Microbiome ecology

A skeptical look at medical practices
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Lance Kennedy
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Microbiome ecology

Post by Lance Kennedy » Sat Sep 08, 2018 11:02 pm

One of the things that annoys me is the ridiculous claims made by those selling those snake oil products called probiotics. There is remarkably little proper empirical evidence that they actually achieve anything, and the claims appear to be based on some form of dubious 'logic '.

There is no doubt that the mix of bacteria in the human gut is important for our health. But in terms of the science, this is a work in progress. Exactly which bacteria are needed and (more importantly) how to get them active, is still not well understood. What is often forgotten is that the human gut is a unique ecosystem in its own right. Simply throwing, for example, a whole lot of Lactobacillus down the old gullet may not achieve what people think it will. The bacteria hits the ecosystem, and if that ecosystem is not to its liking, the bacteria will simply die off.

What appears to be more important than dubious probiotics is the human diet. We all absorb a wide range of bacteria every day. Most will die off, and some will thrive. Which is which depends to a large extent on our diet. Putting a heap of one bacteria into our stomach may not help, if the gut ecosystem is not suitable. A tiny amount of the helpful bacteria that we ingest every day unintentionally may result in a population explosion of that specific species, if the gut ecosystem is to its liking.

So how do we alter the gut ecosystem in the direction of stimulating useful bacteria ? By eating healthy foods, and especially food with lots of fiber. The British National Health Service recommends no fewer than ten different types of fruit and vegetable every day. This would almost certainly stimulate population growth of the useful bacteria.

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Re: Microbiome ecology

Post by fromthehills » Sun Sep 09, 2018 1:05 am

I’ve also read that “god made dirt, dirt don’t hurt”. Just kidding, I never read that. But it was a popular saying when I was a kid. I did read that if you grow your own, vegetables that is, maybe don’t wash them so much.

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Re: Microbiome ecology

Post by TJrandom » Sun Sep 09, 2018 1:30 am

There are meds which kill off gut bacteria. I am on a ‘pre-biotic’ without which the big D comes a calling, and yes - even with a balanced diet. And yes, science based, medical trials supported.

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Re: Microbiome ecology

Post by Gord » Sun Sep 09, 2018 5:57 am

Lance Kennedy wrote:The British National Health Service recommends no fewer than ten different types of fruit and vegetable every day.
I didn't even know there WERE ten different types of fruit and vegetable! Lemme think:

1. Banana
2. Apple
3. Orange
4. Purple
5. Onion
6. Celery
7. Potato
8. Green things
9. ...ummmmmmm....

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Re: Microbiome ecology

Post by Lance Kennedy » Sun Sep 09, 2018 8:17 am

It is easier than you think.
Frozen fruits and vegetables are acceptable on that list. At my local supermarket, I can buy a frozen stir fry mix with four vegetables in it. I can buy frozen peas, broccoli, blueberries, strawberries, raspberries, and lots of other frozen material. I could easily get my ten a day in frozen form and keep them in my freezer.

However, I keep fresh fruit and vege also. Right now, I have in my kitchen the following. Bananas, tomatoes kiwi fruit, oranges, grapes, strawberries, celery, cauliflower, carrots, lettuce, cucumber, and capsicum. It takes a little bit of effort to always eat that ten a day, but it is well worth it. It also helps that fresh, raw, fruit and vegetables are both filling and low in calories. Keeps the physique slim. Also high in fiber to keep you regular.

If your meal habit is McDonald's, then I have no sympathy. You will probably die young, and generally of heart disease.

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Re: Microbiome ecology

Post by ElectricMonk » Sun Sep 09, 2018 9:37 am

I can get 100% nutritional value from Solyent Green.

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Re: Microbiome ecology

Post by TJrandom » Thu Sep 13, 2018 2:22 pm

Mangoes and cashew nuts... - both high in anacardic acid, appear to boost immunotherapy responses for cancer patients.

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Re: Microbiome ecology

Post by Lance Kennedy » Thu Sep 13, 2018 8:37 pm

Interesting stuff, TJ.

Again, a link to food rather than probiotics.

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Re: Microbiome ecology

Post by TJrandom » Thu Sep 13, 2018 9:39 pm

Lance Kennedy wrote:Interesting stuff, TJ.

Again, a link to food rather than probiotics.
Absolutely agree - but then there are many cancer patients who simply cannot eat without pre/probiotics, so as the article says - this finding may lead to new meds. Personally, I`ll be picking up cashews at my next COSTCO visit, to add to my nut mix since I may start immunotherapy in a couple of months. I`ll stay off of the mangos due to their high calories.

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Re: Microbiome ecology

Post by scrmbldggs » Thu Sep 13, 2018 10:27 pm

Cabbage - good in all three states: raw, cooked, sauerkrauted. The fermented latter is said to hold those craved probiotics. And I think it fibers also.
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Re: Microbiome ecology

Post by TJrandom » Fri Sep 14, 2018 2:30 am

Had cabbage today for lunch - with fried oysters. Umm mmm good!

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Re: Microbiome ecology

Post by Lance Kennedy » Fri Sep 14, 2018 8:56 am

Trivia relating to cabbage.

Prof. Bruce Ames several decades ago decided to test cabbage. He extracted over 100 different chemical substances from the food, and subjected each to the Ames test for mutagenicity, which also relates to carcenogenicity. About 60 of the cabbage chemicals tested positive as cancer causing substances. Cabbage produces 49 chemicals which are "designed " by evolution to be natural pesticides, and are quite toxic to people.

Of course, to be fair, they only became cancer causing at doses way, way higher than anyone eating cabbage would ever get. Normal cabbage is a safe and healthy food. But this shows what happens when people ignore dose in their judgements. Lots of quite harmless materials are listed as possible or probable carcinogens, when they are totally safe at normal use levels.

Lots of people get their knickers in a twist about pesticide residues in their food. But the venerable Bruce Ames wrote in a 1990 paper that 99.99% of the pesticides that people consume are actually totally natural, not synthetic sprays.

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Re: Microbiome ecology

Post by ElectricMonk » Fri Sep 14, 2018 9:12 am

Lance Kennedy wrote: Lots of people get their knickers in a twist about pesticide residues in their food. But the venerable Bruce Ames wrote in a 1990 paper that 99.99% of the pesticides that people consume are actually totally natural, not synthetic sprays.
the question is toxicity, not how natural something is.

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Re: Microbiome ecology

Post by TJrandom » Fri Sep 14, 2018 9:50 am

And dose is not always as the manufacturer planned - since farmers can mix improperly by accident or design.

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Re: Microbiome ecology

Post by landrew » Fri Sep 14, 2018 7:59 pm

TJrandom wrote:And dose is not always as the manufacturer planned - since farmers can mix improperly by accident or design.
Less than you might think; due to liabilities and costs.
Product testing has also become ubiquitous in the food industry, so the chances of slipping through are more remote.
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Re: Microbiome ecology

Post by landrew » Fri Sep 14, 2018 8:05 pm

ElectricMonk wrote:
Lance Kennedy wrote: Lots of people get their knickers in a twist about pesticide residues in their food. But the venerable Bruce Ames wrote in a 1990 paper that 99.99% of the pesticides that people consume are actually totally natural, not synthetic sprays.
the question is toxicity, not how natural something is.
It's a variation on the naturalistic fallacy, but "natural" is not always safest. Think nicotine, a natural herb, yet responsible for much misery and death.

The toxicity is in the dose, not in the name. Everything has practically everything else in it, so name-hysteria is all the more ridiculous.
Last edited by landrew on Fri Sep 14, 2018 8:12 pm, edited 1 time in total.
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Re: Microbiome ecology

Post by Lance Kennedy » Fri Sep 14, 2018 8:06 pm

ElectricMonk wrote: the question is toxicity, not how natural something is.
No. Utterly and totally wrong.
The question is always, always and always, dose. The most toxic substance ever discovered is a mixture generated by the bacterium Clostridium botulinum which, when injected into a human, has a toxicity of 1 nanogram per kilogram. That is roughly 1,000 TIMES as toxic as the worst chemical ever jnvented by humans (a member of the dioxin family called 2,3,7,8 TCDD ). Yet this incredibly toxic substance is routinely injected into people's faces to iron out wrinkles. It goes under the trade name Botox. The reason Botox can be used this way, despite its unbelievably high level of toxicity, is that it is injected at incredibly low (almost homeopathic) dose.

Natural pesticides are frequently just as toxic as synthetic ones. The reason they do not cause harm is simply that the levels found in modern vegetables is very low. As always, it is about dose.

Actually, the ancestral cabbages, lettuce, broccoli etc, all had much higher levels of natural pesticides. We have bred them to have less. Not because of health reasons, but simply because high levels of natural pesticides make the food taste bitter.

Two natural pesticides that are well known are caffeine and nicotine. Nicotine especially is very toxic.

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Re: Microbiome ecology

Post by TJrandom » Fri Sep 14, 2018 9:32 pm

landrew wrote:
TJrandom wrote:And dose is not always as the manufacturer planned - since farmers can mix improperly by accident or design.
Less than you might think; due to liabilities and costs.
Product testing has also become ubiquitous in the food industry, so the chances of slipping through are more remote.
I disagree, and believe it to be rampant - at least here in Japan and in China. Here the agricultural associations provide the oversight, such as it is, and over time customers have become accustomed to perfect fruits and vegetables - obtained thru high pesticide/herbicide/antifungal use. Spraying chemicals several times during the growth period, and again just prior to harvest ensures perfection but leaves residue. Here to be safe, you must thoroughly wash and peel – and no government agency at any level checks for safety, though we do have maximum residue limit standards in place.

We do a better job at testing imported foods – testing about 10% of all shipments, vs the US which tests just 1% (according to this now dated 2007 article).

For example, honey from China continues to be a world-wide problem due to improper timing of the use of bee antibiotics and hive beetle pesticides – sufficient to get it banned in some countries but smuggled thru illegal importations. From what I have read elsewhere, this is mostly caused by ignorance in application on the production side, but avarice in the export and sales.

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Re: Microbiome ecology

Post by Lance Kennedy » Fri Sep 14, 2018 9:50 pm

I do not know what it is like in Japan.

Here in NZ, we have a government agency which tests foods. I have spoken to one of their food scientists. Their test results for pesticide residues return "nothing detectable " (meaning less than one part per trillion ) in about half their tests. Almost all the tests return less than one part per million, which is totally non toxic for human consumption. It is very rare to get a result that is of realistic concern.
Last edited by Lance Kennedy on Fri Sep 14, 2018 9:53 pm, edited 1 time in total.

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Re: Microbiome ecology

Post by Lance Kennedy » Fri Sep 14, 2018 9:50 pm

I do not know what it is like in Japan.

Here in NZ, we have a government agency which tests foods. I have spoken to one of their food scientists. Their test results for pesticide residues return "nothing detectable " (meaning less than one part per trillion ) in about half their tests. Almost all the tests return less than one part per million, which is totally non toxic for human consumption. It is very rare to get a result that is of realistic concern.

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Re: Microbiome ecology

Post by Poodle » Fri Sep 14, 2018 10:00 pm

... and they double-check their results.

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Re: Microbiome ecology

Post by Lance Kennedy » Fri Sep 14, 2018 10:41 pm

My apology, Poodle.

It is ridiculously easy to double post.

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Re: Microbiome ecology

Post by TJrandom » Fri Sep 14, 2018 11:05 pm

Here, the only non-import independent testing that occurs, is if an incident has caused illness. Restaurants are periodically tested for cleanliness and procedure compliance (setting aside food samples in case an incident occurs, etc.), but independent ingredient testing of Japan produced food does not occur on even a random basis.

Of course large chain outlets/production facilities can test themselves, but with the high cost of test equipment, those tests will be simple. In addition, we have movements toward grow-for-identified customer/market, and know-your-grower (grower labelling), and both of these help to ensure best practice – but wholesale and retail markets are outside of these.

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Re: Microbiome ecology

Post by ElectricMonk » Sat Sep 15, 2018 4:12 am

landrew wrote: It's a variation on the naturalistic fallacy, but "natural" is not always safest. Think nicotine, a natural herb, yet responsible for much misery and death.

The toxicity is in the dose, not in the name. Everything has practically everything else in it, so name-hysteria is all the more ridiculous.
landrew gets it, Lance doesn't.

yes, to be precise, toxicity determines the safe dosage.

But the issue is in the natural fallacy Lance made was that there is a false scare about industrial pesticides, when there are so many natural ones on our food: both are scary, depending on type and concentration.

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Re: Microbiome ecology

Post by Lance Kennedy » Sat Sep 15, 2018 5:08 am

EM

'Both are scary' is silly.
Toxics are simply part of our world, to be managed like any other hazard, and know how is the key. Which is why I jump on ignorance.

Yes, landrew is aware. His post was sensible. Yours was not. It does not matter how toxic something is. Although knowing the toxin is important. Good data. What matters is being sensible and avoiding too high a dose. Otherwise Botox would not be used.

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Re: Microbiome ecology

Post by ElectricMonk » Sat Sep 15, 2018 6:05 am

this is tedious.

Your post made light of the dangers of pesticides - and that is a problem.

This is a serious issue, mostly caused by ignorance both of consumers and producers: modern pesticides are far more effective, which means that you need less for the same effect. But many farmers operate on the "a lot helps a lot" principle, regularly causing problems. Organic farmers are just as bad, since many are amateurs and think that because it is "organic" means you can out as much as you want.
This might not be a problem in NZ, but in the US, produce certification is a private business: the standards are what a re-seller will accept and what number of recalls stores will swallow. There is virtually no government oversight.
It is very much like "Fight Club":
If the "Formula" says that most people won't get so sick from your produce that they will demand compensation, it's cheaper to sell unsafe food than to go with only top-certified farms.

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Re: Microbiome ecology

Post by Lance Kennedy » Sat Sep 15, 2018 7:47 pm

EM

It is not about "making light of a problem". It is about recognising what is a problem and what is not. The truth is that people getting sick because of synthetic pesticide residues in their food is very, very rare. The suggestion that such incidents often happen is a myth perpetrated by crackpots.

Where synthetic pesticides occasionally cause real problem is among those who handle them. The farmers and contractors who mix and spray them. Because the dose is higher. Consumers getting sick from synthetic pesticide residues in their food are really, really rare.

The most basic principle in the science of toxicology is that it really is all about dose. Among other things, this means that toxins normally found in low levels (like synthetic pesticide residues in food) are not normally a problem. The real harm comes from those substances found in large amounts. This means, for example, that more people suffer the toxic effects of drinking too much water (hypernatremia), or breathing too much oxygen (hyperbaric oxygen toxicity), than getting poisoned by food preservatives, coloring, or synthetic pesticide residues.

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Re: Microbiome ecology

Post by ElectricMonk » Sun Sep 16, 2018 6:18 am

This back-and-forth is a classic WoMBaT.

As usual, the only reason why you think there is no problem is because people have put checks and controls in place to avoid past health issue.
It's like saying hippos in the zoo are safe - they are certainly not; it's just that we have a big fence between us and them.

Your rhetoric makes light of the economic and regulatory efforts necessary to keep these problems marginal. And it is precisely this attitude that allows people like Trump&co. to dismantle health and safety regulations.

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Re: Microbiome ecology

Post by Lance Kennedy » Sun Sep 16, 2018 8:11 pm

No one, EM, and certainly not me, has suggested that we should dismantle safety procedures. But as I have said before, I seriously, really, really, hate bull-{!#%@}. The suggestion that synthetic pesticide residues in food are a significant hazard to those eating the food is total bull-{!#%@}. It is the kind of bull-{!#%@} used by politically active alternative food and environmental organisations to pull the wool over people's eyes, and I co not think anyone who calls him/herself a skeptic should be kowtowing to that form of intellectual crap.

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Re: Microbiome ecology

Post by TJrandom » Sun Sep 16, 2018 10:10 pm

I truly don`t know - having googled for pesticide residue on food that has caused illness, I just cannot find the articles - but we do know that pesticide residues are there, and show up in the food we eat, and the blood, urine, and faeces of humans. And we know that people are getting cancer at higher rates than before, though this could be due to other causes such as the often touted one that people live longer these days so have a longer period in which to get cancer. And there are other diseases that may be caused as well.

At a minimum, I would conclude that immediate deaths are not occurring due to residue – since they do not show up via google, but to determine whether longer term death or other illnesses are caused by residue would require further study IMO.

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Re: Microbiome ecology

Post by Lance Kennedy » Sun Sep 16, 2018 10:44 pm

TJ

How much study do you need ?
There are literally thousands of published studies.

Nor is there any need to speculate. The basic theory is simple. To suffer harm from a toxin requires a harmful dose. Synthetic pesticide residues as determined by chemical analysis of a very, very wide range of foods, shows in almost every case, the amount of such residue is well below one part per million. So no harm.

But of course, there is MASSIVE harm from other food ingredients that are present in large amounts. Like sugar, processed starch, trans fats, saturated fats, and too much salt. If a rational person wants to present data on the harm of 'stuff ' in food, concentrate on these things which GENUINELY cause harm, and not on the idiotic issues that crackpot organisations get into.

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Re: Microbiome ecology

Post by TJrandom » Mon Sep 17, 2018 1:59 am

I didn’t find a study that covered 30 years since ingestion- have you?

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Re: Microbiome ecology

Post by Lance Kennedy » Mon Sep 17, 2018 4:04 am

No. But I have seen an awful lots of claims by crackpots with no backing whatever.

Pesticides have to pass a number of tests before they are permitted to be used. That includes longer term exposures on animals. A laboratory mouse that lives two years is equivalent to a human who lives 70. Long term studies on those mice are readily available. We know what happens to animals exposed to high levels. Human exposures from food run to less than one part per million. That is laughable, and anyone who claims it may cause harm is an idiot. Not you, TJ. But as you know, there are idiots on this forum.

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Re: Microbiome ecology

Post by ElectricMonk » Mon Sep 17, 2018 4:27 am

Stop being so zealous (and pompous), Lance. No one here has claimed that pesticides are a major killer or even a top twenty health risk. Only you are going on and on about how unreasonable any concern is - which is the actual stupid thing here:
We had a fair share of scandals with pesticides that accumulated in breast milk, causing real and permanent damage to children. So the "crackpots" as you call them have legitimate reason for concern, whether you like it or not.

I really don't see how you are making any kind of an argument: farming at any scale needs monitoring because it is the stuff we eat. It's not a major issue, but we cannot ignore it.
Why do we have to spend time on this obviousness?

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Re: Microbiome ecology

Post by Lance Kennedy » Mon Sep 17, 2018 4:48 am

Because this topic skirts bull-{!#%@}, and I oppose bull-{!#%@}. Synthetic pesticides are no more toxic than natural pesticides, and the average person consumes 10,000 times less synthetic pesticide than natural, according to Professor Ames. Synthetic pesticides can be a hazard, but not normally in food. They are a hazard to those who handle them and operate sprays. The old principle still applies. It is all about dose. The only people to get a big enough dose to be of concern are those who handle and spray the actual chemicals. Not those who consume the food later.

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Re: Microbiome ecology

Post by TJrandom » Mon Sep 17, 2018 7:49 am

Lance Kennedy wrote:... The only people to get a big enough dose to be of concern are those who handle and spray the actual chemicals. Not those who consume the food later.
Not true Lance, and you know it. If consumption were not a concern, then there would be no need for monitoring (where it occurs), standards, research, etc. What we do not know, is how MUCH of a concern - for health damage, is reasonable GIVEN the known residuals on food. And... whether we consume more `natural` than synthetic (or simply human applied) is nonsense - since we do not (normally) control the level of naturals in the food we eat. Instead, we either eat it or don`t. But we do control the amount of residual that we apply - hence the concern on what, when, and how much is applied and how much residual is permitted.

My take is that the standards are probably cost-effective. We have much more food available because we apply pesticides. But the ag-chem industry which profits from the sales is also the one that performs the safety tests in most (?) cases, and the farmer does not get zapped by a God if he uses more, or uses it nearer to harvest than he should. Ideally, residuals should not be found on store bought foods, but unfortunately it is. The human health impact from these residuals is what is at question.

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Re: Microbiome ecology

Post by Lance Kennedy » Mon Sep 17, 2018 8:09 pm

Here in NZ it is the Food Safety Authority that performs the tests. I would be surprised if the American F.D.A. failed to do any testing. In Britain, they have the Food Standards Agency. The key to pesticide safety in food is simply following the legal requirements. Using only approved pesticides, in the approved way, and not applying pesticides in the latter weeks before harvesting. As long as this is done, there is no problem, except occasionally to those who do the applying.

Based on the data I have seen, this is almost always done, and it is testing that polices these rules. This is why testing is important. The end result is that synthetic pesticide residues in food is not a safety concern for consumers, which is what I have been saying.

But I have a gripe with those who present bull-{!#%@}. In this case, the bull-{!#%@} is to suggest that synthetic pesticide residues in food are a safety concern. They are not.

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Re: Microbiome ecology

Post by TJrandom » Mon Sep 17, 2018 8:31 pm

I found this 2014 article that is a good read on pesticides in foods and testing in the US. A bit detailed, but informative.

And again to add - residual pesticides in marketed foods IS a concern, and shame on Lance for saying otherwise.

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Re: Microbiome ecology

Post by Lance Kennedy » Mon Sep 17, 2018 10:16 pm

Your reference, TJ, does NOT show that synthetic pesticide residues are a real concern. It goes into detail about testing, which is fine. It also mentions that a tiny percentage of tests in the USA show a result a little above legal recommendations. Since those legal recommendations are normally about 1% of the NOAEL (no observable adverse effect limit ) that is a statement with no meaning.

I would challenge you to show any example of a person suffering health problems as a result of too much synthetic pesticide residue in the food he or she eats, in any advanced western country, in the last couple of decades. I could readily show you a case where natural pesticide in food caused hospitalization. Here in NZ in 2002, when organic zucchini with too much of the natural pesticide cucurbitacin was eaten.

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Re: Microbiome ecology

Post by TJrandom » Tue Sep 18, 2018 1:52 am

Read this. But I will quote this portion...
The presence of pesticides in HM is of great concern due to the potential health effects for the breastfed infant, as many of these pesticides are known to interfere with the function of normal endocrine systems2. Exposure to these xenobiotics has been associated with a wide range of adverse effects, such as delayed neurodevelopment, poor cognitive performance and growth retardation during early childhood9,10,11. High prenatal exposure to OPPs and its metabolites has been associated with attention deficit/hyperactivity disorder in children at 5 years of age12. Similarly, a longitudinal study of 329 children through to 7 years of age confirmed that high maternal OPPs concentrations were associated with poor intellectual development and cognitive performance13

And since you claim that natural pesticides are of concern, maybe you could provide a link on that - preferably including a list if the foods.