Artificial intelligence identifies plant species by looking at them

Machine learning algorithms have successfully identified plant species in massive herbaria just by looking at the dried specimens. According to researchers, similar AI approaches could also be used identify the likes of fly larvae and plant fossils. From Nature:

There are roughly 3,000 herbaria in the world, hosting an estimated 350 million specimens — only a fraction of which has been digitized. But the swelling data sets, along with advances in computing techniques, enticed computer scientist Erick Mata-Montero of the Costa Rica Institute of Technology in Cartago and botanist Pierre Bonnet of the French Agricultural Research Centre for International Development in Montpellier, to see what they could make of the data.

Researchers trained... algorithms on more than 260,000 scans of herbarium sheets, encompassing more than 1,000 species. The computer program eventually identified species with nearly 80% accuracy: the correct answer was within the algorithms’ top 5 picks 90% of the time. That, says (Penn State paleobotanist Peter) Wilf, probably out-performs a human taxonomist by quite a bit.

Such results often worry botanists, Bonnet says, many of whom already feel that their field is undervalued. “People feel this kind of technology could be something that will decrease the value of botanical expertise,” he says. “But this approach is only possible because it is based on the human expertise. It will never remove the human expertise.” People would also still need to verify the results, he adds.

"Going deeper in the automated identification of Herbarium specimens" (BMC Evolutionary Biology) Read the rest

Scientists discover transparent frog

Scientists discovered this new species of "glass frog" in Ecuador's Amazon lowlands. Hyalinobatrachium yaku's belly is so transparent that you can clearly see its kidneys, bladder, and beating heart. From Science News:

Yaku means “water” in Kichwa, a language spoken in Ecuador and parts of Peru where H. yaku may also live. Glass frogs, like most amphibians, depend on streams. Egg clutches dangle on the underside of leaves, then hatch, and the tadpoles drop into the water below. But the frogs are threatened by pollution and habitat destruction, the researchers write. Oil extraction, which occurs in about 70 percent of Ecuador’s Amazon rainforest, and expanding mining activities are both concerns.

"A marvelous new glassfrog (Centrolenidae, Hyalinobatrachium) from Amazonian Ecuador" (ZooKeys) Read the rest

Cats domesticated themselves

In many, animal species are domesticated when humans bring them into their homes whether they want to be there or not. For example, it's mostly accepted that humans domesticated wolves, breeding them in captivity until they became the modern dogs we love today. Now, a new study of cat genetics reveals that cats just kind of hung around humans for thousands of years before they were domesticated. From Casey Smith's article in National Geographic:

The earlier ancestors of today’s domestic cats spread from southwest Asia and into Europe as early as 4400 B.C. The cats likely started hanging around farming communities in the Fertile Crescent about 8,000 years ago, where they settled into a mutually beneficial relationship as humans’ rodent patrol.

Mice and rats were attracted to crops and other agricultural byproducts being produced by human civilizations. Cats likely followed the rodent populations and, in turn, frequently approached the human settlements.

“This is probably how the first encounter between humans and cats occurred,” says study coauthor Claudio Ottoni of the University of Leuven. “It’s not that humans took some cats and put them inside cages,” he says. Instead, people more or less allowed cats to domesticate themselves.

A second lineage, consisting of African cats that dominated Egypt, spread into the Mediterranean and most of the Old World beginning around 1500 B.C. This Egyptian cat probably had behaviors that made it attractive to humans, such as sociability and tameness.

The results suggest that prehistoric human populations probably began carrying their cats along ancient land and sea trade routes to control rodents.

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Thinking of the history of life on Earth in terms of "energy epochs"

Olivia P. Judson's paper in Nature, The energy expansions of evolution, presents a novel, beautifully written and presented frame for looking at the history of life on Earth: as a series of five epochs in which energy became more abundant and available to lifeforms, allowing them to scale up in complexity and fecundity: geochemical energy, sunlight, oxygen, flesh and fire. Read the rest

No matter how cool superblack activated charcoal food looks, it's a bad idea

Activated charcoal makes for some cool-looking chow, like the superblack soft-serve at LA's Little Damage, and you might think that since activated charcoal is given to people with acute poisoning, it's safe to eat. Read the rest

Hacking your microbiome with DIY fecal transplants

Biohacker Josiah Zayner suffered from persistent digestive problems so he decided to undertake an extreme self-experiment: He isolated himself in a hotel room, took massive doses of antibiotics, and then gave himself a fecal transplant to transform his own microbiome. Mark Frauenfelder and I interviewed Josiah about biohacking, cheap genetic engineering kits, and, of course, his own full body microbiome transplant in this episode of For Future Reference, a new podcast from Institute for the Future:

Please subscribe to For Future Reference: iTunes, RSS, Soundcloud Read the rest

Watch researchers modify caterpillars, revealing wing development inside cocoons

Biologist Nipam Patel and his team at UC Berkeley study how butterflies develop wing shape and color by performing surgery on caterpillars, creating translucent windows in their cocoons. Read the rest

Fancy flashlight finds first fluorescent frog

South American polka dot tree frogs are pretty cool, but Julián Faivovich and Carlos Taboada found out they are even cooler when an ultraviolet flashlight is trained on them. They fluoresce.

Many animals can see beyond the spectrum visible to humans, and these frogs adapted with this trait. From the abstract:

Fluorescence, the absorption of short-wavelength electromagnetic radiation reemitted at longer wavelengths, has been suggested to play several biological roles in metazoans. This phenomenon is uncommon in tetrapods, being restricted mostly to parrots and marine turtles. We report fluorescence in amphibians, in the tree frog Hypsiboas punctatus, showing that fluorescence in living frogs is produced by a combination of lymph and glandular emission, with pigmentary cell filtering in the skin. The chemical origin of fluorescence was traced to a class of fluorescent compounds derived from, here named hyloins. We show that fluorescence contributes 18−29% of the total emerging light under twilight and nocturnal scenarios, largely enhancing brightness of the individuals and matching the sensitivity of night vision in amphibians. These results introduce an unprecedented source of pigmentation in amphibians and highlight the potential relevance of fluorescence in visual perception in terrestrial environments.

I'd make a Wikipedia article about dihydroisoquinolinone, but it would probably be an annoying and demoralizing fight.

Naturally occurring fluorescence in frogs (via Nature) Read the rest

Conservation biologist warns that "cyber-poachers" could use tracking tags to hunt endangered animals

In Troubling issues at the frontier of animal tracking for conservation and management, Carleton University biologist Steven Cooke and colleagues describe a series of incidents in which poachers have used tracking tags placed on wild animals for conservation purposes to find and kill those animals. Read the rest

Frog saliva is even stranger than scientists expected

Frog tongue mechanism has been well-documented, but only recently have scientists started looking at the remarkable combo of tongue softness and frog spit's chemical makeup. Read the rest

This fish hunts by spitting water at its prey

The Archerfish of Southeast Asia and Australia spit at perched insects to knock them into the water for an easy meal. From KQED's "Deep Look":

“When the fish fires the shot,” (Wake Forest University biologist Morgan) Burnett explained, citing the work of other researchers in Germany who first used high-speed cameras to observe the projectiles in 2014, “the water leaves the mouth as essentially a very long stream. But during flight, the stream merges into a ball.”

The fish accomplishes this feat of timing through deliberate control of its highly-evolved mouthparts, in particular its lips, which act like an adjustable hose that can expand and contract while releasing the water.

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Meet Saccorhytus, bloblike human ancestor that shat through its mouth

Behold the 540 million-year-old fossil remains of the earliest-known human ancestor! Saccorhytus was "likely an egg-shaped creature that ate and expelled from the same gaping orifice," just like Senior Counselor to the President Stephen Bannon.

"This may represent the primitive beginnings of a very diverse range of species, including ourselves," said co-author Simon Conway Morris, a professor at Britain's University of Cambridge. Saccorhytus belongs to a broad category of organisms called deuterostomes, and is the most ancient specimen unearthed so far...

The sack-like animal's most distinctive feature is a large -- relative to the rest of its body -- mouth ringed by concentric circles of raised bumps. It probably ate by engulfing food particles and microscopic creatures. Intriguingly, the researchers did not find anything corresponding to an anus.

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First ever video of Ghost Shark, with sex organ on its head, alive in the ocean

Ghost sharks, aka chimaeras, are elusive relatives of sharks and rays that live in the black depths of the ocean, as far down as 2,600 meters. The Ghost Shark was captured on video by a remotely operated vehicle deployed on a geology expedition by the Monterey Bay Aquarium Research Institute in waters off Hawaii and California. The scientists who analyzed the video think that it's a pointy-nosed blue chimaera (Hydrolagus trolli) that usually calls the waters off Australia and New Zealand home. This is the first time researchers have known this species to swim in the Northern Hemisphere. From National Geographic:

Unlike those more well-known sharks, chimaeras don’t have rows of ragged teeth, but instead munch up their prey—mollusks, worms, and other bottom-dwellers—with mineralized tooth plates.

A pattern of open channels on their heads and faces, called lateral line canals, contain sensory cells that sense movement in the water and help the ghost sharks locate lunch.

And perhaps most fascinating, male chimaeras sport retractable sex organs on their foreheads.

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Honest mimicry vs. dishonest mimicry

I learned that there are two forms of mimicry in nature -- honest mimicry (e.g., bees and wasps look similar and advertise that they can sting) and dishonest mimicry (e.g., some flies look like bees and wasps to trick predators into thinking they can sting).

Inés Dawson, a graduate and PhD student at the University of Oxford, is the creator of this video, which is part of a science series on YouTube called Draw Curiosity. Read the rest

Scientists find first of its kind two-headed shark

University of Malaga scientists were studying the cardiovascular systems of Atlantic sawmill catsharks (catshark (Galeus atlanticus) when they found one with two heads. This is the first time that dicephaly (two-headedness) has been seen in an egg-laying shark. From National Geographic:

The causes of dicephaly aren't known, but the researchers—led by Valentín Sans-Coma of the University of Malaga—suspect that genetics are the most likely culprit (rather than some environmental factor, à la Blinky, the three-eyed fish, from The Simpsons)...

"We see two-headed sharks occasionally," says George Burgess, director of the Florida program for shark research at the Florida Museum of Natural History. "It's an anomaly, caused by a genetic misfire. There are lots of different kinds of genetic misfires, and most don't make it out of the womb."

"There’s a reason you don’t see a lot of sharks with two heads swimming around: they stand out like a sore thumb, so they get eaten," adds Burgess. "They would have trouble swimming and probably digesting food."

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Royal Society's remarkable 2016 nature photo finalists

Tane Sinclair-Taylor's image of a clownfish and a bleached anemone is one of the many remarkable biological photographs chosen as finalists and winners in Royal Society Publishing's 2016 contest. Read the rest

Tiny Pac-Man game uses real single cell organisms

Researchers in Norway built a 1mm wide Pac-Man board and populated it with single cell organisms.

From PopSci

You can't control them, but it's fascinating (and a bit creepy) to watch Euglena, ciliates, and rotifers wander around the oh-so familiar maze. While the video might give you a creepy-crawly tingle, worry not: there are probably far more microscopic creatures on an old arcade joystick from the original Pac-Man than you could possibly fit in this mini maze.

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