This blog is about the intersection between evolutionary biology and food. But also about practical applications, sustainable agriculture, and general tasty things.
I was fairly young when I started having health problems. One of them was headaches. I had severe headaches and then migraines starting when I was maybe 9. By the time I was in high school, headaches, constant infections, fatigue, and stomach problems caused me to miss over a month of class every single school year. One thing that helped quite a bit was Excedrin Migraine, a combination of ibuprofen and caffeine. I popped those things like candy. I bought them all the time, taking the maximum dose for weeks at a time.
When I was a senior in high school I was diagnosed with my first ulcer and given Nexium. I was diagnosed with another ulcer when I was a freshman in college.
I don't know why doctors never thought to connect my excessive usage of Excedrin Migraine to my ulcers.
I've eaten all sorts of things since I discovered evolutionary medicine. Some of those things were not probably the best things to eat. And sometimes I've had stomach aches, but I've never gone back to my original horrible messed up state.
Except once. I was backpacking through Europe with friends. Let's just say I didn't sleep so well and I also drank my fair share of brandy, mulled wine, and beer. I came down with what was probably strep throat, but the trip was almost over and I didn't know how I could get treated in a place like Budapest. So I took the max safe dosage of ibuprofen for over a week, all through Hungary and Austria. By the time I got back to home base in Sweden, I was having heartburn again. It took a long time for me to get rid of that. It was extremely unpleasant to say the least, requiring a strict elimination diet to fix.
And at that time I did my research and found that NSAIDs could damage the gut lining. Some studies have connected NSAIDS to impaired intestinal permeability in IBS patients. I stopped taking them.
Last year I purchased 23andme for myself and then I also got my dad a kit for Christmas. I ran both of our outputs through Promethease, a cool open-source program I've blogged about before. One thing that I noticed this time was genoset 191, which is related to poor NSAID metabolism. Being super lucky, I have CYP2C8*3 from my father and CYP2C9*2 from my mother. Several studies have shown this genoset is associated with gastric bleeding. Now that's an acute symptom, but you have to wonder it can cause more subtle chronic stomach problems as well.
Both my parents were taking NSAIDS at the time I realized this. Both have a history of stomach problems. My mother discontinued them on my advice and she said it helped.
But when you stop taking NSAIDs, you realize how much our culture depends on them. Last year I messed up my knee while exercising and was kind of sore for a couple of days. I rarely resort to pain killers, but it was affecting my ability to concentrate. The office first aid kit only contained NSAIDs- aspirin, advil, etc. I walked to the drug store in pain and bought tylenol. It doesn't work as well for me as NSAIDs, but it worked OK.
But not being able to rely on pain relievers also forces you to address the real source of problems you might cover up otherwise. It seems like at least once a year, I get bad neck aches. Ususally it's after a big project when I sit hunched over for too long, even though I know it will have consequences. Unfortunate Even a standing desk doesn't fix this for me. Apparently I can hunch while standing.
Usually yoga helps it, but my regular yoga teacher moved away. When I went to another level 1 yoga class nearby, that teacher was really pushy about inversions. Now, I think inversions can be safe, but I don't think they are safe for beginners or people with certain structural issues at all. That's not the way the human body evolved to move and you really need to have good core strength and flexibility (the latter which I do not have) to do them safely. And of course my neck got worse after that class, to the point where I started to get headaches.
And the 8 Steps to Pain-Free Back stuff only helps so much when it's that bad. I can't maintain the recommendations in the book if my muscles are cramped and miserable. So I decided to try other things. I went to the chiropractor next door to my office. Now I am suspicious of a lot of chiropractic stuff, but when my neck is in such a state, it really does seem to help and I can chose to ignore the office woo about food/vaccines/etc. Which is kind of hilarious given how pushy some chiropracters are about getting x-rays, which increase risk for several cancers. They had a video playing in the office of the latest place I went that was about chiropractic care having been around for 2000 years or something. I wondered how it was ever possible it existed before x-rays considering how annoyed they were with me when I said I wouldn't sign off on them.
The other thing I didn't like about the chiropractic stuff is that I didn't feel it was fixing the root causes, just treating the symptoms and frustratingly when I brought that up to the chiropractor, they just said I needed to come in more. When I dialed back on my appointments because I was busy, the pain came back.
I started seeing a rolfing professional on a whim. Rolfing was pretty interesting- is it almost like a massage, but one that tries to correct your structure by interrupting dysfunctional fascia. It provided me relief and the rolfer provided some insight into some of the everyday imbalances that seemed to plague me. I got the book she recommended, The New Rules of Posture by Mary Bond, which I'm currently in the middle of.
It's truly an interesting book in how it points out the potential sources of problems. For example, I was under the impression that I was doing the right thing in terms of my shoes and walking. I walk a lot and I wear flexible thin-soled shoes. Earlier this year I started having some annoying heel pain on my right food. The exercises in the book pointed out that this is my dominant foot, so that makes sense. Or does it? Turns out that dominant doesn't mean what you think it means, the drive for the act of walking according to Bond should be the buttocks and ball/toes of the non-dominant foot, rather than the heel strike, which is how I was driving.
Also the Bond and Gokhale books both pointed out that the fact that my dress straps on many of the sleeveless dresses slipping is not just a minor annoyance, it reveals that my shoulders have become rounded over time, probably from a mixture of hunching (I often put my elbows on my desk and lean onto my hands) and letting my shoulder muscles atrophy. There is also just a host of interesting information about posture in the Bond book, particularly that about posture reflecting mood and social structure. If you think about this it makes sense. How many times have you seen a timid animal hunch down with you tried to pet them? Or cats arching their backs when trying to menace another cat? Or a guilty dog hunch and look down at the ground when confronted? In humans you start to notice this as well, seeing the introverted child or overworked programmer hunching? Perhaps this explains why various studies have tied unhappiness to back pain. They always frustrated me because some used them to imply that back pain is psychosomatic, but in my opinion it seems more likely that unhappiness and unhappy situations can lead to poor posture and also that pain from that can lead to further unhappiness.
So for the new year I plan on finishing the Bond book exercises. And I'd like to try out Feldenkrais and the Alexander technique. More Rolfing too with some gentle yoga, and occasional visits to the chiropractor just to release tension. And perhaps instead of doing group workouts, focus on my own weight training with my own deficits in mind. Any other suggestions?
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, I wrote about how it's impossible for epigenetic changes from very cold environments 3-4 billion years ago to have been conserved. Somehow people thought I was accusing Dr. Kruse of making up cold-adapted monkey ancestors or something.
No, I realize he doesn't mention cold-adapted monkeys, but he also doesn't stick to bacteria living in sad cold slurries either. He also mentions ancient mammals. Dr. Kruse also has an interesting belief that all mammals “evolved in the polar environments on earth.”
I can't find any evidence that early eutherian mammals evolved in such an environment or even a later candidate for a polar eutherian that could be a possible ancestor. They discovered the earliest known (so far) eutherian fossil last year in China, Juramaia sinensis, in a Late Jurassic formation. The climate in the area at the time was relatively warm and dry. Juramaia sinensis' teeth suggests it was an insectivore. Many other early mammal fossils have been found in Asia, but as we know, mammals went on to colonize a variety of environments and climates.
Dr. Kruse says "mammals were ideally adapted for hibernation too, until they got too smart for their own genes sake.” It is indeed true that Juramaia sinensis and other early eutherians did hibernate. Mevolutionary biologists now consider the origin of biological changes distinct to hibernation behaviors to have originated even before the evolution of class mammalia and are displayed even in reptiles who live in very warm environments.
Why did most mammals stop hibernating then? As the excellent paper The Evolution of Endothermy and Its Diversity in Mammals and Birds says “ energy-optimization-related selection pressures, often dictated by the energetic costs of reproduction, apparently favored abandonment of the capacity for short- or long-term torpors." In most primates, it seems this abandonment was characterized by a species with a large brain and increased adaptability to a variety of foods and climates.
That's too bad, because hibernation (or even torpor, a less extreme form) would be very useful for things like organ transplantations, surgery recoveries, or long space flights. In the future, if we figure out how to do it, being able to trigger hibernation would be incredibly useful. Unforunately, the exact way to trigger hibernation is not currently known, though there are many promising candidates. Dr. Kruse however believes that the stimuli is already known: “the stimulus for hibernation in eutherian mammals and their descendants are tied to high dietary carbohydrate intake (proven fact already in science and not controversial).” If only it were that easy. A search of the scientific literature found no papers that posited that carbohydrate consumption triggers hibernation, though it is established that carbohydrate metabolism undergoes changes before and after hibernation. Scientists who propose triggering hibernation believe it would probably involve injection of chemicals produced by hibernating animals. This would be possible because many of the genes related to hibernation are still present in primates, not because we hibernate, but because they have other functions. We'd also have to figure out how to prevent brain damage, which has been a major challenge to such research since humans appear to suffer memory loss from brain changes normal to hibernating mammals.
Evolution is efficient and while genes that had interesting past uses (wouldn't it be cool if we could "reawaken" gills or the ability to lay eggs??) are often conserved in our genome, they are often expressed in radically different ways. It seems the areas that once encoded for gills, for example, are now related to the bones in the ear. As for those that don't seem to be in use now, as geneticist Paul Szauter says:
If genes are not expressed in the human genome, they do not survive intact over evolutionary time, because they accumulate mutations in the absence of selection. If there were squid genes in the human genome that could be "activated," it is likely that the accumulated mutations would result in a truncated gene product (3 of the 64 codons are "stop") with many changes in its sequence.
Dr. Kruse believes that humans, like all mammals, are optimized for hibernation and that remnants of mammalian hibernation are activated in humans based on certain times of the day: "It appears 12-3 AM are the critical hours at night are where the remnants of mammalian hibernation lies for our species". This is a far cry from the current state on literature related to hibernation. The idea that remnants of hibernation occur in humans at night also goes against the definition of hibernation. An excellent paper authored by another McEwen, Dr. Bruce McEwen, has a great concise definition "Hibernation is a highly regulated physiological response to adverse environmental conditions characterized by hypothermia and drastic reductions of metabolic rate"
Re-definition and special unique definitions of terms is another of Melia’s characteristics of bad books: “ The texts of these books all continue in the same excited first-person voice. They often introduce vague, undefined or invented terms.” A good example of this is in Dr. Kruse’s PaleoFX talk, where he references “ geothermal circadian cycles.” It sounds scientific, but there are no known circadian cycles that are tied to Earth’s internal heat* and it appears Dr. Kruse invented the concept since it is found nowhere else. It is a particularly deceptive practice, made easier by the fact that many of the terms that are often mis-used by these authors, such as the species concept or even hibernation, are the subject of some academic contention. But while academics might be arguing about whether or not bears are “true hibernators,” we can be assured that no one is considering that humans are hibernating every night because that doesn’t even fit into the realm of contention or the fringes of what is considered hibernation.
The only known primate that hibernates is Cheirogaleus medius, member of suborder Strepsirrhini, which diverged from the evolutionary line that led to humans over 70 million years ago. They also store a lot of fat beforehand, so I don't know if I'd like to hibernate like them anyway. I don't think I'd look so good and I probably wouldn't get much work done.
Even if it were conserved, Dr. Kruse makes the mistake of tying hibernation to extreme cold: “Cold environments are found as mammals hibernate in normal circadian biology…….this completely reverses IR in mammals and wakes them up when conditions are better for life.” Dr. Kruse’s cold therapy involves exposure to freezing temperatures, because he thinks that is linked to hibernation in humans. Kruses asks his readers if maybe diabetes has “become thought of as a neolithic disease in humans because we we have simultaneously lost the ability to hibernate because we evolved the ability to control our environment completely?” However, there are many animals that hibernate without exposure to very cold temperatures and biologists are still debating whether or not relative cold is even needed to trigger hibernation at all. For example, the only hibernating primate, the aforementioned Cheirogaleus medius, hibernates at 30 degree celsius (86 F). And if humans had lost the ability to hibernate because we control our environment, we would find the ability in related primates who do not control their environments. But we do not. The northernmost living non-human primate, Macaca fuscata, does not show any evidence of hibernation or even torpor, even those that do not visit hot springs. Interestingly, their winter diet does include digging for roots.
Why do so few primates hibernate? Around the equator, where primates evolved, seasons operate quite differently than they do in the arctic and other regions far from the equator. Because the environments and climates of Africa are so diverse, with many micro-climates in certain regions, most primates closely related to humans have evolved to be able to adapt to scarcity regardless of Earth’s axis tilt through the reliance on “fall back foods.” Possibly because of this evolutionary strategy, there is no particular dietary pattern that consistently characterizes the seasons for primates as an order or even within species.
Even in non-primates that live in the north, a very small percentage hibernate. For example, some squirrels hibernate, some don't. Those that don't often will cache food and eat it later. Some humans are known to raid rodent caches for carbohydrates. This contrasts with Dr. Kruse’s idea of seasonal biological changes being triggered by changing to carbohydrates or one season being devoid of carbohydrates: “it appears that dietary carbohydrates, which are only present in long light cycles in the summer in cold places, induce mammals to add PUFA’s to our cells to become fluid so we can function as we hibernate.”
According to Kruse, since carbohydrate consumption is tied to hibernation in cold environments, since we don’t really hibernate now (except sort-of, at night according to Kruse), carbohydrates might not be safe to consume: “Since we no longer hibernate……..maybe you need to consider how you eat carbohydrates within the circadian controls? Maybe what you thought was safe………really is not?” The implication is that carbohydrate consumption is only “safe” for mammals in the context of nature’s “design” for hibernation. In terms of our evolutionary line, that makes little sense. The vast majority of primate species consume diets of mainly carbohydrate, with two main digestive strategies. The evidence is that ancestors of modern hominins relied on a mainly-carbohydrate diet until somewhat recently.
If Dr. Kruse’s line of reasoning is true, most primates are living out of balance with nature and have been for millions of years. Some of his followers have said that this only applies if you live in the north since there are somehow some circadian controls only in the North that are tied to carbohydrates (zero evidence provided), but then the mice and squirrels who are eating stored or underground roots are violating natures law. And the idea that if you put an individual primate in the north that it will change its underlying biology to fit the north's light cycles does not have any evidence behind it (and in fact the fact that individual humans don't adapt particularly well to northern light cycles is perhaps behind the etiology of many modern illnesses).
As I will write in my next post, some human populations (and possibly other hominin lines) have genetic adaptations to more polar light cycles, but these are recent adaptations and are not shared by all humans. And one unique thing is that humans that inhabit cold regions have a raised metabolic rate during the coldest season, not a lowered one characteristic of torpor or hibernation, which suggests adaptations more similar to those found in wolves rather than ground squirrels**. Also, I must also discuss longevity being derived rather than ancestral. But I'll leave that to the next post.
* Geothermal according to the OED is “ 1. Geol. Relating to or resulting from the internal heat of the earth; (of a locality or region) having hot springs, geysers, fumaroles, etc., heated by underlying magma.””
** are non-hibernating squirrels naughty "nature's law" breakers? Particularly if they are eating stored carbohydrates?
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.
Grains are evil. The people in the paleolithic didn't eat them. Amirite? Unfortunately, that hypothesis is contradicted by archeological evidence, but now there is genetic evidence that rice may have been domesticated earlier than thought.
Asian rice, Oryza sativa, is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies of Asian rice, indica and japonica, were domesticated from the wild rice O. rufipogon. In contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species range of wild rice. This latter view has gained much support from the observation of strong genetic differentiation between indica and japonica as well as several phylogenetic studies of rice domestication. We reexamine the evolutionary history of domesticated rice by resequencing 630 gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and domesticated rice accessions. Using patterns of SNPs, we identify 20 putative selective sweeps on these chromosomes in cultivated rice. Demographic modeling based on these SNP data and a diffusion-based approach provide the strongest support for a single domestication origin of rice. Bayesian phylogenetic analyses implementing the multispecies coalescent and using previously published phylogenetic sequence datasets also point to a single origin of Asian domesticated rice. Finally, we date the origin of domestication at ∼8,200–13,500 y ago, depending on the molecular clock estimate that is used, which is consistent with known archaeological data that suggests rice was first cultivated at around this time in the Yangtze Valley of China.
13,500 is older than what many people consider to be the end of the paleolithic, though many consider the paleolithic era to be relative to the region and would characterize a culture eating rice 13,500 years ago to be mesolithic.
The molecular clock also has its share of controversy, as it is based on statistical modeling, but no more than other evidence we have used to build the concept of the paleolithic diet.
I have written about my success with rice and hope to write more about it soon. Maybe I should just start calling my diet the mesolithic diet...
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.
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.
Thanks to Karen who recommended Promethease on my genetics post. I ran myself and got some fun results. Well, this one isn't so fun- I have a rare genotype, Rs12536657(A;A), associated with hypermyopia. Indeed, myopia and retinal detachment issues are common in my family. I thankfully seem to have halted my vision decline around the time I improved my diet, but that could just be vision stablization associated with age.
Last year I took a genetic test for celiac disease and my doctor told me it was impossible for me to have it. Unfortunately, like all things, there are many factors and genes at work. How much genetics coursework do doctors have to do anyway? That's why I feel that much future innovation will be done by biopunks- biologically educated nerds with time on their hands. That is unless our government "protects" us from our own genetic information. Oh the hilarity that people with science degrees and training in molecular genetics wouldn't have access, but older doctors who have never taken a genetics class in their life will...
Turns out I do have a variation strongly associated with celiac disease: Rs3184504(T;T).
In high school and early in undergrad, I was taking lots of NSAIDs for headaches. I developed ulcers because of this. Perhaps my gene associated with impaired NSAID metabolism was at play?
I also have a genotype associated with reduced conversion of beta carotene to retinol: Rs12934922(A;T). People with this genotype must rely more on dietary retinol, only present in animal products. It's interesting that this is most common in people with Northern and Western Europe Ancestry, perhaps reflecting an environment where dietary retinol was plentiful? I better eat liver anyway since I have a genotype associated with impaired folate metabolism.
I definitly recommend Promethease. It's a great way to learn about human genetic variation and your own variation in response to drugs and diet.
A thought provoking book about the possibility that human cultures co-evolved with certain foods.
Since I'm a total nerd, I was very very excited when I got my 23andme genetic test back earlier this week. I know quite a bit about some lines of my family tree, but other lines are quite questionable. My mother's father's family were poor immigrants whose names were changed at Ellis Island and they moved a lot because of gambling debt. The McEwen line also has a criminal element, my great great grandfather seems to have committed some sort of crime and fled to South America before reappearing across the country decades later. There is also the rumored Native American ancestry.
I don't have much Native American, less than 1% it seems, but still enough to show up on my "ancestry painting." I'd like my father to get tested to see my Y lineage and figure out where that Native American came from.
Another reason this was interesting for me was that I have some Ashkenazi Jewish blood. Unfortunately, the Ashkenazi are carriers of some infamous recessive genetic diseases like Tay Sachs. Being Jewish on only one side I don't suffer from these, but if I had children with someone with Ashkenazi blood it would be a danger. Fortunately the only Ashkenazi disease I carry is Factor XI Deficiency, a type of hemophilia. More exciting was matching with possible 4th, 5th, and 6th across Eastern Europe. I'm hoping they can help me fill in the family tree. And maybe if I visit Ukraine someday I can meet them. It's interesting that most of my matches are Jewish. I wonder if that reflects that diaspora's interest in lineage or a worries about genetic disease.
I do find it amusing that most of the third cousins it matched me to haven't responded. Maybe they already know me from family reunions and don't like me or something.
As for health, I wasn't surprised that I am at higher risk for alcoholism considering my family history. The other things I'm higher risk for include lupus, type 2 diabetes, ulcerative colitis, and multiple sclerosis. There isn't much cancer in my family so I wasn't surprised that I don't have any of the major cancer risk genes. It's nearly impossible for me to have Celiac disease. I've been looking at genes related to eosinophilic esophagitis and hypotension on my own since 23andme allows you access to the raw data.
I also wasn't very surprised to find I'm genetically lactose intolerant. I haven't been able to drink plain old milk without discomfort for ages. I do get annoyed when people seem to think that lactose intolerance is truly serious. I can still merrily eat normal butter and most fermented dairy products.
I'm also very happy that I'm not related to my boyfriend, Chris Masterjohn. He also had his DNA done at the same time. His results were more interesting than mine since he actually was able to use it to diagnose a health problem. But I'll let him share that story on his own blog. 23andme has an inheritance calculator that tells me that if we had a baby, there is a 40% chance that baby would have blue eyes :)
The fact that humans cannot digest certain fibers and starches in the diet does not mean they are nothing but bulking matter. In the scientific world, more and more research focus has been on the fact that these seemingly indigestible ingredients actually are often digested in the human body, just not by human enzymes. Instead, they are digested by human gut bacteria.
While the human gut may not rely on its bacterial population for calories to the extent that other primates do, the colonic microbiome remains of vital importance to human health. Scientists are just discovering how the bacterial population and its byproducts play important roles in human nutrition, the immune system, and other vital bodily processes. The gut flora is currently under investigation for its role on hundreds of diseases (Guarner & Malagelada, 2003).
Borne out of this are several new paradigms for studying fiber, not as bulk, but as an interaction agent with gut bacteria. The importance of the species mix, population level, and products has been emphasized. One new term for some fibers is “prebiotic.” A prebiotic fiber is indigestible by human enzymes, but stimulates the growth of certain beneficial gut bacteria such as Bifidobacterium and Lactobactillus (Gibson, Roberfroid, & Louuain, 1995). Among the most effective are fructooligosaccharides such as inulin. These are present in modern foods such as Jerusalem artichoke, chicory, onions, and garlic, but there is extensive evidence inulin-rich foods were eaten in the Paleolithic (Henry, Brooks, & Piperno, 2010; Leach & Sobolik, 2010).
More interestingly, prebiotics are a component of human breast milk as human milk oligosaccharides (HMO), which play an important role in establishing gut bacteria that modulate the immune system (Bode, 2009). They are currently not added to infant formulas and deficiency in them has been linked to diseases such as necrotizing enterocolitis.
Figure 1: HMOs help protect the infant from infections through reducing the ability of pathogens to bind gut cells.
All primates produce milk oligosaccharides, but HMOs differ structurally from those of chimpanzees and bonobos (Urashima et al., 2009). These differences could stem from disease pressures, but since HMOs are important for establishing gut bacteria, it is possible they also evolved to set up the optimal bacterial mix for each primate’s diet and environment. There have been few studies on the differences between different primate gut microflora, but the few available such as an analysis comparing macaques and humans suggest that the human gut microflora is significantly different (McKenna et al., 2008).
Gut flora comparison
Where these species come from is a controversial matter. Studies trying to use orally administered probiotics have failed to establish these prebiotic bacteria in the gut, though implanting feces from healthy donors through enemas (bacteriotherapy) has been found to re-establish the flora of some desperately ill individuals (Khoruts, Dicksved, J. K. Jansson, & Sadowsky, 2010; Tuohy, 2003). Evidence points to most gut bacteria being established through maternal transfer (Ley, Peterson, & Gordon, 2006). Most of the gut bacteria cannot be survive outside the gut, so it is likely they have been our residents for a very long time. Analyzing the roles of various bacteria and trying to determine how long they have been residents in hominid guts is a potential method for analyzing diets of our ancestors.
It also calls into question the origin of gut microbiota differences in human populations. A study of gut bacteria comparing rural children from Burkina Faso to urban children in Italy found that during breastfeeding their gut ecology was not significantly different (De Filippo et al., 2010). However, once they started eating solid foods, their gut bacterial populations differentiated.
Figure 3 rRNA analysis of gut bacteria from chidlren from Burkina Faso and Italy
Children from Burkina Faso had greater levels of Bacteroidetes and lower levels of Firmicutes. Their microbiota contained bacteria from the genuses Prevotella and Xylanibacter, completely absent from the Italian children. The bacteria are known to contain a set of genes for cellulose and xylan hydrolysis, so it is possible they are selected for in the gut due to the high levels of these fibers in the Burkina Fasan diet. It would be interesting to know whether or not these bacteria represent an ancestral condition in humans that was lost in populations with less reliance on fiber. The Italian children also had more bacteria associated with disease, perhaps a relic of urbanizations effects on increased pathogen transmission.
It is not just the species that matter, but genetic variation within species of bacteria. A recent study showed that gut bacteria may obtain genes relating to food digestion from bacteria present in food. Analysis of bacteria from sixteen people found that a gene for producing porphyranases, enzymes used to digest porphyrans, a carbohydrate type only found in seaweed, were only found in Japanese individuals (Hehemann et al., 2010). The only other place porphyranase is found is in marine bacteria, so the hypothesized source was that gut bacteria used horizontal transfer to acquire the genes from bacteria present in seaweed in the diet. When this possible transfer occurred is unknown and one of the individuals studied was an unweaned infant, so it is possible it has been transferred maternally though many generations.
Gene transfer can only occur from living bacteria. Changes in the modern human diet may reduce the incidence of this happening. Cooking destroys bacteria, but there is an increasing drive towards sterilizing “raw” foods such as produce and nuts for food safety purposes. Most milk on the market is now pasteurized in order to kill bacteria and interestingly there have been studies showing that children who consume raw milk have lower levels of allergies and asthma (Waser et al., 2007) and children growing up in rural environments in general have lower levels of these diseases. Out of such observations the “hygiene hypothesis” was born (Yazdanbakhsh, Kremsner, & van Ree, 2002) which posits that lack of other species in our guts from bacteria to parasites is behind many “diseases of civilization.”
There are several recent developments besides dietary changes that make analyzing the gut bacteria of modern humans to provide evolutionary clues somewhat difficult. Maternal transmission is interrupted in children born by Caesarean section, who do not pass through the birth canal (Grönlund, Lehtonen, Eerola, & Kero, 1999). Antibiotics can also alter gut flora, though to what extent is controversial. Current evidence shows anti-biotic changes, including the presence of bacteria with antibiotic-resistant genes, persisting for over four years (Jernberg, Löfmark, Edlund, & J. Jansson, 2010)
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