Posts Tagged ‘biology’

Motion sensor “camera traps” unobtrusively take pictures of animals in their natural environment, oftentimes yielding images not otherwise observable. The artificial intelligence system automatically processes such images, here correctly reporting this as a picture of two impala standing.

A new paper in the Proceedings of the National Academy of Sciences (PNAS) reports how a cutting-edge artificial intelligence technique called deep learning can automatically identify, count and describe animals in their natural habitats.

Photographs that are automatically collected by motion-sensor cameras can then be automatically described by deep neural networks. The result is a system that can automate animal identification for up to 99.3 percent of images while still performing at the same 96.6 percent accuracy rate of crowdsourced teams of human volunteers.

“This technology lets us accurately, unobtrusively and inexpensively collect wildlife data, which could help catalyze the transformation of many fields of ecology, wildlife biology, zoology, conservation biology and animal behavior into ‘big data’ sciences. This will dramatically improve our ability to both study and conserve wildlife and precious ecosystems,” says Jeff Clune, the senior author of the paper. He is the Harris Associate Professor at the University of Wyoming and a senior research manager at Uber’s Artificial Intelligence Labs.

The paper was written by Clune; his Ph.D. student Mohammad Sadegh Norouzzadeh; his former Ph.D. student Anh Nguyen (now at Auburn University); Margaret Kosmala (Harvard University); Ali Swanson (University of Oxford); and Meredith Palmer and Craig Packer (both from the University of Minnesota).

Deep neural networks are a form of computational intelligence loosely inspired by how animal brains see and understand the world. They require vast amounts of training data to work well, and the data must be accurately labeled (e.g., each image being correctly tagged with which species of animal is present, how many there are, etc.).

This study obtained the necessary data from Snapshot Serengeti, a citizen science project on the platform. Snapshot Serengeti has deployed a large number of “camera traps” (motion-sensor cameras) in Tanzania that collect millions of images of animals in their natural habitat, such as lions, leopards, cheetahs and elephants. The information in these photographs is only useful once it has been converted into text and numbers. For years, the best method for extracting such information was to ask crowdsourced teams of human volunteers to label each image manually. The study published today harnessed 3.2 million labeled images produced in this manner by more than 50,000 human volunteers over several years.

“When I told Jeff Clune we had 3.2 million labeled images, he stopped in his tracks,” says Packer, who heads the Snapshot Serengeti project. “We wanted to test whether we could use machine learning to automate the work of human volunteers. Our citizen scientists have done phenomenal work, but we needed to speed up the process to handle ever greater amounts of data. The deep learning algorithm is amazing and far surpassed my expectations. This is a game changer for wildlife ecology.”

Swanson, who founded Snapshot Serengeti, adds: “There are hundreds of camera-trap projects in the world, and very few of them are able to recruit large armies of human volunteers to extract their data. That means that much of the knowledge in these important data sets remains untapped. Although projects are increasingly turning to citizen science for image classification, we’re starting to see it take longer and longer to label each batch of images as the demand for volunteers grows. We believe deep learning will be key in alleviating the bottleneck for camera-trap projects: the effort of converting images into usable data.”

“Not only does the artificial intelligence system tell you which of 48 different species of animal is present, but it also tells you how many there are and what they are doing. It will tell you if they are eating, sleeping, if babies are present, etc.,” adds Kosmala, another Snapshot Serengeti leader. “We estimate that the deep learning technology pipeline we describe would save more than eight years of human labeling effort for each additional 3 million images. That is a lot of valuable volunteer time that can be redeployed to help other projects.”

First-author Sadegh Norouzzadeh points out that “Deep learning is still improving rapidly, and we expect that its performance will only get better in the coming years. Here, we wanted to demonstrate the value of the technology to the wildlife ecology community, but we expect that as more people research how to improve deep learning for this application and publish their datasets, the sky’s the limit. It is exciting to think of all the different ways this technology can help with our important scientific and conservation missions.”

The paper that in PNAS is titled, “Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning.”,-count,-describe-wild-animals.html


The purpose and evolutionary origins of sleep are among the biggest mysteries in neuroscience. Every complex animal, from the humblest fruit fly to the largest blue whale, sleeps — yet scientists can’t explain why any organism would leave itself vulnerable to predators, and unable to eat or mate, for a large portion of the day. Now, researchers have demonstrated for the first time that even an organism without a brain — a kind of jellyfish — shows sleep-like behaviour, suggesting that the origins of sleep are more primitive than thought.

Researchers observed that the rate at which Cassiopea jellyfish pulsed their bell decreased by one-third at night, and the animals were much slower to respond to external stimuli such as food or movement during that time. When deprived of their night-time rest, the jellies were less active the next day.

“Everyone we talk to has an opinion about whether or not jellyfish sleep. It really forces them to grapple with the question of what sleep is,” says Ravi Nath, the paper’s first author and a molecular geneticist at the California Institute of Technology (Caltech) in Pasadena. The study was published in Current Biology.

“This work provides compelling evidence for how early in evolution a sleep-like state evolved,” says Dion Dickman, a neuroscientist at the University of Southern California in Los Angeles.

Mindless sleep
Nath is studying sleep in the worm Caenorhabditis elegans, but whenever he presented his work at research conferences, other scientists scoffed at the idea that such a simple animal could sleep. The question got Nath thinking: how minimal can an animal’s nervous system get before the creature lacks the ability to sleep? Nath’s obsession soon infected his friends and fellow Caltech PhD students Michael Abrams and Claire Bedbrook. Abrams works on jellyfish, and he suggested that one of these creatures would be a suitable model organism, because jellies have neurons but no central nervous system. Instead, their neurons connect in a decentralized neural net.

Cassiopea jellyfish, in particular, caught the trio’s attention. Nicknamed the upside-down jellyfish because of its habit of sitting on the sea floor on its bell, with its tentacles waving upwards, Cassiopea rarely moves on its own. This made it easier for the researchers to design an automated system that used video to track the activity of the pulsing bell. To provide evidence of sleep-like behaviour in Cassiopea (or any other organism), the researchers needed to show a rapidly reversible period of decreased activity, or quiescence, with decreased responsiveness to stimuli. The behaviour also had to be driven by a need to sleep that increased the longer the jellyfish was awake, so that a day of reduced sleep would be followed by increased rest.

Other researchers had already documented a nightly drop in activity in other species of jellyfish, but no jellyfish had been known to display the other aspects of sleep behaviour. In a 35-litre tank, Nath, Abrams and Bedbrook tracked the bell pulses of Cassiopea over six days and nights and found that the rate, which was an average of one pulse per second by day, dropped by almost one-third at night. They also documented night-time pulse-free periods of 10–15 seconds, which didn’t occur during the day.

Restless night
Without an established jellyfish alarm clock, the scientists used a snack of brine shrimp and oyster roe to try to rouse the snoozing Cassiopea. When they dropped food in the tank at night, Cassiopea responded to its treat by returning to a daytime pattern of activity. The team used the jellyfish’s preference for sitting on solid surfaces to test whether quiescent Cassiopea had a delayed response to external stimuli. They slowly lifted the jellyfish off the bottom of the tank using a screen, then pulled it out from under the animal, leaving the jelly floating in the water. It took longer for the creature to begin pulsing and to reorient itself when this happened at night than it did during the day. If the experiment was immediately repeated at night, the jellyfish responded as if it were daytime. Lastly, when the team forced Cassiopea to pull an all-nighter by keeping it awake with repeated pulses of water, they found a 17% drop in activity the following day.

“This work shows that sleep is much older than we thought. The simplicity of these organisms is a door opener to understand why sleep evolved and what it does,” says Thomas Bosch, an evolutionary biologist at Kiel University in Germany. “Sleep can be traced back to these little metazoans — how much further does it go?” he asks.

That’s what Nath, Abrams and Bedbrook want to find out. Amid the chaos of finishing their PhD theses, they have begun searching for ancient genes that might control sleep, in the hope that this might provide hints as to why sleep originally evolved.


Rip Van Winkle, the titular ne’er-do-well of Washington Irving’s 1819 short story, famously spent 20 years napping in a forest. This lengthy slumber, apparently triggered by ghost liquor, caused Van Winkle to sleep through the American Revolutionary War.

Nearly two centuries later, scientists are shedding light on plants that do something similar in real life. A surprisingly diverse mix of plants around the world can live dormant underground for up to 20 years, researchers report in the journal Ecology Letters, a strategy that allows the plants to survive hard times by simply napping until things get better.

At least 114 species from 24 plant families are capable of this trick, in which a plant abandons photosynthesis to focus on survival in the soil. It’s a way for plants to hedge their bets, the study’s authors explain, by accepting certain short-term hardships — like missed opportunities to grow and reproduce — for the longer-term benefits of avoiding mortal dangers on the surface.

“It would seem to be paradoxical that plants would evolve this behavior, because being underground means they cannot photosynthesize, flower or reproduce,” says co-author Michael Hutchings, an ecology professor at the University of Sussex, in a statement. “And yet this study has shown that many plants in a large number of species frequently exhibit prolonged dormancy.”

So how do these Rip Van Winkle plants survive for up to 20 years without sunlight? Many species have found other ways to endure dormancy, Hutchings says, especially “by evolving mechanisms enabling them to obtain carbohydrates and nutrients from soil-based fungal associates.” Befriending soil fungi, he adds, “allows them to survive and even thrive during dormant periods.”

This strategy is used by many orchid species (including the lady’s slipper orchids pictured above), along with a wide variety of other plant types. It typically occurs in only part of a population or species during any given year, the researchers note, so the broader population can keep growing and reproducing while the designated survivors wait underground as backup.

By Elaina Zachos

Cheetahs are synonymous with speed. But past the big cat’s slender build and lean muscles, there’s something inside that aids this animal’s need for speed.

A new report, published February 2 in Scientific Reports, shows that certain parts of the cheetah’s inner ear help to make it a better hunter. The study marks the first time researchers have analyzed the big cats’ inner ear.

If you watch a cheetah sprinting in slow motion, you can see that they tend to keep their heads stable and their eyes fixed on prey even while in motion. To learn how the animal’s bone structure helps with this, lead author Camille Grohé turned to the animals’ inner ear.

The inner ear is crucial for maintaining balance and a steady head posture. It consists of three semicircular canals containing fluid and sensory hair cells that pick up motion in the head. Since each canal is angled differently, they’re each sensitive to different movements: one targets up-and-down motion, one side-to-side, and one tilts from one side to the other.

Using high-resolution imaging, Grohé and the team scanned 21 felid skulls. While some skulls were of other big cats, seven belonged to modern cheetahs. The researchers also imaged the skull of an extinct giant cheetah to see how the inner ear might have evolved.

The inner ears of cheetahs are like that of no other modern felids, the study found. Large vestibular systems—which help with balance—took up more of the inner ear of the cheetah than of any other big cat. Cheetahs also had longer semicircular ear canals, which help with head movement and eye direction.

“This distinctive inner ear anatomy reflects enhanced sensitivity and more rapid response to head motions,” co-author John Flynn says in a press release.

These highly-tuned traits were not seen in the extinct cheetah species, which shows these developments in the cheetah’s inner ear happened relatively recently.

“The living cheetah’s ancestors have evolved slender bones that would allow them to run very fast and then an inner ear ultra-sensitive to head movements to hold their head still, enabling them to run even faster,” Grohé adds.

As the fastest land animal, lightweight cheetahs are built for sprinting. Their spines are long and flexible, which allows them to launch from 0 to 60 miles per hour in just three seconds. While their strong, lean muscles help propel them forward, their large nasal cavities help them gulp in air to recover after a chase.

Federal biologist Jay Orr never knows what’s going to come up in nets lowered to the ocean floor off Alaska’s remote Aleutian Islands, which separate the Bering Sea from the rest of the Pacific Ocean. Sometimes it’s stuff he has to name.

The National Oceanic and Atmospheric Administration biologist is part of a group that uses trawl nets to survey commercially important fish species such as cod in waters off Alaska. Sometimes those nets come up with things no one has seen before.

With co-authors, Orr has discovered 14 kinds of new snailfish, a creature that can be found in tide pools but also in the deepest parts of the ocean. A dozen more new snailfish are waiting to be named. Additional species are likely to be found as scientists expand their time investigating areas such as the Bering Sea Slope, in water 800 to 5,200 feet deep, or the 25,663-foot deep Aleutian Trench.

“I suspect we are just scraping the top of the distributions of some of these deep-water groups,” Orr said from his office in Seattle.

Orr and his colleagues measure the abundance of rockfish, flatfish and other “bottom fish” for the Alaska Fisheries Science Center, the research arm of the NOAA’s National Marine Fisheries Service. The center studies marine resources off Alaska and parts of the West Coast.

Five boats with six researchers each surveyed Alaska waters in late June. The teams trawl on the Bering Shelf every summer and in either Aleutian waters or the Gulf of Alaska every other year.

Their findings on fish abundance are fed into models for managing fish populations.

The scientists put down a 131-foot trawl net that captures whatever is along the ocean bottom. A ton of fish is a standard sample. Along with fish, they get clues to the seafloor habitat. Sponges, for example, indicate a hard seafloor, or substrate.

Fifteen years ago, research biologist Michael Martin suggested a small modification: a net just 2 to 3 feet wide at the front of the trawl net.

“We realized we didn’t have a really good picture of the substrate that we were trawling over, and we figured we were missing some things in the big meshes that the larger net had,” Orr said. “So one of the other guys here decided to put this little net on, mainly as a means to see what the substrate looked like.”

On one of the first hauls, the small net returned with a variety of small, soft-bodied fish, including snailfish, that likely would have fallen out or gotten mashed in the main net. Orr took a look and knew they had found something different.

As someone who studies fish, “I sort of knew what I was looking for and what was known out there,” he said. “The first ones that came up, I saw them right away and said, ‘We don’t know what these are. These haven’t been named.'”

Snailfish have no scales, feel gelatinous and look like fat tadpoles. Aristotle described a Mediteranean variety found in ancient Greece as “sea slugs.”

Many fish have pelvic fins on their bellies, just behind the gills. Most snailfish species, instead of pelvic fins, have a sucking disc that they use to cling to rocks.

Orr identified some new varieties that did not have a sucking disc. Another had a hardened bone in its head. Another had a projecting lower jaw. Others varied by shape, color or body parts, such as vertebrae.

“Nearly all of them have genetic characters that distinguish them, too,” Orr said.

He has wide latitude for giving new species both common and Latin names. A red, white and black snailfish with a big, bulbous nose struck him as funny-looking. He gave it the common name of “comic snailfish” and the Latin name Careproctus comus, after Comus, the god of comedy in Greek mythology.

Snailfish made headlines in 2014 when researchers recorded them swimming nearly 27,000 feet, or more than 4 miles, below the surface in the Marianas Trench, making them the deepest-dwelling vertebrate on the planet. The Marianas Trench is about 200 miles southwest of the Pacific island of Guam and is known as the deepest part of the world’s oceans.

A critical part of the work is on the species his agency actively manages. Orr helped distinguish the northern rock sole, which spawns and grows differently than other rock sole. Fishing at the wrong time could disrupt a population important to the seafood market.

“Ultimately we’re managing an ecosystem,” Orr said. “It’s really important to know what each of the elements are.”

by Michael d’Estries

Back in 1986, during surveys for the location of a power plant near the Black Sea in Romania, construction workers digging more than 60 feet underground broke into a bizarre, previously untouched ecosystem.

Called the Movile Cave, this subterranean wonder has been sealed for an estimated 5.5 million years. The air is warm and deadly, with noxious gases and little oxygen, the tunnels narrow, the pure and utter darkness the stuff of nightmares. But what has shocked the few scientists who’ve entered this underground Middle Earth of Horrors is that the place is absolutely teeming with life.

More specifically, creepy-crawly life.

Water scorpions, worms, spiders, predatory leeches and previously unknown microbes are just a few of the creatures in Movile. In fact, of the 48 species that have been identified, a remarkable 33 are new to science.

“All the creatures we saw are completely white,” Microbiologist Rich Boden, one of only 30 people to have entered Movile, said in an interview. “None of them has any pigmentation in their body as there is no sunlight — you can see right through them.”

Most of the species also have no eyes, evolution having done away with that sense long ago in favor of longer antennae and arms.

“I thought it was odd that the spiders still spin webs down there because there are no flies, but then you see there are these little insects called spring-tails, which bounce into the air and are caught by the webs,” added Boden. “It really is the stuff of science-fiction.”

Because no organic matter from the surface makes its way into Movile, scientists were at first puzzled as to how an entire world could possibly flourish under such harsh conditions. The answer lies in vast “mats” on the surface of the cave’s waters and walls. These mats contain millions upon millions of tiny bacteria called autotrophs. Instead of photosynthesis, these autotrophs use a process called chemosynthesis, which obtains chemical energy from the oxidation of sulfur compounds and ammonia in the cave waters, explains the Murrell Lab, part of the University of East Anglia’s School of Environmental Sciences. The resulting milky film of microorganisms serves as the foundation for the rest Movile’s ecosystem.

“It’s very likely that the bacteria have been there a lot longer than 5 million years, but that the insects became trapped there around that time,” microbiologist J. Colin Murrell of University of East Anglia told the BBC. “They could have simply fallen in and become trapped when the limestone cast dropped, sealing the cave until it was discovered again in 1986.”

Movile’s unique conditions for life are so alien that the Romanian press quoted one scientist as saying that “if a nuclear war swept out life on Earth, that ecosystem would be a survivor.”

By Henry Hanks

It’s not often that someone discovers a new species, especially when it’s been under their nose for years.

A shark collected during a research expedition in 2010 turns out to be a ninja lanternshark, a brand new species of shark, so named because it is all black, which is how a ninja is typically dressed.

The scientific name is Etmopterus benchleyi, a reference to “Jaws” author Peter Benchley.

Grad student Vicky Vasquez and Dr. Douglas J. Long wrote about their findings after being asked to take a closer look at the shark (along with her professor, Dr. David A. Ebert of the Pacific Shark Research Center at Cal State).

“It is also the first lanternshark to ever be discovered off of the central eastern Pacific Ocean near Central America,” Vasquez pointed o

Four children, ages 8 to 14 years old, decided upon the name “ninja lanternshark.”