EDIT: Seriously, how is this not contributing? Please provide a comment if you think it is not contributing.
~2 billion base pairs * ~1 in a billion error rate = 2 mutations per generation (on average)
Edit: Slight clarification and a brief (and greatly oversimplified) lesson on how this works.
Let Ne = effective population size. And I'll define "fitness effect" as the advantage conferred by a particular mutation in a particular fitness landscape. e.g., If you're an E. coli, the fitness conferred by penicillin resistance is very high if you're sitting in a pool of penicillin, but generally mildly negative otherwise because you're wasting energy.
When the fitness effect size is much larger in magnitude than 1/Ne (or 1/2Ne if you're diploid, like us), the fate of the gene is largely determined by natural selection. (But add the occasional coin toss in there b/c the real world is messy.)
When the fitness effect size is much smaller in magnitude than 1/Ne, the fate of the gene is largely determined by genetic drift. https://en.wikipedia.org/wiki/Genetic_drift (tl;dr Mostly chance mod a few other effects, like if the mutation of interest has a physical location close to another mutation with strong selection pressure)
However, there are slightly deleterious or slightly advantageous mutations, whose fitness effect size is close to 1/Ne (or 1/2Ne for diploids), and things get kinda interesting, because it's a combination of genetic drift and natural selection. For instance, if it's a slightly deleterious mutation, it will decrease Ne slightly (increasing the proportion of mutations that are considered neutral of the new value of Ne), and the previously "slightly deleterious" mutation may now be effectively neutral for the new value of Ne.
There is a lot of evidence that the "slightly" deleterious and the "slightly" advantageous mutations contribute substantially to evolutionary dynamics.
This is further complicated by the fact that the fitness (whether a mutation is deleterious or advantageous) is not constant everywhere geographically, or over time.
Sure, and it's also possible the human body has already adapted to processing grains without long term damage, and it's possible that there was never any damage by consuming grains in the first place (the body is highly adaptable). All this line of argument is stating is that without any information, we have no information.
What Retric was stating is different though. There exists digestive adaptations that have happened relatively rapidly in relatively recent history, therefore merely the fact that foods were not available in more ancient history is not sufficient to argue that they "aren't good" for the body.
It’s more likely that gluten sensitivity is just caused by a cross-interaction with an additive used for bleaching or similar.
I'm not suggesting it isn't but your dismissive comment doesn't enlighten those who are not aware of the controversy.
Paleo's basic premise is loosly based on the malnourishment seen when we transitioned from a diverse hunter-gatherer diet to a much less diverse agricultural diet (largely caused by iron deficiencies). Its a misunderstanding of history. We ate those foods before, but they weren't the ONLY things people ate. The result is ultimately still restricting diet to healthier foods which means it's nutricious, but still unnecessarily restrictive and without a realistic premise.
Not to mention the fact that your food has evolved as well.
My question was an oversimplification.
I've been vegan for 10 years, have lived in 3 different countries and have met a lot of vegans, usually in situations where food was involved. My personal experience indicates that, overall, vegans eat less processed/refined foods than non-vegans and are more knowledgeable about nutrition than the average.
Regardless, the rest of my comment points out why the person I was replying to is wrong. Even your comment points it out. All you need to do to be a vegan is not eat animal products. This means you can avoid all of the foods that are good for your biome. That was the entire point of the quote from the article that was completely missed by the op.
In addition, not all vegetables are equal with regards to bacteria.
The other valuable information is why whole grains are OK to eat (I favor them in small portions only) and processed grains are so bad for us.
Is animal welfare the reason for dairy goods being out of fashion? I doubt it; it's easy to come by humane milk and eggs, although humane cheese, butter, kefir, yogurt, etc. are less common. And yet, vegans are the new vegetarians -- even the Jains are going vegan -- while we also get the paleo diet with its own reasons for being anti-dairy...
There's also hostility to bread. Bread and milk are historic European staples; a part of me suspects that hostility to these (at least in white Americans) is really about hostility to the past.
I switched to a2 milk and the difference to my digestive system was extremely obvious. Time will show that for many people, if they consume milk, it should be a2 milk.
Also, change as little else in your life as possible while you're performing the experiment to control for confounding variables.
I'm applying data science to this disease. It's what I do, and can afford. Unfortunately, my doctor thinks that pushing pills is an adequate response, which I heartily doubt.
The more I understand this disease, it has to do with either: pancreas is dead (type 1), or your glucose response/insulin response is badly out of whack due to a metabolic carbohydrate problem (type 1.5/2). I was diagnosed with a fasting glucose of 161 and a1c of 7.1 . Met with doctor, and talked about it shortly. Was prescribed metformin and testing kit with 100 strips. I am currently not taking any drugs.
I keep reading that the problem is carbohydrate overload to my genetics. Can I validate or invalidate that? Indeed. I was told to test blood sugar 1x a day for 3 months. That's inadequate, as it's only an instantaneous sample. What about after I eat? What about when I go to bed and wake up? Can I deduce anything about my pancreas and its slow and fast response to glucose? Indeed.
I've started testing myself 4x every meal(1 before meal, 3 half hour increments after meal ends), and 1 when I wake up and go to bed. Turns out that yes, carbs has, in my body a direct correlation to my blood sugar. And it's pretty stark.
Now, if my hypothesis is correct, I can control my blood sugar purely with carb counting and eating to the glycometer. If after 2 weeks this does not show significant changes in my basal glucose rate, as well as weight losses, then I will go on drugs.
However, I already have 2 good side effects: I'm not craving for food any longer, and I no longer overheat. I'm not sure how to classify those effects, but not being slave to extremely annoying bodily issues does seem very beneficent.
First, you may find a continuous glucose monitor helpful to get a more granular view of what's going on. Dexcom  makes the most popular one, which is also hackable .
Second, keep in mind that all carb avoidance isn't equal. If you up your protein a lot, you could still get postprandial glucose spikes due to gluconeogenesis from protein breakdown. A good low-carb diet for you will be a low-carb, high-fat diet.
Third, for extra bang for your buck, go for a walk after you eat. The CGM, if you get one, will verify the efficacy of that.
Fourth, look into high-intensity exercise, which will help combat your insulin resistance. All exercise is not the same. Weight training is particularly good.
Your MD's reaction is sadly typical. You're taking the right approach by taking matters into your own hands, using her as a backup.
I've looked at the Dexcom unit. I would like to run with it for 2-3 needles (20-30 days) to get accurate data on things I surmise are good, but yet cannot prove.
I've also worked on guessing the score before I test. Interestingly enough, after about 2 days with the meter, I within +-2 points. That really surprised me.
And a very good point about the exercise after I eat. I have been doing that in the evening, not always after I eat. I'm going to believe you without proof, only because my body knows I need the exercise. I've also heard that HIIT is also great (meter backed results).
If I do worsen, I do have the metformin I can fall back on. I'd rather not make that the first response if diet shows more effect.
Have you tried squats after eating.
Use of the largest muscles in the body may help with extra glucose sensitivity.
When I asked my doctor about what kind of exercises to do, and whom to ask about that for safe weight loss via exercise, he said "Oh just do exercises".
I also have an existing shoulder injury, and meeting with an orthopedic surgeon. His answer was "Don't do these 2 exercises because of exacerbating the condition, but the rest are safe. And These will help."
I'm still kind of in the research phase on what I can do that will cause a good amount of change. But my research also shows that a safe amount to lose is 1lb/week.
>Participant A maintained a stable blood glucose level after eating a cookie but responded with elevated glucose levels after eating a banana. Conversely, participant B experienced an increase in blood glucose level after eating a cookie, but not after consuming a banana.
>In another striking example one of the participants, a middle-aged woman who was obese and pre diabetic learned that her “healthy” eating habits may have actually been unhealthy for her. The researchers found that in her case, eating tomatoes resulted in an “unhealthy” blood sugar spike, as the woman ate tomatoes frequently over the course of the week long monitoring period, this “healthy” habit may have been undermining her health.
From what I have read, early type 2 diabetes can be completely controlled via diet changes as you have already started to see. The amount of insulin your body needs to make is by far the largest for carbohydrates, then somewhat less for protein, and then near zero form fat.
I liked this talked which summed up the argument for treating diabetes (type II at least) with diet and not drugs: https://www.youtube.com/watch?v=da1vvigy5tQ
Episode that impressed my wife basically showed a women stop having diabetes 2 a few weeks after being put on a no-carb (well, no sugar and no high-glycemic carbs, but meat, fruit and veg) diet.
My fasting glucose was 99 so I'm not sure what to make of that. I ordered a glucose monitor just to learn how different foods affect me.
And what about accompanying seasoning? Olive oil, coconut oil, fatty meat/fish.
P.S. Absolute fasting can be dangerous.
I'm not a doctor however so take any advice with a grain of salt. (But not sugar, definitely not that.)
> I keep reading that the problem is carbohydrate overload to my genetics.
Read up on "glycemic index". This index tells you how close your food is to pure glucose e.g. table sugar has a glycemic index of 68 so it has 68% of the insulin response of pure glucose. The index correlates to the type of carbohydrate and how processed it is, although there are some surprises e.g. premium ice cream has a G.I. of 37.
You don't have to commit the entire index to memory. Usually you can come up with several heuristics e.g. tropical fruit tends to have higher G.I. than temperate fruit.
Obviously you should test this with your own blood sugar readings as individual response to a carbohydrate challenge can be quite different.
The other components to a meal also affect blood sugar. For example, acid, protein and fat tend to slow down digestion and thus blood sugar spiking. If you must take pasta for example, take it with a tomato-based sauce (acidic) rather than cream-based. YMMV.
> Unfortunately, my doctor thinks that pushing pills is an adequate response, which I heartily doubt.
It's important, although somewhat depressing, to see this disease as a progression. A progression that you have to slow down as much as possible, but still a progression.
Know that in the future, you may have to resort to the first line of pills, and then possibly stronger ones. Try to slow down the progression as much as possible, and research the pills to see their efficacy and benefit.
Metformin is usually the first line of defence and it has a long history and little side effect. It generally fools your body into thinking it's in starvation mode, which means you can lose weight, both fat and muscle. It actually lowers insulin resistance rather than increasing insulin. Generally in amounts >1g it gives you loose bowels, so when you have to use it keep on low doses as long as possible.
When metformin doesn't work as well, generally you'll get prescribed sulfonylureas. Since they increase insulin secretion, they tend to exacerbate your insulin resistance. There is some inconclusive research that they burn out the pancreatic beta cells. Better to avoid these as long as possible, but if your glucose control is bad you may not have a choice.
I'm currently on an incretin enhancer (gliptin) + metformin.
Also look up supplements on examine.com. It's hard to tell the effectiveness of supplements, the only one that had a distinct effect on me was berberine.
The other thing you can do is exercise. Lots of it. Strength training for more muscle and more insulin receptors. Aerobic exercise to burn/absorb more glucose and lose weight. There's even recent evidence that high-intensity interval training improves diabetic markers more than sustained, low-intensity exercise.
However, given some of my previous symptoms (thirst, extreme hunger, overheating) along with family history, a basic test was done. a1c=7.1 and initial fasting glucose = 161mg/dL
I'm approaching this aggressively, as I'm not sure exactly how many medical symptoms were caused/still caused by this, including mental fog during programming.
I'm dieting now, I'm going to re-test each time I drop 5kg to see if it helps.
Now I'm at 314.
And also, watch out about the a1c. They are not reliable readings to use in diagnosis. Studies from last year show a very skewed weighted average from the last 3 months that generate the a1c. Also, if you have any sort of hemoglobin-modifying illness (sickle cell, others), a1c is completely inaccurate.
140mg/dL is scientifically known to kill nerve cells. Every minute above this kills stuff. The ideal healthy human's response is between 85-100mg/dL. A resting rate away from this shows dysfunction.
However, an OGTT shows if you have problems. You take a reading prior to drinking 75g glucose. One big drink. Then you test every 30 minutes until you're back to normal, which is usually 2-2.5 hours. A doc won't say it, but every minute over 140 causes cell death, and most likely lower.
For example, this is what 12 carbs did to me:
18:20 12/09/2015 test 143
18:35 12/09/2015 eat 15m
19:15 12/09/2015 test 182
19:30 12/09/2015 test 172
19:45 12/09/2015 test 168
20:00 12/09/2015 test 150
20:15 12/09/2015 test 144
20:30 12/09/2015 test 123
Following the advice of my wife (a pharmacist!), I've been on a restricted calorie diet (1300kcal) for 10 days and it seems to have worked. My resting a1c is 4.3.
I can recommend trying it - although it's not easy. The first 5 days are horrible. I only managed it because I had a stomach virus (so wasn't eating).
Pills are expensive and it's crazy to be stuck on them if you can control your glucose with diet.
Are you sure you really want that extra side of chips? Or has your gut biome decided it wants that extra fat, and influences you to eat it.
Additionally, you can "reseed" your gut biome by changing your diet. Do you crave greasy food? Go vegan for 2 weeks. The new gut biome that develops and takes hold may soon have you start craving healthier foods. A change in diet can change your biome in as little as 4 days. (2) You can witness this phenomena in the movie Super Size Me. At the start of the movie Spurlock is disgusted by eating McDonalds for every meal. But, by the end of his experiment, his gut biome has significantly changed, and you can literally see his mood darken when he is not eating greasy fries and burgers. He craves, or should I say, his microbiome craves those happy meals, and is influencing both his taste receptors, health, and general mood in order to manipulate him in to a trip to the drive though.
It's worth noting that the study does not suggest that. It says that there has been some "circumstantial evidence for a connection between cravings and the composition of gut microbiota" and notes that there would be evolutionary pressure on microbes to be able to influence cravings, but gives no evidence on this point.
The thing the study was actually researching was ways microbes could influence cravings, not whether or not any of them actually were.
Meanwhile, it does appear you can noticeably change the expression of your microbiome by long term changes in your diet, but the effects we've actually found are still fairly subtle (at least in terms of metabolic outputs), and I've found no studies that indicate you can change cravings due to those changes. For example, in , "chocolate desiring" subjects had noticeably different microbiomes than "chocolate indifferent" subjects, but that difference was significant even when on the exact same diet (which was necessary for the study's methods).
You have to be careful not to extrapolate from actual data to "what makes sense". Spurlock's stuff appeals at a gut instinct level, but that's often the most dangerous kind of thing for science since our brains desperately want to make patterns out of data even when there isn't one.
The experiments basically fed gut bacteria from thin creatures, (mice / humans) to fat ones (mice) and they lost weight and visa versa for fat to thin. I guess you could extend that experiment quite easily to mice and chocolate though I'm not sure it's been done yet. Maybe if anyones got some experimental mice and bars of chocolate knocking around they could report back?
But i'm not saying that there is no such thing as the microbiome directly influencing your brain, bacteria produce a wide array of by-products. In which way these by-products affect our bodies is exactly the question.
I just want to point out that there are types of dysbioses that can reduce the ability to absord certain nutrients and by that could exacerbate the problem of cravings.
"We realize a diet like this doesn’t lend itself to being packaged and sold. It emphasizes how to think about food in the context of one’s microbiome, rather than prescribing a narrow choice of foods, counting calories, or advocating “dieting” as a daily activity. This advice is far from sexy and certainly not earth-shattering."
How you get there is up to you. Calorie counting and avoiding simple carbs works for me. As does training for at least an hour a day.
Actually, you could track cohesion, firmness, gassiness, possibly odor, etc. Unfortunately there's already an online community of people who do this kind of thing.
I'm a bit skeptical to the claim that whole grains is a nearly perfect food, though. Think about it - we apes have not eaten huge amounts of grains for most of evolution. Also grains contain various anti-nutrients, otherwise they would have been eaten by insects. It does not seem inconceivable that some of these insect-harming anti-nutrients could also be harmful for humans.
Many dietary studies are done with rodents, but I think (I'm not an expert here) rodents have eaten far more grains than apes during most of evolution. So studies with rodents showing that high-grain diets are healthy, are perhaps showing just that - that high-grain diets are healthy for rodents (and not necessarily apes).
You might have noticed that we do something other species don't. Cooking! It's a pre-digestion mechanism that saves a lot of work. Combined with our omnivorous digestive system we can probably be considered radically distinct from our ape ancestors (in a good way).
Is this what you were thinking about?
The evidence seems rather sketchy, though. From the article:
"If early humans ate grass-eating insects or large grazing animals like zebras, wildebeest and buffalo, it also would appear they ate C4 grasses.
If they ate fish that ate algae, it would give a false appearance of grass-eating because of the way algae takes up carbonate from water, Cerling says.
If they ate small antelope and rhinos that browsed on C3 leaves, it would appear they ate C3 trees-shrubs."
Seems more likely that they ate the animals, though. I mean, otherwise, shouldn't our teeth have been different by now?
Early humans were probably mostly scavengers anyway until fairly close to the agricultural period. Its unlikely they ate much meat.
Based on that section, I would look for an extract from The Good Gut (1) instead. It leans more towards science and less towards popularization....
I learned a lot about how digestion works and then a lot about how to make a book out of very thin gruel.
Also, Amazon reviewers have given it 4.7 stars out of 5, which suggests quite a few people found it useful.
(1) Justin L. Sonnenburg. Principal Investigator, and Erica D. Sonnenburg. Senior Research Scientist.
Even the most brilliant people quite happily believe dumb things.
Even so, I don't personally have enough background in the area to tell you much more than they publish in Journals with a reasonable impact factor. I can assume they know what they are talking about, but no matter the school, no matter the prestige, they could still be wrong and/or poor researchers and/or poor writers. They study ultra-specific things within an ultra-specific field.
Personally, I'd probably enjoy the book.
> no matter the prestige, they could still be wrong and/or poor researchers and/or poor writers
Sure, but those are generalizations, and they don't apply in this case. As you would know if you could be bothered to read it...
cost is relatively low (compared to typical C. diff treatments) and seems very effective, but isn't without it's risks. Research is still very early.
Do someone has any information on the "relatively large quantities" part? How much meat can I eat before protein putrefaction kicks in?