The other path to creating a living organism is eerily reminiscent of the movie Jurassic Park. As is likely to be true in real-life de-extinction projects, Jurassic Park scientists were only able to recover parts of the dinosaur genome—in the case of the movie, from the mosquito blood that was preserved in amber. When they came across holes in the dinosaur genome, they used frog DNA to complete the sequence. Unfortunately, they weren’t able to know beforehand which bits of DNA were important to making a dinosaur look and act like a dinosaur, and which bits were just junk. We can only assume that these fictional scientists were hoping that the holes that they were filling in were mostly in the junk-containing regions of the dinosaur genome. But, of course, they were wrong, and some of that frog DNA let the unextinct dinos switch sexes miraculously, leading to disaster and $400 million in box office earnings.
In real-life de-extinction science, the plan is to know which parts of the genome are important in making the extinct species look and act the way it did. We would then find the corresponding parts of the genome of a close living relative, cut out these important sequences, and replace them with the extinct species’ version.
Of course, this is all easier said than done.
Let’s say we want to bring a mammoth back to life by editing an elephant genome to look like a mammoth genome. First, we have to learn what all the differences between the elephant genome and the mammoth genome are. Then, because making all the changes might be too much to accomplish (at least in the first de-extinctions), we could narrow down which changes to make by deciding which of the differences are important. We might learn, for example, that mammoths have a different copy of a gene called Ucp1—mitochondrial brown fat uncoupling protein 1—than elephants do. Experiments with mice have shown that Ucp1 is involved with thermoregulation. Since mammoths lived in very cold places and elephants do not, we might hypothesize that the mammoth version of this gene helped mammoths to stay warm. Our goal is to turn an elephant into an animal that can survive in cold places, and converting this gene from the elephant version to the mammoth version would help to achieve that goal. So, we construct a molecular tool that can go into an elephant cell, find the spot in the genome that codes for the Ucp1 gene, and edit that gene so that it looks like the mammoth version.
To make the complete mammoth genome, all we have to do is repeat this for every important difference between mammoths and elephants.
Next, we take the cell with the edited genome and inject it into an egg cell that has had its nucleus removed. That cell begins to divide and develop into an embryo, following the familiar path of cloning by nuclear transfer. We then place that embryo into the uterus of a surrogate mom, where it continues to develop and is eventually born.
That last step, in which one species is developing within the uterus of another species, might sound pretty straightforward. However, it also requires some careful consideration. Imagine a project to resurrect Steller’s sea cows. Dugongs, the closest living relative of Steller’s sea cows and therefore the most likely surrogate mom, have a thirteen- to fifteen-month gestation period, after which they give birth to a single calf. Newborn dugongs weigh about thirty kilograms and are a bit over a meter long—about one-third to one-half the length of an adult dugong. If the same size ratio applies to Steller’s sea cows, a newborn calf will be somewhere in the range of three to six meters long. Longer, at birth, than his surrogate mom.
To get around this, one might design a giant sea cow artificial womb. Or, perhaps, a better solution is to choose a species for de-extinction with more suitable options for surrogacy.
Will It Be Possible to Move the Resulting Living Organism from Captivity to a Natural Habitat?
Although much of this has been covered in the answers to the first four questions, I’d like to raise a few additional points here that should be considered when selecting a species for de-extinction. I discussed above whether appropriate habitat exists and what might happen to that habitat and ecosystem if an un-extinct species were suddenly reintroduced. Here, I’m thinking of the more technical aspects of reintroduction. How behaviorally hard-wired was the species? How much parental care was involved with rearing offspring? Were their behaviors learned, or were they born already knowing how to survive, find food, and find a mate? How social were they? Although I brought this up briefly when discussing the additional complexities of bringing back a species with no close living relatives, these are challenges that, to some extent, will face any de-extinction. The first unextinct individual of any species will necessarily be all alone in this world. If behaviors have to be learned, from whom will they be learned? Interaction with the surrogate mom or surrogate community might replace some of the missing social interactions. However, if behaviors are learned from these interactions, will they be the same behaviors that the extinct species would have exhibited? And is that important?
We know from ongoing conservation work that some species survive and seem to do well in captivity but fail to thrive once they are released into the wild. The reason for failure to survive in the wild differs among species. Sometimes animals bred and raised in captivity are easier prey when released, never having been trained to sense and flee from predators. Sometimes they lack the social structure in the wild that they need to be successful. And sometimes they simply never learn how to find their own food. In all of these situations, the only way the species would survive in the wild is if the wild was not actually the wild but instead a site that is actively managed by people. The economic cost of such hands-on management, which may not be small and is likely to take resources away from other conservation and wildlife management programs, needs to be weighed against what is gained by the de-extinction.
THE ELEPHANT IN THE ROOM IS A MAMMOTH
At the beginning of this chapter, I raised the question of who gets to decide what the first targets of de-extinction should be. When I asked the students in my de-extinction class which candidate they thought should have that privilege, they responded with complete silence. Eventually, they offered the only solution appropriate for a group of Californian students: it should be a group decision. But what group? And, even groups have to have a leader, someone who decides ultimately how the group will respond.
The truth is that, at least in these early stages of de-extinction research, the decisions about which species to bring back are going to be made by the people with the interest, money, and expertise to make it happen. The European team working to bring the bucardo back to life is just as unlikely to refocus its attention on the Tasmanian tiger as the Australian team working on the Lazarus frog is to lead the de-extinction of the Yangtze River dolphin. Unfortunately, money is probably the most important determining factor in whether a de-extinction project gains traction. After the death of the baby bucardo in 2003, the bucardo project went silent due to lack of funds. In 2013, after the fresh bout of attention to the project that followed the TEDx event in Washington, DC, the Hunting Federation of Aragón allocated new funds, and the team restarted their cloning efforts. Money, rather than any of the ideas discussed above, may also decide which species are selected for de-extinction. In their campaign to raise funds for de-extinction efforts more broadly, Ryan Phelan and Stewart Brand of Revive & Restore are targeting potential donors on Martha’s Vineyard, a wealthy enclave in Massachusetts just south of Cape Cod, asking residents to consider whether they’d like to see Heath hens roaming the island just as they did during the early twentieth century.
And then there is the mammoth. There may be compelling ecological reasons to bring the mammoth back to life, and I will discuss these later. It is also true that mammoths may face fewer technical hurdles in their de-extinction than other species might face. They lived in cold places and many well-preserved bones can be collected and used for DNA analysis. Their closest living relative is the Asian elephant, from which it diverged around 5–8 million years ago, and elephant moms are probably reasonable surrogates for baby mammoths. There is even a place for resurrected
mammoths to go: Pleistocene Park is likely to provide a suitable place for mammoths to live, although the steppe tundra that dominated the landscape during the mammoth’s reign is not found anywhere on Earth today. That is not to say that mammoth de-extinction would be without challenges. Elephants reach sexual maturity between ten and eighteen years old and have a nearly two-year gestation, which means that genetic engineering experiments will take a long, long time. Also, elephants are extremely social creatures, and there is no reason to suspect mammoths were not highly social as well. Recreating social contexts into which mammoths can be placed will be key to their survival and an additional challenge to overcome.
What inspired the mammoth de-extinction project was not that it would be easy or hard to accomplish, or that it might be ecologically beneficial to have mammoths roaming around Pleistocene Park (although, as I discuss later, the latter is almost certainly true and has become a motivating force as this research continues). The reason that George Church and his group at Harvard’s Wyss Institute selected mammoths, rather than kangaroo rats, as the focal species for developing the genetic engineering technology necessary for de-extinction is that mammoths are mammoths whereas kangaroo rats are, well, rats.
Stewart Brand says that his motivation to bring back the passenger pigeon is that these birds, in cultural terms, are as iconic as bald eagles. He believes that the highest value of resurrected passenger pigeons would be to inspire people to be more aware of and engaged in conservation. He puts it more poetically: “Flocks in memory, and flocks in prospect, can make the heart sing.” Of course, passenger pigeons are iconic because they formed ludicrously large flocks, which may be difficult to recreate, sustain, or tolerate.
In addition to the challenges of creating and sustaining enormous flocks, passenger pigeon de-extinction faces more (or at least different) technical challenges than does mammoth de-extinction. A high hurdle for passenger pigeon de-extinction is that it is not currently possible to transfer engineered nuclei into bird eggs. There is also no assembled genome sequence yet available either for the passenger pigeon or for its closest living relative, the band-tailed pigeon, but we’re working on that (plate 3). We also don’t know the extent to which the passenger pigeon was a social creature. The enormity of their flocks suggests they may have been highly social, but whether they need these large flocks to survive remains unknown. The Bronx Zoo, part of the Wildlife Conservation Society, is creating a habitat for the captive breeding of passenger pigeons, but as for whether they will ever be released into the wild, that’s also a big unknown. One benefit of choosing passenger pigeons is their generation time. They reproduce every year, so the research necessary to bring them back to life could proceed at a relatively quick rate.
Both the mammoth de-extinction project and the passenger pigeon de-extinction project will require new technologies in order to succeed. But how close are we to seeing either of these species brought back to life? What are the next steps, now that these two species have been selected for de-extinction? Knowing what to do first is easy. First, we have to find the right specimens and extract their DNA.
CHAPTER 3
FIND A WELL-PRESERVED SPECIMEN
One winter morning a few years ago, I met Mathias Stiller and Tara Fulton—two postdoctoral research fellows working in my lab—in a dark, sub-basement hallway of the physics building on our university campus. The dark hallway was home to our ancient DNA lab, which was a purpose-built facility for extracting DNA from poorly preserved samples. Artificial lights flickered ominously overhead as we shed our coats, bags, and shoes, leaving them in the row of outside lockers. Anything that might carry hitchhiking fragments of DNA from the outside world was strictly forbidden to enter the lab. We unlocked the door and moved into the anteroom. The air reeked of the bleach we routinely use to sterilize the floors, surfaces and walls. We dressed in the traditional getup of an ancient DNA scientist: full-body suit, sterile boots, two layers of sterile gloves, hairnet, facemask, and goggles. When we were ready, meaning that no skin or hair or piece of nonsterile clothing was exposed, we moved from the anteroom into the main part of the lab. Tara carried a smoking container of dry ice. Mathias carried an enormous mallet (sterilized, of course). And I carried a tiny plastic bag.
In the plastic bag was a stunning seventeen-million-year-old piece of amber. We had acquired this treasure from my colleague, Blair Hedges, who purchased it for precisely the purpose we had in mind. The amber weighed around eight grams, measured five centimeters long and three centimeters tall, and was a centimeter or two thick at the center. Encased within the amber were hundreds of tiny bees that had become trapped in the sticky tree resin millions of years ago and, to our eyes at least, were perfectly preserved.
We proceeded to the back corner of the lab, where we had installed a thick, sterile stone plate, above which hung a bright white light and movable magnifying glass. We removed the amber from the bag and wiped it down with a bleach solution so that DNA from anyone that may have touched it over the years would be destroyed. We then rinsed it twice with ethanol to wash off the bleach and allowed it to dry for a few minutes. As it dried, we waited in silence.
When we were certain that enough time had passed, Mathias picked up the amber with sterile forceps and placed it gently into the container of dry ice. Then, we waited again.
Although amber is fossilized tree resin, it is still somewhat malleable—anyone who has ever touched amber jewelry will know what I mean. Stabbing amber with something sharp might dent it, but amber is nearly impossible to break or chip. We wanted to get this piece of amber really, really cold, so that it would be hard and rigid. Brittle.
After ten very long minutes, Mathias picked the amber out of the dry ice with the forceps and placed it carefully on the stone. I then raised the mallet and smashed the little glimmering piece of geological history over and over again until it shattered into a zillion tiny, shining, sticky chunks. Then, using the magnifying glass, we sorted the amber from the bees (plate 4). This involved a lot of re-freezing, re-smacking, and skilled operation of tweezers. After a few hours, we had one tube of mostly amber and another of mostly bees. We took the tube of bees and stuck it in the freezer. We were done for the day.
The next morning, Mathias began the process of extracting ancient DNA from the amber-preserved bees. Over the years, people working in the field of ancient DNA have developed highly sensitive DNA extraction protocols for situations like this one. If DNA had survived in these bees, there certainly wouldn’t be much of it left. Mathias opted for the extraction protocol that had proved most successful in recovering very old DNA. We were giving it our best shot.
When the extraction experiments were complete, it was time to send the results off to be sequenced. And then wait. The sequencing results came back three weeks later. We got nothing.
I was disappointed. How incredible would it be to recover DNA from insects preserved in amber? And by incredible, I mean implausible. Far-fetched. Unbelievable. Mathias, I think, was relieved. We both knew that if we did get a result that suggested that millions-of-years-old DNA was preserved, that result would have taken over our lives. We would have had to spend considerable time and energy first convincing ourselves that it was real, and later convincing our colleagues that we had not made a mistake.
When staring into a piece of amber that contains a preserved biological organism, it is hard to understand why the community of ancient DNA scholars would be so skeptical of DNA recovered from that organism. Insects, frogs, and even a 23-million-year-old lizard have been found in fossilized amber, all in perfect physical condition. Why should their DNA not be preserved to the same extent?
The unfortunate truth is that DNA simply does not survive for millions of years. If we did recover authentic ancient DNA sequences from amber, we would have broken all the rules that we’ve come to understand about DNA preservation and decay.
WHAT? NO JURASSIC PARK?
Millions of years before amber is amber, amber is a s
ubstance called copal. Thousands of years before it is copal, it is tree resin. Tree resin is a sticky, amorphous, organic substance that is secreted mainly by conifers—pines, cypresses, cedars, sequoias, for example. The resin serves a variety of purposes. It protects the tree from injuries and infections. It may help to heal major wounds, like broken branches. It is also pretty smelly, which might attract curious insects. As the resin oozes out of the tree, bits of plants, insects, and other small animals get trapped and sometimes covered entirely by the sticky substance. Over millions of years, the volatile organic compounds in the resin evaporate, leaving behind only the nonvolatile compounds that make up the amber and anything encased within the amber.
Key to the remarkable preservation of amber-preserved animals is probably the speed in which they are engulfed by resin. If the animal is completely encapsulated and killed almost instantly, that leaves little time for bacteria from the gut or the environment to colonize and start the decomposition process. The tissues also become rapidly dehydrated, killing the enzymes within that would otherwise break down their DNA.
This idea—that amber might provide an exceptional environment for ultra-long-term DNA preservation—is precisely the rationale used by scientists in the early 1990s when they tried this experiment for the first time. Unlike us, however, these scientists claimed success. They shouted it, in fact, in reports that appeared in the most respected scientific journals.
How to Clone a Mammoth Page 6