Nature Generates More Data Than The Internet … For Now
September 26th, 2023
Via Popular Science, a look at how – in the next century – the information transmitted over the internet might eclipse the information shared between Earth’s most abundant lifeforms:
Is Earth primarily a planet of life, a world stewarded by the animals, plants, bacteria, and everything else that lives here? Or, is it a planet dominated by human creations? Certainly, we’ve reshaped our home in many ways—from pumping greenhouse gases into the atmosphere to literally redrawing coastlines. But by one measure, biology wins without a contest.
In an opinion piece published in the journal Life on August 31, astronomers and astrobiologists estimated the amount of information transmitted by a massive class of organisms and technology for communication. Their results are clear: Earth’s biosphere churns out far more information than the internet has in its 30-year history. “This indicates that, for all the rapid progress achieved by humans, nature is still far more remarkable in terms of its complexity,” says Manasvi Lingam, an astrobiologist at the Florida Institute of Technology and one of the paper’s authors.
But that could change in the very near future. Lingam and his colleagues say that, if the internet keeps growing at its current voracious rate, it will eclipse the data that comes out of the biosphere in less than a century. This could help us hone our search for intelligent life on other planets by telling us what type of information we should seek.
To represent information from technology, the authors focused on the amount of data transferred through the internet, which far outweighs any other form of human communication. Each second, the internet carries about 40 terabytes of information. They then compared it to the volume of information flowing through Earth’s biosphere. We might not think of the natural world as a realm of big data, but living things have their own ways of communicating. “To my way of thought, one of the reasons—although not the only one—underpinning the complexity of the biosphere is the massive amount of information flow associated with it,” Lingam says.
Bird calls, whale song, and pheromones are all forms of communication, to be sure. But Lingam and his colleagues focused on the information that individual cells transmit—often in the form of molecules that other cells pick up and respond accordingly, such as producing particular proteins. The authors specifically focused on the 100 octillion single-celled prokaryotes that make up the majority of our planet’s biomass.
“That is fairly representative of most life on Earth,” says Andrew Rushby, an astrobiologist at Birkbeck, University of London, who was not an author of the paper. “Just a green slime clinging to the surface of the planet. With a couple of primates running around on it, occasionally.”
This colorized image shows an intricate colony of millions of the single-celled bacterium Pseudomonas aeruginosa that have self-organized into a sticky, mat-like colony called a biofilm, which allows them to cooperate with each other, adapt to changes in their environment, and ensure their survival. Scott Chimileski and Roberto Kolter, Harvard Medical School, Boston
As all of Earth’s prokaryotes signal to each other, according to the authors’ estimate, they generate around a billion times as much data as our technology. But human progress is rapid: According to one estimate, the internet is growing by around 26 percent every year. Under the bold assumption that both these rates hold steady for decades to come, the authors stated its size will continue to balloon until it dwarfs the biosphere in around 90 years’ time, sometime in the early 22nd century.What, then, does a world where we create more information than nature actually look like? It’s hard to predict for certain. The 2110s version of Earth may be as strange to us as the present Earth would seem to a person from the 1930s. That said, picture alien astronomers in another star system carefully monitoring our planet. Rather than glimpsing a planet teeming with natural life, their first impressions of Earth might be a torrent of digital data.
Now, picture the reverse. For decades, scientists and military experts have sought out signatures of extraterrestrials in whatever form it may take. Astronomers have traditionally focused on the energy that a civilization of intelligent life might use—but earlier this year, one group crunched the numbers to determine if aliens in a nearby star system could pick up the leakage from mobile phone towers. (The answer is probably not, at least with LTE networks and technology like today’s radio telescopes.)
On the flip side, we don’t totally have the observational capabilities to home in on extraterrestrial life yet. “I don’t think there’s any way that we could detect the kind of predictions and findings that [Lingam and his coauthors] have quantified here,” Rushby says. “How can we remotely determine this kind of information capacity, or this information transfer rate? We’re probably not at the stage where we could do that.”
But Rushby thinks the study is an interesting next step in a trend. Astrobiologists—certainly those searching for extraterrestrial life—are increasingly thinking about the types and volume of information that different forms of life carries. “There does seem to be this information ‘revolution,’” he says, “where we’re thinking about life in a slightly different way.” In the end, we might learn that there’s more harmony between the communication networks nature has built and computers.
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Read More »The Race to Save the World’s DNA
September 23rd, 2023
Via The New Yorker, a look at a scientific rescue mission which aims to analyze every plant, animal, and fungus before it’s too late:
Four years ago, a few hundred miles off the coast of West Africa, a crane lifted a bulbous yellow submarine from the research vessel Poseidon and lowered it into the Atlantic. Inside the sub, Karen Osborn, a zoologist at the Smithsonian Institution who was swaddled in warm clothes, tried to ward off nausea. During half an hour of safety checks, Osborn watched water slosh across the submarine’s round window, washing-machine style. Then the crew gave the all-clear and the vessel descended. In the waters of Cape Verde, a volcanic archipelago that is famous for its marine life, Osborn felt the seasickness dissipate. She pressed her face against the glass, peering out at sea creatures until her forehead bruised. “You’re just completely mesmerized by getting to look at these animals in their natural habitat,” she told me.
Osborn was on a mission to find several elusive species, including a bioluminescent worm called Poeobius, and to sequence their genes for a global database of DNA. “We need the genome to figure out how these things are related to each other,” she explained. “Once we have that tree, we can start asking interesting questions about how those animals evolved, how they’ve changed through time, how they’ve adapted to their habitats.” Eventually, such genomes could inspire profound innovations, from new crops to medical cures. Osborn was starting to worry, however: she had already made several trips in the submarine and had not seen a single Poeobius. Each worm measures just a few centimetres in length and feeds on marine snow, or organic detritus that falls from the surface. Because it is yellow on one end, like a cigarette, it is sometimes called the butt worm.
As the pilot steered into deeper waters, Osborn operated a suction hose at the end of a robotic arm. Whenever she spotted organisms that she wanted to sample—crustaceans, sea butterflies, jellies—she’d suck them through a tube and into a collection box that was filled with seawater. She started to wish that the submarine had a rest room on board. Then, a few hundred metres down, she finally saw a group of Poeobius. “Oh, that’s what we want!” she remembers exclaiming. “Go! Go get that!” The pilot slowly turned the sub and Osborn sucked up the worms.
Back on the ship, even before using the rest room, Osborn deposited her boxes in an onboard laboratory. “It’s always exciting to climb out and go look at all the samplers, and take them into the lab and see what animals you’ve gotten,” she told me. She placed one of the Poeobius worms under a microscope, anesthetized it, sliced off a bit of gelatinous tissue, and placed it into a vial, which contained a liquid that would protect the DNA from deterioration. (The butt worm did not survive.) Back at the Smithsonian, a team would extract the genetic material and sequence it. It would soon become a new branch on a growing tree of life.
The evolution of life on Earth—a process that has spanned billions of years and innumerable strands of DNA—could be considered the biggest experiment in history. It has given rise to amoebas and dinosaurs; fireflies and flytraps; even mammals that look like ducks and fish that look like horses. These species have solved countless ecological problems, finding novel ways to eat, evade, defend, compete, and multiply. Their genomes contain information that humans could use to reconstruct the origins of life, develop new foods and medicines and materials, and even save species that are dying out. But we are also losing much of the data; humans are one of the main causes of an ongoing mass extinction. More than forty thousand animal, fungal, and plant species are considered threatened—and those are just the ones we know about.
Osborn is part of a group of scientists who are mounting a kind of scientific salvage mission. It is known as the Earth BioGenome Project, or E.B.P., and its goal is to sequence a genome from every plant, animal, and fungus on the planet, as well as from many single-celled organisms, such as algae, retrieving the results of life’s grand experiment before it’s too late. “This is a completely wonderful and insane goal,” Hank Greely, a Stanford law professor who works with the E.B.P., told me. The effort, described by its organizers as a “moonshot for biology,” will likely cost billions of dollars—yet it does not currently have any direct funding, and depends instead on the volunteer work of scientists who do. Researchers will need to scour oceans, deserts, and rain forests to collect samples before species die out. And, as new species are discovered, the task of sequencing all of them will only grow. “That’s a heavy aspiration that will probably never be entirely achieved,” Greely, who is seventy-one, told me. “It’s like, when you’re my age, planting a young oak tree in your yard. You’re not going to live to see that be a mature oak, but your hope is somebody will.”
For hundreds of years, biologists have roamed the globe in an epic effort to collect and categorize the life on Earth. In the seventeen-hundreds, after traversing Sweden to document its flora and fauna, Carl Linnaeus helped create the system that scientists still use to classify and name species, from Homo sapiens to Poeobius meseres. In 1831, Charles Darwin set out aboard H.M.S. Beagle to collect living and fossilized specimens, which inspired his theory of natural selection. The discovery of DNA, in the nineteenth century, offered a new way to classify species: by comparing their genetic material. DNA’s four building blocks—adenine (A), thymine (T), guanine (G), and cytosine (C)—encode profound differences between organisms. By studying their sequence, we might come to speak life’s language.
Scientists didn’t even begin to sequence a DNA molecule until 1968. In 1977, they sequenced the roughly five thousand base pairs in a virus that invades bacteria. And, in 1990, the Human Genome Project started the thirteen-year process of sequencing almost all of the three billion base pairs in our DNA. Its organizers called the endeavor “one of the most ambitious scientific undertakings of all time, even compared to splitting the atom or going to the moon.” Since then, researchers have been filling in gaps and improving the quality of their sequences, in part by using a new format known as a telomere-to-telomere, or T2T, genome. The first T2T human genome was sequenced only last year, but already scientists with the Earth BioGenome Project are talking about repeating this process for every known eukaryotic species. (Eukaryotes are organisms whose cells have nuclei.)
Because the E.B.P. does not have its own funding, it does not sample or sequence species on its own. Instead, it’s a network of networks; its organizers set ethical and scientific standards for more than fifty projects, including the Darwin Tree of Life, Vertebrate Genomes Project, the African BioGenome Project, and the Butterfly Genome Project. This way, “when we get to the end of the project, it’s not the Tower of Babel,” Harris Lewin, an evolutionary biologist at the University of California, Davis, who chairs the E.B.P. executive council, told me. “You know—your genomes are produced this way, and mine are produced that way, and they’re of different quality, so that, when you compare them, you get different results.”
By 2025, the participants hope to assemble about nine thousand sequences, one from every known family of eukaryotes. By 2029, they aim to have one sequence from every genus—a hundred and eighty thousand in all. After the third and final phase, which could be completed a decade from now, they aim to have sequenced all 1.8 million species that scientists have documented so far. (Roughly eighty per cent of eukaryotic species are still undiscovered.) This database of genomes, including annotations and metadata, will require close to an exabyte of data, or as much as two hundred million DVDs. The amount of information involved is more than “astronomical,” Lewin said; it’s “genomical.” He compared the project to the Webb Space Telescope, which received about ten billion dollars of government funding. Given how much these projects change the way that humans see the world, Lewin said, “the cost is really not that much.”
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Natural-history museums already have some of the samples needed to outline a genetic tree of life. The Smithsonian, for instance, has about fifty million biological samples. But, because DNA degrades quickly, it’s difficult to extract a high-quality sequence from, say, a frog in formaldehyde or an old taxidermy parrot. For this reason, the E.B.P. usually restricts itself to recent samples, which are often frozen. It relies on the Global Genome Biodiversity Network to keep track of who has what; another database, called Genomes on a Tree, tracks which species have been sequenced already, and whether they meet exacting standards. Scientists such as Osborn will have to find the rest—and their jobs will only become more difficult as the low-hanging fruit is plucked.
After Osborn collected her butt worms, she had to transport them to her colleagues at the Smithsonian. This process can be more difficult than it sounds. Many researchers keep their samples intact by packing them with dry ice or liquid nitrogen in the field; airport-security workers sometimes flag these packages as suspicious, leading to delays that can spoil the DNA and waste an expedition. Osborn, for her part, checked a large insulated box on the flight from Cape Verde, and then waited a few hours in Newark for Fish and Wildlife officials to approve it for entry. As it turned out, her samples came from an entirely new species of Poeobius; a paper announcing the discovery is forthcoming.
The first stop in the journey from sample to sequence is a genetics laboratory such as the Vertebrate Genome Lab, at the Rockefeller University, on the eastern shore of Manhattan. On a drizzly day last May, I visited the V.G.L. to see how scientists turn a bit of animal tissue into a string of billions of letters. Olivier Fedrigo, a bespectacled geneticist who was then the lab’s director, led me down a hallway decorated with photos of species that had been sequenced there: a snake, a swan, a shark. It was a kind of trophy wall on which inclusion signified not death but a kind of immortality.
Researchers extract DNA from animal tissue in a biosafety-level-two room, which requires goggles, gloves, coats, and special ventilation to protect people and samples. Nivesh Jain, a scientist who works there, told me that he minces the tissue and places it in a lysis buffer—a chemical that breaks open cells—and then uses one of two methods to get the DNA out. The first is a type of microscopic magnetic bead, which is treated with chemicals that help it stick to genetic material; magnets hold the beads and their attached DNA in place while Jain washes everything else away. The second is a glass wafer called a Nanobind disk, which similarly sticks to DNA while Jain removes the rest of the sample. When we met, Jain was standing at a lab bench, checking the concentration of DNA in a vial. The vial would then go to another room, where Jennifer Balacco, the lab-operation lead, would pipette pieces of extracted DNA into little plastic tubes. Special enzymes attach short, recognizable pieces of DNA, called adapters, to the animal DNA, which readies them for the sequencer.
Finally, the samples travel into refrigerator-size PacBio sequencing machines, which, in this case, were labelled with nicknames from “Star Trek.” Enzymes latch onto the adapters and traverse the strands, attaching a color-coded molecule to every building block of DNA. The machine detects the colors and “reads” the sequence that they represent.
It’s not enough to sequence DNA in pieces: scientists must figure out how each fragment connects to make a genome. Genomes tend to be bundled up in complicated shapes. A technique called Hi-C mapping “helps you to sort out the puzzle pieces,” Fedrigo told me. The resulting map of folded DNA is crowded with colorful squiggles. At some computers down the hall from the sequencers, the maps help another team of researchers assemble sequence fragments into a full T2T genome. Nadolina Brajuka, a bioinformatician, was assembling an Asian-elephant genome. “I can physically use key and mouse controls and pick pieces of the genome up and move them around,” she said. The last step is for a “data wrangler” on the team to upload the raw-sequence data file, the final genome assembly, and background information about the sample—including where, when, and how it was collected, and a photo of the species—to a public server called GenomeArk.
One goal of the E.B.P. is to compare and contrast large numbers of genomes, revealing how they are related. Benedict Paten, a computational biologist at the University of California, Santa Cruz, has developed software to align genomes and determine which genes correspond to one another. “It’s a really rich and difficult problem,” he told me, “because genomes evolve by a bunch of really complicated processes.” For a 2020 Nature paper, Paten and several collaborators used powerful computers to align more than a trillion As, Ts, Gs, and Cs and create a tree of six hundred bird and mammal species. On a typical home computer, such an undertaking could have taken more than a million hours. “If you wanted to do it for all plants and animals, it’s just a vast computational challenge,” Paten told me.
During my trip to the Rockefeller University, I visited Erich Jarvis, a well-dressed neurogeneticist who leads the Vertebrate Genomes Project, and asked him to show me the kinds of experiments that the E.B.P. will unlock. Jarvis, the son of two musicians, grew up in Harlem and originally trained as a dancer; today he studies the genes that help animals learn to imitate sounds.
We walked through Jarvis’s expansive laboratory toward a scientist who was peering through a microscope at a bird embryo. In this early stage of development, the scientist explained, it was possible to inject the embryo with cells that contain modified DNA. When the so-called transgenic bird hatched, the lab would be able to study whether the foreign genes affected its ability to learn songs.
A nearby room was filled with caged birds and mice; speakers played sounds while cameras and microphones recorded how animals responded. I bent down to look at a zebra finch, which was chirping away. A surprisingly small number of animals have been shown to imitate sounds, Jarvis told me: songbirds, hummingbirds, parrots, dolphins, whales, seals, bats, elephants, and humans. Figuring out what these animals have in common could help us understand the genetic roots of spoken language. This kind of research, Jarvis went on, is possible only with high-quality complete DNA sequences.
“We humans would benefit so much from nature’s experiment,” Jarvis said. Some species are resistant to sars-CoV-2. Some, including parrots and elephants, rarely get cancer. Some crops produce more food than others. “We’re going to lose that information if we don’t do something about it soon,” he said. The E.B.P. could also empower scientists to study the health of ecosystems. A researcher with access to full genomes can sample some pond water and figure out which species are living there. Such studies could help humans reverse the harms of agriculture, urbanization, and climate change—and fulfill what Jarvis called a “moral duty” to save fellow-species.
The Earth BioGenome Project “is going to blow the door wide open on conservation genomics,” Bridget Baumgartner, who works for an organization called Revive & Restore, told me. Her project, Wild Genomes, is trying to use DNA for the management of endangered species. In Bolivia, scientists are sequencing jaguars to determine which population individual jaguars came from, and also to track illegal wildlife trafficking. In the Mojave Desert, researchers are comparing the genomes of trees that survive in different temperatures, so they’ll know which individuals of that species could be planted in other places as the climate changes. And, in the archipelago of Indonesia, binturongs have been rescued from smugglers and returned to their specific island of origin, which can be determined through DNA. The other part of Revive & Restore aims for the de-extinction of lost species such as the passenger pigeon, with help from the genomes of living animals. Much of the funding for this work originally came from wealthy Bay Area tech investors—“not the typical conservation funder,” Ryan Phelan, Revive & Restore’s executive director and co-founder, said—but increasingly comes from governments.
Right now, the sequencing process is so cumbersome that scientists can’t hope to repeat it a million-plus times in the coming decade. To achieve the necessary pace of hundreds of genomes a day, they will need to automate much of it, perhaps with robots that can prepare samples and improved algorithms that can assemble genomes—though the bottleneck, Lewin stressed, is still the sampling. Of course, all of this will require funding. There’s little precedent for a government project that touches so many scientific fields, Lewin told me. “In the U.S., if you can eat it, U.S.D.A. will fund it. If it’ll kill you, N.I.H. will fund it. If it’s good for energy production, the Department of Energy will fund it. And, if you have some interesting scientific questions, the National Science Foundation will fund it. But there’s no agency that owns it all.” For that reason, Lewin said, the E.B.P.’s organizers are less focussed on assembling a patchwork of grants than finding what he called “a visionary philanthropist.”
Sooner or later, a global database of genomes will have profound practical implications. Some creatures can regrow their limbs; others do not appear to die unless they suffer an injury. If the basis for such traits can be pinpointed in genes, humans might be able to borrow them, perhaps by using gene therapies. “Evolution has already done nearly every experiment, right?” Lewin told me. “There are organisms that’ll eat oil spills, there are organisms that’ll eat heavy metals. I mean, it’s incredible.” But, when genomes inspire new products, to whom will they belong? This question makes the E.B.P. not only a scientific project but a political one.
In the nineties, scientists from the Human Genome Project argued that DNA sequences should be in the public domain, meaning that anyone, anywhere, would be able to use them. “That has been an animating principle for genomics for the past, like, thirty years,” Jacob Sherkow, a professor at the University of Illinois College of Law, told me. More recently, views have changed. “ ‘Public domain’ is a deceptive term used to deny Indigenous peoples rights from things important to them,” Ben Te Aika, an expert on the traditional knowledge of the M?ori people, in New Zealand, told me. “It would be more honest to say ‘domain of the élites.’ ” In the two-thousands, many observers worried that wealthy nations would exploit biological samples without compensating the countries that they come from. This concern helped inspire the Nagoya Protocol, a piece of international legislation that encourages “benefit sharing,” and instructs countries to agree on terms before biological samples are shared. More than a hundred countries have ratified it. (The U.S. is not one of them.)
Te Aika told me that, after centuries of European colonialism, his community has been reasserting its mana, or traditional authority, over native species. He argues that the M?ori people should have the opportunity to benefit from any scientific samples that are gathered in New Zealand. With a colleague from Ireland, Ann Mc Cartney, Te Aika has co-authored papers in support of data sovereignty, or the right of local and Indigenous people “to control data from and about their communities, land, species, and waters.” They described E.B.P. as “an opportunity to leave no one behind.” The scientific collaboration that Te Aika works for, Genomics Aotearoa, is not affiliated with the E.B.P. and has adopted an unusual structure: its data is accessible only to researchers who apply and are invited to travel to New Zealand. Outside scientists may see such restrictions as a kind of red tape, Te Aika said, but “ ‘red tape’ can become necessary when self-regulating systems fail.”
Several scientists told me that the Nagoya Protocol is already outdated. “Benefit sharing in the Nagoya Protocol is getting more strict and confusing,” in part because of debates about how to interpret it, Jarvis said. Currently, he argued, the protocol is discouraging scientists from developing products at all—an outcome that, in his view, helps no one. One argument for commercializing genomes is that “then you can get financial benefit going back to the people that are the caretakers of the land where the animal came from,” he said. “Something has to change.”
The most complex debate, Sherkow told me, is about whether a digital DNA sequence counts as a biological sample. If not, the Nagoya Protocol wouldn’t apply to the strings of letters stored in the E.B.P., and, as Sherkow put it, “It’s everyone for themselves.” Any scientist, company, or country could download a sequence and use it for their own ends, without consulting or compensating the community that the sequence originated from. But, if the sequence is a sample, then genomes will be governed by Nagoya, and many difficult questions will follow. How should the benefits of a discovery or product be shared? Are they owed to the country that the sequence came from, or someone else, such as an Indigenous group? Communities need an opportunity to voice their own priorities: some may want to build capacity for their own research, and others may want compensation or simply credit for their contributions to a discovery. Some of the scientists I spoke to felt that new international laws would need to be written to answer these questions.
The E.B.P. has formed an Ethical, Legal, and Social Issues Committee to work through such challenges. Sherkow described its work as a balancing act: “What’s best for science? What’s best for the world? What’s best for the particular country that we’re taking samples from?” Greely, who chairs the committee, said that it also develops best practices in other areas: interactions with local communities, the humane treatment of animals being sampled, whether to sample in countries ruled by “nasty regimes,” authorship on papers, and even risks of bioterrorism. He added that he was stunned to learn how many international treaties affect biological resources—treaties on food and agriculture, migratory species, whaling, the law of the sea, and more. “A lot of the hangups are not scientific or even engineering hangups,” Sherkow told me. “The biggest hangup to sequencing all the world’s non-human eukaryotes is humans.”
The quest to document life spans scientific disciplines, continents, and generations. Darwin first drew a tree of life in his notebook around 1837; two hundred years later, the E.B.P. could finish some of what he started. Last May, Mark Blaxter, an evolutionary biologist in the U.K. who contributes to the project and is the director of the Darwin Tree of Life, sat down in the grass in his back yard, cracked open a beer, signed on to Zoom from his laptop, and told me about the new era of biology that he foresees. Periodically, Blaxter, who has long white hair and a graying beard, interrupted himself to identify the creepies that were crawling around him: ladybug, bee, pill bug. “There’s two species of ant on this piece of grass,” he observed. “Only one of them’s biting me, though.”
Charlotte Wright, a twenty-five-year-old doctoral student who likes catching bugs, was drinking a beer with Blaxter that day. Wright studies moths, which, along with butterflies, make up a tenth of all known eukaryotic species. They, too, are mysterious. Human genomes typically have twenty-three pairs of chromosomes; Lepidoptera can have anywhere from five to two hundred and twenty-six. “That gives them the greatest range in chromosome number of any group of organisms on Earth,” Wright said. “They’re completely bonkers.” Because it’s difficult for animals with different numbers of chromosomes to produce offspring, studying chromosome evolution can shed light on how one species diverges into many—one of biology’s fundamental questions.
Blaxter watched a bee fly into his house. Then he reflected on the many drugs that have come from the natural world over the years. Aspirin was first derived from willow bark, which was used to relieve pain since ancient times. “We think that by sequencing, for example, fungi, there’s going to be a huge new pharmacopoeia opened up,” he told me. “Think about the transformative effect that the human genome had on our understanding of human biology and medicine and disease and health. We want that to be available for everyone.”
When Blaxter became a biologist, in the eighties, scientists had not even begun to sequence the human genome. Back then, “biodiversity” was still a new term; humans were only starting to grasp just how many species were vanishing forever, and how much our activities were transforming the planet and its climate. Blaxter, who is sixty-three, seemed conscious that he might not live long enough to see all the impacts of the genomic revolution. “I’m on my way out,” he said. “I’m the old generation, right?” Wright’s generation would inherit unprecedented challenges, but she would also build on an unprecedented foundation of knowledge about the natural world. “Charlotte’s going to be one of the first generation of genome natives,” Blaxter told me. “What we want to do with this project is to change the way biology is done forever.”
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Read More »Animal CSI: Forensics Comes For The Wildlife Trade
September 22nd, 2023
Via Knowable Magazine, a look at how scientists are using the latest in DNA fingerprinting to combat the multibillion-dollar business of trafficking plants and animals:
Campbell’s death was as gruesome as the killers’ previous nine known crimes. Found mutilated in a pool of blood at his home in the district of Albany, South Africa, in June 2016, Campbell had been drugged but was likely in pain before he died from his injuries.
Genetics extends the long arm of the law
Campbell was a white rhinoceros living on a private reserve, and his killing would be the last hurrah of the now notorious Ndlovu Gang. The three poachers were arrested days later at the Makana Resort in Grahamstown, South Africa, caught red-handed with a bow saw, a tranquilizer dart gun and a freshly removed rhino horn. A variety of evidence, including cellphone records and ballistics analysis of the dart gun, would link them to the crime. But a key element was Campbell’s DNA, found in the horn and on the still-bloody saw.Among the scientific techniques used to combat poaching and wildlife trafficking, DNA is king, says Cindy Harper, a veterinary geneticist at the University of Pretoria. Its application in animal investigations is small-scale but growing in a field with a huge volume of crime: The value of the illegal wildlife trade is as much as $20 billion per year, Interpol estimates.
“It’s not just a few people swapping animals around,” says Greta Frankham, a wildlife forensic scientist at the Australian Center for Wildlife Genomics in Sydney. “It’s got links to organized crime; it is an enormous amount of turnover on the black market.”
The problem is global. In the United States, the crime might be the illegal hunting of deer or black bears, the importing of protected-animal parts for food or medicinal use, the harvesting of protected cacti, or the trafficking of ivory trinkets. In Africa or Asia, it might be the poaching of pangolins, the globe’s most trafficked mammal for both its meat and its scales, which are used in traditional medicines and magic practices. In Australia, it might be the collection or export of the continent’s unique wildlife for the pet trade.
The illegal trade of wildlife may include live animals or plants, or parts of them, such as roots, stems, skin, bones or antlers. In the case of tigers and rhinos, trading in products that purport to contain parts of those animals — even if they do not — is also illegal.
Techniques used in wildlife forensics are often direct descendants of tools from human crime investigations, and in recent years scientists have adapted and tailored them for use in animals. Harper and colleagues, for example, learned to extract DNA from rhinoceros horns, a task once thought impossible. And by building DNA databases — akin to the FBI’s CODIS database used for human crimes — forensic geneticists can identify a species and more: They might pinpoint a specimen’s geographic origin, family group, or even, in some cases, link a specific animal or animal part to a crime scene.
Adapting this science to animals has contributed to major crime busts, such as the 2021 arrests in an international poaching and wildlife trafficking ring. And scientists are further refining their techniques in the hopes of identifying more challenging evidence samples, such as hides that have been tanned or otherwise degraded.
“Wildlife trafficking investigations are difficult,” says Robert Hammer, a Seattle-based special agent-in-charge with Homeland Security Investigations, the Department of Homeland Security’s arm for investigating diverse crimes, including those involving smuggling, drugs and gang activity. He and his colleagues, he says, rely on DNA and other forensic evidence “to tell the stories of the animals that have been taken.”
First, identify
Wildlife forensics generally starts with a sample sent to a specialized lab by investigators like Hammer. Whereas people-crime investigators generally want to know “Who is it?” wildlife specialists are more often asked “What is this?” — as in, “What species?” That question could apply to anything from shark fins to wood to bear bile, a liver secretion used in traditional medicines.“We get asked questions about everything from a live animal to a part or a product,” says Barry Baker, deputy laboratory director at the US National Fish and Wildlife Forensics Laboratory in Ashland, Oregon.
Investigators might also ask whether an animal photographed at an airport is a species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora, or CITES, in which case import or export is illegal without a permit. They might want to know whether meat brought into the US is from a protected species, such as a nonhuman primate. Or they might want to know if a carved knickknack is real ivory or fake, a difference special lighting can reveal.
While some identifications can be made visually, DNA or other chemical analyses may be required, especially when only part of the creature is available. To identify species, experts turn to the DNA in mitochondria, the cellular energy factories that populate nearly every cell, usually in multiple copies. DNA sequences therein are similar in all animals of the same species, but different between species. By reading those genes and comparing them to sequences in a database such as the Barcode of Life, forensic geneticists can identify a species.
To go further to try to link a specimen to a specific, individual animal, forensic geneticists use the same technique that’s used in human DNA forensics, in this case relying on the majority of DNA contained in the cell’s nucleus. Every genome contains repetitive sequences called microsatellites that vary in length from individual to individual. Measuring several microsatellites creates a DNA fingerprint that is rare, if not unique. In addition, some more advanced techniques use single-letter variations in DNA sequences for fingerprinting.
Comparing the DNA of two samples allows scientists to make a potential match, but it isn’t a clincher: That requires a database of DNA fingerprints from other members of the species to calculate how unlikely it is — say, a one-in-a-million chance — that the two samples came from different individuals. Depending on the species’ genetic diversity and its geographic distribution, a valid database could have as few as 50 individuals or it could require many more, says Ashley Spicer, a wildlife forensic scientist with the California Department of Fish and Wildlife in Sacramento. Such databases don’t exist for all animals and, indeed, obtaining DNA samples from even as few as 50 animals could be a challenge for rare or protected species, Spicer notes.
Investigators use these techniques in diverse ways: An animal may be the victim of a crime, the perpetrator or a witness. And if, say, dogs are used to hunt protected animals, investigators could find themselves with animal evidence related to both victim and suspect.
For witnesses, consider the case of a white cat named Snowball. When a woman disappeared in Richmond, on Canada’s Prince Edward Island, in 1994, a bloodstained leather jacket with 27 white cat hairs in the lining was found near her home. Her body was found in a shallow grave in 1995, and the prime suspect was her estranged common-law husband, who lived with his parents and Snowball, their pet. DNA from the root of one of the jacket hairs matched Snowball’s blood. Though the feline never took the stand, the cat’s evidence spoke volumes, helping to clinch a murder conviction in 1996.
A database for rhinos
The same kind of specific linking of individual animal to physical evidence was also a key element in the case of Campbell the white rhino. Rhino horn is prized: It’s used in traditional Chinese medicine and modern variants of the practice to treat conditions from colds to hangovers to cancer, and is also made into ornaments such as cups and beads. At the time of Campbell’s death, his horn, weighing north of 10 kilograms, was probably worth more than $600,000 — more than its weight in gold — on the black market.The DNA forensics that helped nab the Ndlovu Gang started with experiments in the early 2000s, when rhino poaching was on the rise. Scientists once thought rhino horns were nothing but densely packed hair, lacking cells that would include DNA, but a 2006 study showed that cells, too, are present. A few years later, Harper’s group reported that even though these cells were dead, they contained viable DNA, and the researchers figured out how to access it by drilling into the horn’s core.
In 2010, a crime investigator from South Africa’s Kruger National Park dropped by Harper’s lab. He was so excited by the potential of her discovery to combat poaching that he ripped a poster describing her results off the wall, rolled it up and took it away with him. Soon after, Harper launched the Rhinoceros DNA Index System, or RhODIS. (The name is a play on the FBI’s CODIS database, for Combined DNA Index System.)
Today, thanks to 2012 legislation from the South African government, anyone in that nation who handles a rhino or its horn — for example, when dehorning animals for the rhinos’ own protection — must send Harper’s team a sample. RhODIS now contains about 100,000 DNA fingerprints, based on 23 microsatellites, from African rhinoceroses both black and white, alive and long dead, including most of the rhinos in South Africa and Namibia, as well as some from other nations.
RhODIS has assisted with numerous investigations, says Rod Potter, a private consultant and wildlife crime investigator who has worked with the South African Police Service for more than four decades. In one case, he recalls, investigators found a suspect with a horn in his possession and used RhODIS to identify the animal before the owner even knew the rhino was dead.
In Campbell’s case, in 2019 the three poachers were convicted, to cheers from observers in the courtroom, of charges related to 10 incidents. Each gang member was sentenced to 25 years in prison.
Today, as rhino poaching has rebounded after a pandemic-induced lull, the RhODIS database remains important. And even when RhODIS can’t link evidence to a specific animal, Potter says, the genetics are often enough to point investigators to the creature’s approximate geographic origin, because genetic markers vary by location and population. And that can help illuminate illegal trade routes.
Elephants also benefit
DNA can make a big impact on investigations into elephant poaching, too. Researchers at the University of Washington in Seattle, for example, measured DNA microsatellites from roving African elephants as well as seized ivory, then built a database and a geographical map of where different genetic markers occur among elephants. The map helps to determine the geographic source of poached, trafficked tusks seized by law enforcement officials.Two line maps of Africa. The left map shows the origins of ivory seized in the Philippines between 1996 and 2005; the one on the right illustrates origins of ivory seized in Singapore in 2007. Red diamonds mark the ports by which the ivory left Africa. Crosses mark the locations of elephants in a genetic database. Blue circles mark the origins of the seized ivory, based on that database.
Researchers used elephant DNA from animals in different locations (orange crosses) to create a database mapping where different gene markers are likely to occur. This information allows them to pinpoint the elephant populations where seized ivory originated (blue circles). Analyses of ivory confiscated in the Philippines (left) and in Singapore (right) indicated that the poaching occurred primarily in the eastern Democratic Republic of Congo and Zambia, respectively.Elephants travel in matriarchal herds, and DNA markers also run in families, allowing the researchers to determine the relatedness of different tusks, be they from parents, offspring, siblings or half-siblings. When they find tusks from the same elephant or clan in different shipments with a common port, it suggests that the shipments were sent from the same criminal network — which is useful information for law enforcement officials.
This kind of information came in handy during a recent international investigation, called Operation Kuluna, led by Hammer and colleagues at Homeland Security Investigations. It started with a sting: Undercover US investigators purchased African ivory that was advertised online. In 2020, the team spent $14,500 on 49 pounds of elephant ivory that was cut up, painted black, mixed with ebony and shipped to the United States with the label “wood.” The following year, the investigators purchased about five pounds of rhino horn for $18,000. The undercover buyers then expressed interest in lots more inventory, including additional ivory, rhino horns and pangolin scales.
The promise of such a huge score lured two sellers from the Democratic Republic of the Congo (DRC) to come to the United States, expecting to seal the $3.5 million deal. Instead, they were arrested near Seattle and eventually sentenced for their crimes. But the pair were not working alone: Operations like these are complex, says Hammer, “and behind complex conspiracies come money, organizers.” And so the investigators took advantage of elephant genetic and clan data which helped to link the tusks to other seizures. It was like playing “Six Degrees of Kevin Bacon,” says Hammer.
Shortly after the US arrests, Hammer’s counterparts in Africa raided warehouses in the DRC to seize more than 2,000 pounds of ivory and 75 pounds of pangolin scales, worth more than $1 million.
Two photos show pieces of elephant tusks from a warehouse. On the left is a large pile of ivory and on the right are three pieces on a scale.
Following arrests of smugglers in Washington state, law enforcement officials in the Democratic Republic of the Congo raided warehouses, recovering elephant ivory, rhinoceros horns and pangolin scales.Despite these successes, wildlife forensics remains a small field: The Society for Wildlife Forensic Science has fewer than 200 members in more than 20 countries. And while DNA analysis is powerful, the ability to identify species or individuals is only as good as the genetic databases researchers can compare their samples to. In addition, many samples contain degraded DNA that simply can’t be analyzed — at least, not yet.
Today, in fact, a substantial portion of wildlife trade crimes may go unprosecuted because researchers don’t know what they’re looking at. The situation leaves scientists stymied by that very basic question: “What is this?”
For example, forensic scientists can be flummoxed by animal parts that have been heavily processed. Cooked meat is generally traceable; leather is not. “We have literally never been able to get a DNA sequence out of a tanned product,” says Harper, who wrote about the forensics of poaching in the 2023 Annual Review of Animal Biosciences. In time, that may change: Several researchers are working to improve identification of degraded samples. They might work out ways to do so based on the proteins therein, says Spicer, since these are more resistant than DNA is to destruction by heat or chemistry.
Success, stresses Spicer, will require the cooperation of wildlife forensic scientists around the world. “Anywhere that somebody can get a profit or exploit an animal, they’re going to do it — it happens in every single country,” she says. “And so it’s really essential that we all work together.”
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Read More »Five Ways AI Is Saving Wildlife
September 11th, 2023
Via The Guardian, a look at why artificial intelligence has been identified as one of the top three emerging technologies in conservation, helping protect species around the world:
There’s a strand of thinking, from sci-fi films to Stephen Hawking, that suggests artificial intelligence (AI) could spell doom for humans. But conservationists are increasingly turning to AI as an innovative tech solution to tackle the biodiversity crisis and mitigate climate change.
A recent report by Wildlabs.net found that AI was one of the top three emerging technologies in conservation. From camera trap and satellite images to audio recordings, the report notes: “AI can learn how to identify which photos out of thousands contain rare species; or pinpoint an animal call out of hours of field recordings – hugely reducing the manual labour required to collect vital conservation data.”
AI is helping to protect species as diverse as humpback whales, koalas and snow leopards, supporting the work of scientists, researchers and rangers in vital tasks, from anti-poaching patrols to monitoring species. With machine learning (ML) computer systems that use algorithms and models to learn, understand and adapt, AI is often able to do the job of hundreds of people, getting faster, cheaper and more effective results.
Here are five AI projects contributing to our understanding of biodiversity and species:
1. Stopping poachers
Zambia’s Kafue national park is home to more than 6,600 African savanna elephants and covers 22,400 sq km, so stopping poaching is a big logistical challenge. Illegal fishing in Lake Itezhi-Tezhi on the park’s border is also a problem, and poachers masquerade as fishers to enter and exit the park undetected, often under the cover of darkness.Automated alerts mean that just a handful of rangers are needed to provide around-the-clock surveillance. Photograph: Game Rangers International
The Connected Conservation Initiative, from Game Rangers International (GRI), Zambia’s Department of National Parks and Wildlife and other partners, is using AI to enhance conventional anti-poaching efforts, creating a 19km-long virtual fence across Lake Itezhi-Tezhi. Forward-looking infrared (FLIR) thermal cameras record every boat crossing in and out of the park, day and night.Installed in 2019, the cameras were monitored manually by rangers, who could then respond to signs of illegal activity. FLIR AI has now been trained to automatically detect boats entering the park, increasing effectiveness and reducing the need for constant manual surveillance. Waves and flying birds can also trigger alerts, so the AI is being taught to eliminate these false readings.
“There have long been insufficient resources to secure protected areas, and having people watch multiple cameras 24/7 doesn’t scale,” says Ian Hoad, special technical adviser at GRI. “AI can be a gamechanger, as it can monitor for illegal boat crossings and alert ranger teams immediately. The technology has enabled a handful of rangers to provide around-the-clock surveillance of a massive illegal entry point across Lake Itezhi-Tezhi.”
2. Tracking water loss
Brazil has lost more than 15% of its surface water in the past 30 years, a crisis that has only come to light with the help of AI. The country’s rivers, lakes and wetlands have been facing increasing pressure from a growing population, economic development, deforestation, and the worsening effects of the climate crisis. But no one knew the scale of the problem until last August, when, using ML, the MapBiomas water project released its results after processing more than 150,000 images generated by Nasa’s Landsat 5, 7 and 8 satellites from 1985 to 2020 across the 8.5m sq km of Brazilian territory. Without AI, researchers could not have analysed water changes across the country at the scale and level of detail needed. AI can also distinguish between natural and human-created water bodies.The Negro River, a major tributary of the Amazon and one of the world’s 10 largest rivers by volume, has lost 22% of its surface water. The Brazilian portion of the Pantanal, the world’s largest tropical wetland, has lost 74% of its surface water. Such losses are devastating for wildlife (4,000 species of plants and animals live in the Pantanal, including jaguars, tapirs and anacondas), people and nature.
“AI technology provided us with a shockingly clear picture,” says Cássio Bernardino, WWF-Brasil’s MapBiomas water project lead. “Without AI and ML technology, we would never have known how serious the situation was, let alone had the data to convince people. Now we can take steps to tackle the challenges this loss of surface water poses to Brazil’s incredible biodiversity and communities.”
3. Finding whales
Knowing where whales are is the first step in putting measures such as marine protected areas in place to protect them. Locating humpbacks visually across vast oceans is difficult, but their distinctive singing can travel hundreds of miles underwater. At National Oceanic and Atmospheric Association (Noaa) fisheries in the Pacific islands, acoustic recorders are used to monitor marine mammal populations at remote and hard-to-access islands, says Ann Allen, Noaa research oceanographer. “In 14 years, we’ve accumulated around 190,000 hours of acoustic recordings. It would take an exorbitant amount of time for an individual to manually identify whale vocalisations.”In 2018, Noaa partnered with Google AI for Social Good’s bioacoustics team to create an ML model that could recognise humpback whale song. “We were very successful in identifying humpback song through our entire dataset, establishing patterns of their presence in the Hawaiian islands and Mariana islands,” says Allen. “We also found a new occurrence of humpback song at Kingman reef, a site that’s never before had documented humpback presence. This comprehensive analysis of our data wouldn’t have been possible without AI.”
4. Protecting koalas
Australia’s koala populations are in serious decline due to habitat destruction, domestic dog attacks, road accidents and bushfires. Without knowledge of their numbers and whereabouts, saving them is challenging. Grant Hamilton, associate professor of ecology at Queensland University of Technology (QUT), has created a conservation AI hub with federal and Landcare Australia funding to count koalas and other endangered animals. Using drones and infrared imaging, an AI algorithm rapidly analyses infrared footage and determines whether a heat signature is a koala or another animal. Hamilton used the system after Australia’s devastating bushfires in 2019 and 2020 to identify surviving koala populations, particularly on Kangaroo Island.“This is a gamechanger project to protect koalas,” says Hamilton. “Powerful AI algorithms are able to analyse countless hours of video footage and identify koalas from many other animals in the thick bushland. This system will allow Landcare groups, conservation groups and organisations working on protecting and monitoring species to survey large areas anywhere in Australia and send the data back to us at QUT to process it.
“We will increasingly see AI used in conservation,” he adds. “In this current project, we simply couldn’t do this as rapidly or as accurately without AI.”
5. Counting species
Saving species on the brink of extinction in the Congo basin, the world’s second-largest rainforest, is a huge task. In 2020, data science company Appsilon teamed up with the University of Stirling in Scotland and Gabon’s national parks agency (ANPN) to develop the Mbaza AI image classification algorithm for large-scale biodiversity monitoring in Gabon’s Lopé and Waka national parks.Conservationists had been using automated cameras to capture species, including African forest elephants, gorillas, chimpanzees and pangolins, which then had to be manually identified. Millions of pictures could take months or years to classify, and in a country that is losing about 150 elephants each month to poachers, time matters.
The Mbaza AI algorithm was used in 2020 to analyse more than 50,000 images collected from 200 camera traps spread across 7,000 sq km of forest. Mbaza AI classifies up to 3,000 images an hour and is up to 96% accurate. Conservationists can monitor and track animals and quickly spot anomalies or warning signs, enabling them to act swiftly when needed. The algorithm also works offline on an ordinary laptop, which is helpful in locations with no or poor internet connectivity.
“Many central African forest mammals are threatened by unsustainable trade, land-use changes and the global climate crisis,” says Dr Robin Whytock, post-doctoral research fellow at the University of Stirling. “Appsilon’s work on the Mbaza AI app enables conservationists to rapidly identify and respond to threats to biodiversity. The project started with 200 camera traps in Lopé and Waka national parks in Gabon but, since then, hundreds more have been deployed by different organisations across west and central Africa. In Gabon, the government and national parks agency are aiming to deploy cameras across the entire country. Mbaza AI can help all these projects speed up data analysis.”
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Read More »How to Use AI to Talk to Whales—and Save Life on Earth
September 3rd, 2023
Via Wired, a look at how – with ecosystems in crisis – engineers and scientists are using AI to decipher what animals are saying, with the hope that – by truly listening to nature – humans will decide to protect it:
BEFORE MICHELLE FOURNET moved to Alaska on a whim in her early twenties, she’d never seen a whale. She took a job on a whale watching boat and, each day she was out on the water, gazed at the grand shapes moving under the surface. For her entire life, she realized, the natural world had been out there, and she’d been missing it. “I didn’t even know I was bereft,” she recalls. Later, as a graduate student in marine biology, Fournet wondered what else she was missing. The humpbacks she was getting to know revealed themselves in partial glimpses. What if she could hear what they were saying? She dropped a hydrophone in the water—but the only sound that came through was the mechanical churn of boats. The whales had fallen silent amid the racket. Just as Fournet had discovered nature, then, she was witnessing it recede. She resolved to help the whales. To do that, she needed to learn how to listen to them.
Fournet, now a professor at the University of New Hampshire and the director of a collective of conservation scientists, has spent the past decade building a catalog of the various chirps, shrieks, and groans that humpbacks make in daily life. The whales have huge and diverse vocabularies, but there is one thing they all say, whether male or female, young or old. To our meager human ears, it sounds something like a belly rumble punctuated by a water droplet: whup.
Fournet thinks the whup call is how the whales announce their presence to one another. A way of saying, “I’m here.” Last year, as part of a series of experiments to test her theory, Fournet piloted a skiff out into Alaska’s Frederick Sound, where humpbacks gather to feed on clouds of krill. She broadcast a sequence of whup calls and recorded what the whales did in response. Then, back on the beach, she put on headphones and listened to the audio. Her calls went out. The whales’ voices returned through the water: whup, whup, whup. Fournet describes it like this: The whales heard a voice say, “I am, I am here, I am me.” And they replied, “I also am, I am here, I am me.”
Biologists use this type of experiment, called a playback, to study what prompts an animal to speak. Fournet’s playbacks have so far used recordings of real whups. The method is imperfect, though, because humpbacks are highly attentive to who they’re talking to. If a whale recognizes the voice of the whale in the recording, how does that affect its response? Does it talk to a buddy differently than it would to a stranger? As a biologist, how do you ensure you’re sending out a neutral whup?
One answer is to create your own. Fournet has shared her catalog of humpback calls with the Earth Species Project, a group of technologists and engineers who, with the help of AI, are aiming to develop a synthetic whup. And they’re not just planning to emulate a humpback’s voice. The nonprofit’s mission is to open human ears to the chatter of the entire animal kingdom. In 30 years, they say, nature documentaries won’t need soothing Attenborough-style narration, because the dialog of the animals onscreen will be subtitled. And just as engineers today don’t need to know Mandarin or Turkish to build a chatbot in those languages, it will soon be possible to build one that speaks Humpback—or Hummingbird, or Bat, or Bee.
The idea of “decoding” animal communication is bold, maybe unbelievable, but a time of crisis calls for bold and unbelievable measures. Everywhere that humans are, which is everywhere, animals are vanishing. Wildlife populations across the planet have dropped an average of nearly 70 percent in the past 50 years, according to one estimate—and that’s just the portion of the crisis that scientists have measured. Thousands of species could disappear without humans knowing anything about them at all.
To decarbonize the economy and preserve ecosystems, we certainly don’t need to talk to animals. But the more we know about the lives of other creatures, the better we can care for those lives. And humans, being human, pay more attention to those who speak our language. The interaction that Earth Species wants to make possible, Fournet says, “helps a society that is disconnected from nature to reconnect with it.” The best technology gives humans a way to inhabit the world more fully. In that light, talking to animals could be its most natural application yet.
HUMANS HAVE ALWAYS known how to listen to other species, of course. Fishers throughout history collaborated with whales and dolphins to mutual benefit: a fish for them, a fish for us. In 19th-century Australia, a pod of killer whales was known to herd baleen whales into a bay near a whalers’ settlement, then slap their tails to alert the humans to ready the harpoons. (In exchange for their help, the orcas got first dibs on their favorite cuts, the lips and tongue.) Meanwhile, in the icy waters of Beringia, Inupiat people listened and spoke to bowhead whales before their hunts. As the environmental historian Bathsheba Demuth writes in her book Floating Coast, the Inupiat thought of the whales as neighbors occupying “their own country” who chose at times to offer their lives to humans—if humans deserved it.
Commercial whalers had a different approach. They saw whales as floating containers of blubber and baleen. The American whaling industry in the mid-19th century, and then the global whaling industry in the following century, very nearly obliterated several species, resulting in one of the largest-ever losses of wild animal life caused by humans. In the 1960s, 700,000 whales were killed, marking the peak of cetacean death. Then, something remarkable happened: We heard whales sing. On a trip to Bermuda, the biologists Roger and Katy Payne met a US naval engineer named Frank Watlington, who gave them recordings he’d made of strange melodies captured deep underwater. For centuries, sailors had recounted tales of eerie songs that emanated from their boats’ wooden hulls, whether from monsters or sirens they didn’t know. Watlington thought the sounds were from humpback whales. Go save them, he told the Paynes. They did, by releasing an album, Songs of the Humpback Whale, that made these singing whales famous. The Save the Whales movement took off soon after. In 1972, the US passed the Marine Mammal Protection Act; in 1986, commercial whaling was banned by the International Whaling Commission. In barely two decades, whales had transformed in the public eye into cognitively complex and gentle giants of the sea.
Roger Payne, who died earlier this year, spoke frequently about his belief that the more the public could know “curious and fascinating things” about whales, the more people would care what happened to them. In his opinion, science alone would never change the world, because humans don’t respond to data; they respond to emotion—to things that make them weep in awe or shiver with delight. He was in favor of wildlife tourism, zoos, and captive dolphin shows. However compromised the treatment of individual animals might be in these places, he believed, the extinction of a species is far worse. Conservationists have since held on to the idea that contact with animals can save them.
From this premise, Earth Species is taking the imaginative leap that AI can help us make first contact with animals. The organization’s founders, Aza Raskin and Britt Selvitelle, are both architects of our digital age. Raskin grew up in Silicon Valley; his father started Apple’s Macintosh project in the 1970s. Early in his career, Raskin helped to build Firefox, and in 2006 he created the infinite scroll, arguably his greatest and most dubious legacy. Repentant, he later calculated the collective human hours that his invention had wasted and arrived at a figure surpassing 100,000 lifetimes per week.
Raskin would sometimes hang out at a startup called Twitter, where he met Selvitelle, a founding employee. They stayed in touch. In 2013, Raskin heard a news story on the radio about gelada monkeys in Ethiopia whose communication had similar cadences to human speech. So similar, in fact, that the lead scientist would sometimes hear a voice talking to him, turn around, and be surprised to find a monkey there. The interviewer asked whether there was any way of knowing what they were trying to say. There wasn’t—but Raskin wondered if it might be possible to arrive at an answer with machine learning. He brought the idea up with Selvitelle, who had an interest in animal welfare.
For a while the idea was just an idea. Then, in 2017, new research showed that machines could translate between two languages without first being trained on bilingual texts. Google Translate had always mimicked the way a human might use a dictionary, just faster and at scale. But these new machine learning methods bypassed semantics altogether. They treated languages as geometric shapes and found where the shapes overlapped. If a machine could translate any language into English without needing to understand it first, Raskin thought, could it do the same with a gelada monkey’s wobble, an elephant’s infrasound, a bee’s waggle dance? A year later, Raskin and Selvitelle formed Earth Species.
Raskin believes that the ability to eavesdrop on animals will spur nothing less than a paradigm shift as historically significant as the Copernican revolution. He is fond of saying that “AI is the invention of modern optics.” By this he means that just as improvements to the telescope allowed 17th-century astronomers to perceive newfound stars and finally displace the Earth from the center of the cosmos, AI will help scientists hear what their ears alone cannot: that animals speak meaningfully, and in more ways than we can imagine. That their abilities, and their lives, are not less than ours. “This time we’re going to look out to the universe and discover humanity is not the center,” Raskin says.
Raskin and Selvitelle spent their first few years meeting with biologists and tagging along on fieldwork. They soon realized that the most obvious and immediate need in front of them wasn’t inciting revolution. It was sorting data. Two decades ago, a primate researcher would stand under a tree and hold a microphone in the air until her arm got tired. Now researchers can stick a portable biologger to a tree and collect a continuous stream of audio for a year. The many terabytes of data that result is more than any army of grad students could hope to tackle. But feed all this material to trained machine learning algorithms, and the computer can scan the data and flag the animal calls. It can distinguish a whup from a whistle. It can tell a gibbon’s voice from her brother’s. At least, that’s the hope. These tools need more data, research, and funding. Earth Species has a workforce of 15 people and a budget of a few million dollars. They’ve teamed up with several dozen biologists to start making headway on these practical tasks.
An early project took on one of the most significant challenges in animal communication research, known as the cocktail party problem: When a group of animals are talking to one another, how can you tell who’s saying what? In the open sea, schools of dolphins a thousand strong chatter all at once; scientists who record them end up with audio as dense with whistles and clicks as a stadium is with cheers. Even audio of just two or three animals is often unusable, says Laela Sayigh, an expert in bottlenose dolphin whistles, because you can’t tell where one dolphin stops talking and another starts. (Video doesn’t help, because dolphins don’t open their mouths when they speak.) Earth Species used Sayigh’s extensive database of signature whistles—the ones likened to names—to develop a neural network model that could separate overlapping animal voices. That model was useful only in lab conditions, but research is meant to be built on. A couple of months later, Google AI published a model for untangling wild birdsong.
Sayigh has proposed a tool that can serve as an emergency alert for dolphin mass strandings, which tend to recur in certain places around the globe. She lives in Cape Cod, Massachusetts, one such hot spot, where as often as a dozen times a year groups of dolphins get disoriented, inadvertently swim onto shore, and perish. Fortunately, there might be a way to predict this before it happens, Sayigh says. She hypothesizes that when the dolphins are stressed, they emit signature whistles more than usual, just as someone lost in a snowstorm might call out in panic. A computer trained to listen for these whistles could send an alert that prompts rescuers to reroute the dolphins before they hit the beach. In the Salish Sea—where, in 2018, a mother orca towing the body of her starved calf attracted global sympathy—there is an alert system, built by Google AI, that listens for resident killer whales and diverts ships out of their way.
For researchers and conservationists alike, the potential applications of machine learning are basically limitless. And Earth Species is not the only group working on decoding animal communication. Payne spent the last months of his life advising for Project CETI, a nonprofit that built a base in Dominica this year for the study of sperm whale communication. “Just imagine what would be possible if we understood what animals are saying to each other; what occupies their thoughts; what they love, fear, desire, avoid, hate, are intrigued by, and treasure,” he wrote in Time in June.
Many of the tools that Earth Species has developed so far offer more in the way of groundwork than immediate utility. Still, there’s a lot of optimism in this nascent field. With enough resources, several biologists told me, decoding is scientifically achievable. That’s only the beginning. The real hope is to bridge the gulf in understanding between an animal’s experience and ours, however vast—or narrow—that might be.
ARI FRIEDLAENDER HAS something that Earth Species needs: lots and lots of data. Friedlaender researches whale behavior at UC Santa Cruz. He got started as a tag guy: the person who balances at the edge of a boat as it chases a whale, holds out a long pole with a suction-cupped biologging tag attached to the end, and slaps the tag on a whale’s back as it rounds the surface. This is harder than it seems. Friedlaender proved himself adept—“I played sports in college,” he explains—and was soon traveling the seas on tagging expeditions.
The tags Friedlaender uses capture a remarkable amount of data. Each records not only GPS location, temperature, pressure, and sound, but also high-definition video and three-axis accelerometer data, the same tech that a Fitbit uses to count your steps or measure how deeply you’re sleeping. Taken together, the data illustrates, in cinematic detail, a day in the life of a whale: its every breath and every dive, its traverses through fields of sea nettles and jellyfish, its encounters with twirling sea lions.
Friedlaender shows me an animation he has made from one tag’s data. In it, a whale descends and loops through the water, traveling a multicolored three-dimensional course as if on an undersea Mario Kart track. Another animation depicts several whales blowing bubble nets, a feeding strategy in which they swim in circles around groups of fish, trap the fish in the center with a wall of bubbles, then lunge through, mouths gaping. Looking at the whales’ movements, I notice that while most of them have traced a neat spiral, one whale has produced a tangle of clumsy zigzags. “Probably a young animal,” Friedlaender says. “That one hasn’t figured things out yet.”
Friedlaender’s multifaceted data is especially useful for Earth Species because, as any biologist will tell you, animal communication isn’t purely verbal. It involves gestures and movement just as often as vocalizations. Diverse data sets get Earth Species closer to developing algorithms that can work across the full spectrum of the animal kingdom. The organization’s most recent work focuses on foundation models, the same kind of computation that powers generative AI like ChatGPT. Earlier this year, Earth Species published the first foundation model for animal communication. The model can already accurately sort beluga whale calls, and Earth Species plans to apply it to species as disparate as orangutans (who bellow), elephants (who send seismic rumbles through the ground), and jumping spiders (who vibrate their legs). Katie Zacarian, Earth Species’ CEO, describes the model this way: “Everything’s a nail, and it’s a hammer.”
Another application of Earth Species’ AI is generating animal calls, like an audio version of GPT. Raskin has made a few-second chirp of a chiffchaff bird. If this sounds like it’s getting ahead of decoding, it is—AI, as it turns out, is better at speaking than understanding. Earth Species is finding that the tools it is developing will likely have the ability to talk to animals even before they can decode. It may soon be possible, for example, to prompt an AI with a whup and have it continue a conversation in Humpback—without human observers knowing what either the machine or the whale is saying.
No one is expecting such a scenario to actually take place; that would be scientifically irresponsible, for one thing. The biologists working with Earth Species are motivated by knowledge, not dialog for the sake of it. Felix Effenberger, a senior AI research adviser for Earth Species, told me: “I don’t believe that we will have an English-Dolphin translator, OK? Where you put English into your smartphone and then it makes dolphin sounds and the dolphin goes off and fetches you some sea urchin. The goal is to first discover basic patterns of communication.”
So what will talking to animals look—sound—like? It needn’t be a free-form conversation to be astonishing. Speaking to animals in a controlled way, as with Fournet’s playback whups, is probably essential for scientists to try to understand them. After all, you wouldn’t try to learn German by going to a party in Berlin and sitting mutely in a corner.
Bird enthusiasts already use apps to snatch melodies out of the air and identify which species is singing. With an AI as your animal interpreter, imagine what more you could learn. You prompt it to make the sound of two humpbacks meeting, and it produces a whup. You prompt it to make the sound of a calf talking to its mother, and it produces a whisper. You prompt it to make the sound of a lovelorn male, and it produces a song.
NO SPECIES OF whale has ever been driven extinct by humans. This is hardly a victory. Numbers are only one measure of biodiversity. Animal lives are rich with all that they are saying and doing—with culture. While humpback populations have rebounded since their lowest point a half-century ago, what songs, what practices, did they lose in the meantime? Blue whales, hunted down to a mere 1 percent of their population, might have lost almost everything.
Christian Rutz, a biologist at the University of St. Andrews, believes that one of the essential tasks of conservation is to preserve nonhuman ways of being. “You’re not asking, ‘Are you there or are you not there?’” he says. “You are asking, ‘Are you there and happy, or unhappy?’”
Rutz is studying how the communication of Hawaiian crows has changed since 2002, when they went extinct in the wild. About 100 of these remarkable birds—one of few species known to use tools—are alive in protective captivity, and conservationists hope to eventually reintroduce them to the wild. But these crows may not yet be prepared. There is some evidence that the captive birds have forgotten useful vocabulary, including calls to defend their territory and warn of predators. Rutz is working with Earth Species to build an algorithm to sift through historical recordings of the extinct wild crows, pull out all the crows’ calls, and label them. If they find that calls were indeed lost, conservationists might generate those calls to teach them to the captive birds.
Rutz is careful to say that generating calls will be a decision made thoughtfully, when the time requires it. In a paper published in Science in July, he praised the extraordinary usefulness of machine learning. But he cautions that humans should think hard before intervening in animal lives. Just as AI’s potential remains unknown, it may carry risks that extend beyond what we can imagine. Rutz cites as an example the new songs composed each year by humpback whales that spread across the world like hit singles. Should these whales pick up on an AI-generated phrase and incorporate that into their routine, humans would be altering a million-year-old culture. “I think that is one of the systems that should be off-limits, at least for now,” he told me. “Who has the right to have a chat with a humpback whale?”
It’s not hard to imagine how AI that speaks to animals could be misused. Twentieth-century whalers employed the new technology of their day, too, emitting sonar at a frequency that drove whales to the surface in panic. But AI tools are only as good or bad as the things humans do with them. Tom Mustill, a conservation documentarian and the author of How to Speak Whale, suggests giving animal-decoding research the same resources as the most championed of scientific endeavors, like the Large Hadron Collider, the Human Genome Project, and the James Webb Space Telescope. “With so many technologies,” he told me, “it’s just left to the people who have developed it to do what they like until the rest of the world catches up. This is too important to let that happen.”
Billions of dollars are being funneled into AI companies, much of it in service of corporate profits: writing emails more quickly, creating stock photos more efficiently, delivering ads more effectively. Meanwhile, the mysteries of the natural world remain. One of the few things scientists know with certainty is how much they don’t know. When I ask Friedlaender whether spending so much time chasing whales has taught him much about them, he tells me he sometimes gives himself a simple test: After a whale goes under the surface, he tries to predict where it will come up next. “I close my eyes and say, ‘OK, I’ve put out 1,000 tags in my life, I’ve seen all this data. The whale is going to be over here.’ And the whale’s always over there,” he says. “I have no idea what these animals are doing.”
IF YOU COULD speak to a whale, what would you say? Would you ask White Gladis, the killer whale elevated to meme status this summer for sinking yachts off the Iberian coast, what motivated her rampage—fun, delusion, revenge? Would you tell Tahlequah, the mother orca grieving the death of her calf, that you, too, lost a child? Payne once said that if given the chance to speak to a whale, he’d like to hear its normal gossip: loves, feuds, infidelities. Also: “Sorry would be a good word to say.”
Then there is that thorny old philosophical problem. The question of umwelt, and what it’s like to be a bat, or a whale, or you. Even if we could speak to a whale, would we understand what it says? Or would its perception of the world, its entire ordering of consciousness, be so alien as to be unintelligible? If machines render human languages as shapes that overlap, perhaps English is a doughnut and Whalish is the hole.
Maybe, before you can speak to a whale, you must know what it is like to have a whale’s body. It is a body 50 million years older than our body. A body shaped to the sea, to move effortlessly through crushing depths, to counter the cold with sheer mass. As a whale, you choose when to breathe, or not. Mostly you are holding your breath. Because of this, you cannot smell or taste. You do not have hands to reach out and touch things with. Your eyes are functional, but sunlight penetrates water poorly. Usually you can’t even make out your own tail through the fog.
You would live in a cloud of hopeless obscurity were it not for your ears. Sound travels farther and faster through water than through air, and your world is illuminated by it. For you, every dark corner of the ocean rings with sound. You hear the patter of rain on the surface, the swish of krill, the blasts of oil drills. If you’re a sperm whale, you spend half your life in the pitch black of the deep sea, hunting squid by ear. You use sound to speak, too, just as humans do. But your voice, rather than dissipating instantly in the thin substance of air, sustains. Some whales can shout louder than a jet engine, their calls carrying 10,000 miles across the ocean floor.
But what is it like to be you, a whale? What thoughts do you think, what feelings do you feel? These are much harder things for scientists to know. A few clues come from observing how you talk to your own kind. If you’re born into a pod of killer whales, close-knit and xenophobic, one of the first things your mother and your grandmother teach you is your clan name. To belong must feel essential. (Remember Keiko, the orca who starred in the film Free Willy: When he was released to his native waters late in life, he failed to rejoin the company of wild whales and instead returned to die among humans.) If you’re a female sperm whale, you click to your clanmates to coordinate who’s watching whose baby; meanwhile, the babies babble back. You live on the go, constantly swimming to new waters, cultivating a disposition that is nervous and watchful. If you’re a male humpback, you spend your time singing alone in icy polar waters, far from your nearest companion. To infer loneliness, though, would be a human’s mistake. For a whale whose voice reaches across oceans, perhaps distance does not mean solitude. Perhaps, as you sing, you are always in conversation.
MICHELLE FOURNET WONDERS: How do we know whales would want to talk to us anyway? What she loves most about humpbacks is their indifference. “This animal is 40 feet long and weighs 75,000 pounds, and it doesn’t give a shit about you,” she told me. “Every breath it takes is grander than my entire existence.” Roger Payne observed something similar. He considered whales the only animal capable of an otherwise impossible feat: making humans feel small.
Early one morning in Monterey, California, I boarded a whale watching boat. The water was slate gray with white peaks. Flocks of small birds skittered across the surface. Three humpbacks appeared, backs rounding neatly out of the water. They flashed some tail, which was good for the group’s photographers. The fluke’s craggy ridge-line can be used, like a fingerprint, to distinguish individual whales.
Later, I uploaded a photo of one of the whales to Happywhale. The site identifies whales using a facial recognition algorithm modified for flukes. The humpback I submitted, one with a barnacle-encrusted tail, came back as CRC-19494. Seventeen years ago, this whale had been spotted off the west coast of Mexico. Since then, it had made its way up and down the Pacific between Baja and Monterey Bay. For a moment, I was impressed that this site could so easily fish an animal out of the ocean and deliver me a name. But then again, what did I know about this whale? Was it a mother, a father? Was this whale on Happywhale actually happy? The AI had no answers. I searched the whale’s profile and found a gallery of photos, from different angles, of a barnacled fluke. For now, that was all I could know.
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