Tag Archives: Science

Ivan Pavlov in 22 surprising facts

  • Pavlov didn’t use a bell, and for his real scientific purposes, couldn’t. English-speakers think he did because of a mistranslation of the Russian word for zvonok (buzzer) and because the behaviorists interpreted Pavlov in their own image for people in the U.S. and much of the West.

  • He didn’t use the term and concept “conditioned reflex,” either – rather, “conditional,” and it makes a big difference. For him, the conditional reflex was not just a phenomenon, but a tool for exploring the animal and human psyche – “our consciousness and its torments.”

  • Unlike the behaviorists, Pavlov believed that dogs (like people) had identifiable personalities, emotions, and thoughts that scientific psychology should address. “Essentially, only one thing in life is of real interest to us,” he declared: “our psychical experience.”

  • As a youth, he identified worriedly with Dostoevsky’s Ivan Karamazov – fearing that his devotion to rationality might strip him of human morality and feelings – but also believed that science (especially physiology) might teach humans to be more reasonable and humane.

    Daniel P. Todes - Pavlov 2
    Ivan Pavlov. Public domain via Wikimedia Commons

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Sapiens: A Brief History of Humankind by Yuval Noah Harari – review

Human beings (members of the genus Homo) have existed for about 2.4m years. Homo sapiens, our own wildly egregious species of great apes, has only existed for 6% of that time – about 150,000 years. So a book whose main title is Sapiens shouldn’t be subtitled “A Brief History of Humankind”. It’s easy to see why Yuval Noah Harari devotes 95% of his book to us as a species: self-ignorant as we are, we still know far more about ourselves than about other species of human beings, including several that have become extinct since we first walked the Earth. The fact remains that the history of sapiens – Harari’s name for us – is only a very small part of the history of humankind.

Can its full sweep be conveyed in one fell swoop – 400 pages? Not really; it’s easier to write a brief history of time – all 14bn years – and Harari also spends many pages on our present and possible future rather than our past. But the deep lines of the story of sapiens are fairly uncontentious, and he sets them out with verve.

For the first half of our existence we potter along unremarkably; then we undergo a series of revolutions. First, the “cognitive” revolution: about 70,000 years ago, we start to behave in far more ingenious ways than before, for reasons that are still obscure, and we spread rapidly across the planet. About 11,000 years ago we enter on the agricultural revolution, converting in increasing numbers from foraging (hunting and gathering) to farming. The “scientific revolution” begins about 500 years ago. It triggers the industrial revolution, about 250 years ago, which triggers in turn the information revolution, about 50 years ago, which triggers the biotechnological revolution, which is still wet behind the ears. Harari suspects that the biotechnological revolution signals the end of sapiens: we will be replaced by bioengineered post-humans, “amortal” cyborgs, capable of living forever.

This is one way to lay things out. Harari embeds many other momentous events, most notably the development of language: we become able to think sharply about abstract matters, cooperate in ever larger numbers, and, perhaps most crucially, gossip. There is the rise of religion and the slow overpowering of polytheisms by more or less toxic monotheisms. Then there is the evolution of money and, more importantly, credit. There is, connectedly, the spread of empires and trade as well as the rise of capitalism.

Harari swashbuckles through these vast and intricate matters in a way that is – at its best – engaging and informative. It’s a neat thought that “we did not domesticate wheat. It domesticated us.” There was, Harari says, “a Faustian bargain between humans and grains” in which our species “cast off its intimate symbiosis with nature and sprinted towards greed and alienation”. It was a bad bargain: “the agricultural revolution was history’s biggest fraud”. More often than not it brought a worse diet, longer hours of work, greater risk of starvation, crowded living conditions, greatly increased susceptibility to disease, new forms of insecurity and uglier forms of hierarchy. Harari thinks we may have been better off in the stone age, and he has powerful things to say about the wickedness of factory farming, concluding with one of his many superlatives: “modern industrial agriculture might well be the greatest crime in history”.
He accepts the common view that the fundamental structure of our emotions and desires hasn’t been touched by any of these revolutions: “our eating habits, our conflicts and our sexuality are all a result of the way our hunter-gatherer minds interact with our current post-industrial environment, with its mega-cities, airplanes, telephones and computers … Today we may be living in high-rise apartments with over-stuffed refrigerators, but our DNA still thinks we are in the savannah.” He gives a familiar illustration – our powerful desires for sugar and fat have led to the widespread availability of foods that are primary causes of unhealthiness and ugliness. The consumption of pornography is another good example. It’s just like overeating: if the minds of pornography addicts could be seen as bodies, they would look just like the grossly obese.

Read on http://www.theguardian.com/books/2014/sep/11/sapiens-brief-history-humankind-yuval-noah-harari-review

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When science meets aboriginal oral history

In Inuit oral history, the Tuniit loom both large and small.

They inhabited the Arctic before the Inuit came, and they were a different stock of people — taller and stronger, with the muscularity of polar bears, the stories say. A Tuniit man could lift a 1,000 pound seal on his back, or drag a whole walrus. Others say the Tuniit slept with their legs in the air to drain the blood from their feet and make them lighter, so they could outrun a caribou.

But despite their superior strength and size, the Tuniit were shy. They were “easily put to flight and it was seldom heard that they killed others,” according to one storyteller in the book “Uqalurait: An Oral History of Nunavut.” The Inuit took over the best hunting camps and displaced the conflict-averse Tuniit. Soon enough, these strange people disappeared from the land.

This week, the prestigious journal Science published an unprecedented paleogenomic study that resolves long-held questions about the people of the prehistoric Arctic. By analyzing DNA from 169 ancient human specimens from Canada, Alaska, Siberia, and Greenland, the researchers concluded that a series of Paleo-Eskimo cultures known as the Pre-Dorset and Dorset were actually one population who lived with great success in the eastern Arctic for 4,000 years — until disappearing suddenly a couple generations after the ancestors of the modern Inuit appeared, around 1200 A.D. There is no evidence the two groups interbred.

The Dorset are almost certainly the Tuniit of Inuit oral history.

“The outcome of the genetic analysis is completely in agreement, namely that the Paleo-Eskimos are a different people,” says Eske Willerslev, a co-author of the Science study.

It’s not the first time his genomic research has synchronized neatly with indigenous oral traditions.

In February, when Willerslev and colleagues announced they had sequenced the genome of a 12,500-year-old skeleton found in Montana, the results showed that nearly all South and North American indigenous populations were related to this ancient American. Shane Doyle, a member of the Crow tribe of Montana, said at the time: “This discovery basically confirms what tribes have never really doubted — that we’ve been here since time immemorial, and that all the artifacts and objects in the ground are remnants of our direct ancestors.” The sequenced genome of an Aboriginal from Australia also revealed findings in line with the local communities’ oral histories, Willerslev says.

“Scientists are sitting around and academically discussing different theories about peopling of Americas, and you have all these different views on how many migrations, and who is related to,” he says. “Then when we actually undertake the most sophisticated genetic analysis we can do today, and this is state of the art, genetically — we could have just have listened to them in the first place.”

He was laughing when he said that. But he and many others are serious when they say that scientists need to revaluate the weight they give traditional indigenous knowledge

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Tiny, Vast Windows Into Human DNA by Carl Zimmer

In the history of biology, two little animals loom large.

In the early 1900s, scientists began studying Drosophila melanogaster, the common fruit fly. Research on these fast-breeding insects revealed that genes lie on chromosomes, which turned out to be true for other animals, including us. For more than a century, scientists have continued to glean clues from the lowly fly to other mysteries of biology, like why we sleep and how heart disease develops.

In the 1960s, another unassuming animal joined biology’s pantheon: a tiny worm called Caenorhabditis elegans. The biologist Sydney Brenner realized that its body, made up of just a couple of thousand cells, offered an singular opportunity to learn how a single egg gives rise to a complete animal. Today, many scientists are studying the worm for clues to how our own brains are wired and why we age.

Now the two species are providing even deeper insights in biology. A team of hundreds of scientists has exhaustively recorded the choreography of their genes as the animals develop from eggs to adults.

“It’s not just this gene or that gene,” said Robert H. Waterston, a geneticist at the University of Washington who is among the scientists working on the project, called modENCODE. “We can get a picture of the whole.”

Dr. Waterston and his colleagues published overviews of the modENCODE results in five papers last week in Nature. In their initial analysis, they find a striking similarity between the choreography of genes in flies and worms and that of our own DNA. Exploring that similarity may provide scientists with new insights into genetic disorders and diseases like cancer.

In 1998, Dr. Waterston and a large group of fellow scientists cataloged all 19,000 protein-coding genes in C. elegans, along with a rough guide to the rest of its DNA. In 2000, researchers did the same for D. melanogaster. These two efforts were a huge help to scientists studying the biology of the animals. But these two efforts revealed little about what the genes actually do in an organism. It was as if they had inventoried all the instruments in an orchestra but weren’t able to see the sheet music.

A gene contains information that a cell can use to make a particular molecule. But an animal may only use a given gene at a particular time in its life, or in a particular organ.

Cellular DNA is coiled around spool-like molecules called histones. When DNA is tucked away, gene-reading molecules cannot reach it. By adding certain compounds, known as histone marks, to the histones, a cell opens up a stretch of DNA.

When a gene is exposed this way, a protein called a transcription factor latches onto it, recruiting other molecules to “read” it and produce a new protein or RNA molecule. Sometimes, a single transcription factor may switch on dozens of other genes. And sometimes, those genes encode transcription factors of their own, enabling a cell to produce hundreds of kinds of molecules at once.

The modENCODE team took on an enormous task: to create a detailed picture of this molecular dance. For the past five years, hundreds of biologists have been recording DNA activity in flies and worms, and systematically comparing the results to what they see in humans.

To study genes in humans, the scientists focused on a wide variety of cells, like neurons, blood cells and liver cells. In the experiments on flies and worms, the scientists examined the entire bodies of the animals as they matured from eggs.

The scientists cataloged the parts of the genome that cells were using. They also mapped the histone marks and located the transcription factors latching onto the DNA. Because the scientists used the same methods to gather data from all three species, they were able to compare them on a scale never before attempted.

Flies, worms and humans come from distant branches on the evolutionary tree. The last common ancestor lived 700 million years ago. Despite the tremendous differences among the three species, the modENCODE team found some striking parallels in the workings of their DNA.

In all three, it turned out, many genes tended to turn on and off in the same pattern, following a predictable rhythm. All told, the researchers found 16 such sets of genes, each containing hundreds of genes working together. While it’s not clear yet what these genes are doing in all three species, the scientists did observe that a dozen clusters were especially active at some stages of development in the worm and the fly. They may be essential for transforming an egg into an adult animal.

The scientists also found that histone marks control DNA in much the same way in all three species. If certain marks were present around a gene, the scientists usually could predict how active it was, whether fly, worm or human.

“The neat thing is that it works — it really works well,” Mark Gerstein of Yale University, a modENCODE team member, said of the group’s predictive model.

Read on (NYT)

 

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Peter Godfrey-Smith Takes On The Philosophy Of Biology

Peter Godfrey-Smith’s Philosophy of Biology (Princeton University Press), may not sound like the kind of book even science enthusiasts want to crack open for pleasure, but it’s a great way to get up to speed on all the issues that working biologists love to debate amongst themselves.

Godfrey-Smith is a professor in the Philosophy Program at City University of New York. His more academic books include, Darwinian Populations and Natural Selection (Oxford University Press), and Theory and Reality: An Introduction to the Philosophy of Science (University of Chicago Press). His main areas of interest include the philosophy of mind and pragmatism.

In just 200 pages, Philosophy of Biology includes short, succinct chapters on mechanisms and models, natural selection, genes, adaptation and function, species and the Tree of Life, evolution and social behavior, and information.

But as I mentioned in my last post, the question for many science geeks is: why even bother with a book on philosophy at all–let alone the philosophy of science?

What good is it?

So, I asked Scott Carson, an associate professor of philosophy at Ohio University*, what he tells his students at the start of each semester.

Carson’s main areas of interest are the history of evolutionary biology and the biomedical sciences, and among his publications is this fascinating essay he co-authored on how quantum indeterminacy may effect evolution.

“Typically,” he said via email, “I tell my students that philosophy of science is important because we live in a society that is very much a product of what Bas Van Fraassen called ‘The Scientific Image’. That is, we are, as persons, largely shaped by the culture that surrounds us and we are presently surrounded by a culture that is increasingly impacted by science and technology.

“If we are to be intelligent and well-informed members of the society and culture in which we find ourselves, it is essential that we understand not only the results of scientific research, but the foundations of science itself.”

In Carson’s view, this will put us in a better position to evaluate questions about the nature of the authority of the sciences and the reliability of the conclusions and recommendations made by scientists.

“Ideally a philosopher of science is not someone who hopes to make any positive contributions to the working sciences,” he said, “but someone who is interested in answering philosophical questions that are informed by the discoveries of the sciences and who wants to describe and assess scientific practice as accurately as possible.”

In terms of the current book, he added, “I think you will find that this is very close to what Godfrey-Smith believes is the proper function of the philosopher of science.”

Read on @Forbes

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‘Supercomputers make discoveries that scientists can’t’ by Hal Hodson

IN MAY last year, a supercomputer in San Jose, California, read 100,000 research papers in 2 hours. It found completely new biology hidden in the data. Called KnIT, the computer is one of a handful of systems pushing back the frontiers of knowledge without human help.

KnIT didn’t read the papers like a scientist – that would have taken a lifetime. Instead, it scanned for information on a protein called p53, and a class of enzymes that can interact with it, called kinases. Also known as “the guardian of the genome”, p53 suppresses tumours in humans. KnIT trawled the literature searching for links that imply undiscovered p53 kinases, which could provide routes to new cancer drugs.

Having analysed papers up until 2003, KnIT identified seven of the nine kinases discovered over the subsequent 10 years. More importantly, it also found what appeared to be two p53 kinases unknown to science. Initial lab tests confirmed the findings, although the team wants to repeat the experiment to be sure.

KnIT is a collaboration between IBM and Baylor College of Medicine in Houston, Texas. It is the latest step into a weird world where autonomous machines make discoveries that are beyond scientists, simply by rifling more thoroughly through what we already know, and faster than any human can.

Read on: @New Scientist

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Heaven’s Gaits – What we do when we walk

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Why people walk is a hard question that looks easy. Upright bipedalism seems such an obvious advantage from the viewpoint of those already upright that we rarely see its difficulty. In the famous diagram, Darwinian man unfolds himself from frightened crouch to strong surveyor of the ages, and it looks like a natural ascension: you start out bending over, knuckles dragging, timidly scouring the ground for grubs, then you slowly straighten up until there you are, staring at the skies and counting the stars and thinking up gods to rule them. But the advantages of walking have actually been tricky to calculate. One guess among the evolutionary biologists has been that a significant advantage may simply be that walking on two legs frees up your hands to throw rocks at what might become your food—or to throw rocks at other bipedal creatures who are throwing rocks at what might become their food. Although walking upright seems to have preceded throwing rocks, the rock throwing, the biologists point out, is rarer than the bipedalism alone, which we share with all the birds, including awkward penguins and ostriches, and with angry bears. Meanwhile, the certainty of human back pain, like the inevitability of labor pains, is evidence of the jury-rigged, best-solution-at-hand nature of evolution.

Over time, though, things we do for a purpose, however obscure in origin, become things we do for pleasure, particularly when we no longer have to do them. As we do them for pleasure, they get attached either to a philosophy or to the pursuit of some profit. Two new accounts of this process have recently appeared, and although they occasionally make you want to throw things, they both illuminate what it means to be a pedestrian in the modern world.

Matthew Algeo’s “Pedestrianism: When Watching People Walk Was America’s Favorite Spectator Sport” (Chicago Review) is one of those books which open up a forgotten world so fully that at first the reader wonders, just a little, if his leg is being pulled. How could there be an account this elaborate—illustrated with sober handbills, blaring headlines, starchy portrait photographs, and racy newspaper cartoons—of an enthusiasm this unknown? But it all happened. For several decades in the later nineteenth century, the favorite spectator sport in America was watching people walk in circles inside big buildings.
The story Algeo tells begins in 1860, at the start of the Civil War, when a New Englander named Edward Payson Weston made a facetious bet with a friend that, if Lincoln won the Presidential election, he would walk all the way from the State House in Boston to the unfinished Capitol, in Washington, in ten days. Lincoln won, and, ten days before the inaugural, Weston set off. Though he didn’t get there quite in time, his progress, chronicled by the newspapers, enthralled a nation in need of some small fun, and he became an improbable American hero, a kind of Lindbergh of the corns and calluses. Liking his new celebrity, and the money it brought, Weston decided to keep a good thing going and, when the war ended, began to engage in competitive, six-day (never on Sunday) walking marathons in Chicago, New York, and, eventually, London.

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