Cheerful or not

The Common Hand || National Geographic

The hand is where the mind meets the world. We humans use our hands to build fires and sew quilts, to steer airplanes, to write, dig, remove tumors, pull a rabbit out of a hat. The human brain, with its open-ended creativity, may be the thing that makes our species unique. But without hands, all the grand ideas we concoct would come to nothing but a very long to-do list.

The reason we can use our hands for so many things is their extraordinary anatomy. Underneath the skin, hands are an exquisite integration of tissues. The thumb alone is controlled by nine separate muscles. Some are anchored to bones within the hand, while others snake their way to the arm. The wrist is a floating cluster of bones and ligaments threaded with blood vessels and nerves. The nerves send branches into each fingertip. The hand can generate fine forces or huge ones. A watchmaker can use his hands to set springs in place under a microscope. A pitcher can use the same anatomy to throw a ball at a hundred miles an hour….

Our hands began to evolve at least 380 million years ago from fins—not the flat, ridged fins of a goldfish but the muscular, stout fins of extinct relatives of today’s lungfish. Inside these lobe fins were a few chunky bones corresponding to the bones in our arms. Over time the descendants of these animals also evolved smaller bones that correspond to our wrists and fingers. The digits later emerged and became separate, allowing the animals to grip underwater vegetation as they clambered through it.

Early hands were more exotic than any hand today. Some species had seven fingers. Others had eight. But by the time vertebrates were walking around on dry land 340 million years ago, the hand had been scaled back to only five fingers. It has never recaptured the original exuberance of fingers—for reasons scientists don’t yet know.

Still, there is a great diversity of hands in living species, from dolphin flippers to eagle wings to the hanging hooks of sloths. By studying these living hands, scientists are beginning to understand the molecular changes that led to such dramatic variations—and to understand that despite the outward differences, all hands start out in much the same way.

Entire genome of extinct human decoded from fossil || Physorg

In 2010, Svante Pääbo and his colleagues presented a draft version of the genome from a small fragment of a human finger bone discovered in Denisova Cave in southern Siberia. The DNA sequences showed that this individual came from a previously unknown group of extinct humans that have become known as Denisovans. Together with their sister group the Neandertals, Denisovans are the closest extinct relatives of currently living humans.

The Leipzig team has now developed sensitive novel techniques which have allowed them to sequence every position in the Denisovan genome about 30 times over, using DNA extracted from less than 10 milligrams of the finger bone. In the previous draft version published in 2010, each position in the genome was determined, on average, only twice. This level of resolution was sufficient to establish the relationship of Denisovans to Neandertals and present-day humans, but often made it impossible for researchers to study the evolution of specific parts of the genome. The now-completed version of the genome allows even the small differences between the copies of genes that this individual inherited from its mother and father to be distinguished. This Wednesday the Leipzig group makes the entire Denisovan genome sequence available for the scientific community over the internet.

DNA Turning Human Story Into a Tell-All || New York Times

The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins.

The new view is fast supplanting the traditional idea that modern humans triumphantly marched out of Africa about 50,000 years ago, replacing all other types that had gone before.

Instead, the genetic analysis shows, modern humans encountered and bred with at least two groups of ancient humans in relatively recent times: the Neanderthals, who lived in Europe and Asia, dying out roughly 30,000 years ago, and a mysterious group known as the Denisovans, who lived in Asia and most likely vanished around the same time.

Their DNA lives on in us even though they are extinct.

Evolution World Tour: Wadi Hitan, Egypt || Smithsonian Magazine

Scientists had long suspected that whales were terrestrial mammals that had eased into the ocean over millions of years, gradually losing their four legs. Modern whales, after all, have vestigial hind leg bones. But little in the fossil record illustrated the transition—until Gingerich began excavating Wadi Hitan’s hundreds of whale fossils, finding legs and knees.

Those skeletons “are the Rosetta stones,” says Nick Pyenson, a curator of fossil marine mammals at the National Museum of Natural History. “It’s the first time we could say we know what the hind limbs of these animals look like. And they’re bizarre.” Older specimens of footed whales have since been identified, but Wadi Hitan’s are unmatched in their numbers and state of preservation. The valley—about a three-hour drive from Cairo—is now a Unesco World Heritage site visited by some 14,000 people each year.

Gingerich speculates that whales’ landlubber ancestors were deer- or pig-like scavengers living near the sea. About 55 million years ago, they started spending more time in the water, first eating dead fish along the shore, and then chasing prey in the shallows, and then wading deeper. As they did, some evolved traits that facilitated hunting in water. Over time—since they no longer had to bear their full body weight at sea—they got bigger, their backbones elongating and their rib cages broadening.

Into the mind of a Neanderthal || New Scientist

Humour is just one aspect of Neanderthal life we have been plotting for some years in our mission to make sense of their cognitive life. So what was it like to be a Neanderthal? Did they feel the same way we do? Did they fall in love? Have a bad day? Palaeoanthropologists now know a great deal about these ice-age Europeans who flourished between 200,000 and 30,000 years ago. We know, for example, that Neanderthals shared about 99.84 per cent of their DNA with us, and that we and they evolved separately for several hundred thousand years. We also know Neanderthal brains were a bit larger than ours and were shaped a bit differently. And we know where they lived, what they ate and how they got it.

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The only obvious difference between Neanderthal technical thinking and ours lay in innovation. Although Neanderthals invented the practice of hafting stone points onto spears, this was one of very few innovations over several hundred thousand years. Active invention relies on thinking by analogy and a good amount of working memory, implying they may have had a reduced capacity in these respects. Neanderthals may have relied more heavily than we do on well-learned procedures of expert cognition.

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Neanderthals’ short lifespan - few lived past 35 - meant that other features of our more recent social past were absent: elders, for example, were rare. And they almost certainly lacked the cognitive abilities for dealing with strangers that evolved in modern humans, who lived in larger groups numbering in the scores and belonged to larger communities in the hundreds or more. They also established and maintained contacts with distant groups.

One cognitive ability that evolved in modern humans as a result was the “cheater detection” ability described by evolutionary psychologist Leda Cosmides, at the University of California, Santa Barbara. Another was an ability to judge the value of one commodity in terms of another, what anthropologist Alan Page Fiske at the University of California, Los Angeles, calls the “market pricing” ability. Both are key reasoning skills that evolved to allow interaction with acquaintances and strangers, neither of which was a regular feature of Neanderthal home life.

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So we could have recognised and interacted with Neanderthals, but we would have noticed these significant cognitive differences. They would have been better at well-learned, expert cognition than modern humans, but not as good at the development of novel solutions. They were adept at intimate, small-scale social cognition, but lacked the cognitive tools to interact with acquaintances and strangers, including the extensive use of symbols.

Evolution World Tour: Mendel's Garden, Czech Republic || Smithsonian Magazine

For seven centuries, the skyline of Brno—the second-largest city in the Czech Republic—has been dominated by Spilberk Castle. Built on the summit of the highest hill in the city, it was one of Europe’s most notorious prisons, and a conspicuous warning to those who would oppose the rule of the Hapsburg dynasty.

Yet, for many, the most impressive site in Brno is a four- acre patch of land near the base of the hill. This is where Gregor Mendel, a friar at the Augustinian Abbey of St. Thomas, spent eight growing seasons (1856-63) cultivating and breeding as many as 10,000 pea plants (Pisum sativum), and meticulously counting some 40,000 blossoms and 300,000 peas. His experiments laid the foundations for modern genetics. And unbeknown to Mendel at the time, his discovery of how physical traits are passed down from one generation to the next revealed a crucial biological mechanism underlying Darwin’s theory of evolution through natural selection.

“Mendel is a giant in the history of genetics,” says David Fankhauser, a professor of biology and chemistry at the University of Cincinnati Clermont College, who made a “pilgrimage” to the abbey in 2006.

How to Build a Dog || National Geographic

In a project called CanMap, a collaboration among Cornell University, UCLA, and the National Institutes of Health, researchers gathered DNA from more than 900 dogs representing 80 breeds, as well as from wild canids such as gray wolves and coyotes. They found that body size, hair length, fur type, nose shape, ear positioning, coat color, and the other traits that together define a breed’s appearance are controlled by somewhere in the neighborhood of 50 genetic switches. The difference between floppy and erect ears is determined by a single gene region in canine chromosome 10, or CFA10. The wrinkled skin of a Chinese shar-pei traces to another region, called HAS2. The patch of ridged fur on Rhodesian ridgebacks? That’s from a change in CFA18. Flip a few switches, and your dachshund becomes a Doberman, at least in appearance. Flip again, and your Doberman is a Dalmatian.

“The story that is emerging,” says Robert Wayne, a biologist at UCLA, “is that the diversity in domestic dogs derives from a small genetic tool kit.”

Lichen evolved on two tracks, like marsupials and mammals || Science Blog

Lichen, those drab, fuzzy growths found on rocks and trees, aren’t as cuddly and charismatic as kangaroos or intriguing as opossums, but they could be a fungal equivalent, at least evolutionarily.

A Duke research team has found that lichen that seem identical in all outward appearances and produce the same internal chemicals are in fact two different species, one living in North America and one in Australia. They’re an example of “convergent evolution,” in which two species evolve separately but end up looking very similar, like the Tasmanian wolf and the American wolf.

The lichens developed the same adaptations to survive and thrive in vastly different regions of the world. Since they show the same evolutionary patterns as marsupials and mammals, but are easier to study, they could become model organisms to further probe how mammals and other groups of organisms evolve[.]

Bacteria Divide People Into 3 Types, Scientists Say || New York Times

[They’ve] discovered a new way to classify humanity: by bacteria. Each human being is host to thousands of different species of microbes. Yet a group of scientists now report just three distinct ecosystems in the guts of people they have studied.

Blood type, meet bug type.

“It’s an important advance,” said Rob Knight, a biologist at the University of Colorado, who was not involved in the research. “It’s the first indication that human gut ecosystems may fall into distinct types.”

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The discovery of enterotypes follows on years of work mapping the diversity of microbes in the human body — the human microbiome, as it is known. The difficulty of the task has been staggering. Each person shelters about 100 trillion microbes.

(For comparison, the human body is made up of only around 10 trillion cells.) But scientists cannot rear a vast majority of these bacteria in their labs to identify them and learn their characteristics.

300 Years of Wondering || Babel's Dawn

The history of ideas becomes especially provocative when it shows people wrestling with thoughts we still haggle over today; those old struggles reminds us that everything we know is hard won, and they keep us humble too by pointing out that very clever people can be missing things in front of their face. If those serious thinkers of old could be fooled, what spares us today?

I’m reminded of the quiet pleasures of intellectual history because I’ve been reading a recent paper on one of the first thinkers about language evolution. That was Hugh Blair (1718-1800), a Scottish divine and participant in the Scottish Enlightenment….

It strikes me as fairly astonishing that for at least 300 years people have been stuck on the matter of whether language shapes thought or thought shapes language. There is empirical evidence supporting both ideas, and there are conflicting axioms which seem to boil down to differences in tastes about metaphysics. The solution is bound to be some third choice, possibly something like Niels Bohr’s complementarity, or maybe the position urged on this blog: language directs the mind by piloting attention (thus explaining the ability of language to clarify thought) while the nature of perception determines the basic structure of language (hence, the ability of non-verbal people to think).

Evolution of Feathers || National Geographic

Most of us will never get to see nature’s greatest marvels in person. We won’t get a glimpse of a colossal squid’s eye, as big as a basketball. The closest we’ll get to a narwhal’s unicornlike tusk is a photograph. But there is one natural wonder that just about all of us can see, simply by stepping outside: dinosaurs using their feathers to fly.

Birds are so common, even in the most paved-over places on Earth, that it’s easy to take for granted both their dinosaur heritage and the ingenious plumage that keeps them aloft. To withstand the force of the oncoming air, a flight feather is shaped asymmetrically, the leading edge thin and stiff, the trailing edge long and flexible. To generate lift, a bird has merely to tilt its wings, adjusting the flow of air below and above them.

Airplane wings exploit some of the same aerodynamic tricks. But a bird wing is vastly more sophisticated than anything composed of sheet metal and rivets. From a central feather shaft extends a series of slender barbs, each sprouting smaller barbules, like branches from a bough, lined with tiny hooks. When these grasp on to the hooklets of neighboring barbules, they create a structural network that’s featherlight but remarkably strong. When a bird preens its feathers to clean them, the barbs effortlessly separate, then slip back into place.

The origin of this wonderful mechanism is one of evolution’s most durable mysteries.

[See also: photo gallery of feathers and fossils]

"This Paper Should Not Have Been Published" || Slate

On Thursday, Dec. 2, Rosie Redfield sat down to read a new paper called “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.” Despite its innocuous title, the paper had great ambitions. Every living thing that scientists have ever studied uses phosphorus to build the backbone of its DNA. In the new paper, NASA-funded scientists described a microbe that could use arsenic instead. If the authors of the paper were right, we would have to expand our notions of what forms life can take.

Redfield, a microbiology professor at the University of British Columbia, had been hearing rumors about the papers for days beforehand…. As soon as Redfield started to read the paper, she was shocked. “I was outraged at how bad the science was,” she told me.

Redfield blogged a scathing attack on Saturday. Over the weekend, a few other scientists took to the Internet as well. Was this merely a case of a few isolated cranks? To find out, I reached out to a dozen experts on Monday. Almost unanimously, they think the NASA scientists have failed to make their case. “It would be really cool if such a bug existed,” said San Diego State University’s Forest Rohwer, a microbiologist who looks for new species of bacteria and viruses in coral reefs. But, he added, “none of the arguments are very convincing on their own.” That was about as positive as the critics could get. “This paper should not have been published,” said Shelley Copley of the University of Colorado.