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New Book - "Metagenomics of the Human Body"
 Moderated by: Prof Trevor Marshall Page:  First Page Previous Page  1  2  3  Next Page Last Page  
 

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Prof Trevor Marshall
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 Posted: Tue Dec 7th, 2010 12:10

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My copy of the book arrived from Amazon yesterday, Monday 6th December :)

Total number of pages 337, of the 16 chapters ours is the most detailed, at 46 pages :)

The best way to read the parts you are most interested is via Amazon.com's preview. Remember that you will have to erase the Amazon cookies every time they decide you have read enough for free :)

http://www.amazon.com/Metagenomics-Human-Body-Karen-Nelson/dp/1441970886#reader_1441970886

..Trevor..
ps: I note some of the information is out of date. For example, the chapter on the lung microbiome was written before the COPD study showed that healthy lungs had a prolific microbiome. The chapter says there is no healthy lung microbiota. It is a pity when mistakes like this get through to final print, but this is a rapidly moving field, and the preliminary COPD lung data has only been presented at a conference...
 

eClaire
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 Posted: Wed Dec 8th, 2010 13:41

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Given your comment then it is safe to assume that you now think that there might be "healthy" bacteria?



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Prof Trevor Marshall
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 Posted: Wed Dec 8th, 2010 14:33

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 All genomes will have both negative and positive interactions with the human genome. Based on what we know now, I would prefer no pathogens at all, so that the human genome can get on with doing what it evolved to do...

Teresa Green
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 Posted: Wed Dec 8th, 2010 15:18

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Trevor,

Did not the Human Genome evolve from  early bacterial life forms?   And does it not continue to evolve in concert with the baterial metagenome

The other day I was sitting and thinking about our modern society, evolutionary biology, epigenetics and the metagenome.  I could not help thinking that with the advent of and overuse of antobiotics, the human genome has undergone such transformatios due to epigenetic changes resulting from pathogenic microbes, that within mine and my children's generation we have created a human race that will continue to exhibit chronic illness symptoms earlier and earlier in their lifetimes.

Much more research needs to be focused on earlier intervention to avoid impending future health disasters.


Teresa

Prof Trevor Marshall
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 Posted: Wed Dec 8th, 2010 16:38

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First, the word "epigenetic" does not necessarily fit into the argument you are making.

I think the biggest single contributing factor to the surge in chronic disease is the globalization of food supplies, especially meat, the surge in travel, especially International travel, and a total lack of understanding about how the microbiota are spread between an increasingly social modern population.

Yes, use of antibiotics which were never properly test in-vivo, is also a problem. How can it be that, just today, a paper comes out disclosing that a 1968 antibiotic -- minocycline -- has a direct affect on cancer autophagy, on apoptosis:

http://www.ncbi.nlm.nih.gov/pubmed/21079420

Antibiotics were thought to just kill bugs. Nobody bothered to see if they had any other actions in the human body. This was a terrible mistake.

Finally, the introduction of Vitamin-D supplementation of milk on a grand scale by Nestle in the 1950s, such that essentially all shipment of milk to less developed nations has been heavily supplemented since that date, gave the Th1 microbiota a big help in knocking out the human innate immune system, and paving the way for HIV, EBV, and other VDR-centric organisms to flourish.
 

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 Posted: Thu Dec 9th, 2010 06:35

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Here's an image from a presentation by Karesh on the globalization of food.



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 Posted: Thu Dec 9th, 2010 15:40

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Wow, Paul, what a fabulous illustration of Trevor's point about the globalization of food supplies! It's a great map, and would do Edward Tufte* proud.

*author of the classic The Visual Display of Quantitative Information

Thanks for sharing it so promptly!

All best,
Dody
geography major and GIS (geographic info systems) analyst



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 Posted: Thu Dec 9th, 2010 17:17

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I love Edward Tufte. :)



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Lottis
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 Posted: Thu Dec 9th, 2010 23:20

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In a nutshell! :)


Dr Trevor Marshall wrote:

...
I think the biggest single contributing factor to the surge in chronic disease is the globalization of food supplies, especially meat, the surge in travel, especially International travel, and a total lack of understanding about how the microbiota are spread between an increasingly social modern population.

Yes, use of antibiotics which were never properly test in-vivo, is also a problem. How can it be that, just today, a paper comes out disclosing that a 1968 antibiotic -- minocycline -- has a direct affect on cancer autophagy, on apoptosis:

http://www.ncbi.nlm.nih.gov/pubmed/21079420

Antibiotics were thought to just kill bugs. Nobody bothered to see if they had any other actions in the human body. This was a terrible mistake.

Finally, the introduction of Vitamin-D supplementation of milk on a grand scale by Nestle in the 1950s, such that essentially all shipment of milk to less developed nations has been heavily supplemented since that date, gave the Th1 microbiota a big help in knocking out the human innate immune system, and paving the way for HIV, EBV, and other VDR-centric organisms to flourish.



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Sallie Q
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 Posted: Fri Dec 10th, 2010 14:06

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forget Julian Assange 'in the frame' for Wikileaks'
I'd like to see a class action against Nestle for cruelty to children
Sallie



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 Posted: Fri Dec 17th, 2010 06:35

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Hi !

I did not know who Craig Venter (of the Craig Venter institute that is responsible for the book we are discussing in this thread) was.

Some time ago someone here on the site posted a link to a Ted-conference-talk about people whose taste is in color.

That presentation was so incredibly interesting that I have been watching all sorts of presentations on TED.com since then.

To my astonishment I ran into a presentation of Craig Venter !

It blew my mind, a must see:
- http://tinyurl.com/nxo4wu

It gives me a good feeling to see that a pioneering organisation like JCVI gives credibility to the MP-pathogenesis.

There are more presentations of Craig Venter on TED.com  btw.

Best, Frans



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 Posted: Tue Apr 19th, 2011 11:49

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This study indicates that a nutrient, choline or lecithin (often found in supplements, but also in fish and some other foods), when combined with a particular gut microorganism, can produce a pro atherogenic substance:

http://www.sciencedaily.com/releases/2011/04/110406131814.htm

Just showing another link between the microbiome and health, adding complexity to figuring out effects of things we ingest.

Joyce Waterhouse



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Prof Trevor Marshall
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 Posted: Tue Apr 19th, 2011 12:59

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Frans,
Here are two more excellent videos:

http://www.charlierose.com/view/interview/11024

http://www.youtube.com/watch?v=HLP6x4h1tOM

..Trevor..
 

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 Posted: Wed Apr 20th, 2011 07:26

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These are very thought provoking videos, and Thank you for the link.

The work does raise ethical and philosophical questions:  is the computer the "parent" of this new synthetic life form, or is the true "parent" the intelligence and creativity of human beings?  Isn't the computer merely a tool?

Excellent videos.

Sherry



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Prof Trevor Marshall
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 Posted: Wed Apr 20th, 2011 07:59

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The computer is merely a tool. It slavishly does what I tell it to do. It is up to me to tell it what I want to look at, and up to me to interpret the results when they are displayed. Other scientists look at the videos I show them and they see nothing. They notice nothing. They learn nothing.

At the Nuclear Receptors conference I was showing a video emulation of exactly how the VDR activates, how each helix has to be displaced. Nobody was interested. The movie was not something they could relate to. To this day I am the only person I have met who understands precisely how 1,25-D and Olmesartan deform the VDR in order to enhance binding to DRIP205. Even though the 4 key hydrogen bonds are shown on this poster from 2007:

http://AutoimmunityResearch.org/transcripts/dmm2007-harvard.pdf
 

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 Posted: Wed Apr 20th, 2011 12:20

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I agree, very interesting videos ... thanks for posting them!

It must be very frustrating Dr Marshall to have your discoveries fall on deaf ears of scientists!  They just do not grasp how monumental a breakthrough you have achieved.  There is a LOT of ego in the scientific world!! 



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 Posted: Wed Apr 20th, 2011 12:20

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Thanks Joyce and Trevor for posting these links.  Lots of fascinating stuff!

Here's another youtube video of Venter speaking at CalTech just a few months ago.  It might have been posted elsewhere, but this is the first time I saw it.

http://www.youtube.com/watch?v=HdgfzdlgUHw
:)
Marysue



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Rico
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 Posted: Wed Apr 20th, 2011 14:15

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Why do you think that is, Trevor? The lack of interest and inability to grasp ...  Are medical scientists intimidated by computer models or are your explanations/theories just too contradictory to what they know/believe/learned that they just instinctively dismiss it?



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 Posted: Fri Apr 22nd, 2011 12:27

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In the "science" of creating a learning environment, it is my understanding that the first order of business is to help the student feel at ease (safe) because only then is the brain in the proper state to take in new information. The second is to provide a context for the student so that they see the value in the knowledge presented.

Perhaps the first part that is why civility on our forums is so important to me personally. :)

Of course, those checking us out online are most likely very motivated to discern if what we are reporting can help them, or a loved one, with a medical condition that has not turned around with standard of care, so the second part is easier for the patient than it is for the researcher of health professional to grasp. You think?



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Prof Trevor Marshall
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 Posted: Fri Apr 22nd, 2011 13:28

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Rico wrote: Are medical scientists intimidated by computer models or are your explanations/theories just too contradictory to what they know/believe/learned that they just instinctively dismiss it?
All of the above. Different emphasis in different people. Nobody likes change. Medicine (as a whole) really hasn't come to grips with Helicobacter pylori yet, let alone the Microbiome.
 


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