Author Message
 Prion disease is really a fungus transposon disease

It is becoming much clearer to me. That is, the likely theory of prion
disease.

  Notice these three clues: (1) prion disease is mostly a brain disease
(2) some parasitic fungus are brain diseases, one in particular is the
ant fungus Cordyceps Ascomycetes Clavicipitacea  that drives the ant to
climb the nearest tree, die, and then fungus spores emitt out of its
brain. (3) yeast, which are fungus, have the bad and good prions, and
yeast is the only known species other than the 'victim species' that
has the good and bad prions.

  All known prion diseases are brain diseases. And the behaviour of the
victim species such as kuru, CJD, mad cow, and scrapie are somewhat
similar in a desire to so to speak "return the spores to the ground to
further disseminate the spores in a new cycle"

  Now the mechanism of the disease is clearer to me but has many gaps.

Mechanism of prion disease:

1) A normal individual seldom needs the prion protein for coating of
brain cells.  Call this the normal prion.

2) A fungus infects the normal individual and it leaves part of its
genetic code, a snippet or fragment of its DNA/RNA which manages to
find the manufacturing site of normal prion proteins. Call this fungus
fragment the fungus transposon.

3) The fungus transposon attaches to the prion protein manufacture site
of the normal individual. Then when a new prion protein is manufactured
at this infected site, the fungus transposon is split in half
vertically with two compliments. At this moment the disease has started
and the normal individual is no longer normal but diseased.

4) The manufacture site has 1/2 of the fungus transposon and the
manufactured prion protein has the other 1/2 of the fungus transposon.
The manufacturing site of prion proteins with the attached fungus
compliment churns out the reverse of the attached fungus transposon and
spews out a multitude of these prion proteins. Call them good prion
proteins (but really they are diseased prion proteins).

5) The original prion protein with the other attached fungus transposon
compliment is roaming around. Call this prion protein the bad prion
protein. It is a sole wanderer.

6) Back at the infected manufacturing site. It is spewing out an
enormous number of so called good prion proteins. Remember that it is
the 'reverse compliment' of the roaming bad solitary prion.

7) Once the good prions have increased in population, the frequency of
a encounter with the bad prion becomes high probability. When the bad
prion encounters the reverse compliment good prion the two combine at
the fungus nucleic acid transcription.

8) The good prion has more energy and is more unstable than the bad
prion. The bad prion has stability and lowest energy. The good prion in
the binding site of the nucleic acids decays. In the decay process of
the good prion, it becomes an identical copy of the bad prion. Thus
there now are 2 bad prions in a ocean of many good prions all waiting
to be converted.

9) When the population of the bad prion, which is stable increases to a
point, the individual dies.

  What I need now to confirm or support this theory, is for a
sequencing of prion proteins, both the good and bad prion proteins to
see whether they have an attached nucleic acid snippet. And to see
whether the attached nucleic acid is a fungus DNA/RNA fragment and to
see whether they are compliments of each other, or nearly compliments.

  The different shapes of the good prion protein compared to the bad
prion protein is simply the fact that one is a reverse compliment of
the other.

  So, I please need the biochemist researchers to look for nucleic acid
_on_ or _in_ good and bad prion proteins.



Sat, 18 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease
And I just spyed an article in SCIENCE NEWS about how enzymes erase
DNA's molecular coating in 20FEB99 issue. It is about methylation and
demethylating enzyme. Perhaps there is a connection here to prion
disease. I will have to think about it.


Sat, 18 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease


Fri, 19 Jun 1992 00:00:00 GMT
 Prion disease is really a fungus transposon disease
 The deciding experiment of Prusiner's prion disease. I really suspect
that the reason the biology community overlooked a deciding experiment
for the Prusiner theory is because, well, biologists are more
muddle-headed than physicists or chemists.

 Place a new theory in the physics community, and those boys are quick
and sharp to figure out the deciding experiment. Well, I take that
back, not so quick, but sharp. A fine example is EPR, when finally John
Bell led the path to the deciding experiment and A. Aspect did the
actual experiment. It was a clinching final deciding experiment.

  In the biology community, when you propose a new theory such as what
S. Prusiner did a long time ago, well, biologists are really not that
sharp enough to seek a "Deciding Experiment". Biologists compared to
physicists are not that well equipped in logic and in science
intuition. But propose a new theory in physics, well, those boys will
run you over with "implications" of your new theory.

  Propose a new theory and your new theory makes predictions, or
implications.

  It is strange how the social history of the Prusiner theory went.
Instead of making implications and formulating the deciding experiment,
the Prusiner believers, like sheep, demanded and dictated that unless
other researchers find a virus, that the Prusiner theory was correct.
And since no researcher could find a virus to link to prion disease, it
was assumed that Prusiner had a true theory. And we know the history
from there on, that in rapid order, rush rush pell mell, Mr. Prusiner
was awarded a Nobel prize for his half-baked theory where no 'energy
account' was given. And worse, never a Deciding experiment was
formulated. Prusiner could never have gotten away with his theory if it
were physics.

So, let me give the Deciding experiment for the Prusiner theory. And I
must add, that I am the first to give Prusiner theory a Deciding
Experiment.

Deciding Experiment of the Prusiner prion theory:

 The Prusiner prion theory implies that a bad prion protein without any
nucleic acid present, collides/contacts/interacts with a good prion
protein and turns that good prion protein into an identical copy of the
bad prion protein. So, to decide the truth of Prusiner's theory, one
only need make certain that no nucleic acid is present whether _on_ or
_in_ or _near_ the prion proteins when they are interacting.

  Some experiments to date have come close to checking the Deciding
Experiment such as the Glover et al printed in CELL  89:811, 30MAY97.
But they are not thorough enough to prove one way or another whether
Prusiner's theory is true of false. They need to conclusively show that
no nucleic acid is present when a bad prion turns a good prion into
another bad prion.

  Oh, well, it was not the first Nobel mistake, but it surely was one
of the most rush, rush and sloppy science mistakes. Every scientist
should have Deciding experiments on the front of his mind when judging
the merits of a new theory.



Sat, 18 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease


Fri, 19 Jun 1992 00:00:00 GMT
 Prion disease is really a fungus transposon disease

Quote:

> It is becoming much clearer to me. That is, the likely theory of prion
> disease.

>   Notice these three clues: (1) prion disease is mostly a brain disease
> (2) some parasitic fungus are brain diseases,

And some parasitic fungi like to spend enormous amounts of Internet
bandwidth spewing fact-ignoring "theories".  Does that mean that *you*
are a prion, Archie?  Or perhaps it just means that you are a mad cow.

        Eric Lucas



Sat, 18 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease

=
= It is probably best at this point to not worry how the proposed DNA
= gets to the protein. It isn't obvious, but it also isn't important
= (for now).
=
=
=
= About the only way to show a role for such a piece of DNA would be to
= find it, show that it works. If one has a guess as to what the DNA
is,
= there might be some short-cuts. If one can isolate any DNA from prion
= preparations, that could be a starting point. If one suspects  a
= particular small size, or size range, it is now practical to test all
= DNA of length  5 or 6 or so.
=

  My guess is that it is a fungus RNA/DNA sequence. Some parasitic
fungus. Has the fungus of the ant disease Cordyceps Ascomycetes
Clavicipitacea been sequenced?

=
= You question my use of the term ligand or binding. But that is what
= you propose. If the DNA is not working by its coding function, the
= only way it could work is by binding to the prion, thus affecting its
= shape.
=

  Well, Bob, I not versed in the terms that you use. I can only use
what I know in simple language. If it is ligand and binding, then that
is what it is.

= Let us suppose that a particular prion conversion uses a small DNA
= molecule binding to the prion to "catalyze" the conversion. Nothing
= particularly wrong with this -- tho it can only be an idea until
= someone finds the DNA.
=

  I suspect the Glover experiment found RNA/DNA because it could not
get 100% free of RNA/DNA.

  And so the Glover experiment is a falsification of the Prusiner prion
theory.

= But a few important points...
=
= It is 'widely suspected' that some factor in addition to prion
protein
= is needed for the conversion. You have mentioned the mysterious
factor
= X. In yeast, a chaperone protein is needed in vivo.
=

  I do not even know what a chaperone is.

= The essence of your proposal is that a small piece of DNA is factor x
= (or part of it). Yes?
=

  You say that a protein can only be made by messenger RNA. If true,
then the factor x is a small piece of Messenger RNA.

= There is no particular advantage to using DNA. DNA does not have any
= properties that make it _especially_ suited for this. Proteins change
= shape all the time, binding oxygen, various chemicals in the body,
= proteins, DNA, whatever.
=
= It is quite plausible that different factors will be used in
different
= cases and under different conditions. In fact the yeast results
= (glover) in vitro do not seem to require any factor, whereas in vivo
a
= chaperone is required. This is all reasonable, since protein folding
= kinetics may be very sensitive to conditions. As I mentioned earlier,
= the glover expt should be best thought of as 'proof of principle'.
Its
= direct relevance to anything is unclear.
=

  The Glover experiment supported my theory that some RNA/DNA content
was there to cause the changes. Thus Glover experiment falsifies the
Prusiner prion theory.

= Mammalian prion diseases are very slow. Whatever it is that happens
is
= rare and/or slow. This is a difficulty in studying them!
=
=
= What would Prusiner or any 'reasonable biochemist' think of your
= proposal that DNA is factor X? Certainly consistent with the current
= standard model. No one would be bothered by it. They might be
somewhat
= surprised, because I don't think we are expecting a small DNA
molecule
= to be there, to be playing this role. But if it were found to be
doing
= so, fine, no problem. Would even be 'interesting'.
=

  I need RNA/DNA to preserve the science of biology as the lowest
fundamental unit of biology to be the RNA/DNA for
reproduction/copy/replication. Not only for reproduction but also for
energy balance so that no laws of physics of thermodynamics are
violated.

=
= If a piece of DNA is needed for prion conversion in some cases, that
= would certainly be interesting. It would not change the basic story,
= but merely identify 'factor x' -- the detailed conditions needed for
= conversion.

= sense of the word (as animals do, or as DNA does). You are merely
= using DNA as a factor x, to catalyze the conversion. A protein might
= work, or maybe no catalyst is needed.
=

=
= see above. It is likely that their protein was essentially DNA free,
= but that is hard to prove. Further, it might be true for one prion
and
= not another.

=
= don't know.
=
= The new paper bennett posted needs follow up.
=
=

=
= doesn't seem likely. (And you must mean RNA here.) If something like
= this happened, presumably it involves the messenger RNA for the prion
= protein. By identifying a specific candidate nucleic acid, would be
= easier to test.

=
= maybe. The big problem is that DNA is not directly involved in making
= proteins; it is in a different part of the cell. RNA does not mend.
=
=
=

=
= well, that is not coding in the normal sense of the genetic role of
= DNA. It is simply one molecule affecting the shape of another, by
= binding. Proteins do that all the time.
=
=

=
=
= as discussed above, for binding, a small amount is enough.
=

=
= but that is a binding role; see above.There is  no other way DNA
could
= affect the prion shape.
=

=
= well, that would be a stretch. A transposon is a piece of DNA  that
= moves from one location of the chromosome to another.
=

  My definition of a transposon is more broad. I define them as any
snippet or fragment of RNA or DNA that moves and performs a specific
function that is observable. Prion diseases are easily observable. And
this fungus RNA attachment to the protein molecule causes the prion
disease characteristics. It is movable. Let us not be bound to narrow
definitions.

=
= I don't know of any case where a transposon is commonly associated
= with a particular disease. (My ignorance of that is not necessarily
= significant.)
=
= There are examples known where a particular mutation was shown to be
= due to a transposon. the first known case was reported in late 80s, i
= think. A child had a genetic disease, but analysis of the parents
= showed that neither carried the mutation. The mutation was due to a
= transposon. Thus the transposon must have 'jumped' during production
= of one of the germ cells for the child. (Can find reference, i
think.)
= A few examples of this have been shown. But of course, the disease is
= most commonly due to some mutation other than that caused by a
= transposon. BTW, a transpson jumping into a gene _usually_
inactivates
= the gene.

----




=
= ==
= ==
= ==Bennett posted an item about a new article of concern (in vitro
prion
= ==that is not infectious). All I know is what he posted. Sounds
= ==interesting, and I am sure it will be followed up. For the moment I
= ==think we just need to be aware of it, and watch to see what
happens. I
= ==can think of simple reasons why it is not a 'problem.' But maybe it
is
= ==a problem; time will tell.
= ==
= =
= =
= =The simplest "not a problem" scenario is that the PrPres produced
wasn't in
= =the right configuration - since it's not possible to work out the
structure
= =of PrPres we might never know ;-)
=
= agreed.
=
= This  is a can of worms. Not all protease-resistant forms are
= necessarily equal. In fact, the notion of prion strains seems to
= depend on multiple biologically significant forms.
=
= The yeast in vitro prion conversion also need this reservation, I
= think. They are in a good sense 'proof of principal', but relevance
is
= harder to determine.
=
=
=
= =
= =It does sound interesting, but I know only what I posted.  I've been
out of
= =the literature for a while with regards to prions.  What made me sit
up was
= =the Narang papers about the 1.2kb ssDNA.  What is _that_ doing
there??!  Is
= =it important?  Is it somehow resistant to UV?  What does it code for
(it's
= =not PrP according to GenBank).
= =
=
= I'm going to try to find both this weekend.
=
= In the long run, the question will be whether the intriguing results
= suggested in these papers are reproducible.

  I guess two experiments have now falsified Prusiner prion theory.
Both the Glover experiment and the 1.2kb ssDNA have rooted out nucleic
acids in prion proteins. Thus, prions contain attached nucleic acids.

  Is the chemistry difficult to be able to recognize an attached
snippet of nucleic acid on the surface of a protein? How does one find
attached nucleic acid upon a protein molecule?



Sun, 19 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease


Fri, 19 Jun 1992 00:00:00 GMT
 Prion disease is really a fungus transposon disease

Quote:
>  The deciding experiment of Prusiner's prion disease. I really suspect
> that the reason the biology community overlooked a deciding experiment

Overlooked??...it was a common topic of conversation as I wandered round
the prion section of a meeting last June. What we need and what we can do
do not necessarily coincide....you are intelligent to recognise that
shortfalls exist, why do you then go off on harebrained rampages as to the
whys?

Quote:
>   It is strange how the social history of the Prusiner theory went.
> Instead of making implications and formulating the deciding experiment,
> the Prusiner believers, like sheep, demanded and dictated that unless
> other researchers find a virus, that the Prusiner theory was correct.
> And since no researcher could find a virus to link to prion disease, it
> was assumed that Prusiner had a true theory. And we know the history

This is plain drivel, Archimedes..It doesn't describe the setup at
all...the prion hypothesis was around for a very very long time before it
started getting accepted as a possibility. And the idea of protein only
was suggested by earlier researchers (a fact Prusiner always refers back
to). The agent didn;t behave like a virus, and didn't behave like a
nucleic acid based object (as sdomeone else has suggested, virology may
not be the best place for it to be, bu tthats its historical location)
so people started considering the theory

Quote:
> So, let me give the Deciding experiment for the Prusiner theory. And I
> must add, that I am the first to give Prusiner theory a Deciding
> Experiment.

Crap, self inflating, self aggrandising crap.....what is required to nail
the prion theory one way or another has been mooted around the research
community for ages....you put down plenty of 'only' and 'simply' notes
in your descriptions of what you think is needed, showeing you have a
blatant lack of knowledge in the technicalities involved in the procedures
you demand.

Tim
When playing rugby, its not the winning that counts, but the taking apart
ICQ: 5178568



Sun, 19 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease
Quote:


>>  The deciding experiment of Prusiner's prion disease. I really suspect
>> that the reason the biology community overlooked a deciding experiment

<snip> why do you then go off on harebrained rampages as to the whys?

1)  Tim smells something funny.

Quote:
>>   It is strange how the social history of the Prusiner theory went.
>> Instead of making implications and formulating the deciding experiment,
>> the Prusiner believers, like sheep, demanded and dictated that unless
>> other researchers find a virus, that the Prusiner theory was correct.
>> And since no researcher could find a virus to link to prion disease, it
>> was assumed that Prusiner had a true theory. And we know the history

>This is plain drivel, Archimedes.  <snip>

2)  He realizes it's a rat.

Quote:
>> So, let me give the Deciding experiment for the Prusiner theory. And I
>> must add, that I am the first to give Prusiner theory a Deciding
>> Experiment.

>Crap, self inflating, self aggrandising crap.....<snip>

3)  He finds the rat.

Just so you know TIm, Archie has absolutely zero interest in understanding
prion biochemistry, he's just trying to be outrageous.  I've enjoyed reading
your comments nonetheless.

mike



Sun, 19 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease

Quote:

> > So, let me give the Deciding experiment for the Prusiner theory. And I
> > must add, that I am the first to give Prusiner theory a Deciding
> > Experiment.

> Crap, self inflating, self aggrandising crap.....what is required to nail
> the prion theory one way or another has been mooted around the research
> community for ages....you put down plenty of 'only' and 'simply' notes
> in your descriptions of what you think is needed, showeing you have a
> blatant lack of knowledge in the technicalities involved in the procedures
> you demand.

  And in your paragraph of nearly 100% ad hominem, there is little
constructive information.

  You still do not know, nor understand what it means to have a
Deciding Experiment for a theory of science. You probably never had
training in physics, but that is a huge shortfall of nearly every
biologist.

  Yes, I am the first to give the Deciding Experiment for the Prusiner
Prion theory and let me restate it. If I state it long enough, and
differently each time, then pikes such as you maybe able to finally
understand prion theory.

 Prusiner Prion theory implies: that 2 different protein molecules in
the total absence of nucleic acid can combine to give the end result of
2 identical protein molecules.

  For the benefit of biologists who are so much weaker in logic than
physicists, when you make a theory, your theory has predictions.
Predictions are implications. A theory implies something. The Prusiner
prion theory implies something. And what it implies is that there is no
nucleic acid present in the reaction of turning 2 different protein
molecules into 2 identical protein molecules.

  To date, all of the prion experiments have shown or indicated that a
nucleic acid was present in the reaction. That is, the Glover
experiments, and this 1.2kb ssDNA experiment.

  Unless you can get an experiment that is 100% absent free of all
nucleic acid where 2 different prion proteins result in 2 identical
prion proteins, then the Prusiner prion theory is a fake theory.

  Now I can understand that after 2 decades of foisting this fake
Prusiner theory about, and even awarding Mr. Prusiner a Nobel prize
that this comes as a shock. But it is no shock to a physics genius. The
Nobel prizes, even in physics are littered with mistakes, some worse
than the Prusiner prion theory fakery in biology.



Sun, 19 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease


Fri, 19 Jun 1992 00:00:00 GMT
 Prion disease is really a fungus transposon disease
In article

Quote:


> >   For the Prusiner theory to be correct implies that no nucleic acid is
> > present when a bad prion turns a good prion into another bad prion.

> Yes....but so does every ion channel interaction...the channels change
> shape and they have long since departed interaction with nucleic acids.

 Does this ion channel copy for an identical ion channel upon reaction
completion?
  You, like Bob and Bennett still do not understand the Prusiner Prion
theory and what constitutes the deciding experiment for the Prusiner
prion theory.

Deciding Experiment: In the reaction: bad-prion + good-prion -> 2 bad
prions, in that reaction there is no nucleic acid, none whatsoever
involved in the reaction and that before, during, and after the
reaction it is *protein only*. Thus, to prove the Prusiner Prion
Theory, if it is correct, would require a reaction that had no nucleic
acid present. All of the experiments on prions to date indicate that
some nucleic acid was present. Hence, all the experiments to date show
that the Prusiner prion theory is a fake.

  If you cannot understand that, for it is quite clear, then you do not
have a clear and logical and scientific mind, and you do not deserve to
talk with me any longer.

Quote:
> >   From what I have seen so far, no experiment, Glover or any others
> > have taken the painstaking removal of all nucleic acid and then checked
> > to see if prions replicated.

> >   I take it that scientists have not been able to sequence the prion
> > protein completely and have not found a nucleic acid sequence.

> You take it very very very wrong then. the Prion gene has been sequenced
> in a number of species from end to end, as has the protein....we got the
> ovine one cloned into a vector here in the lab.

  Have they really, or are you just spouting. Have they checked to see
if any nucleic acid was attached to the prions?

  By the way, what is a chemical test to see if a nucleic acid is
attached to a protein molecule? And have these researchers been
thorough enough in their examinations for attached nucleic acids?

Quote:
> >   I take it that no scientist has checked the DNA site where prions
> > were produced as to whether the DNA prion gene had become a jumping
> > gene, a transposon and had moved from the DNA. And that is damaged
> > section of DNA was now copying for prions of a different sequence.

> You'd get multiple hits on a Southern, since they could locate the gene
> (as sinc etc before prion gene was sequenced) to a single locus in the
> sheep and mouse this would indicate no transposon, unless it was very very
> close hopping. The data is likely scattered over papers but the answer
> will be in the early work...ie pre computer databases....

  Read my "mechanics of prion disease". There I make a broad definition
of a transposon as a genetic entity that is phenotypically observable.
Prion disease is an observable phenomenon. In my Mechanics, you will
see that I posit that the RNA fragment does not jump around. It is
attached 1/2 vertical fragment to the messenger RNA and spewing reverse
compliments called good prions (but really they are diseased proteins)
and the other 1/2 vertical fragment is attached to the solitary bad
prion protein that is now roaming the body. When this solitary roamer
comes in contact, or collision with a good prion (really an abnormal
protein) the two compliments bind, or as Bob calls ligand) and the bad
prion turns the reverse compliment into another bad prion.

  This picture that I have just painted you is very clear, and even you
should be able to understand this picture, although you have been
brainwashed with the Prusiner bologna for the past 2 decades.



Sun, 19 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease

Quote:

> the DNA fragment
> >is the trigger that changes the normal or good prion into another bad
> >prion copy.

> Ahh - now this may have been inspired....  Narang has said that he's found a
> 1.2kb ssDNA associated with the PrP, and he assumes (I've seen no proof)
> that it encodes a protein which acts as a chaperone for the prion reaction.
> What if the DNA molecule _itself_ acts as the chaperone?  After all it has
> hydrogen bonds like proteins, and could conceivably do such a thing
> (although it's unlikely...)

  Bennett, what is this 1.2kb ssDNA. Could you describe it in further
details. I am a physic genius with no more than a few High School
biology courses. In your explanation omit these biology terms and speak
in just ordinary language. And please explain this "chaperone" stuff
while you are at it. Thanks in advance


Sun, 19 Aug 2001 03:00:00 GMT
 Prion disease is really a fungus transposon disease


Fri, 19 Jun 1992 00:00:00 GMT
 
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