How to Clone a Mammoth

by Shapiro, Beth

  It was this experiment that motivated Iritani and his team to try to clone cells from the Yukagir mammoth’s leg. Although Iritani’s team was unsuccessful (none of the mammoth cells developed to a stage where it was possible to try to make cell lines), he remains undeterred. His team had, after all, managed to isolate a nucleus from a mammoth cell, which was a remarkable feat in itself.

  In August 2011, a mammoth thigh bone was found in the Sakha Republic that was so well preserved that it still contained greasy bone marrow. Certain that this was the ticket to cloned mammoths, Iritani used this find as a springboard to reinvigorate his mammoth-cloning plans. That December, Iritani announced that he would clone a mammoth by 2016. His timeline required that (1) they find a perfectly preserved mammoth during the following field season; and (2) they would be able to establish cell lines from that mammoth immediately. Given that elephants have a 600-day gestation period, his plan left no room for error.

  Iritani’s announcement was embraced by the global media, which delighted in the opportunity to publish yet another round of mammoth-cloning-is-inevitable stories. The most intriguing response, however, came from South Korea, where one more contestant in the race to clone a mammoth was about to emerge.

  In March 2012, Hwang Woo-Suk at the Sooam Biotech Research Foundation announced with great fanfare that Sooam had established a new collaboration with the North-Eastern Federal University in Sakha (with which the Mammoth Museum is affiliated, and with which Iritani had been working since 1997), and that he was going to clone a mammoth. The announcement went viral, complete with pictures of a smiling Hwang shaking hands with Vasily Vasiliev, vice-rector of North-Eastern Federal University, over official-looking documents. Almost immediately, the Moscow News published a clarification of the report. Without identifying its source, the Moscow News stated in strong and clear language that while the Russian Academy of Sciences certainly was planning to clone a mammoth, it would do so in collaboration with Iritani and the team from Kinki University and not with Hwang.

  It is not surprising that reaction to Hwang’s involvement in the high-profile cloning project would bring about mixed emotions. I mentioned Hwang earlier in this chapter, with a brief reference to his work to produce the first cloned dog, Snuppy. Hwang is, however, better known for his work in human cloning. In the early 2000s, Hwang was leading a research group at Seoul National University that was at the absolute cutting edge in human stem cell research. His group published two major breakthrough papers in 2004 and 2005. The first claimed that they had cloned the first human embryos, and the second indicated that they had made stem cells that were genetically matched to specific people; these were enormous advances for biomedical research. In Korea, Hwang was praised widely as a national hero. And then the walls came crumbling down. In 2006, Hwang retracted both papers after it was revealed that the data had been faked. He lost his job at the university and was stripped of his license to conduct stem cell research. He was also charged with fraud, embezzlement, and bioethics infractions and was eventually found guilty of the two latter counts.

  Hwang’s trial lasted for three years from 2006 to 2009. During this time, he joined the Sooam Biotech Research Foundation and continued his research, which was now focusing on cloning animals. The first official mention of Sooam’s plans to clone a mammoth came in 2012, with the announcement of collaboration with the North-Eastern Federal University. Hwang’s interests were already well established by that time, however. During his trial in 2006, Hwang explained why so much of the standard documentation of research expenses was missing from his files: he needed to pay the Russian Mafia for access to the best mammoth carcasses.

  In the autumn of 2012, on the heels of their big announcement, Hwang Woo-Suk and his student, Hwang Insung, joined Semyon Gregoriev of the North Eastern Federal University on a three-week expedition up the Yana River to find a mammoth to clone. The trip was being filmed for National Geographic by a London-based documentary maker who intended to tell the story of Sooam’s project from start to, well, start. Although the expedition did not succeed in finding a mammoth mummy, reports emerged as soon as they returned from the field that a remarkably well-preserved piece of skin had been found buried in the frozen ground. Most importantly, the skin was said to contain cells with intact nuclei.

  A few weeks prior to the trip, the filmmaker contacted me about joining the expedition as the genetics expert. Unfortunately, I had to stay behind (to give birth to my second son), but recommended my friend and colleague, Love Dalén, who runs an ancient DNA lab at the Swedish Museum of Natural History. Love tells a slightly less fantastic rendition of the story than the documentary portrays. In Love’s version, the team already knew where to look for a mammoth before the expedition began. Yakutian mammoth hunters had spent the early part of the season looking for tusks along the river. In doing so, they blasted a series of long tunnels into the permafrost along the riverbanks using high-pressure water. At the end of one such tunnel, someone had spotted a perfectly preserved baby mammoth. The mammoth—sans tusks, of course, as these would already have been removed by the first people to encounter the freshly exposed mummy—was still in place, and the plan for the show was to go back and get it. Unfortunately, by the time the expedition team arrived and filming began, late season rains and flooding had caused the tunnel to collapse, leaving the expedition/documentary team desperately searching those tunnels that remained for anything that would suffice for their show. The skin in question was found by Hwang Insung after he maneuvered into one such tunnel despite warnings from the expedition’s safety officer that it was dangerous to do so. Hwang found the piece of skin deep within the tunnel, just before getting word from the outside that the tunnel was about to collapse. After a few moments of desperate panic, those who had dared enter the tunnel emerged, narrowly escaping being crushed by several thousands of kilograms of frozen dirt.

  Did the bit of mammoth skin that they found have cells that contained intact nuclei? Perhaps. Finding what appears to be cellular structure is not uncommon in permafrost-preserved remains. Will the genome within those cells be sufficiently intact to be cloned? Doubtful. Love was able to take a subsample of the specimen to Stockholm where he extracted and amplified DNA. He confirmed that the skin was, in fact, from a mammoth. But the longest fragments of DNA that Love could amplify were around 800 nucleotides long. That is a remarkably long fragment for ancient DNA (the average length of fragments from permafrost-preserved specimens is closer to seventy nucleotides long), and it certainly indicates that the specimen is well preserved. Still, 800 nucleotides is a far cry from the length of an intact chromosome.

  In the summer of 2013, a new partial mammoth carcass was discovered frozen in a lake on Malolyakovsky Island, part of the New Siberian Islands. The find was absolutely stunning. The part of the mammoth that had been exposed was beginning to rot, but other bits of flesh were so well preserved that they were described as looking like fresh meat. Most intriguingly, a deep red substance suspiciously reminiscent of blood was found in the permafrost beneath the carcass. While most experts (myself included) are highly skeptical that the substance actually is blood—there is no animal with blood capable of staying unfrozen in the conditions in which this sample was recovered—research has been inconclusive so far with regard to what it actually is. The specimen has been kept frozen and is currently being studied in Yakutsk by scientists from around the world.

  Is this latest mammoth the “best preserved mammoth in the history of paleontology,” as Semyon Gregoriev, who led the expedition to recover its remains, is quoted as having said? Dan Fisher was one of the first to examine the specimen, and he confirms that parts of it are indeed impeccably well preserved. As to whether it is sufficiently well preserved to contain intact nuclei, we will have to wait and see. I remain skeptical.

  AND SO THE SEARCH CONTINUES

  It so happened that the two men who appeared suddenly outside of our enclosure on the third day of our ill-fated Taimyr expedition were
related to the Jarkovs—the family that found and alerted Bernard of the Jarkov mammoth in 1997. They were Dolgans, a group of people who are indigenous to that part of the Taimyr. While the rest of us were trying to pretend that the sudden appearance of strangers with guns had not nearly caused us to have simultaneous heart attacks, Bernard was inviting them into the enclosure and exchanging hearty handshakes and bises. Bernard, it appears, knows everyone in Siberia.

  Dolgans are nomadic reindeer herders. During the summer months, they move around the tundra, allowing their large herds to graze. They settle in one spot for a few weeks, until the reindeer have eaten everything in sight, and then pack up and move to the next place. In doing so, they have a chance to scope out pretty much the entire region. If bones, tusks, or mummified mammoths had been exposed when the ground thawed that spring, the Dolgans would know about it. The two men who joined us had seen our helicopter fly in a few days earlier and were curious to know what was going on. So, while the rest of their families were packing up to move on to their next location, the pair set out in search of us.

  As the initial shock of the men’s surprise appearance wore off, the heaviness that had settled in among the members of our expedition team began to lift and be replaced by the familiar, excited anticipation of what was to come. We gave them all the fish and rice they could eat and apologized for the lack of vodka. When the French couple opened the cooler and pulled out two giant cheeses—a gouda the size of a human head and what must have been three kilograms of brie—the entire crew erupted into laughter. Of course a French family working alone in Siberia would have a cooler filled with cheese. Even Pasha, who had managed to inch his face into the enclosure in a desperate attempt to keep the mosquitoes out of his nose, sniffed and flopped his tail onto the tundra. The whole scene was completely absurd, and we were only on day three.

  We invited the Dolgan men to stay in our camp for the night and, the next morning, took them back to their families in our outboard-powered inflatable boats. The entertained us for a while; we chatted about the weather, shared some French cheeses, and ate some of their prepared dried fish. We asked whether any of the Dolgans knew of sites that were actively producing bones. They had a few ideas but no strong leads. Then they finished packing up, hooked up their houses and gear to the reindeer, and set off for their next stop on the tundra.

  During the rest of the summer, we found only a few scraps of mammoth bone, as well as intact but poorly preserved bones from horses, steppe bison, and woolly rhinos. We later learned that the area we were searching had been covered by ice for most of the Pleistocene, which explains our lack of success. Luckily, before we left Siberia, Ian and I were able to take samples from some extremely well preserved bones that had been collected during previous years’ expeditions and that were stored in Bernard’s collection in Khatanga, so the trip was not entirely wasted.

  These bones did not contain cells with intact genomes. Fortunately, however, perfectly preserved genomes are not critical to de-extinction.

  CHAPTER 5

  BREED THEM BACK

  So, mammoth cloning is not going to happen. No intact genomes will have survived the 3,700 years since the last mammoth walked on Wrangel Island. No mammoth chromosomes will be found that are sufficiently repairable to transform the cells in which they are found into pluripotent stem cells. From my perspective, it doesn’t matter how many trips are made to deepest Siberia or how many tunnels are blasted into the permafrost. It’s just not going to happen.

  Should we just give up? Walk away dejectedly with our tails between our legs? Go back to the rest tent and cry into our mosquito-laden rice soup? Of course not! As it turns out, there are perfectly reasonable, perfectly feasible ways of bringing back a mammoth. Well, of bringing back kind of a mammoth. But let us not drown ourselves in the semantic argument just yet. First, the science.

  There are two ways to bring an extinct species back to life that are feasible in the present day. One of these is so straightforward that most people probably have not thought of it in the context of de-extinction. The other is more magical, and by “magical,” I mean the most-incredible-scientific-advance-in-a-long-while kind of magical. Let’s begin with the more straightforward approach.

  It is possible to bring an extinct species back right now using technology that our species began to refine some twenty or thirty thousand years ago. It is around this time that we find the first genetic and archaeological evidence of domestication—changing the course of evolution to suit our needs and desires. The approach is not overly sophisticated and requires only a reasonable grasp of basic evolutionary biology. Mainly, the idea is to take advantage of three facts. First, the physical and behavioral characteristics that define an individual—that individual’s phenotype—are determined by the sequence of the individual’s genome—its genotype—and the interaction of that genotype with the environment. Second, genotypes are passed down from parents to offspring. Third, natural selection can change the relative frequencies of different phenotypes within a population. In the wild, phenotypes that are better adapted to the environment in which the organism lives will become more common than phenotypes that are less well adapted to the same environment.

  To bring a mammoth back, we can simply take advantage of nature’s own process of genetic engineering. All we have to do is find the hairiest, most cold-tolerant elephants that exist and breed them with each other. After a few generations, we will have created, without calling upon any DNA-sequencing technology at all, an elephant that can live in Siberia.

  BACK-BREEDING

  Henri Kerkdijk-Otten is a friend of mine who lives in the Netherlands and loves cows. Specifically, he loves large brutish cows that may or may not taste very good and probably don’t enjoy being milked. Henri loves aurochs. Unfortunately for Henri, aurochs have been extinct since the middle of the seventeenth century.

  Henri, however, has a plan. He will bring his beloved aurochs back from extinction not by finding well-preserved fossils in European forests and not by nuclear transfer but by the comparatively simpler process of selective breeding. His hope is that he can create an auroch by carefully selecting and breeding animals that have physical and behavioral traits reminiscent of the ancient aurochs. After this process of choosing which cow gets to mate with which bull continues for many generations, the aurochs (or at least a close rendition of the aurochs) will be back. They will be able to roam free in the Dutch grasslands, where they will presumably thrive on the ubiquitous tulips.

  Aurochs are the wild ancestors of domestic cattle. Around 10,000 years ago, human populations in the Near East and South Asia began farming and taming wild aurochs. Eventually, this gave rise to the two main variations of domestic cattle—humpless taurine cattle and humped zebu. Today, taurine cattle are widely distributed across the globe and belong to familiar-sounding breeds like Holstein, Angus, and Hereford. Zebu tend to be farmed in the tropics, thanks to adaptations that allow them to survive better than taurine cattle in very warm climates. Because domestic cattle are descended from aurochs, much of the genetic diversity that was present in wild aurochs is probably still present in living cattle. It may, however, be distributed among the various breeds. To reengineer an auroch, one simply has to concentrate into a single new lineage all of the auroch-like traits that are present in living zebu and taurine cattle. The end product will not contain the genome sequence of a purebred auroch. It will, however, look like an auroch.

  The first genetic-engineering experiments performed by humans involved genetic manipulation of wolves, probably gray wolves that lived in Europe as long as 30,000 years ago. It is at this time that we find the first probable evidence of domestic dogs: bones found in archaeological sites that look similar to but distinct from the bones of gray wolves. These early stages of dog domestication were, of course, not hardcore genetic-engineering experiments. Instead, wolves that were more tolerant of humans and humans who were more tolerant of wolves both benefited from a closer association. Just l
ike my own dogs, these first dogs benefited from access to table scraps. The people living in proximity to these early dogs benefited from early warnings of approaching danger, much the same way I benefit from knowing that the mail has arrived. Once the symbiosis was established, humans put genetic engineering to work. Today we have big dogs, small dogs, strong dogs, fluffy dogs, dogs with short legs, dogs with long ears, hunting dogs, herding dogs, dogs that can find people buried in avalanches, dogs that provide life support for people with disabilities, and dogs that can be carried in leopard-spotted purses on trips to the grocery store.

  Henri and his colleagues plan to reverse-engineer the domestication process in cattle. Instead of breeding for traits that we tend to associate with domestic animals—tameness and manageability, for example—they want to re-create the wild ancestor of the domestic cow. Beginning with the more “primitive” breeds—including Maremmana, Moronesa, and two Dutch breeds, Limia and Sayaguesa—they have developed a selective breeding program designed to capture the physical and behavioral characteristics of aurochs and, in doing so, create a new cattle breed. The process is known as back-breeding, which is a name that highlights the goal: to breed back traits that used to exist and hopefully still exist somewhere in the gene pool of living individuals.

  Today’s effort is not the first attempt to back-breed the auroch. In the 1920s and ’30s, the German brothers Heinz and Lutz Heck, who happened to be directors of the Hellabrunn Zoological Gardens in Munich and the Berlin Zoological Gardens, respectively, were instructed to re-create the auroch. This directive is said to have come from Hermann Göring, who, as an avid hunter, wished to re-create the folkloric prey of Roman hunters. (Although it is unappealing to attribute the first back-breeding experiments to the Nazis, one cannot ignore the timing of this work in interpreting its motivation.) The Heck brothers had the same goal but performed their experiments separately. They each selected different cattle breeds and used these breeds in different crosses. At the time, no scientific reconstructions of the auroch were available, and so neither brother had a particularly good sense of what an auroch actually looked like.