China-backed Sumatran dam threatens the rarest ape in the world

By Bill Laurance, James Cook University

The plan to build a massive hydropower dam in Sumatra as part of China’s immense Belt and Road Initiative threatens the habitat of the rarest ape in the world, which has only 800 remaining members.

This is merely the beginning of an avalanche of environmental crises and broader social and economic risks that will be provoked by the BRI scheme.




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How we discovered a new species of orangutan in northern Sumatra


The orangutan’s story began in November 2017, when scientists made a stunning announcement: they had discovered a seventh species of Great Ape, called the Tapanuli Orangutan, in a remote corner of Sumatra, Indonesia.

In an article published in Current Biology today, my colleagues and I show that this ape is perilously close to extinction – and that a Chinese-sponsored megaproject could be the final nail in its coffin.

Forest clearing for the Chinese-funded development has already begun.
Sumatran Orangutan Society

[Read more…]

We reconstructed the genome of the ‘first animal’

File 20180502 153908 1choet4.jpg?ixlib=rb 1.1

Shutterstock

By Jordi Paps, University of Essex

The first animals emerged on Earth at least 541m years ago, according to the fossil record. What they looked like is the subject of an ongoing debate, but they’re traditionally thought to have been similar to sponges.

Like today’s animals, they were made up of many, many different cells doing different jobs, programmed by thousands of different genes. But where did all these genes come from? Was the emergence of animals a small step in evolution, or did it represent a big leap in the DNA that carries the instructions for life?

To answer these questions and more, my colleague and I have reconstructed the set of genetic instructions (a minimal genome) present in the last common ancestor of all animals. By comparing this ancestral animal genome to those of other ancient lifeforms, we’ve shown that the emergence of animals involved a lot of very novel changes in DNA. What’s more, some of these changes were so essential to the biology of animals that they are still found in most modern animals after more than 500m years of independent evolution. In fact, most of our own genes are descended from this “first animal”.

Previous research on lifeforms that are closely related to animals – single-celled organisms such as choanoflagellates, filastereans and ichthyosporeans – has shown they share many genes with their animal cousins. This means that these genes are older than animals themselves and date back to some common ancestor of all these creatures. So the recycling of old genes into new functions, a kind of genome tinkering, must have been an important force in the origin of animals.

But Professor Peter Holland and I wanted to find out which new genes emerged when animals evolved. We used sophisticated computer programs to compare 1.5m proteins (the molecules that genes contain the instructions for) across 62 living genomes, making a total of 2.25 trillion comparisons to find out which genes are shared between different organisms today.

[Read more…]

Person of the forest

Why the human brain is so efficient

Liqun Luo writes:

An important difference between the computer and the brain is the mode by which information is processed within each system. Computer tasks are performed largely in serial steps. This can be seen by the way engineers program computers by creating a sequential flow of instructions. For this sequential cascade of operations, high precision is necessary at each step, as errors accumulate and amplify in successive steps. The brain also uses serial steps for information processing. In the tennis return example, information flows from the eye to the brain and then to the spinal cord to control muscle contraction in the legs, trunk, arms, and wrist.

But the brain also employs massively parallel processing, taking advantage of the large number of neurons and large number of connections each neuron makes. For instance, the moving tennis ball activates many cells in the retina called photoreceptors, whose job is to convert light into electrical signals. These signals are then transmitted to many different kinds of neurons in the retina in parallel. By the time signals originating in the photoreceptor cells have passed through two to three synaptic connections in the retina, information regarding the location, direction, and speed of the ball has been extracted by parallel neuronal circuits and is transmitted in parallel to the brain. Likewise, the motor cortex (part of the cerebral cortex that is responsible for volitional motor control) sends commands in parallel to control muscle contraction in the legs, the trunk, the arms, and the wrist, such that the body and the arms are simultaneously well positioned to receiving the incoming ball.

This massively parallel strategy is possible because each neuron collects inputs from and sends output to many other neurons—on the order of 1,000 on average for both input and output for a mammalian neuron. (By contrast, each transistor has only three nodes for input and output all together.) [Continue reading…]

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Only a tiny fraction of the genes inside our bodies are human

James Gallagher writes:

Prof Rob Knight, from University of California San Diego, told the BBC: “You’re more microbe than you are human.”

Originally it was thought our cells were outnumbered 10 to one.

“That’s been refined much closer to one-to-one, so the current estimate is you’re about 43% human if you’re counting up all the cells,” he says.

But genetically we’re even more outgunned.

The human genome – the full set of genetic instructions for a human being – is made up of 20,000 instructions called genes.

But add all the genes in our microbiome together and the figure comes out between two and 20 million microbial genes.

Prof Sarkis Mazmanian, a microbiologist from Caltech, argues: “We don’t have just one genome, the genes of our microbiome present essentially a second genome which augment the activity of our own.

“What makes us human is, in my opinion, the combination of our own DNA, plus the DNA of our gut microbes.” [Continue reading…]

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Burning coal may have caused Earth’s worst mass extinction

Dana Nuccitelli writes:

Recently, geologist Dr Benjamin Burger identified a rock layer in Utah that he believed might have formed during the Permian and subsequent Triassic period that could shed light on the cause of the Great Dying [the Earth’s deadliest mass extinction 252 million years ago].

During the Permian, Earth’s continents were still combined as one Pangea, and modern day Utah was on the supercontinent’s west coast. Samples from the end-Permian have been collected from rock layers in Asia, near the volcanic eruptions, but Utah was on the other side of Pangaea. Burger’s samples could thus provide a unique perspective of what was happening on the other side of the world from the eruptions. Burger collected and analyzed samples from the rock layer, and documented the whole process in a fascinating video:

 

Burger’s samples painted a grim picture of Earth’s environment at the end of the Permian period. A sharp drop in calcium carbonate levels indicated that the oceans had become acidic. A similar decline in organic content matched up with the immense loss of life in the oceans during this period. The presence of pyrite pointed to an anoxic ocean (without oxygen), meaning the oceans were effectively one massive dead zone.

Bacteria ate the oversupply of dead bodies, producing hydrogen sulfide gas, creating a toxic atmosphere. The hydrogen sulfide oxidized in the atmosphere to form sulfur dioxide, creating acid rain, which killed much of the plant life on Earth. Elevated barium levels in the samples had likely been carried up from the ocean depths by a massive release of methane.

Levels of various metals in the rock samples were critical in identifying the culprit of this mass extinction event. As in end-Permian samples collected from other locations around the world, Burger didn’t find the kinds of rare metals that are associated with asteroid impacts. There simply isn’t evidence that an asteroid struck at the right time to cause the Great Dying.

However, Burger did find high levels of mercury and lead in his samples, coinciding with the end of the Permian period. Mercury has also been identified in end-Permian samples from other sites. Lead and mercury aren’t associated with volcanic ash, but they are a byproduct of burning coal. [Continue reading…]

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How Lyme disease the first epidemic of climate change

Mary Beth Pfeiffer writes:

In the tally of species that will evolve or perish as temperatures rise, now consider the moose. The lumbering king of the deer family, known for antlers that can span six feet like giant outstretched fingers, the moose faces a litany of survival threats, from wolves and bears to brain worms and liver fluke parasites. But in the late 1990s in many northern states and Canada, something else began to claim adult cows and bull moose and, in even greater numbers, their single or twin calves.

Lee Kantar is the moose biologist for the state of Maine, which means that he makes a living climbing the rugged terrain of north-central Maine when a GPS collar indicates a moose has died. A lean man with a prominent salt-and-pepper moustache who wears flannel shirts and jeans to work, Kantar tagged 60 moose in January of 2014 around Moosehead Lake in the Maine Highlands. By the end of that year, 12 adults and 22 calves were dead – 57 per cent of the group. When biologists examined the carcasses, they found what they thought was the cause. Calves not even a year old harboured up to 60,000 blood-sucking arthropods known as winter ticks. In Vermont, dead moose were turning up with 100,000 ticks – each. In New Hampshire, the moose population had dropped from 7,500 to 4,500 from the 1990s to 2014, the emaciated bodies of cows, bulls and calves bearing similar infestations of ticks. These magnificent animals were literally being bled to death. [Continue reading…]

The interstitium, the largest organ we never knew we had

Tanya Basu writes:

What is an organ? Anatomy textbooks are rather fuzzy about what defines an “organ,” requiring one to have primary tissue—parenchyma—and “sporadic” tissue, called stroma, which can be nerves, vessels, and other connective tissue. Organs are the necessary building blocks of organisms (hence, the name), and can be gigantic or microscopic. So long as cells clump together to form tissues, and these tissues organize themselves into organs that perform specific functions in the survival of an organism, that mass of tissues and cells can be called an organ.

Theise, Carr-Locke, and Benias weren’t sure what to call this space with its collagen bundles and fluid. The fluid itself appeared rich in proteins typical of lymphatics and serum, but the space was neither lymphatic nor vascular (meaning that it contained neither veins nor arteries), so what could it be?

That’s when it dawned on them that what they’d stumbled upon was actually talked about in medical textbooks, but that they were the first to actually define it.

This thing they were looking at, struggling to understand with its bizarre structure and rule-breaking form, was the interstitium, a space vaguely described in textbooks as where “extracellular fluid” is found, the fluid that isn’t contained within cells. What doctors had defined as “dense connective tissue” wasn’t dense connective tissue at all. In fact, they were all fluid-filled structures that only appeared to be densely compacted when tissues were made into slides, the fluid draining away, the collagen lattice collapsing onto itself.

They had a theory—that the space was the interstitium—and a way to prove it. They were on to something.

So far they had only recognized this in the bile duct. But Theise began to recognize through his daily lot of diagnostic slides from surgical resections and biopsies of all sorts of tissues and tumors that the dense connective tissue layers of other parts of the body also had the same appearance as this layer in the bile duct. He noticed it in stomach and intestine and esophageal specimens, then he saw it in fascia around muscles and in fat. And then he noticed it around veins and arteries. Then skin.

It seemed to be everywhere, and Theise realized the potential enormity of what they’d discovered, calculating that it was largest organ of the body by volume—larger even than that of skin due to its wrapping around every organ, including the skin. At about 20 percent of all the fluid of the body, and about 10 liters, it was gigantic despite the fact that it could only be seen by peering through a microscope: The cardiovascular system (heart, veins, arteries, and capillaries) weighed in at about a third of that volume, the cerebrospinal fluid 20 times smaller. [Continue reading…]

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How new data is transforming our understanding of place cells — the brain’s GPS


Adithya Rajagopalan writes:

The first pieces of the brain’s “inner GPS” started coming to light in 1970. In the laboratories of University College London, John O’Keefe and his student Jonathan Dostrovsky recorded the electrical activity of neurons in the hippocampus of freely moving rats. They found a group of neurons that increased their activity only when a rat found itself in a particular location. They called them “place cells.”

Building on these early findings, O’Keefe and his colleague Lynn Nadel proposed that the hippocampus contains an invariant representation of space that does not depend on mood or desire. They called this representation the “cognitive map.” In their view, all of the brain’s place cells together represent the entirety of an animal’s environment, and whichever place cell is active indicates its current location. In other words, the hippocampus is like a GPS. It tells you where you are on a map and that map remains the same whether you are hungry and looking for food or sleepy and looking for a bed. O’Keefe and Nadel suggested that the absolute position represented in the hippocampal place cells provides a mental framework that can be used by an animal to find its way in any situation—be that to find food or a bed.

Over the next 40 years, other researchers—including the husband and wife duo of Edvard and May-Britt Moser—produced support for the idea that the brain’s hippocampal circuitry acts like an inner GPS. In recognition of their pioneering work, O’Keefe and the Mosers were awarded the 2014 Nobel Prize in physiology or medicine. You’d think that this would mean that the role of the hippocampus in guiding an animal through space was solved.

But studying the brain is never that straightforward. Like a match lighting a fuse, the 2014 Nobel Prize set off an explosion of experiments and ideas, some of which have pushed back against O’Keefe and Nadel’s early interpretation. This new work has suggested that when it comes to spatial navigation, the hippocampal circuit represents location information that is relative and malleable by experience rather than absolute. The study of the hippocampus seems to have stumbled into an age-old philosophical argument. [Continue reading…]

3.5 billion-year-old fossils challenge ideas about early life on Earth

Rebecca Boyle writes:

In the arid, sun-soaked northwest corner of Australia, along the Tropic of Capricorn, the oldest face of Earth is exposed to the sky. Drive through the northern outback for a while, south of Port Hedlund on the coast, and you will come upon hills softened by time. They are part of a region called the Pilbara Craton, which formed about 3.5 billion years ago, when Earth was in its youth.

Look closer. From a seam in one of these hills, a jumble of ancient, orange-Creamsicle rock spills forth: a deposit called the Apex Chert. Within this rock, viewable only through a microscope, there are tiny tubes. Some look like petroglyphs depicting a tornado; others resemble flattened worms. They are among the most controversial rock samples ever collected on this planet, and they might represent some of the oldest forms of life ever found.

In December, researchers lobbed another salvo in the decades-long debate about the nature of these forms. They are indeed fossil life, and they date to 3.465 billion years ago, according to John Valley, a geochemist at the University of Wisconsin. If Valley and his team are right, the fossils imply that life diversified remarkably early in the planet’s tumultuous youth.

The fossils add to a wave of discoveries that point to a new story of ancient Earth. In the past year, separate teams of researchers have dug up, pulverized and laser-blasted pieces of rock that may contain life dating to 3.7, 3.95 and maybe even 4.28 billion years ago. All of these microfossils — or the chemical evidence associated with them — are hotly debated. But they all cast doubt on the traditional tale. [Continue reading…]

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