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Metagenomics and the blurring of Species...
 Moderated by: Prof Trevor Marshall
 

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Prof Trevor Marshall
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 Posted: Wed Apr 4th, 2007 22:35

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The American Society for Microbiology has released a new (FREE) document

"Reconciling Microbial Systematics and Genomics," March 2007

which explains in detail how pathogens engage in lateral transfer of DNA (and other miscellany) to morph into species which can no longer be readily regarded as distinct.


Another older document from the same source is

"Microbial Triggers of Chronic Human Illness," April 2005

Which we have seen before, but is worth review now. Especially the summary of 'problems' starting on page 9.

Enjoy!:)

ps: I totally agree with this passage:
The criteria used to ascribe etiology to non-microbial causes like genetics and non-infectious environmental influences are far less rigorous than those applied to identify microbial causes. For example, the autism community has all but concluded that autism is a genetic disease, but the dizygotic twin and sibling concordance studies do not support a dominant role for genetic cause. These potential etiologies need to be held to the same experimental standards for causation as microbial etiologies.

Last edited on Wed Apr 4th, 2007 22:53 by Prof Trevor Marshall

Jacko
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 Posted: Thu Apr 5th, 2007 01:56

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This quote is interesting. It may be old hat to you but they have found increased amounts of cytokines and other inflammatory markers in the brains of autistics.



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Prof Trevor Marshall
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 Posted: Thu Apr 5th, 2007 02:35

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Jacko,
It will be old hat to you in 5 years time, too. As you recover on the MP you will find that many symptoms of ASD were present, albeit at extremely low levels, when you were ill. Further, you will note they disappear as you get better. Difficulty relating to peers, lack of focused concentration, disruptive behaviour, are all symptoms we can look back upon and see that we have thrown off...

tickbite
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 Posted: Thu Apr 5th, 2007 07:18

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I love the 21st century. I also love it when I read this stuff and it blows old dogma out of the window.

Thanks!



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eClaire
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 Posted: Sat Apr 7th, 2007 00:49

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Interesting Trevor that you say that about our relating to ASD symptoms as we get better.  I've already related to it (e.g., Asperger's Syndrome)--that is, beyond what psychologists pin on ADD.  However, my psychologist tells me that if I really had some of those symptoms I wouldn't be aware of them, as part of the illness is a lack of self awareness. 

Well, in a similar "you couldn't possibly know" vein, I was once was having pain that started at around the time of ovulation (i.e., a pain in my gut that extended at times for days or for weeks) and I told my gynecologist about it.  I told him that inside my gut it felt like a little tight rubber ball was being pelted from the inside, then there would be this initial stab of pain after which several days to a couple weeks of pain would begin.  (Turns out, the doc explained, that the long-term pain was actually from blood in the intestine from a pretty intense ovulation, and blood in the intestine makes you hurt--survival of the species sort of thing.) 

At any rate, the Gyn explained to me that what I had described was in fact happening to me--the pelting scenario--, and then he said,  "But you couldn't possibly feel that."  I changed gyns. 

Since I've had that discussion with my psychologist, I've already heard scientists linking autism and CFS.  Right now, I'm just waiting for my psychologist to someday eat his words. 

Claire



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Prof Trevor Marshall
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 Posted: Sat Apr 7th, 2007 03:49

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eClaire,
In a way, the psychologist is correct. When you are ill with those symptoms it is hard to notice that you have them, even harder to admit that you have them. But after they have gone, and you remember back, and your friends tell you how they appreciate the change, that's when you realize how much you were made to suffer by these tiny little bugs...

VEZ R.N.
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 Posted: Tue Apr 10th, 2007 05:41

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Dr. M.

I am counting on this.....All of these symptoms I have learned to live with for years will hopefully be history soon.  I read both articles and am thrilled beyond words at the science finally getting out but......it will take years to change the machine of current medical practice.  Thank You again......VEZ

tickbite
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 Posted: Fri May 4th, 2007 12:21

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Thought this was interesting....quorom sensing

Say What? Bacterial Conversation-Stoppers

My blog about quorom sensing 

i'm not saying we should be taking these types of antimicrobials. Dr. Marshall has made it quite clear that the abx we are using do the job sufficiently well. It's just nice to "know thy enemy."

One point I would like to make is that say a dominant species which is squelching a lesser species succumbs to the abx combos first, that would enable the lesser species to quorom sense and perhaps change the way it interacted with our bodies. In other words, make our disease change in nature. Maybe....:)



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Prof Trevor Marshall
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 Posted: Fri May 4th, 2007 12:45

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Greg,
The actual situation is too complex to talk in terms of "dominant species" and "lesser species." Each species has a genome, and elements of those genomes, and of the host genome, all interact in an interactive manner. Not just multiple species are involved, but mutiple genes. Millions of them.

I know this is a difficult concept. I think I am a long way along toward understanding it at the moment, but even I think it is too early to try and put it into words, as these writers have done. It just gives you all the wrong impression. The scale of interaction is actually semi-infinite...

tickbite
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 Posted: Sat May 5th, 2007 15:48

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Dr Trevor Marshall wrote: Greg,
The actual situation is too complex to talk in terms of "dominant species" and "lesser species."

Let me have my fantasies! :) :)

Anyway, for simplicity's sake I said that...however we would want to say it, "dominant genes" then. There must be some sort of hierarchy functionality to the whole soup, however complicated.

Well I agree it is crazy complicated....but even you have to agree we must start somewhere......reminds me of the MP :)



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tickbite
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 Posted: Mon May 14th, 2007 11:28

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You may enjoy reading this news article Dr. Marshall.

http://www.sciencedaily.com/releases/2007/05/070514101100.htm

DOE JGI Sets 'Gold Standard' For Metagenomic Data Analysis

To what extent beyond your own knowledge of these gene swapping collectives do scientists understand this phenomenon in your opinion? Reading the article above gives me evidence that such understanding must be talked about in some circles.



____________________
"Lyme","CFS", Meningitis
Phase3 8-2-07, MP on hold 11/2007

Prof Trevor Marshall
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 Posted: Mon May 14th, 2007 13:39

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The problem is with clinicians' understanding, IMO. The scientists seem to have a good handle on what is happening, although they haven't been able to tie their understanding with the pathogenesis of disease.


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