Rethinking of disease

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Rethinking of disease

Postby BDK » Thu Apr 07, 2016 4:22 am

Rethinking of “germ” or disease theory.

This is very simplistic, and a rough outline. I’m not providing cites, etc. This may be more of a small book/phD, to properly explain.

Essentially, germ theory is, conventionally, viewed as “We have found a vile beastie, we must kill it with Broadband Killer X, toxic to almost all of a wide category.”

So, as it turns out, the human body is better modeled as a ecosystem, than a machine – some of this change is an inevitable result of technological change, but it does seem to be more accurate. (Our organs are more of a diverse array of connected and interdependent ecosystems, than machines.)

We have more bacterial cells, than we have our own cells, on our body, and we are vitally dependent on the balance of yeast, bacteria, bacteriophage (viruses which infect bacteria), and I would suspect, viruses which prey on the yeast.

This is more of a complex predator prey model, which is both dependent on the ecosystem, and which supports it - which is true of macro ecosystems as well.

Now, the term I have heard used is "microecology," but no one's formally named it, yet, TMK.

Antibiotics act as an intense fire, in an environment which isn’t centered on fire. Lots of species are lost, and the ratios seem to skew drastically. (It is currently thought that an indigenous human has about 8,000 species of bacteria in their digestive tract alone, someone in the first world has 250.)

We have long known of a link between food preservatives and cancer – and food preservatives act by mutating the DNA in bacteria (its one of their uses in a laboratory), so this is not a surprise – however, a lifetime of consuming chemicals which are directly toxic to what is a vital part of our body, will most likely prove to be a very significant issue.

We have also found that bacteria which we thought were purely pathogenic, are in fact very widespread in the populace. (There are invasive pathogens, these would be things like whatever hellish fever pops out of some place with horrible sanitation – think of them like kudzu, zebra mussels, etc.)

In a very simple way, say we envision this ecosystem as a lush Bermuda grass lawn. Very healthy, and vibrant, lots of nutrients, and good soil. Due to some damage/other defect, some dollar weed gets established.

Now, the correct solution (as I’ve been told, not a lawn expert), is to closely mow the lawn, as the desired species can very easily outcompete the invader, if kept mown.

Or, we could burn the lawn, and then let whatver willl regrow, sprout up, and continue to burn it, as long as we keep seeing dollar weed.

So, rather than burn the lawn, we need to start looking at A) what went wrong which let the weed get established, and B) what can be done to allow the ecosystem to rebalance, and most importantly C) how can we establish a healthy ecosystem in the first place, when its been lost in so much of the developed world.

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Re: Rethinking of disease

Postby blackeagle603 » Thu Apr 07, 2016 2:39 pm

Would seem to relate to the suggestion that a ketogenic diet is beneficial in that (among other things) it starves sugar hungry beasties like cancers.

...and feeding the beneficial gut beasties with prebiotics.
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Re: Rethinking of disease

Postby BDK » Thu Apr 07, 2016 4:03 pm

Yes, though ideally there would be a more specific process to re-seed missing elements/provide environmental conditions to more specifically address any inadequacies.

Essentially exactly how you would address a weed-filled pasture which you want to re-establish a healthy natural forest or pasture

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Re: Rethinking of disease

Postby BDK » Thu Apr 07, 2016 4:04 pm

This works great on MRSA - but the FDA provides some structural hurdles in actually marketing it.

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Re: Rethinking of disease

Postby AggieWalt » Thu Apr 07, 2016 4:20 pm

So in essence you are getting on to some critical points that we are just coming to understanding. One thing that that you need to understand that in areas (especially the gut) the human body through production of general antimicrobial molecules and specific immune responses act in concert with the constituents of the normal commesal microbiome to restrict the effects of certain pathogens and opportunistic pathogens while acting in a nutrient breakdown chain to support one another. It is important to note that microbomes and what is normal varies due to exposures and immunological tolerance. There are a lot of niches in the gut and the skin and other sites that can be filled by multiple species and which one occupies that niche is largely due to what the host recognizes as normal and will allow to grow. Short term alterations (days to weeks) in the composition of the microbiome are actually pretty typical and there is a degree of flux that is normal and tolerated usually do to diet, stress, disease, antibiotics etc. but over longer periods the microbiome is stable due to the immune system of the host and the the relative abundance of nutrients and other members of the microbiome that rely upon one another. However there are cases where this is not true. Sometimes certain pathogens can subvert the population dynamics after external disturbances or have developed ways of disturbing the dynamics themselves. A classic example of this is C. difficile after antibiotic treatment, this nasty bug stays around and is pathogenic after broad spectrum antibiotics due to subversion of the dynamics (being more fit int he new environment) and we are finding out that is has multiple ways of shutting down our immune system which really are cool is a terrifying way. Another example off the other end is IBD where your immune system goes haywire and then there is a change in the microbiome because the host is no longer pruning the microbial garden and this change perpetuates inflammation that is already happening. One final example then I will leave it off is the case of hyperphagia and over nutrition, this chronic change in the nutrient load causes low level inflammation and changes the population of the microbiome during these event the host learns that the new population is the correct and there is little to no long term response to the population change that become semi-permanent due to environmental (nutrient load) changes.
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Re: Rethinking of disease

Postby AggieWalt » Thu Apr 07, 2016 4:21 pm

BDK wrote:Yes, though ideally there would be a more specific process to re-seed missing elements/provide environmental conditions to more specifically address any inadequacies.

Essentially exactly how you would address a weed-filled pasture which you want to re-establish a healthy natural forest or pasture



Look up re-poopulate

It's a real product.
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Re: Rethinking of disease

Postby BDK » Thu Apr 07, 2016 6:37 pm

Walt, are you at A&M? If so, and you like this stuff, there are a couple prof's working on this, coming from bacteriophage - it would probably really tie in w your work you have mentioned on water sources

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Re: Rethinking of disease

Postby BDK » Thu Apr 07, 2016 6:40 pm

The issue w repopulating is that we cannot culture the vast majority of species.

Hell, I don't think anyone was even really looking at flora seriously until fairly recently - which is odd, as I remember being taught the importance of the genital and skin biomes in undergrad

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Re: Rethinking of disease

Postby BDK » Thu Apr 07, 2016 6:43 pm

The folks I know we're looking more at it from how bacteriophage based therapies should work.

But that is probably simplistic - it's not that Beastie X has over-populated, it's that it has had the opportunity to do so - and I strongly suspect that will tie into diet/stress/exercise the macro level

I've been trying to think of how to elegantly and simply express it, but, essentially, our overall health, micro biotic health and living conditions are all interlocked - which I find a bit fascinated by it, as it makes pop gen important, which we all hated.

And... I think pop gen models may be able to be adapted to economic models as well

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Re: Rethinking of disease

Postby AggieWalt » Thu Apr 07, 2016 8:00 pm

BDK wrote:Walt, are you at A&M? If so, and you like this stuff, there are a couple prof's working on this, coming from bacteriophage - it would probably really tie in w your work you have mentioned on water sources


Yep and I am working closely with Robert Alaniz who is setting us up a gnotobiotic core and microbiomics core.
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Re: Rethinking of disease

Postby BDK » Thu Apr 07, 2016 8:02 pm

Cool. Ryland Young and Carlos Espinoza were the two prof's who talked to me about it - along with the issue that many profs aren't aware of what other prof's are researching.

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Re: Rethinking of disease

Postby AggieWalt » Thu Apr 07, 2016 8:03 pm

BDK wrote:The issue w repopulating is that we cannot culture the vast majority of species.

Hell, I don't think anyone was even really looking at flora seriously until fairly recently - which is odd, as I remember being taught the importance of the genital and skin biomes in undergrad


True, we knew it but until the really neat deep seq methods were well developed and cheap (the most important part) we couldn't do much about it. But re-poopulate is literally freeze-dried poop in a capsule. We no longer have to take a bite of the shit sandwich, it comes in pill form now :lol:
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Re: Rethinking of disease

Postby AggieWalt » Thu Apr 07, 2016 8:04 pm

BDK wrote:Cool. Ryland Young and Carlos Espinoza were the two prof's who talked to me about it - along with the issue that many profs aren't aware of what other prof's are researching.



What college are they in at A&M? I'm in the HSC so we are pretty cloistered.
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Re: Rethinking of disease

Postby AggieWalt » Thu Apr 07, 2016 8:08 pm

BDK wrote:The folks I know we're looking more at it from how bacteriophage based therapies should work.

But that is probably simplistic - it's not that Beastie X has over-populated, it's that it has had the opportunity to do so - and I strongly suspect that will tie into diet/stress/exercise the macro level

I've been trying to think of how to elegantly and simply express it, but, essentially, our overall health, micro biotic health and living conditions are all interlocked - which I find a bit fascinated by it, as it makes pop gen important, which we all hated.

And... I think pop gen models may be able to be adapted to economic models as well


Are you a modeler?
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Re: Rethinking of disease

Postby BDK » Thu Apr 07, 2016 8:54 pm

No, I'm an ice cream maker/lawyer.

They are in the Biochem department, over in the bio-bio building. Technically we were Ag students in undergrad.

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Re: Rethinking of disease

Postby Jered » Sat Apr 09, 2016 4:44 am

I think that part of the thing that the medical profession (AKA doctors) get wrong, at least as far as disease is concerned is that they look, essentially, at the disease through a microscope, and they don't see the whole picture of the big person.

If you look at the history of medicine, it's only in about the past, probably sixty years or so, that we've really fundamentally been able to start to grasp how the human body functions at the microscopic level.
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Re: Rethinking of disease

Postby BDK » Sat Apr 09, 2016 6:01 am

60 years ago or so we didn't even know what DNA was.

We still don't have a clue at the micro level

For the most part doctors do a pretty good job with the large scale stuff. "Eat lots of veggies, get exercise and rest and don't stress too much."

I think we are handling pathogens really poorly.

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Re: Rethinking of disease

Postby Jered » Sat Apr 09, 2016 7:28 am

For pathogens and disease, the two most effective things that we've done, ever, are probably our clean tap water and indoor flush toilets.
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Re: Rethinking of disease

Postby Cobar » Sat Apr 09, 2016 1:55 pm

Reminds me of the story I heard about some leper colony where some nun made sure everyone washed their hands and they found the leprosy didn't spread. Rome did pretty well overall, possibly due to their rather obsessive cleanliness.

I wonder sometimes if we aren't tipping the scales the other way with all of our anti-microbial stuff. Maybe it is just alarmist hippie anti-chemical stuff, but aren't we supposed to have a whole colony of benign stuff living on our skin?

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Re: Rethinking of disease

Postby BDK » Sat Apr 09, 2016 4:45 pm

Yes, the biome on the skin is one of the things AggieWalt mentioned.

We know now, that keeping that biome is vital.

I suspect where we are heading, both in trying to keep environments sanitary and in overall disease, is more biome focused, if we can get the testing methods correct.

It's much easier to keep fermented sausage save than a sterile nutrient broth, as the fermented sausage is loaded full of bacteria which outcompete the pathogens.

Just like a rich, fertile field - if it has native sod over it, just keep it burned every few years.

It is laying bare and exposed, you'll go nuts trying to keep the weeds out.

Given all the oral antibiotics, food preservatives, and, probably, sanitary foods instead of preserved and fresh foods we eat, our organs resemble something like those bare fields.

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Re: Rethinking of disease

Postby slowpoke » Sun Apr 10, 2016 5:24 pm

In the future I have no doubt that oral antibiotics will be thought of as worse than leeching.
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Re: Rethinking of disease

Postby MarkD » Mon Apr 11, 2016 2:32 pm

I've been pondering this since you posted, and thought I'd make a couple observations just because.

Please note, I am not a doctor, nor to I play one on TV, and I didn't stay in a Holiday Inn Express last night. I have no training in biology/biochemistry beyond basic High School biology and what just about anyone can gain thru internet searches.

That said.....

Comparing the 8,000 species of bacteria in the gut of an indigenous person to the 250 in someone living in "modern" conditions: How many of those lost species are truly beneficial, how many are a response to a pressure that's not present in modern life, and how many are at best mildly parasitical? I don't know if this is caused by a bacteria, but I recall reading that the sickle cell played a role in preventing malaria, trading something that MAY kill you years down the road to protect against something that may kill you NOW. Life is always a trade-off.

While I'm certainly not a fan of anti-bacterial everything, and I'm a firm believer that killing off all the germs in our environment is what brings about an increase in allergies (the immune system responding to something that's not a threat because it's never had a chance to respond to something that IS), lots of people are alive today because of antibiotics and vaccines. My mother had a cousin who died of tetanus (she called it lockjaw) after burning himself with a cap gun (which is why cap guns were verboten in the D household growing up). Today that wouldn't even be an issue, a quick shot in the arm at the ER, or just a booster as part of a routine check-up. How often did people (even healthy people) die of the flu before antibiotics? Now only the people who are already compromised in some manner do so. While a more targeted approach would probably be even better, if given the choice between dying of infection in the next few days, or surviving then having to deal with rebuilding my intestinal environment, well option 2 sounds pretty good.

(Just as an aside, note that most of the diseases that are BIG killers don't naturally use humans as hosts, they've jumped species. Killing your host, especially quickly, isn't a good choice for a disease that wants to be passed on, note how quickly Ebola tends to burn out when it hits an area in Africa. IIRC rodents can carry Plague for years, but it kills humans quickly.)

How much of the increase in diseases like cancer is simply because we live longer? Diseases that kill you after your children are grown are genetically irrelevant. I recall being told once that if he lives long enough, a man will either die OF prostate cancer or WITH it. Add 20 years to the average life expectancy in a century and all sorts of things become issues that never were before, things like cancer and alzhiemers. Plus, significant numbers of people now survive cancer when they're younger and reproduce, for cancers with a genetic component, those genes are passed on.

Mind you, I'm not saying your wrong in looking at the human body as an ecosystem instead of a machine, nor am I saying that our view of diseases (of all sorts) doesn't need to change. I'm just noting that within my lifetime I've seen it go from 90 being an extremely old person spending their days in a chair in an "old people's home" to having a mother-in-law who's 88 and still plays tennis.

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Re: Rethinking of disease

Postby AggieWalt » Mon Apr 11, 2016 8:26 pm

BDK wrote:No, I'm an ice cream maker/lawyer.

They are in the Biochem department, over in the bio-bio building. Technically we were Ag students in undergrad.


Ah makes sense now
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Re: Rethinking of disease

Postby BDK » Tue Apr 12, 2016 2:02 am

Those 8,000 species are not believed to be pathogenic. They are thought to be of the same nature as the indigenous ones, which cannot be cultured - pretty much, by definition, a pathogen would be able to be cultured.

The situation with food allergies is becoming quite serious - and there appears to be a link between digestive flora and obesity.

Provided they aren't done irresponsibly, vaccines are up there with hygiene as a benefit of modern life

I know antibiotics have saved lives - but they aren't a panacea, and, frankly, they are rapidly losing any effectiveness.

In theory, a bacteriophage based therapy would work - and has worked well on MSRA - and bacteria couldn't become resistant to it.

But, getting the FDA onboard would take an act of Congress, and some serious brow-beating, and someone in that area of research - which was a tiny handful of folks - may have increased some with the new interest in intestinal flora - to start talking to politicians.

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Re: Rethinking of disease

Postby Termite » Thu Apr 14, 2016 12:36 am

BDK wrote: there appears to be a link between digestive flora and obesity.

So naturally carbonated home brewed beer and real kim chi are weight loss foods?
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Re: Rethinking of disease

Postby Windy Wilson » Sat Jul 09, 2016 10:58 am

The FDA will never get on board. All they have to do is say "Thalidomide" and the other side shuts up.
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Re: Rethinking of disease

Postby BDK » Mon Jul 11, 2016 1:08 am

? Totally different scenario/mechanism. Bacteriophage therapy, more or less, is based on amplifying the bacteriophage already present/normally present, to control an overgrowth of bacteria - its about restoring environmental balance to the biome, rather than clear cutting it.

(It has to be done carefully, and has been, thus far. Some "surprises" have been found (probably the "plague of sores.), but seems to have good results.)


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