Tag Archives: Ancient DNA

De-Extinction Is On Its Way

“What’s the point of bringing back some pigeons that have been gone for a century, or some hairy elephants that disappeared four millennia ago? Well, what’s the point of protecting unhairy elephants in Africa or over-specialized pandas in China or dangerous polar bears in the Arctic, or any of the endangered species we spend so much money and angst on preserving?”

– Stewart Brand

It’s difficult to argue with that logic. In 2012, the US spent over $3 billion on conservation efforts.

I don’t know about you, but I always dreamt of a real-life Jurassic Park. Unfortunately, it doesn’t seem like dinosaurs will ever have the chance to roam the Earth again. Quite frankly, with new research showing that most dinosaurs probably had feathers, I’m not sure it would even live up to what our minds are conditioned to believe dinosaurs to look like anyway. They’d be giant, carnivorous chickens, more or less. But what about a mammoth or a thylacine?

While the DNA that once inhabited a dinosaur bone is long gone, victim to over 65 million years of radiation, hydrolysis, and other forms of degradation, DNA can be found in some more recent specimens. But how would it work? How could we possibly bring back – that is, De-Extinct – an organism. Well, actually, it’s already been done.

The Sad Saga of the Pyrenean Ibex 

The last surviving Pyrenean Ibex died in 2000. Of all the ways for a species to go out, this one was found dead underneath a fallen tree. It seems as though Mother Nature was just out to get them. So, naturally, humans did what humans do best – try to one-up Mother Nature. Pre-emptively thinking in 1999, biologists cryogenically froze a tissue sample of Celia, the last surviving member of her species. When Celia died, scientists were ready to bring her back.

The technique used is called somatic cell nuclear transfer. You can find a short video of it happening in real time here. Essentially, an oocyte – egg cell – from a domestic goat was de-nucleated and the nucleus from one of Celia’s somatic (body) cells was inserted into the empty oocyte. The resulting cells were then transferred into a domestic goat surrogate. Unfortunately, the process proved technically difficult. 285 embryos were reconstructed. Of those, 54 were transferred to 12 ibex and ibex-goat hybrids. Only two survived the two months of gestation before they too died. One clone was finally birthed in 2009 – the very first de-extinction. Unfortunately, the clone had a lung defect, and died of a collapsed lung only 7 minutes after birth. One of the problems was likely the fact that Celia was already 13 years old – old age for a goat – when the tissue sample was taken. This means that her telomeres, the caps on chromosomes that protect the supercoiled DNA, were already very short. As DNA replicates, the enzymes cannot make it to the very end of the DNA (where the telomeres are located), so the telomeres are truncated. They act as a sort of buffering system to keep the actual genes from being damaged (on a side note, your age is essentially a function of your telomere length).

The procedure seemed to doom any idea of de-extinction. After all, if we can’t even bring back a species that has been dead for under a decade, how can we ever hope to bring back a 30,000 year-old wooly mammoth? Fortunately, scientists are incredibly stubborn, and didn’t just drop the idea all at once. With advances in technology, science fiction often becomes reality. In the field of de-extinction, the limiting factor is DNA extraction and sequencing technology, which seems to be growing faster than Moore’s Law predicts it should.

A New Method

So, is there another way – a better way – to clone an animal than by somatic cell nuclear transfer? Maybe, and it’s called induced-pluripotent stem cell (IPS)-Derived sperm and egg cloning. The idea behind this is to splice your target species DNA (say, from a mammoth) into a surrogate stem cell genome (say, from an Asian elephant). Because these are stem cells (or pluripotent cells), they can become anything. So you coax the newly modified stem cells into becoming germ cells – those that will make the testes and ovaries. You then insert the germ cells into the embryos of a male and female surrogate (Asian elephants, in our example). Now you have a male and female Asian elephant embryo with mammoth precursory germ cells. You grow up the two surrogates, and they will exhibit target species (mammoth) gonads (testes and ovaries). So, you then mate the two and out comes a “full-blood” mammoth (click here and skip ahead to about the 10 minute mark to see this example with falcons and chickens. I recommend watching the entire TED talk. It’s my favorite one, and will explain a lot about De-Extinction).

You will see a second De-Extinction in your lifetime, and hopefully more to follow. Expect it from – Passenger Pigeons, Gastric Brooding Frogs, and, hopefully, Mammoths.

Maybe We Can… But Should We?

This, to me, is one of the biggest hurdles. You have to convince people that something, at least of this caliber, is a good idea. I began the post with a quote from Stewart Brand that I think idealizes the argument for De-Extinction. Hank Greely, a Stanford Law School professor specializing in biomedical technology ethics gives an excellent TED talk on this (found here). To outline his talk, here are the 10 things we must consider, 5 risks and 5 benefits:

  • Animal Welfare
  • Health
  • Environment
  • Political Concerns
  • Morality
  • Scientific Knowledge
  • Technological Progress
  • Environment
  • Justice
  • Wonder

I will flesh these out quickly, but won’t spoil the TED talk.

Animal Welfare

  • Cloning isn’t a very “safe” process. It can take hundreds of embryos, and often the few who survive don’t last long. We need to ensure the welfare of the animals that we try to bring back.


  • What if we bring back an animal and it happens to be a great vector for a terrible disease? Oftentimes the beginning of an epidemic is a new, better vector.


  • If we bring back a species, is it going to cause ecological problems?

Political Concerns

  • If we make De-Extinction a plausible conservation effort, will it undermine current efforts to preserve what we have? Why try to save them if we can just bring them back? Similarly, is it worth it financially?


  • To be short, we are playing God. We are doing something that, presumably, has never really happened in almost 4 billion years of life. We are redrawing the branches of the tree of life. It’s not something to be taken lightly

Scientific Knowledge

  • We could learn things previously unknowable about genetics, evolution, and biology.

Technological Progress

  • De-Extinction is the edge of science. It is pushing technology to its outer bounds, making technological development increase faster than it normally would. This provides technological offshoots for many medical procedures.


  • Bringing back a species can actually be good for the community. See, for example, the effect of wolf reintroduction at Yellowstone.


  • Are reparations due? Its arguable whether or not we caused megafaunal extinction – mammoths, wooly rhinoceros, cave bear, etc. – but there’s no doubt that some species, such as the passenger pigeon, went extinct due to human activity, namely hunting. And, sadly, we continue this destructive path, which is stripping the Earth of some of its most precious large mammals – tigers, elephants, and rhinoceroses, just to name a few.


  • My favorite. This is what science does. It inspires us. It awes us. It brings our imagination outside of our minds and places in front of us. Wonder isn’t all that impractical either. Wonder is what drives scientific knowledge further. It’s a self-perpetuating field that is snowballing into the ever-decreasing realm of science fiction.

The “can we” of De-Extinction is coming to a close. It’s time to start discussing the “should we” aspect. The technology will be here very soon, but are we ready?


The Paleo Diet – Brilliantly Simple, or Simply Wrong?

Introduction to the Paleo

 According to thepaleodiet.com, “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 http://anthronow.com/wp-content/uploads/2016/04/AnthroZine_1601.pdf