A Listening Network To Detect Nuclear Bomb Tests Found Blue Whales Instead
October 3rd, 2023
Via BBC, an article on how a listening built to detect nuclear bomb tests found blue whales instead:
Since the 1990s, a global network of sensors has listened for unauthorised nuclear detonations. But as Richard Fisher discovers, its creation has led to unanticipated upsides for science – such as identifying a previously unknown pod of pygmy blue whales.
For generations, the creatures swam through the ocean without crossing paths with any human beings. Some of them grew to 24m (80ft) long and weighed 90 tonnes. But if these enormous animals did encounter any boats, those meetings went unrecorded. Until recently, we didn’t even know they were there: a pod of pygmy blue whales in the Indian Ocean.
Their discovery in 2021 was all the more striking because of how they were found. We wouldn’t have come across them if it wasn’t for nuclear weapons.
What have atomic bombs got to do with a pod of whales? The answer lies in a global network of sensors, placed in some of the world’s most remote locations. Since the 1990s, its operators in a control room in Vienna, Austria have been listening for rogue nuclear tests. But as the years have passed, their network has also picked up many other sounds and rumblings throughout the ocean, ground and atmosphere – and that’s now proving a surprising boon to science.
The story of how the blue whales were found can be traced all the way back to the 1940s, when human beings discovered they could unlock the terrible power of the atom. After the US Trinity test and the bombing of Japan, decades of instability and fear followed, as nations raced to build their own arsenals and test ever-more powerful weapons.
After 50 years, many governments accepted that transparency was needed. If nuclear escalation was to be avoided, the world needed a way to know if any rogue nation or actor was conducting unauthorised tests. Only then could they trust one another.
So, in the 1990s, a number of nations signed and ratified the Comprehensive Nuclear-Test-Ban Treaty (CTBT), including the UK and many Western European nuclear powers. A few did not, including China, India and the US. While these hold-outs meant the treaty failed to come into force, the process did create a global norm against testing. And crucially, it also led to the establishment of a network capable of hearing, sniffing or sensing a nuclear detonation anywhere on Earth.
With sensors all over the world, the International Monitoring System – run by the CTBT Organisation in Vienna – has been operating ever since, growing to more than 300 facilities worldwide that can detect the sound, shockwaves and radioactive materials of nuclear explosions. This includes more than 120 seismic stations, 11 hydro-acoustic microphones in the oceans, 60 “infrasound” stations that pick up very low-frequency inaudible noise, and 80 detectors of radioactive particles or gases.
Many facilities can be found in quiet, relatively undisturbed locations. The US, for example, operates a station on Wake Island in the Pacific, one of the world’s most isolated atolls. Others can be found in Antarctica. However, a few are a little closer to civilisation, such as the seismic array in the village of Lajitas in Texas – 650km (400 miles) west of San Antonio – or the radionuclide station in Sacramento, California. (Here’s a map of all of them.)
Their widespread distribution means that if there’s a nuclear detonation somewhere on Earth, the operators of the Vienna control room will know, says Xyoli Perez Campos, director of the International Monitoring System division [IMS] of the CTBTO in Austria. “Wherever it happens, we have the technologies to cover it,” she says. “If there is an underground nuclear test, then we have the seismic technology to catch it. If the nuclear testing is underwater, then we have the hydro-acoustic stations. If testing happens in the atmosphere, then we have the infrasound. And the radionuclide stations allow us to distinguish if there was a nuclear component; that’s the smoking gun.”
Indeed, when North Korea conducted nuclear weapons tests in the 2000s and 2010s, various seismic sensors in the IMS picked up the waves from the blasts, and analysis of radioactive isotopes in the atmosphere confirmed it. The network has also sensed large non-nuclear blasts, like the enormous explosion in the port of Beirut in 2020, or the Hunga Tonga-Hunga Ha’apai volcanic eruption in January 2022.
The non-nuclear explosion in the port of Beirut in 2020 produced infrasound and seismic waves that could be detected from far away (Credit: Getty Images)
The non-nuclear explosion in the port of Beirut in 2020 produced infrasound and seismic waves that could be detected from far away (Credit: Getty Images)Recently, however, the IMS nuclear network has uncovered much more than big bangs. Over the past decade or so, as scientific access to the data has opened up, researchers have turned to the IMS to sense events that might otherwise go unnoticed. That includes the songs of whales, but also much more.
In June, hundreds of these scientists met at a conference in Vienna to share their findings. Researchers from Germany showed how the network’s hydro-acoustic sensors can monitor noise caused by shipping, a team from Japan presented findings about how they’d used the IMS to study submarine volcanic activity, and a Brazilian researcher spoke about the infrasound generated by the aurora borealis and aurora australis.
Others described efforts to detect the crash of avalanching glaciers from afar – building on previous research that deployed the network to keep tabs on calving icebergs in Antarctica.
The physicist Elizabeth Silber of Sandia National Laboratories in Albuquerque, New Mexico even demonstrated how the IMS’s detectors had picked up an “Earth-grazing fireball” – a meteoroid larger than 10cm (4in) that generated shockwaves as it struck the atmosphere on 22 September 2020.
As for the pygmy blue whales – a tropical subspecies of blue whale – they were discovered when researchers in Australia decided to listen a little closer to ocean sounds using the IMS’s hydro-acoustic network.
In 2021, bioacoustician Emmanuelle Leroy at the University of New South Wales, in Sydney, and colleagues analysed the songs of various whale populations in the central Indian ocean. A few years prior, a new song had been noticed, known as the “Chagos song”, or “Diego Garcia Downsweep”, named after the place it was detected: the Diego Garcia atoll in the Chagos archipelago.
At the time, five blue whale pods were known in the Indian Ocean, along with populations of Omura’s whales. But it wasn’t clear which group the Chagos song belonged to. Scientists know that each pod has strongly personalised calls, which means they can be sorted into “acoustic populations”, and this one did not match.
Leroy and colleagues realised that the IMS network would allow them to study the Chagos song over almost two decades, at various locations in the ocean, ranging from Sri Lanka to Western Australia. Their analysis concluded that the Chagos song must belong to an entirely new population of pygmy blue whales.
Finding this new pod was a significant piece of good news, not least because pygmy blue whales are so rare. In the 20th Century, blue whales were hunted close to extinction, from an estimated 239,000 in the 1920s to a low of around 360 in 1973.
When the architects of the IMS built their detection network, they did so hoping that the world would be a little safer. “What is really amazing for me is that these smart people decided that nuclear testing is a hazard for humanity, and not only did they write a treaty saying let’s stop it, but they came up with the technologies to monitor it. That is putting science and technology into good use for humanity,” says Perez Campos.
But even with that foresight, the network’s founders probably did not anticipate all of the IMS’s uses today. Its 300-plus stations have evolved into the ultimate planetary listening network. Right now, at remote locations all over the world, sensors are monitoring humanity and nature for sounds and rumbles that might otherwise go unnoticed – and that includes a family of whales singing a unique song. We might not be able to see this elusive pod, but they can nonetheless be heard.
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Read More »Can a Map of the Ocean Floor Be Crowdsourced?
October 3rd, 2023
Via BBC, an article on the potential for crowdsourcing to help map the ocean floor:
Tucked inside a federal government building in the American Rockies is the world’s best collection of seafloor maps. Occasionally a hard drive arrives in the mail, filled with new bathymetric – or seafloor – charts collected by survey vessels and research ships cruising the seas. The world’s largest public map of Earth’s oceans grows just a little bit more.
Cloaked in ocean, the seafloor has resisted human exploration for centuries. Folklore and myths told of it as the domain of terrifying sea monsters, gods, goddesses and lost underwater cities. Victorian-era sailors believed that there was no ocean floor at all, just an infinite abyss where the bodies of drowned sailors came to rest in watery purgatory.
Throughout the last century, modern scientific techniques and sonar have dispelled the stories and revealed a little understood seascape of crusted brine lakes, steaming volcanoes, and vast undulating underwater plains. We have only just begun to map, much less explore, this enormous subsea world.
One organisation wants to change this – and quickly. In 2023, Seabed 2030 announced that its latest map of the entire seafloor is nearly 25% complete. The data to make the world’s first publicly available map is stored at the International Hydrography Organization (IHO)’s Data Centre for Digital Bathymetry (DCDB) in a government building in Boulder, Colorado.
So far, the DCDB holds over 40 compressed terabytes of seafloor data. The biggest contributor is the US academic fleet: 17 research vessels owned by American universities which constantly circle the globe studying the deep ocean. Other contributors include the National Oceanic and Atmospheric Administration (NOAA) fleet, the Geological Survey of Ireland, and Germany’s Federal Maritime and Hydrographic Agency. The biggest users are scientists all over the world who rely on the data to conduct research.
Seabed 2030 has made extraordinary progress by asking countries and corporations to share maps with the DCDB. But unfortunately, the map is not growing quickly enough. Between 2016 and 2021, the map leapfrogged from 6% to 20%. Since then, the pace has slowed. In 2022, it reached just 23.3% complete; in 2023, 24.9%. The ocean mappers came up with a new plan: crowdsourcing.
By attaching a data logger to a boat’s echosounder, any vessel can build a simple map of the seafloor
“Crowdsourced bathymetry came about a few years ago when the IHO was saying: ‘At this rate, we’re never going to map the whole darn ocean; we need to start looking outside the box,'” says Jennifer Jencks, the director of the DCDB and the chair of a crowdsourced working group at the IHO.By attaching a data logger to a boat’s echosounder, any vessel can build a simple map of the seafloor. This is crucial in developing coastal and island nations. Tion Uriam, the head of the Hydrographic Unit at the Republic of Kiribati’s Ministry of Communications, Transport and Tourism Development, recently received two data loggers that he’s planning to install on local ferries. “It’s a win to be part of that initiative,” he says. “Just to put us on the map and raise our hands [to say] we want to be part of a global effort. Our contribution might be small – but it’s a contribution.”
Kiribati is a Pacific island nation of about 130,000 people spread across 33 coral atolls, only 20 of which are inhabited. British charts published in the 1950s and 1960s have been the most accurate maps to date; the United Kingdom and United States claimed various islands as protectorates or territories, mining them for phosphate or using them as whaling stations. Other British maps used are old and inaccurate; some date back to the late Victorian age or list depth measurements in fathoms, which most countries moved on from years go (the US only retired it in 2022).
That isn’t so unusual in the Pacific, according to marine geologist Kevin Mackay, who oversees Seabed 2030’s South and West Pacific Regional Centre at New Zealand’s National Institute of Water and Atmospheric Research (Niwa) in the capital Wellington. “The big problem in the Pacific is the relic of the colonial system. So, in the Pacific, who looks after the mapping? It’s the Americans through their territories, or the UK through their territories, or the French and their islands, even though they’re now officially independent.” Kiribati gained independence in 1979, but there’s been little progress on surveying since then. In 2020, the World Bank funded a $42m (£34.1m) project to improve maritime infrastructure in the outer islands. A portion of that will go toward seabed mapping.
As one of the least developed countries in the world, most i-Kiribati (the name for Kiribati’s inhabitants) live in the capital of South Tawara: a 17 sq km (6.5 sq mile) crescent-shaped atoll with a population density equal to Tokyo. More people are crowding into the capital in search of a modern life, while the rest live on remote islands where poverty and unemployment is high, amenities are poor and the long-term future uncertain because of rising sea levels and severe tropical storms.
The military or commercial value of nautical charts will always be a barrier to achieving complete coverage of the world map
Improved charts could boost trade, transit and tourism on the outer islands. They could help communities plan for tsunamis, storm surges and rising shorelines. Many islands lack basic tide gauges, and so visiting ships time their arrival for high tide. In his meetings with government ministers, Uriam tries to stress the economic benefits of improving nautical charts in Kiribati.However, there’s a roadblock when it comes to sharing maps with the DCDB archive back in Boulder. Around a third of the IHO’s 98 member states allow crowdsourcing inside territorial waters. However, the Pacific island nations of Kiribati, the Independent State of Samoa and the Cook Islands, which all recently received data loggers from Seabed 2030, are not among them. Until the governments give their blessing, the new crowdsourced maps will remain under wraps.
Despite Seabed 2030’s publicly stated scientific goal, the military or commercial value of nautical charts will always be a barrier to achieving complete coverage of the world map. “Sea charts, by their very nature, were destined to be removed from the academic realm and from general circulation,” wrote the map historian Lloyd Brown in his book The Story of Maps. “They were much more than an aid to navigation; they were in effect, the key to empire, the way to wealth.”
In a world where only a quarter of the seafloor is charted, there’s still an advantage in knowing more than your rivals. Niwa’s Mackay experienced this himself on a scientific-mapping expedition. He received a call from a military he chooses not to name and “they said ‘you need to destroy that data because there was military value in what you’re mapping, because it’s a place where submarines like to hide’,” he recalls. “Obviously, we ignore them because we’re [mapping] for science, we don’t care. But the military, they find lots of value in bathymetry that, as a scientist, we don’t even think about.”
For some nations, it’s also suspicious that the DCDB is based in the United States, which has the world’s most powerful military. “We have seen concerns as well, that the DCDB is hosted by the United States. Not everyone loves that,” says Jencks. She tries to assuage these concerns by stressing that the DCDB was endorsed by all IHO member states back when it was created in 1990.
In Kiribati, the challenges are less political, more practical, according to Uriam. His position as the head of the Hydrographic Unit only became permanent about a year ago. He used to work in the fisheries department and he knows just how hard is to share data across departments, let alone with outsiders. There’s also hurdles around storing data and hiring people with the right expertise to manage them. Another concern: foreign research vessels have mapped some of Kiribati’s territorial waters before and neglected to share data with the country’s government.
With just over six years left until the deadline, Seabed 2030 faces serious challenges in finishing the first public map of the seafloor. The staggering size of the ocean, the depths, the hostile offshore working environment where ocean mappers are constantly contending with wind, waves, and the corrosive effects of salt water. Then there’s the cost of mapping remote international waters where no country has a responsibility to map.
However, all these challenges seem small compared to the work of uniting countries behind a collective goal, particularly ones as diverse as the US and the Republic of Kiribati. The differences help explain why the goal of finishing a complete map of the seafloor may remain out of reach for many decades to come.
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Read More »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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