Forget The Woolly Mammoth -- Let's Resurrect Some Extinct Plants

Illustration: Angelica Alzona, Gizmodo

From Jesus to “Jurassic Park,” people dream of resurrection, cheating death, defying nature, and uncovering the mysteries of the past. We debate the ethics of reviving extinct species like the passenger pigeon or woolly mammoth, with scientists clamoring to make some poor, hairy proboscidean clone baby take its first awkward steps out onto the ice. Yet somehow, the idea of resurrecting long-lost plants never really caught on in the public imagination. Maybe that’s because most people probably couldn’t even name an extinct plant, let alone one they’d want to smell, see, or study, though Rachel Meyer, an assistant professor of ecology and evolutionary biology at the University of California, Santa Cruz, has a hard time picking just one.

She likes silphium, a mysterious herb prized by ancient Romans as a food, perfume, and aphrodisiac that, according to the BBC, was “overharvested and overgrazed” to extinction almost 2,000 years ago. But if she could actually resurrect any now-extinct flora, “I’d probably just opt to bring back some of the melon diversity that was lost,” she told Gizmodo. She cites bygone melon varieties eaten by ancient Egyptians, and others that, according to legend, were so good a Renaissance-era pope died after overdosing on the sweet, pulpy fruit.

“There are a lot of delicious ancient things,” Meyer said, “and I’m like ‘man, how did we lose that?’” Meyer rhapsodizes about “eggplant varieties in ancient ayurvedic texts” and extinct varieties of carrots “of beautiful different colours, flavours, and aromas,” used not just as food, but “in ceremony, and as medicines, and in embalming.” There’s a broad, storied slate of lost plant species and varieties “that have been sort of forgotten that maybe we want again,” she said, and it’s looking increasingly likely that “we could bring these things back.”

True, an island of prehistoric ferns probably wouldn’t have the same cinematic appeal as a T. rex, but in theory, the ability to bring a plant back from nonexistence could be a boon to conservationists, a way to restore long-lost wild biodiversity or traits that helped ancient crops endure harsh conditions. More than 99 per cent of all species that have ever existed are now extinct, there has to be some good stuff hidden in the genetic compost pile—what might we find if we start pawing through botanical history for forgotten foods or medicines? Now, gene-editing technology and advances in recovering DNA have opened up the possibilities for plucking treasures from the past, but there are already a few cases in which humans have brought back plant life, ages after it completely disappeared from the planet.

In 2012, a Russian research team reported growing ice-age flowers from fruit and seed material first buried by squirrels along the banks of the Kolyma river more than 30,000 years ago. The seeds, from a paleolithic version of a white flower called the narrow-leafed campion that still grows in Siberia, wouldn’t germinate; however, the scientists were able to use placental tissue to generate new plants, which bore viable seeds, making it the oldest ever regenerated flora. According to the team’s findings, the ice age flowers constitute a “distinct phenotype” from modern versions of the plant, and the experiment helped establish permafrost as a “depository for an ancient gene pool... long since vanished from the earth’s surface.”

The previous record for oldest resurrected plant—and current record holder for oldest viable seed—came from opposite climes, a date palm named “Methuselah,” germinated in 2008 from a 2,000-year-old seed found amidst ruins at Masada, a desert fortress in Israel. “In Israel, there’s a medical facility where there’s a garden, where they are mixed in with other dates, so you’ll never know,” said Meyer, who extracted the DNA and sequenced genetic information from leaf samples of the ancient palms. A new paper, published February 2020 in Science Advances, announced the researchers had successfully germinated six more of the ancient plants, which they note were “described in antiquity for the quality, size, and medicinal properties of its fruit, but lost for centuries.”

If one actually wanted to actually select the resurrected plant though, trying to find, let alone germinate, seeds like Methuselah’s is “a lottery that you’re likely to lose,” said Dorian Fuller, a professor of archaeobotany at University College, London. Usually, organic material like a seed eventually “gets recycled by other organisms,” Fuller told Gizmodo. “Most archaeobotanical material is preserved by charring, by coming into contact with fire,” he explained, keeping seeds from moldering and unattractive to hungry wildlife, but also preventing them from germinating.

Seeds like Methuselah’s are lucky accidents, the freak product of very specific conditions, like sheltered sites in extreme desert, the deep freeze of permafrost, or “waterlogged preservation” in a peat bog or the mud beneath a lake. Even in ideal conditions, most seeds are damaged or age out of viability eventually (with date palms seeds having a bit of an advantage, due to their large size and hard outer shell). Seed banks, which preserve collections for agriculture and science, only go back a little more than a century, and must grow specimens occasionally to produce new seeds, since “most seeds are non-viable within a decade,” said Fuller. Space and time are limited, he said, and many stored now-extinct varieties were never regrown, leaving their seeds as nonviable historic specimens.

Still, Fuller believes that currently extinct plants are “potentially an untapped resource” for humanity. While trying to sprout old seeds may not be a great bet, he sees possibilities in combining gene-editing technology like CRISPR and advances in recovering DNA from historical specimens. “Theoretically,” he said, “You could take genetic material out of an ancient plant and insert it into a modern seed.”

He explained how the last century or so of agriculture has increased dependence on heavy fertiliser use and irrigation, producing high crop yields but also low genetic diversity. These conditions have made crops unsustainably resource-intensive and left food supplies vulnerable to diseases, pests, and environmental woes. Shifting climate conditions are already causing chaos for growers around the world, as Earth experiences its hottest years in recorded history. Considering these trends, “a lot of traditional varieties, lost varieties, and even lost crop species might be more resilient,” said Fuller. It’s worth experimenting with “either taking lost varieties of crops we have today or even crops that we don’t really grow anymore and potentially bringing them back,” he said.

Fuller was part of a team that recovered seeds from a lost Nubian barley variety that thrived in some of the hottest parts of Africa, including northern Sudan, for thousands of years, eventually disappearing sometime before the medieval period. First, a few seeds were ground with a mortar and pestle, and the material was then put through a series of processes and solutions to prepare, extract, and purify the ancient barley DNA, taking great care to avoid any modern contaminants. The DNA was then sequenced, creating a picture that could be studied closely. His team identified clusters of genes in the ancient barley that don’t exist in modern counterparts, which they hypothesised to be related to water metabolism, in an adaptation to aridity. “In theory,” he said, “you could take those genes, engineer them into modern barley and see whether these revised genes made it more suitable for hyper-arid conditions.”

All researchers studying ancient life must ensure their samples aren’t contaminated by modern materials. Indeed, scientists in 1967 claimed to have grown a flowering plant from seeds found in a burrow dating back to the Pleistocene. In 2009, however, an analysis of the “ancient” seeds revealed that they were actually modern and had likely fallen into the burrow not long before their discovery. Researchers working with DNA today must take great care to keep their samples pristine.

Jamming DNA from extinct plants into living relatives certainly opens up the possibilities for resurrecting lost genes, but even speculatively speaking, there are limits to what could be retrieved. Scientists interested in plants from prehistoric periods would probably love to study, say, a real, live Gilboa tree, the tall, brush-crowned Devonian plant whose stumps populate the world’s oldest fossil forest. But DNA decays over time, and remains that old tend to only exist as impressions left behind on stones, or because they’ve fossilized, in a process that replaces the plants’ original material with minerals over time.

It’s not clear what the limits on gathering ancient DNA really are. Recent advances have allowed scientists to reach back further and further, piecing together fragments of time-ravaged DNA to recreate whole genomes. In late 2019, DNA was reportedly recovered from a 1.7-million-year-old rhino tooth, but according to Fuller, plant material usually doesn’t fare as well. The oldest ancient plant DNA ever recorded was pulled from frozen sediment cores in Greenland and estimated to be more than 300,000 years old. In parts of the world that haven’t been frozen for millennia, Fuller said, you could probably only retrieve plant DNA that goes back a few thousand years. Even in deserts, “you probably can’t find material that’s older than about 6,000 years, just because the world was wetter before that.”

Fuller said he’s not aware of any current, real-world experiments attempting to implant genes from extinct plants into modern seeds. Asked why he thinks that is, he replied, “it’s not cheap… and it seems to me that the institutions that do traditional crop breeding, crop growing agronomy, are not the same institutions that are doing ancient DNA and genome sequencing of crops.” For now, he said, “it’s just a quest to show that you can get parts of ancient genomes and say something interesting about them.”

The DNA wasn’t ancient, but last year, Boston-based synthetic biology firm Ginkgo Bioworks tried to do a little more than just “say something interesting,” when it announced it had roughly recreated the scent of two extinct plants, including a lost hibiscus variety. Once native to Hawaii, Hibiscadelphus wilderianus was “decimated by colonial cattle ranching,” according to the Ginkgo site, “and the final tree was found dying in 1912.” The project “started about six years ago from a conversation about whether it would be possible,” said Christina Agapakis, the company’s creative director. “Could we smell something that went extinct?” The project was a way “to use art as a way to experience something that’s impossible to experience without synthetic biology,” a chance to encounter “a ghost—a memory of something that’s gone,” she told Gizmodo.

Agapakis is a biologist, but she’s also something of a scientific art provocateur; in 2013 she was part of a team that crafted cheeses using bacteria from human feet and armpits. For the extinct scent project, she said her team spent years looking for the right species and samples, eventually hitting paydirt at the Harvard Herbarium, where tiny bits of leaves yielded the DNA they needed. The DNA was read and reassembled using a still-living hibiscus as a reference, then the gene sequences underlying the plants’ production of odorous compounds were identified. Rather than trying to host that genetic information in a modern relative, it was “reprogrammed into the genomes of yeast,” she said. The engineered yeast, living in vats, would then “eat” sugar and excrete the scent-related molecules once produced by the plants. “You can actually chemically separate the molecules of the fragrance,” said Agapakis, “and then you take that liquid, and then you purify it.”

Even once Ginkgo had reproduced those scent-related molecules, “we needed to work with an artist,” said Agapakis. Sissel Tolaas, a scent expert, created “a composition of a smell, to imagine what it might have smelled like... because we didn’t know how those molecules might have been mixed together, what else might have been there to make the full smell.” Agapakis described the result as “Less of a kind of floral smell,” and instead, “really woody and resinous.”

The Ginkgo extinct scent project highlights an important point: Experiencing the taste or smell of a lost fruit or flower might not require resurrecting the whole plant. In theory, if researchers knew what they were looking for, the same process could be used to recreate say, resins, poisons, waxes, or unique compounds that might have health benefits for humans. Could extinct plants be a trove of undiscovered medicines? Gizmodo asked Barry O’Keefe, chief of the Natural Products Branch at the National Cancer Institute and acting chief of the Molecular Targets program at the Centre for Cancer Research, who called the idea a “potentially fascinating possibility.” O’Keefe’s work involves the collection, extraction, and testing of material from organisms like plants in the search for unique compounds and chemical structures that might lead to cancer drugs.

When it comes to extinct plants though, O’Keefe said at this point, there’s just no particular reason to start rooting around in the genetic graveyard for new drugs. For one thing, it’s a lot easier to access still-living plants, many of which have yet to be evaluated for clinical potential. Also, while species go extinct for a wide range of reasons and there are surely many valuable, totally unknown natural products, he said, probability dictates that there would be fewer of them in extinct species, since any history indicating benefits to human health would increase a plant’s likelihood of ongoing cultivation. (You could apply a similar argument to foods, which is why Meyer notes that we’re likely to find better-tasting stuff in plants that were domesticated before disappearing.)

Ultimately, said O’Keefe, “we can’t know for sure that a resurrected plant wouldn’t be of [medicinal] use, but it would be hard to pick which one or to know in advance which one that might be.” That said, he adds, “bringing back attributes and plants might be highly advantageous. It would be good to know we can do that, should we need to.” So for example, said O’Keefe, “if we lost the capability to make a natural product in the future,” being able to resurrect a plant or retrieve a valuable chemical would be “an important capacity to have.” In that light, he sees Ginkgo’s scent project as “a good proof-of-principle system.”

Sure, given the layer of guesswork, Ginkgo’s project was not an exact recreation, but then again neither would be anything resurrected, in whole or part, from extinction, whether that be fruit, fragrance, or a whole cloned woolly mammoth. No organism is an island, and without the exact same environment, relationships to other organisms, and ecological niche of its predecessors, even a perfect genetic copy would be something new and distinct.

“I often say that once a species is gone, there really is no way to bring it back,” said Beth Shapiro, author of “How to Clone a Mammoth: The Science of De-Extinction,” whose UCSC paleogenomics lab extracted the DNA and identified the gene sequences used by Ginkgo. “I guess it depends on what you’re willing to accept as a copy of something that used to be alive,” she told Gizmodo. “But the technologies that are involved with doing this, I think have tremendous potential for conservation of species that are still alive, that still exist.” By sequencing and assembling genomes and figuring out how genetic data corresponds with behaviours and physical characteristics, we could, in theory, “tweak living species so that we can assist them in adapting to a changing habitat,” she said.

To Shapiro, the best reason to actually bring anything out of extinction would be a kind of resurrection rewilding project: “Let’s say an ecosystem has been destabilized because something has become extinct, and that destabilization might lead to even more extinctions because of some sort of cascade,” she said. If one could “put something back into that community of organisms, which restabilized that ecosystem, then I think that is a compelling thing to do.”

This is exciting science, but it’s important to remember that interventions can come with unintended consequences, warned O’Keefe. “There are certainly ethical concerns,” he said, and reintroducing historically extinct plants into the wild “is something that has to be done with a great, great deal of caution.” For example, introducing something from the past could potentially have an effect analogous to releasing a non-native invasive species, further tilting out-of-whack ecosystems. “We have to try and protect the biodiversity we already have,” he said, “because it’s easier to keep a lot of these species from becoming extinct in the first place than trying to resurrect them afterwards.”

As Shapiro and O’Keefe both mention, any discussion about resurrection is also a discussion about conservation. The researchers who exhumed ancient Judean date palms and cultured new life from ice age placentas wanted to better understand how extreme conditions preserve genetic material, in part, so seed banks—like the so-called “doomsday” seed vault in Svalbard, Norway—can help humanity stave off future extinctions, biodiversity losses, and agricultural disasters. With one in five plant species threatened with extinction, in theory, resurrection could be a backstop when conservation fails.

According to a 2019 article in the journal Nature Ecology and Evolution, more than 500 known plant species have gone extinct over the last 250 or so years, though that number is likely far from a precise count—in the same amount of time, hundreds of other species have been declared extinct, only to later be rediscovered, growing in some far-flung garden or grove. “We don’t have a real count of what’s gone extinct,” said Meyer. Even with better official numbers or measurement metrics, she asks, “how are you going to really know, especially when common names change?” Other species and varieties are headed for extinction or extinct in the wild, she said, or some, like the American chestnut, are endangered to the point of being “functionally extinct,” persisting in small, isolated populations, studied in greenhouses and labs, or carefully preserved by conservationists and indigenous communities. Tragic loss of biodiversity can’t be reduced to when the last of something dies.

“It would be really great,” said Meyer, to “broaden people’s definitions of extinction,” which could be thought of less as a hard ending for one particular thing and more of a slow process that involves many other codependent organisms and often leaves more behind than one might think. It might not have the mad-science magic of gene editing a long-lost plant into existence, but Meyer said there are plenty of conventional ways to create something both old and new, like “taking a functionally extinct species and making hybrids,” or re-domesticating a plant no longer used for food. She gives the example of sumpweed, or marsh elder, a plant with edible, high-protein seeds that was domesticated by Native American people in the ancient Midwest.

With some undesirable traits, like a pronounced smell, sumpweed was eventually abandoned for crops like corn. Though the wild variety is still around, the domesticated version, which grew much bigger seeds, is now extinct. “So if you consider that a species that was lost that we could easily bring back, we already know what it could become,” said Meyer. These days, we could likely reduce or eliminate sumpweed’s unwanted aspects, making it once again “a food source that would be potentially low input,” she said.

“There are things we used heavily and then for whatever reason, abandoned,” she said. Experiencing them again is not only a theoretical path to more resilient crops or botanical novelties; Meyer wants to open a window to human history, to how crops moved across continents and how “flavours catalyzed new economies, wars, cultural connections, competitive feasting, ecosystem changes, and much more.” Now, she said, “we have this chance to bring things back, to redomesticate things, to add new species to our dinner plates.” In this “very creative time” for the exploration of plant diversity, said Meyer, long-lost treasures from our botanical past could very well “end up being our crops for the future.”

Editor's Note: This article has the US release date. We will update this article as soon as possible with an Australian release date, if available.

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