🚀 go-pugleaf

On Sun, 14 Jul 2002 00:50:46 GMT, "Stef Duncan"
<robandstef2000@earthlink.net> wrote:

>
>"Mark Addinall" <addinall@myownemail.com> wrote in message
>news:3d2f6e1d.343537991@news.optusnet.com.au...
>> On Fri, 12 Jul 2002 22:45:51 GMT, "Stef Duncan"
>> <robandstef2000@earthlink.net> wrote:
>>
>> >
>> >"Mark Addinall"
>> >
>> >> I fail to see the purpose of posting biological untruths
>> >> on a support group.  Seems an odd hobby.
>> >>
>> >> Mark Addinall.
>> >
>> >I would see it to be an odd hobby as well.
>>
>> Then stop doing it.
>
>What "lie or half-truth" have I ever posted?  How would doing so cure any of
>us?  Mine, as well as everybodys motivation isnt attention, its to be cured.

I don't know what your agenda is.  But the seemingly "no-one in the
world" scenario you propose for the cuture of mycoplamas is clearly
untrue.  Some of the fastidious mycoplasmas take more care to
culture than other strains.  Having care does not
make a task impossible, or technically difficult.  The preference
given
for DNA sequencing is based on time and money.  It is far easier
to test for the presence in this way.  Being destructive, the
test will not allow futher population dynamics observations
as is with cultured pathogens.  Cultured pathogens also come in
damn handy when testing new drugs, delivery systems,
absorbtion and exretrion.

The transport mechanisms are not well defined at a molecular level,
and to dat, no toxin has been isolated.  A good reason to have
controlled, live culture.


Before I reply to this any futher.  Taking your word at face value,
then would not this discussion be better served in one of the sci.*
newsgroups?  That way some wandering practitioners can call us
both mad, ot hopefully, be inclined to investigate with some more
depth.  I would be more than happy to continue our conversation in a
more appropriate newsgroup.  I can't devote a lot of time into 
doing so, as I have my own work to get on with.  I am sure
that the readers of a support group are not terribly interested
in Beowulf clustering, Petaflops, Markov chains, parrallel RDBMS
techniques, extentions to BioPerl:: objects, BLAST and FASTA
algorithms, load-sharing, proteomics, gene-transfer therapies,
in silico predictions of absorbtion, distribution, metabolism and
excretion properties of a drug, and a drug target.

It fills volumes and annoys people.

This seems to be a place to ask "How do I stop feeling ill?".
"How do I take a holiday?".

Support.  Not R&D.

Pick one or more groups.  I am happy to read your collected research.

>
>
>
>> >You still haven't shown that
>> >mycoplasmas can reliably be cultured.  You show labs requirements and
>> >methods, but no valid support of success.
>>
>> For $28 you can get a mycoplasma culture grown anywhere.
>> Most labs have a time getting rid of the stuff.
>
>Nope.  Go to a universities research library.  

Once or twice a week.

>there are dozens of studies
>showing that its nearly impossible to culture mycoplasmas from synovial
>fluid... yet they are there, and everybody knows it.

Painstaking is not nearly impossible.


>
>
>> You mentioned in on of your earlier rants that you hate
>> acadeamia?  Why is that?
>>
>> You also seem to be worried about a peer review?  Why is that?
>
>Publish or perish.  And you dont publish unless you have researched an
>issue.  And you cant research an issue, (once out of the university setting)
>without funding.  And you get no funding unless your "research" suits
>somebodys agenda and they are willing to pay you to prove their point.
>Thats academia in this worlds pharmaceuticaly controlled scientific
>environment.  Look how AIDs research has been taken over by a select few
>acemics who are in the pockets of the pharms.  Its no accident.

Such a limited view.  I have many friends at various Universities
that are always more than willing to vet an idea of mine.
(of course, I am genuilly brilliant ;-)
None I know of are 'in the pocket' of anyone, and would likely
to be most upset if you suggested they were.  Dunno what it
is like over your neck of the woods, but in Australia scientists
get paid crap.  And I spend a LOAD of time trying to figure out
how to do research on the cheap.

Being fortunate my 'lab' doesn't require a billion dollars to
run.

>
>> > In arthritis cases, where the
>> >patient has a known mycoplasmal infection, most times no labs can culture
>> >anything.  That's the nature of the beast.  The stuff is oddly slow
>growing
>> >and highly resistant to being forced to do something it doesn't want to
>do.
>> >It has its own time-table  No lab anywhere claims a good success record
>in
>> >culturing mycoplasmas.  From synovial fluid some cases report zero
>success
>> >of growing it... even when its shown to be there with DNA testing over
>and
>> >over again.
>
>
>> Utter crap.
>> "Beast"?  "Stuff"?  "forced to do something IT doesn't want to do"?
>> Is this another example of your scientific method?  Projecting
>> a personality onto a bug?
>
>I think the personification of a pathogen was made by you.  Not I.  

I think not.  It usually represents a string of '1's and '0's to me.
It is difficult to personify a molecular interaction at quantum level.



>"beast"?
>Maybe you arent familiar with American coloquealisms?  Youve never heard,
>its the "nature of the beast" before?  LOL, no, I wasnt calling our
>pathogen, "beasts".  "want" was simply a quick term for proclivity,
>programming, and opportunity.

As you say.

>
>
>
>> Millions of labs will happily culture you any of the mycoplasmas for
>> a small fee.  Why do you persist in telling lies in a support
>> group?
>
>Obviously melodramatic statements arent mine alone.  Millions? 

True.  Gross overstatement.

> And no, the
>vast majority of labs cant even culture a simple mycoplasma from a serum
>sample.  Even when its know to be in it.  Im suprised by your vehement
>stance on this issue.  Its not easy.  The medium is very important to the
>bug.

Isn't that the case with every pathogen?
Mycoplasmas are part of the human (and other species) bodies
natural bio-sphere.  Some grow anywhere, others are more reluctant
to be cultured in gereral media.

>
>
>
>> Which mycoplamoids are you referring to?
>> The bacteria with the smallest known genomes are found among
>> members of the class Mollicutes. This class presently comprises
>> the six eubacterial genera Acholeplasma, Anaeroplasma,
>>  Asteroleplasma, Mycoplasma, Spiroplasma and Ureaplasma (however,
>> the term mycoplasma has been frequently used to denote any
>> species included in the class Mollicutes).
>
>Mollicutes.  There are six that we are concerned with.  The fermentans
>strains, the chlamydia strains, and a few others.

Ok.

>
>>
>> The common characteristics are the complete lack of a bacterial cell
>> wall, osmotic fragility, colony shape and filterability through
>> 450-nm pore diameter membrane filters. The relatively
>> close phylogenetic relationship of these genera was measured
>> by comparative sequence analysis of the 5S and 16S ribosomal
>> RNA (rRNA). The rRNA sequence analyses also revealed that
>>  the Mollicutes are not at the root of the bacterial
>> phylogenetic tree, but rather developed by degenerate evolution
>> from gram-positive bacteria with a low mol% G+C (guanine
>> plus cytosine) content of DNA, the Lactobacillus group
>> containing Lactobacillus, Bacillus, Streptococcus and two
>> Chlostridium species. The Mollicutes lost during the process
>> of evolution a substantial part of their genetic information.
>
>Im not sure of the context in which you use the word "lost".  They didnt
>"lose" anything.  The rid themselves of it.  They evolved beyond the need
>for a cellular wall.  (they kind of have one... its difficult to describe.)
>Its an entirely unridged pathogen.  Much like how an octoppus the size of
>your fist can squeeze into the opening of a coke bottle... thats how these
>pathogens are.

That's a poor anology.  And I think lost is apt, until the
phylogenisis of Mollicutes is better known.  It seems to me
that the mutation from bacterial forms to mcyplasmas is
a retrograde one.  I do not know what caused this evolutionary
inversion, nor do I think does anyone.

To attest a causitive effect from the presence is speculation
in its' purest form.  You may as well state that E. Coli is the
culprit behind MS, as all MS patients show E. Coli.


100% correlation.  No causation.

>
>
>>This
>> is reflected by significantly smaller genome sizes as low as 600
>> kbp and extending to 2300 kbp as compared with 2500-5700
>> kbp long genomes of their ancestor bacteria. The loss of
>> coding capacity could probably be tolerated because of the
>> parasitic life style of the Mollicutes.
>
>Im not sure if you are typing this, or if you are paraphrasing it.  They
>didnt "lose" anything.  They evolved beyond the need for it.  They developed
>through selective pressure the advantage of not having one.  They dont need
>one.  They would be at a disadvantage if they had one.  So, "lost" is a word
>out of context.  They developed into a pathogen unrestricted by the need for
>it.  Its not as if they "lost" it.  But, I am pretty sure I may be
>discussing a point thats not even on topic.  Semantics... lovely game.  If
>so, my apologies.

Lost is appropraite.  Some bottleneck had to have occured at a point
in the past that a pathogen would lose its' more complex function
and revert to a simple opportunistic form.  This may have happened as
the pool vector species became threatened, or any number
of other biological events.  This we may never know.

You mention Anthrax in one of your posts.  Point in question.
Anthrax is a wonderfully complex bug with its' changing morpholgy,
and the complex series of toxic agents that allow it to work as it
does.  This one followed the more usual progression of building
complexity to better suit:

- The target organism
- Vector organisms
- Extended life cycle

Virus are a mish-mash.  The filovirus remain simple, quick 
and horrific.
HIV/AIDS is a lot more complex and better suited to 
perpetuatingthe phenotype.
Influenza just relies on a zoonotic shape shift twice a year.

Pick one and study it to death.



>
>
>
>> They have never been found
>> as freely living organisms. In nature Mollicutes depend on a host
>> cell, respectively on a host organism. For instance, Mycoplasmas
>> and Ureaplasmas are parasites in different vertebrates, from
>> which they obtain essential compounds such as fatty acids,
>> amino acids, precursors for nucleic acid synthesis and cholesterol,
>> a compound normally not found in bacteria. Only Acholeplasma
>>  and Asteroleplasma do not require cholesterol for growth.
>
>Mycoplasms can live in or outside of a cell.  They can live and reproduce
>within a cell and within free serum.  You are right.  They must acquire
>their nutrition from a host, but not necessarily "within" a cell.

Fine.

>
>
>> Molecular Systematics is a good starting read for information
>> regarding phylogenetics and mutations.
>
>ok?

Yes.  Good book BTW.

>
>
>> >But I think the point was about the doctors credentials and the
>reliability
>> >of his opinion...
>>
>> Shifting blame will not help.  I am addressing your posts.  Clearly
>> false.
>
>"Shifting blame"?  No, the originol point was about the doctors credentials.
>In your addressment of my points... youve stated nothing that contradicts a
>thing I have said.

I have.  Several times.  I can be more blunt, but this is not the
appropriate forum for flame either.

>
>
>> >In anycase, even with a record as inscrutable as his, I
>> >place no importance on any single persons opinion.  If he didn't exist
>the
>> >evidence wouldn't change.
>>
>>
>> Are you a nutter or just a troll?
>> A troll I think.
>>
>> Hint Rob/Steph/whoever.  You are not the brightest on the block by
>> far.
>> You miss most of the basics of mundane biochemical work,
>> and seem to post wild fantasy as fact.
>
>I think youve been taking what youve been reading a little too close to
>heart.  You find the most qualified expert on myoplasms that you like.  Give
>me his name.  Ill contact him.  This is the sort of interaction I want.

I can read well enough for myself.

>Your education on the matter is stilted, 

I thought I was doing rather well ectually.

>so I am sure you will take your
>experts opinion of mycoplasms as gospel.

Whatever you think.  Mind reading another one of your
skill set?

>
>
>
>>
>> If you have anything to say, then take it to a university and publish.
>> It will be read by others, your new peer group.  If they
>> dismiss you as a lunatic, then so be it.  If they give
>> you a prize then God's speed.  Failing that, your rants
>> on a support group are not only mis-leading, but unwanted, from the
>> posts I read around your missives.
>
>Ulcers were caused by stress.  Heart disease was caused by eggs.  Freud
>wasnt mentally ill.  Polio was caused by potatos.  And prions were a
>wildmans hallucination...  These peers you want me to educate, they wouldnt
>be these same pharm educated ones responcible for the former opinions would
>they be?

The Earth is flat.
There are canaluea on Mars.
Liquid tetra-elthylene lead is as safe as houses.

All science progresses.  So will medical and
computational biology.  And yes, if you want to educate the
'establishment', then get into it.  Have a convincing argument,
and a conviction for your passion.

But first pick an appropriate audience.

>
>
>> So when can we expect your abstract?
>>
>>
>> I think you are full of it Rob/Steph/Whoever
>> and if you do want to take your work seriously you
>> can contact me at
>>
>> addinall@members.bioinformatics.org
>>
>> And I will have a look.
>> Failing that, stop bothering the nice people.
>>
>> Mark Addinall.
>
>Mr. Mark, 

Just Mark will do for now.

>you are right about one thing.  These are nice people.  But
>submitting work to peers whose reality is based on something divorced from
>reality is an effort in futility.  

Then it is futile posting here.  What do you hope to gain?  A whole
bunch of nice but ill people will take up your banner, do a quick
degree in biochemistry and carry the mcyo flag into battle for you?


If you feel that strongly about it, then do something constructive.

>Ive no problem providing collected
>research to prove my point however.  If that is what you like I will take
>some time to compile it in a manner suitable for discussion.  I will e-mail
>you  in time about a rather LARGE file that will be delivered to you.  (its
>hard to bother someone when you've taken over the newsgroup by being put in
>everyone's kill-file)

Cut it into manageable chunks and I'll look at it.  Be glad to.
Meanwhile, I have added aus.science in the headers as a jumping of
point until you suggest a more appropriate forum.  Suggestions for
bioinformatics
searches are most welcome.

I am convinced you are off topic in here, as would I be if I published
all my research into a support group.  Being plonked into kill-files
should give you a hint.  Start a new group.  Moderate it if you wish.
I'll vote for you.

"Oh, I'm feeling chipper today, lessee what my mates have
to say......"

"Oh goodie, there's Mark again giving us all a lecture on the
function of breakdown laser induced spectrometry and the
resultant context free Basyian language required to
analyise the atomic wave functions from the
induced plasma....(with XML extentions)"

"Well, that made me feel better..."

See how you are annoying people?

>
>
>Rob/Stef/Whoever
>(Its an "F", not "ph", my alternate persona hates that)

Whatever.

Mark Addinall.



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