genetics

 Over the years I've been involved in this community, I've met many many people who have seen their health improve when they eliminated wheat gluten from their diet. But I also see it as part of a worrying trend that relies all too much on self-experimentation and self-diagnosis. Often when I meet these people they are noshing on a burger without a bun at a regular restaurant or ordering a salad a restaurant like Hanna's Bretzel where gluten-free ingredients are laid side by side with non-gluten free ingredients.

If these people actually have celiac disease, this is probably not an acceptable behavior. To be clear, celiac disease, which is an autoimmune disorder, is an extremely serious disease. Any gluten in the diet can contribute to long-term health problems and even cancer. 

Scary stuff. Scary enough that celiacs need to seriously consider cross-contamination at places like restaurants. Fries that are fried in the same oil as breaded chicken nuggets, eggs cooked in a pan that was used to cook French toast, salad made from lettuce served with tongs used to pick up croutons, these can introduce damaging gluten into a celiac's system. So it's not acceptable to just go to a regular restaurant and order a burger with a bun and some fries. Doing so might mean subjecting yourself to chronic damage. Senza, which is the gluten-free restaurant I reviewed recently, does not allow any gluten at all in its building ever. That is the level of strictness required to achieve remission of damage in most celiacs.

It's not surprising to find that in our culture where eating out is so common, many celiacs still present with intestinal damage years after initiating a gluten-free diet. 

I've asked many of these people who eliminated gluten from their diets and saw an improvement why they do not get tested for celiac. Sometimes it's a financial issue. They feel they cannot afford the tests. Other times they are concerned because a true diagnosis by intestinal biopsy requires that they eat gluten for some time before getting the test. I'd say that a month of feeling sick is worth it in order to avoid years of chronic damage. The alternative would be to commit to a truly strict gluten-free diet and stop eating at the local Irish pub. 

Which is think is totally unnecessary and silly for those of us who are not actually celiac. There is growing evidence non-celiac wheat sensitivity exists, but none that show that trace gluten could cause the kind of damage seen in celiac. It is likely it is more similar to lactose intolerance, which is dependent on dose (few lactose intolerants can truly never tolerate any lactose ever), than an autoimmune condition like celiac. 

I'm completely against strictness when it is unnecessary. For me it absolutely is. I was able to avoid a biopsy because I did a genetic test that showed I completely lack any of the genes related to celiac. Through the FODMAPs elimination diet, I found out it was the fructans that were causing trouble for me. I do occasionally consume wheat products, primarily fermented wheat and those made with heritage grains. They are not a staple for me because I don't think they are particularly great for you (that doesn't mean they are "bad") and they require quite a bit more effort than just making a meal with fresh meat and vegetables. I will continue to eat whatever I can get away with on special occasions and when traveling unless I see conclusive science that says any gluten ever is bad for anyone. 

But if you have the genes, that doesn't mean you have celiac, it just means it's possible for you to have it and you should pursue the matter further. I created this chart once to explain it to a friend:

Yes, it's crappy to have to go through all that to get a diagnosis and it can be hard to find a doctor that cares, but I truly believe it's worth it to know. Especially since celiac is becoming more and more common. I'm not a fan of Wheat Belly, (also see Dr. Deans' review) which essentially took a blog with some interesting ideas, and I suspect the publisher said "find everything that could possibly be bad about wheat and mention it without any nuance whatsoever." You can write such a book about almost any food. It reminds me of Whitewashed, which is about milk. I'm still waiting for the book about how evil shrimp is because some people are allergic to it. 

Shrimp is Actually EVIL SEA BUGS THAT CAUSE LEAKY GUT- the book

 On that note, a professor associated with the grain industry recently published a critique of the book. There are some good points there on Davis' hyperbole, misuse of studies (not citing the follow-up that disproves his theory, irrelevant in vitro studies, studies on genetically engineered mice) and use of the same tactics that plant-based zealots use (acidification! AGES! glycemic!), but right off the bat I spotted a bunch of mistakes. One of the most obvious is that the author mentions the Joe Murray study on historical blood samples. It says "the analysis shows that 0.2% of recruits had the gene in 1950 compared with 0.9% of recent recruits." And then it goes on to say increase prevalence might be due to better identification and awareness. But that study specifically refuted that, as it was not even studying genes, it was studying antibodies. It was an important study in pointing to increased prevalence, which should surprise no one who studies autoimmune diseases, most of which have increased in prevalence. 

“This tells us that whatever has happened with celiac disease has happened since 1950,” Dr. Murray says. “This increase has affected young and old people. It suggests something has happened in a pervasive fashion from the environmental perspective.”

Dr. Murray lists several possible environmental causes of celiac disease. The “hygiene hypothesis” suggests the modern environment is so clean that the immune system has little to attack and turns on itself. Another potential culprit is the 21st century diet. Although overall wheat consumption hasn’t increased, the ways wheat is processed and eaten have changed dramatically. “Many of the processed foods we eat were not in existence 50 years ago,” Dr. Murray says. Modern wheat also differs from older strains because of hybridization. Dr. Murray’s team hopes someday to collaborate with researchers on growing archival or legacy wheat, so it can be compared to modern strains.

Murray's team also used those blood samples to show that the undiagnosed airmen were more likely to have died young, possibly as a consequence of undiagnosed celiac. Undiagnosed celiac is frankly dangerous, particularly since it takes so little gluten to cause damage. There is still an argument about whether or not gluten is bad for everyone, but we aren't going to win over the medical profession if we use hyperbole instead of saying "hey did you consider whether or not your patient with diabetes/ibs/osteoporosis/arthritis/etc. might have celiac or wheat sensitivity?" 

So if you suspect that wheat is an issue for you, I strongly recommend taking time to get a firm diagnosis so you can know if you need to be 100% gluten-free. 

 In my last post on the subject of Dr. Jack Kruse, AKA, The Quilt, I briefly touched on the misuse of the ideas of quantum theory. Not long after, the WSJ had an excellent article on the mis-use of that subject. 

Actually, it's pretty interesting because I agree that both the mis-use of evolutionary biology and quantum science aren't that bad, because they show that people really are interested in science. They are just suseptible to bad science, which isn't a surprise considering the abysmal state of scientific education in this country. Only about 4 in 10 Americans actually believe that evolution is a real thing.

Well, here is some background for new readers. My original post confused some people who do not post on Paleohacks, where my rivalry with Dr. Kruse has a very long history.

The question of what drives popular interest in such evolutionary fantasies is a difficult one. Frequently, they are bundled in with good advice, further increasing credibility among laymen. They contrast with legitimate evolutionary biology in that they contain simple and often epic “just so” narratives that appeal to people, in contrast with the complexities and fervent debates in the academic study of human evolution.

An example of one such internet popularizer is the aforementioned Dr. Jack Kruse, a Tennessee neurosurgeon and dentist who started plying a “paleo” diet and lifestyle program called the Leptin RX Reset on various popular paleo diet websites (particularly Mark’s Daily Apple, which is ranked 2000 on the Alexa web traffic rating system in the US, and Paleohacks, which is ranked 8000) in 2010. Calling himself “The Quilt,” his posts quickly became some of the most popular on these sites. In June of 2011, he launched his own website, containing a blog and his master “Quilt” manifesto and cracked Alexa’s top 100,000 sites in the US within months, hitting 26,581 in March 2012. He gained a further audience from the online Paleo Summit, where his talk was among the most popular and where many people learned about the next part of his Leptin RX Reset program, the Cold Thermogenesis Protocol (CT). Then he was a keynote speaker at PaleoFX, an Austin paleo conference sponsored by The Ancestral Health Society that drew many of the movement’s most popular speakers. In the fall of 2012, he will be a panelist on a debate about “safe starches” at the Ancestral Health Society’s main conference, the Ancestral Health Symposium.

Evolution is central to Dr. Kruse’s ideas and recommendations. In a comment to reader he explained “ Adapting evolutionary biology to what we learn makes us a better physician not matter what we do.” His writings contain many references to human evolutionary origins and how his readers can use them to improve their health in a modern context. Many of his readers have reported success from using his recommendations, but is the evolutionary basis behind them sound?

During a panel at PaleoFX in Austin Dr. Kruse said

Only humans who fail to listen to evolutions rule book of engagement die. You can eat a banana in the winter and feel fine but Mother Nature says it’s impossible………therefore we ought not to do it. I will follow her lead over a diet book guru or the opinions of a bunch of people who let their thoughts subjugate their genes. Feelings and thoughts do not trump neural biochemistry …

But his writings reveal a more ambivalent view of evolution. On one hand, on one blog post he says that “The speed of evolutionary change has far out stripped the ability of our paleolithic genes to catch up.#” But in his Quilt manifesto he outlines an extremely plastic view “A human is the only animal that can actually change its DNA just by thinking. Moreover, what we really think is just a biologic secretion. No different than any hormone released by the pituitary gland. Thinking is… well it is a meme that hijacks our brain’s chemistry. Any one thought can alter our genetic and biologic purpose in life.#” Therein lies an essential paradox- on one hand our genes are “paleolithic,” but on the other they are malleable simply by thinking differently. Perhaps it is just part of our genes that are “paleolithic.” For example, he refers to our brains being neolithic and able to “subjugate” our paleo genes, with negative consequences: "our neolithic brains allow us to make decisions that subjugate out paleolithic genes all too often.”

The idea that human genetics have not changed since the end of the Paleolithic roughly 10,000 years ago and that they are mismatched to the modern neolithic environment is a common one in paleo diet circles. Unfortunately, its origin can be traced back to academia and it lives on as a popular principle despite the fact that it has been the subject of considerable controversy in evolutionary biology. A common citation in paleo books is to An evolutionary perspective enhances understanding of human nutritional requirements, a paper written by Boyd Eaton, Melvin Konner, and Marjorie Shostak in 1996:

Geneticists believe that the increased human number and mobility associated with civilization have produced more, not less, inertia in the gene pool and that when the humans of 3000-10,000 years ago (depending on locality) began to take up agriculture, they were, in essence, the same biological organisms as humans are today (Neel 1994).

More recent research has come to the opposite conclusion, as newer statistical genetics models have actually found that human evolution has accelerated greatly in the past 40,000 years, certainly not freezing with the advent of agriculture. However, along with many other paleo authors, Dr. Kruse is still of the less dynamic mindset, writing that “Evolutionary pressures are selected for by the environments of our ancestors were exposed to and not for what we face today.”

n academic anthropology, new discoveries in archaeology and rapid advances in genetics have spawned a discipline in which textbooks are outdated as soon as they are published. Human origins are constantly under debate, which means that even if scientific education were adequate in the US, it is fairly hard for anyone to keep up. But even a basic outdated education on the topic would help a layman be critical of several pop-science fringe evolutionary theories that have cropped up, such as the “aquatic ape” theory. Why do such theories become popular? As anthropologist Jim Moore put it:

Even among scientists, as we've seen with Hoyle, there are times when assertions are put forth which are poorly drawn, yet, because they strike a chord, often of wishful thinking, they catch on and are repeated. Yet refuting them can be an exercise in futility. A good scientific review and critique is a lot of work, and takes a lot of time. But it's far easier to pop off with a theory that's poorly researched than it is to accurately go over all the things that the original theorist should've, and to provide a point by point refutation.

In the case of the Aquatic Ape theory, Jim Moore did a major service by creating a website to refute it, since as he elucidates there, there is very little incentive for academics to engage in debates with popular pseudoscientific theories, since they are so focused on doing their own original research for the benefit of their careers.

This is unfortunate, because pseudoscience has great power to shape the public’s consciousness. As anthropologist John Hawks puts it:

Is the Aquatic Ape Theory fairly described as pseudoscience? Every statement of natural causes is potentially scientific. What distinguishes science from pseudoscience is social. Pseudoscience is supported by assertions of authority, by rejection or ignorance of pertinent tests, by supporters who take on the trappings of scientific argument without accepting science's basic rules of refutation and replication. Pseudoscience is driven by charismatic personalities who do not answer direct questions. When held by those in power, like Lysenkoism, it destroys honest scientific inquiry. When held by a minority, it pleads persecution.

In a world where many people are unhappy and unhealthy despite our scientific advances, the idea that conventional science is wrong can be quite appealing. It allows people to buy into fringe pseudoscience for which little evidence exists and not question the lack of evidence.

Dr. Kruse has a new interesting spin on the "paleo" diet, though whether his approach is "paleolithic" is up for debate. His spin on the evolutionary approach lately has emphasized cold. Why?

Considering that 90% of the earth’s current biome lives in extreme conditions on our own planet today still, we might need to consider that what we think is “our normal environment” is not so normal for most of life on our planet or our evolutionary history. Life on Earth evolved in an environment much like we see on Titan today; in a deep ocean frozen solid at its surface with the capability of life buried deep with in it. The only escape was due to ejectants of water vapor from super heated water from underwater volcano’s. All these things are present today on Earth’s crust too. There is one major difference now between the two. We are warmer today than life began. There are others, but when one looks at Titan we see a frozen giant moon with a monsterous ocean beneath it.

This creates an issue of whether or not Dr. Kruse is even promoting a paleo diet or if instead he is promoting a Archean diet. But if he is referring to the Archean, it is mystifying that he emphasizes cold, considering that the Archean was probably warmer than today. Dr. Kruse has "references" on his blog, but I would challenge anyone to tie the meandering list on his blog post with any actual "facts" in his writing, like that cold promotes autophagy or that Neuropeptide Y is downregulated in cold weather. 

Either way, debates as to the origin of life on Earth are still happening, with some (but not a consensus!) emphasizing the possibility that colder temperatures were the ideal place for single-celled life forms to originate. Dr. Kruse believes this is important because “life first adapted to extreme environments and then was naturally selected and adapted to a cyclic warming trend on our planets crust over time.” But he seems to believe that this adaptation was somehow incomplete: “Our hominid species may have adapted during this warming trend, but the DNA we inherited came from animals that were cold adapted.” Did DNA not adapt during this warming trend even through our hominin ancestors themselves adapted? It seems strange since Dr. Kruse believes that “One thought might just alter your DNA!”

Instead, he believes that these adaptations were mostly epigenetic, once again appealing to the idea that he knows more than conventional science “We know today that the power of epigenetics dictates a lot more about newer generations adaptations than we even knew ten years ago.” While epigenetics has become an important field, it is clear that a species adaptation to changing environments involves both epigenetic and genetic adaptations. Unfortunately, epigenetic is an appealing buzzword, which has been co-opted to absurdity. Dr. Kruse says that the warm paleoclimate that our primate ancestors were exposed to might not matter as much as we think it does because we might still carry an epigenetic imprint from the cold that engulfed Earth 3-4 billion years ago:

The modern science of epigenetics shows that who we came from and what they faced has a direct biologic effect upon subsequent generations DNA and phenotypes. It is crystal clear today, but the biologic implications remain unexplored in all modern day literature. What is happening on Titan maybe like opening up a blackhole back to a reality that used to be our own. The ability to see Earth at life’s evolutionary beginning.

This is confusing, because while here he blames epigenetic relics, in other writings he blames static genetics: “ The speed of evolutionary change has far out stripped the ability of our paleolithic genes to catch up. This mismatch causes major problems for modern humans.” Dr. Kruse seems to want to have it both ways.

The idea that epigenetic relics from billions of years ago are affecting us today is questionable, since the latest evidence shows that epigenetic changes are not stable enough to carry on from thirty generations and certainly not from 3-4 billion years ago. Evolutionary biologist Jerry Coyne has addressed people who hype up the evolutionary significance of epigenetics: “ There are a handful of examples showing that environmentally-induced changes can be passed from one generation to the next. In nearly all of these examples, the changes disappear after one or two generations, so they couldn’t effect permanent evolutionary change.“ This is in direct opposition to Dr. Kruse’s view of how evolution works:

I think evolution found that epigenetic modifications to be quite effective way to pass on environemental information to succeeding generations. So successful that it became a backbone law of genomic functioning. Evolution follows fractal patterning. So it is also highly conserved in all species. Today that appears to be true too.

While epigenetics has indeed led to important new understandings, it is less of a game-changer than Dr. Kruse presents: “Evolution uses epigenetics to determine adaptation to environments. We have discarded the strict definition of genetic determinism that came from Watson and Crick, as founders of DNA.” As evolutionary biologist Rama S. Singh succinctly put it:

While the new discoveries of the laws of developmental transformations are enriching our knowledge of the intricate relationship between genotype and phenotype, the findings of epigenetic inheritance do not challenge the basic tenets of the neo-Darwinian theory of evolution, as other than producing new variation no new processes of evolutionary change have been added to the ones we already know — mutation, migration, selection, and drift

Unfortunately, Dr. Kruse’s erroneous beliefs on human evolution have wide-ranging consequences holistically on his philosophy and recommendations, since it causes him to believe in conservation of many traits for which there is no evidence of conservation in Hominidae. Daniel F. Melia, professor of Celtic studies, recently wrote an article about characteristics of bad books that promote pseudoscience in his discipline. One of these characteristics is “Confident conclusions are often the result of chains of circumstance and supposition so long that even remembering their origin points while reading the books is difficult.” It’s easy to see that here and it shows how particularly ingenious this characteristic is since it makes anyone who tries to criticize the absurdities wade through the mire, further dis-incentivizing criticism.

A reasoning that Dr. Kruse uses for carbohydrate restriction is that epigenetics has sped up: “epigenetics has sped up and you eat a warm climate diet you by definition increase mitochondrial ROS that slowly kills you” A search of the scientific literature and academic databases found zero papers on epigenetics speeding up in modern humans. His article cites Wikipedia and himself. 

The phenomena he blames on an epigenetic speed up also often do not have known epigenetic causes.

This is more fuel or proof that the “metabolic trap door” I found makes all starches less safe when they are eaten outside how our circadian biology accounts for them in our sped up systems. Evolution power laws has sped up too simultaneously to compound the issue. This explains why kids today are huge and bigger than their preceding genrations. It explains also why they reach puberty faster today.

Scientists are not sure what is causing earlier puberty(NYtimes article yesterday). If Dr. Kruse really knows, he should be eligible for a Nobel prize. It’s also interesting because paleo authors are often quick to point out that Paleolithic humans were bigger and stronger than modern humans because of their healthier diets and lifestyles. Yet Dr. Kruse is portraying this phenomenon as a bad thing, which begs the question as to why the paleolithic humans were bigger. Were they eating too many carbs? Why modern humans are catching up to paleolithic humans in terms of height is a matter of debate, but the best theory is it has to do with greater access to calories and less malnutrition stress.

Overall, on the issue of genetics and epigenetics, Dr. Kruse seems willing to rewrite definitions and build a pseudoscientific narrative that has little basis in reality. It shows that new scientific discoveries that become buzzwords in the public consciousness are very easy to manipulate in order to build such narratives. They make them sound scientific and cutting-edge, when in reality they are empty and devoid of factual basis.  

I have MUCH more to write on this subject, including more on the evolution of mammals, hibernation, and hominin adaptations to cold. Also, a history of how he did not invent most of the regimens his followers praise so highly, as well as the actual non-pseudoscience evolutionary biology reasons that they work for those people. 

 A poor evolutionary nutrition narraive posits that because we didn't have X food in the paleolithic, we are maladapted to it. I think Mat Lalonde covered issues with this nicely at AHS and in the latest Paleo Solution podcast. 

Here is a funny twist to the story if it turns out to be true:

John Hawks, a biological anthropologist at the University of Wisconsin-Madison, notes that many HLA genes pre-date humans' split from Neanderthals and Denisovans, and that the differences may have arisen by chance as the groups evolved.

Hawks, too, has been digging into the archaic genomes, and his team has already discovered that Neanderthals and Denisovans lack certain forms of genes that may help modern humans to fend off epidemic diseases, such as measles. This is hardly surprising: the low population density of hunter-gatherers meant that epidemics were unlikely, so they probably would not have benefited from these immune genes.

But Hawks's team is now using the find to test whether the defensive genes are linked to autoimmune diseases. In September, Hawks and his colleague Aaron Sams are scheduled to present data at a meeting of the European Society for the Study of Human Evolution in Leipzig, Germany, showing that the Denisovans lacked nearly all of the gene variants linked to coeliac disease, a gut autoimmune disorder present in modern humans. Hawks suspects that the variants may actually be in the same genes that are linked to epidemic resistance — if they are, further study could reveal how recently such autoimmune diseases arose in humans.

Haha, it would be funny if an adaptation to civilization (diseases worsened by high population density), would also turn out to be a maladaptation as civilization progressed. 

A thought provoking book about the possibility that human cultures co-evolved with certain foods.