The Paleo Diet – Brilliantly Simple, or Simply Wrong?

Introduction to the Paleo

 According to, “the Paleo Diet, the world’s healthiest diet, is based upon the fundamental concept that the optimal diet is the one to which we are genetically adapted.” Who can disagree with that? After all, it does make sense that the best diet would be one that, according to our genetics, our body can utilize most efficiently. However, is this what the Paleo Diet actually offers?

The Paleo Diet claims to offer “modern foods that mimic the food groups of our pre-agricultural, hunter-gatherer ancestors.” First we have to look at what the Paleo Diet means by our “ancestors.” Being a “paleo” diet, it is referring to our ancestors in the Paleolithic era, which extends from about 2.5 million years ago to about 10,000 years ago, just after the end of the last ice age and around the dawn of the Neolithic – or agricultural – revolution. 2.5 million years is a pretty broad range to select a diet from, but perhaps not so broad on an evolutionary timescale.

One issue that arises when studying the diets of ancient hominids is the fact that archaeological sites aren’t all too common past 10,000 years ago. The reason probably lies in the fact that prior to the Neolithic revolution, people were hunter-gatherers. They didn’t really have permanent settlements. Hunter-gatherers travel to where the food – presumably that which can be hunted (migratory animals such as elk, bison, caribou, etc. depending upon geographic location) and gathered (berries, nuts, shellfish, and so on) – is. This would vary by the season and even by the century as animals permanently migrated to new locations or became over-hunted in their current location. However, when mankind developed agriculture about 10,000 years ago, people began to establish permanent settlements. These settlements, which were fueled by the domestication of plants and animals and thus liberation from hunting and gathering, provide a rich source for archaeological artifacts. It’s difficult to find the few material bits and pieces of a nomadic lifestyle. When people settle for hundreds or even thousands of years in a location, artifacts build up, and the chances of finding something 10 millennia later are much greater.

How do we know about their diet? Archaeological evidence

So, how do we know what the hunter-gatherers ate? One way is to look through the archaeological sites that we do have. Animal bones are often signs that the inhabitants ate meat. Furthermore, we might find tools that could have been used for butchering along with cut marks on the bones that imply that the animal was butchered. Along with this, we can track morphological changes over time. Changes in the size and structure of certain bones, such as the mandible and cranium, might indicate a change in diet. A diet heavier in meat could require a larger mandible and would imply an increase in calories that would be necessary to support a larger brain in the larger cranium.

Osteological analysis, though, is qualitative at best. It’s important to remember that an archaeological site is merely a snapshot in time. For example, a site that was abandoned in the winter (maybe to move somewhere warmer, a death of the inhabitants, or something completely different) might show a heavy use of meat due to the fact that not many plants grow in the colder months. With so few sites, there isn’t very strong evidence one way or the other about diets. Small sample sizes can be incredibly biased.

Stable Isotopes

Another way is to study ancient diets is by using stable isotope analysis. If you remember from chemistry class, isotopes are two elements with the same number of protons but a differing number of neutrons. Because proton (atomic) number defines elemental properties, the two elements are actually the same element, but with slightly different weights. For example, about 99% of the carbon in the atmosphere is C12 – carbon with an atomic mass number (combined number of protons and neutrons) of 12. This is the most stable form of carbon, and thus the most abundant. Carbon has two other isotopes that are relevant to scientific studies, C13 and C14. Though there are many more isotopes, they are found in minute amounts and are so unstable that they decay rather quickly.

You have probably heard of carbon dating, which measures the relative abundance of C14 in an organic artifact and derives an approximate date based on known rates of decay for C14. This works based on the fact that there is a certain ratio of C12 to C14 in the atmosphere, which is taken up by organisms. After the organism dies, C14 begins to decay due to its heavier weight. While this is based on the assumption that C14 to C12 ratios were the same in the past, it can often be cross-verified with other forms of dating, such as stratification, phylogenetic dating, other forms of radiometric dating, and sometimes even early writings (for example, the date derived from carbon dating an item purportedly from some event can be compared to a written, dated historical document describing the event).

Stable isotope analysis works, as the name implies, by measuring a stable, rather than radioactive isotope. Because C13 is not heavy enough to decay (C12 and C13 are the only stable isotopes of carbon, and C14 is the most stable radioactive isotope), it will remain in the bones and teeth in the same C12:C13 ratio as when the organism was alive. Great! Although C12 and C13 are not discriminated in our bodies, some plants distinguish between C12 and C13, ever so slightly. Ribulose-1,5-biphosphate carboxylase/oxygenase – commonly known as RuBisCO – is an enzyme that, in most plants, binds to the CO2 entering the stoma. Rubisco happens to have a slight affinity for C12, meaning the plant – and everything that eats the plant – has a disproportionate amount of C12 to C13. These plants are known as “C3” pathway plants.

In arid climates, where water is even most precious, plants had to adapt. A problem arose due to the fact that water escapes from the stoma when it opens to have rubisco capture CO2. Therefore, some plants, known as C4 pathway plants, evolved to use another enzyme, PEP-carboxylase, to bind CO2. PEP-carboxylase binds much more strongly to CO2 than rubisco, and doesn’t present a preference for either C12 or C13.

Carbon isotopes are used in conjunction with other elemental isotopes, such as nitrogen, to assess relative ratios of plant to meat in diets. This is all based on small differences between heterotrophs and autotrophs, carnivores, herbivores, and omnivores. For example, organisms higher in the food chain tend to have more N15 than organisms lower in the food chain. It is important to understand the isotopic variation of the ecosystem, however, they can vary, especially when environmental manipulation (such as cooking) comes into play. Ultimately, stable isotope analysis has a modest amount of discriminatory power, but is not comprehensive. It utilizes quantitation to make a qualitative claim, and does so on a limited number of samples.

Problems with the logic of a Paleo Diet

Which “paleo” should we eat like? 10,000 B.C.E. Inuit people? 200,000 year old Mitochondrial Eve? 1 million year old Homo erectus? Clearly there were times, and species, of hominids that ate more meat than others. An Inuit living in north Canada survived largely off of seal fat. However, Homo erectus probably lived more off of fruits and nuts. Humans survived and came to dominate the planet due largely to their adaptability, including our omnivorous diet. Our ability to adapt to mostly nuts or mostly blubber has granted us freedom to roam from the heart of Africa to the frozen lakes of Canada. Paleolithic hunter-gatherers simply ate what was available to them.

Many Paleo dieters cite articles discussing health disparities that arose when agriculture entered the picture. While this is true, it’s not necessarily because we stopped eating a “paleo diet.” More likely, health problems arose because we stopped eating such a wide variety of foods. Many ancient peoples went from elk, bison, nuts, and berries to what we could domesticate. Eventually, our domesticated crops and animals grew in variety and things leveled out a little more. This was likely not a rapid transition. Domestication may have started out as simply a way to supplement hunting and gathering before the boom of the Neolithic Revolution. Regardless of your diet, it is important to eat a variety of food in order to encompass all nutritional ingredients. Many people in Westernized cultures today eat a much more monotonous diet than they should.

Are we genetically identical to our “Paleo” brothers and sisters?

One of the main arguments of the Paleo Diet is that our genome has changed little since the end of the Paleolithic period, meaning our bodies are still best adapted to the diet of that time. This argument is a bit short-sighted. To claim that our genome has not adapted to our Neolithic lifestyle is simply incorrect. It is true that our genome evolution lags far behind our cultural evolution, and is often overshadowed by it. However, there do exist some key differences in our genomes from those of a Paleolithic hominid. The two most well known adaptations are the amylase and lactase mutations. Amylase is an enzyme that allows for digestion of starch from grain. As the Neolithic Revolution kicked into gear, those with an extra copy of the amylase gene better metabolized all of the new grain they could grow. This extra gene places amylase in the saliva, helping break down the starch at the beginning of digestion rather than beginning halfway through in the gut.

The second mutation is a regulatory mutation. People are born with a gene that regulates the production of lactase, an enzyme that breaks down the biologically unusable dairy sugar lactose into the biologically usable sugars galactose and glucose. Before animal husbandry practices of the Neolithic Revolution, the lactase gene would be transcriptionally inactive, or “turned off” in most people around the age of 5-7. After this age, the child no longer breast fed, and really had no need for lactase. However, once people began raising dairy animals, such as goats and cattle, dairy products such as milk and yogurt became an important staple food. This seems to have caused positive selection for the genetic mutation that allowed the lactase gene to remain “on” throughout life. Those with the lactase and amylase mutations could better exploit dairy and grain products than those without the mutations. So, while our genomes are not radically different, they are indeed different, and have adapted to some of the Neolithic diet changes.


Although our genome is relatively similar to our ancestors, our microbiome certainly isn’t. The microbiome is the summation of microorganisms that inhabit us. This might not seem like a big deal, so let me put it in perspective. If we were to take the entire amount of DNA in your body, including that of the microorganisms, human DNA would comprise only about 10%. The other 90%? That would be the microbiome. You are 90% microorganism. With the recent completion of the human microbiome project, expect to see some incredible discoveries about the differences between ourselves and our Paleo ancestors in the near future.

So how do we study the Paleo microbiome? One way is through ancient DNA. Unfortunately (or fortunately, for researchers today), there were no Paleo dentists around, nor were there any Paleo toothbrushes. When people ate, plaque built up and calcified on their teeth. This calcified plaque is called dental calculus, and it preserves the DNA of the microorganisms that made up the plaque along with some of the DNA from the actual food. From this, using Next Generation Sequencing techniques, we can learn more about the kinds of food and the microorganisms that were present in the bodies of our ancestors. By comparing what we find to oral microbiomes today, we can have a better understanding of what Paleo people ate. Also, microfossils can be preserved in the dental calculus, allowing for a visual confirmation of food in the plaque. Again, these are qualitative measures that are inhibited by sample size. But, these are the best methods we have and they are producing some excellent research.

Is the food still the same?

People freak out about GMOs. The truth is basically everything we eat – meats and plants alike – are genetically modified. Over thousands of years we have artificially selected plants and animals for particular traits. As our genome has changed since Paleolithic times, plant and animal genomes have radically changed, largely due to human manipulation. So, even if you eat according to the Paleo Diet, you are eating the modern-Paleo Diet, not the Paleo-Paleo Diet. So, really, you aren’t even eating like you think the ancestors ate. Our modern plants are “human inventions,” as Dr. Christina Warinner – a leading Dental calculus expert at the University of Oklahoma – puts it.

Ultimately, the Paleo Diet, as it is marketed, isn’t really a Paleo Diet at all. There’s no harm, and definitely some benefit, in cutting refined sugars and overly processed meats out of your diet. However, eating modern versions of nuts, fruits, veggies, and more meat isn’t going to make you any more like a Paleo-man or Paleo-woman than if you just eat a normal, balanced diet. If anything, skipping out on legumes, dairy, and multi-grain wheat, which are prohibited in the Paleo Diet, could cause a lapse of certain nutrients. Technological and agricultural advances have produced some amazing foods that our Paleo ancestors could have only dreamt about. If you really want to be Paleo, then take advantage of the advances in food science. It’s what our ancestors would have done.

*A form of this is also published at



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