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Assorted Personal Notations, Essays, and Other Jottings

Posts Tagged ‘science

[LINK] “Neanderthals Lived in Small, Isolated Populations, Gene Analysis Shows”

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This analysis, reported by National Geographic News‘ Dan Vergino, is fascinating. The sample size is small–three Neanderthals and one Denisovan–but the preliminary conclusions are quite noteworthy. How were ancient humans different from each other? We’re learning.

Compared to Neanderthals, humanity appears to have evolved more when it comes to genes related to behavior, suggests a team headed by Svante Pääbo, a pioneer in ancient genetics at Germany’s Max Planck Institute for Evolutionary Anthropology. Their study was published today in the Proceedings of the National Academy of Sciences.

They note in particular that genes linked to hyperactivity and aggressive behavior in modern humans appear to be absent in Neanderthals. Also missing is DNA associated with syndromes such as autism.

“The paper describes some very interesting evolutionary dynamics,” said paleoanthropologist John Hawks of the University of Wisconsin at Madison.

The Neanderthal genes suggest that sometime after one million to 500,000 years ago, Neanderthal numbers decreased and the population stayed small, Pääbo’s group determined. A small population size would have been bad news for Neanderthals, Hawks said, because it would have meant that “natural selection had less power to weed out bad mutations.”

Pääbo and colleagues looked at the genes of two ancient Neanderthals, one from Spain and one from Croatia. They compared the DNA of those individuals to that of a third Neanderthal who had lived in Siberia and whose DNA had been analyzed in an earlier study, and to the DNA of several modern humans.

Written by Randy McDonald

April 23, 2014 at 7:16 pm

[BLOG] Some Wednesday links

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  • The Dragon’s Tales links to news of remarkably thorough reconstruction of Neanderthal and Denisovan genomes.
  • Eastern Approaches visits eastern Ukraine’s Donbas region.
  • Geocurrents’ Martin Lewis notes that Pakistan still apparently lays claim to the former Muslim-run princely state of Junagadh in Gujarat.
  • Joe. My. God. and Towleroad both note a proposed bill before the Russian parliament that would require the fingerprinting of all HIV-positive people in a national database.
  • The Power and the Money’s Noel Maurer notes a continuing crisis in the availability of rental spaces in the American housing market, linking it to low-density zoning.
  • Torontoist notes the sad loss of a pet pigeon on Queen Street West.
  • Towleroad notes continuing controversy over the use of the HIV drug Truvada as a prophylactic against infection.
  • The Volokh Conspiracy visits controveries over affirmative action in the United States where different minorities (here, Asian-Americans) have different claims.
  • Window on Eurasia visits the increasingly problematic lot of Crimean Tatars in their Russian-occupied homeland, notes that traditionally pro-Russian Belarus is newly wary of its eastern partner, and quotes from a journalist who predicts catastrophe from a Russian pursuit of empire.

[CAT] “What Are Cats Thinking?”

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Writing at Slate, David Grimm writes about the state of research into cat intelligence. It seems that it’s not very advanced, largely because cats have a different sort of intelligence from us (and from dogs).

In 1998, [Ádám Miklósi] and Duke University biological anthropologist Brian Hare independently showed that dogs can understand human pointing. Both labs conducted experiments demonstrating that when a volunteer pointed at one of two cups containing a treat, dogs almost always went for the correct cup. Though it may seem a simple test, our closest relatives, chimpanzees, fail miserably; they ignore the volunteer, pick cups at random, and rarely score above chance. The ability to follow a pointed finger isn’t just a neat trick; it shows that dogs may have a rudimentary “theory of mind”—an ability to understand what another animal is thinking (in this case, that the human volunteer was trying to show them something). The skill is so important to our species that without it, we would have trouble learning and interacting with the world around us. That’s why so many labs have begun studying the canine mind; dogs, the thinking goes, may provide clues to the evolution of the human mind.

But what about cats? Miklósi, I was surprised to learn, had also conducted the pointing test with felines. Like Agrillo, he had a hard time getting cats to cooperate in his laboratory—so he went to their homes instead. Even then, most of the animals weren’t interested in advancing science; according to Miklósi’s research paper, seven of the initial 26 test subjects “dropped out.” But those that did participate performed nearly as well as dogs had. Cats too, it appears, may have a rudimentary theory of mind.

But when Miklósi took the study a step further, he spotted an intriguing difference between cats and dogs. This time, he and his colleagues created two puzzles: one solvable, the other impossible. In the solvable puzzle, the researchers placed food in a bowl and stuck it under a stool. Dogs and cats had to find the bowl and pull it out to eat. Both aced the test. Then the scientist rigged the exam. They again placed the bowl under a stool, but this time they tied it to the stool legs so that it could not be pulled out. The dogs pawed at the bowl for a few seconds and then gave up, gazing up at their owners as if asking for help. The cats, on the other hand, rarely looked at their owners; they just kept trying to get the food.

Now before you conclude that cats are dumber than dogs because they’re not smart enough to realize when a task is impossible, consider this: Dogs have lived with us for as many as 30,000 years—20,000 years longer than cats. More than any other animal on the planet, dogs are tuned in to the “human radio frequency”—the broadcast of our feelings and desires. Indeed, we may be the only station dogs listen to. Cats, on the other hand, can tune us in if they want to (that’s why they pass the pointing test as well as dogs), but they don’t hang on our every word like dogs do. They’re surfing other channels on the dial. And that’s ultimately what makes them so hard to study. Cats, as any owner knows, are highly intelligent beings. But to science, their minds may forever be a black box.

Written by Randy McDonald

April 22, 2014 at 12:56 am

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[BLOG] Some Monday science links

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  • Centauri Dreams’ Paul Gilster notes that there is a class for bright F-class stars to host Earth-like worlds, and observes that the ESA’s Rosetta probe is set to rendezvous with Comet 67P/Churymov-Gerasimenko.
  • D-Brief suggests that mitochondrial damage might be responsible for so-called “Gulf War syndrome”.
  • The Dragon’s Gaze notes that the Kepler satellite can detect large exomoons, links to a paper suggesting that Jupiters aren’t needed to deliver water to the surfaces of rocky habitable-zone planets, and observes that the geological cycles of the Earth are necessary for life.

Written by Randy McDonald

March 31, 2014 at 7:07 pm

[LINK] On cosmic inflation, the Big Bang, and Andrei Linde

CBC’s article

The new results were announced by a collaboration that includes researchers from the Harvard-Smithsonian Center for Astrophysics, the University of Minnesota, Stanford University, the California Institute of Technology and NASA’s Jet Propulsion Laboratory. The team plans to submit its results to a scientific journal this week, said its leader, John Kovac of Harvard.

For their research, astronomers scanned about 2 percent of the sky for three years with a telescope at the South Pole, chosen for its very dry air to aid in the observations.

They were looking for a specific pattern in light waves within the faint microwave glow left over from the Big Bang. The pattern has long been considered evidence of the rapid growth spurt, known as inflation. Kovac called it “the smoking gun signature of inflation.”

The scientists say the light-wave pattern was caused by gravitational waves, which are ripples in the interweaving of space and time that sprawls through the universe. If confirmed, the new work would be the first detection of such waves from the birth of the universe, which have been called the first tremors of the Big Bang.

Arizona State’s Krauss cautioned that it’s possible that the light-wave pattern is not a sign of inflation, although he stressed that it’s “extremely likely” that it is. It’s “our best hope” for a direct test of whether the rapid growth spurt happened, he said.

The New Yorkergoes into more detail, here too.

What went viral about all this is the video of physicist Andrei Linde, the man who suggested the theory of cosmic inflation in the first place, being informed at his door of the news of his theory’s confirmation.

This joyous video has just under 1.6 million views as of this posting.

Written by Randy McDonald

March 19, 2014 at 4:00 am

[LINK] “Making Babies with 3 Genetic Parents Gets FDA Hearing”

Dina Fine Maron’s Scientific American article concerning new technologies that could marry DNA from three individuals, creating three-parent children, is a good overview of the technology’s position in the United States right now. (I’m for it, for whatever it’s worth, in that preventing inherited mitochondrial DNA diseases in children is a good thing.)

Scientists have already had successes with this type of reproductive approach in monkeys and in human embryos, and are now eager to launch human clinical trials. First, however, they must get the green light from the U.S. Food and Drug Administration, which will convene a public hearing before an advisory committee on February 25.

The technology, called oocyte modification (but sometimes nicknamed “three-parent IVF”), involves scooping out potentially mutated mitochondrial DNA (mtDNA) from a woman’s egg and replacing it with the mtDNA of an unaffected donor woman. The process is designed to prevent the transmission of some debilitating inherited mitochondrial diseases, which can result in vision loss, seizures and other maladies. Such inherited diseases, often unfortunately known by acronyms for complex medical names that include LHON, for Leber’s Hereditary Optic Neuropathy, along with MELAS, MERRF and NARP, occur in about one in every 5,000 live births and are incurable.

Once the mtDNA has been swapped out, the egg could be fertilized in the lab by the father’s sperm and the embryo would be implanted back into mom where pregnancy would proceed. The resulting child would be the genetic offspring of the intended mother but would carry healthy mitochondrial genes from the donor.

[. . .]

Scientists already have evidence for the promise of this type of oocyte modification. Shoukhrat Mitalipov of the Oregon Health & Science University and his colleagues created human embryos in this way, although they did not implant those embryos to make babies. Their findings were published in October 2012 in Nature. Other work from that same team also found that in monkeys the process could lead to the birth of healthy offspring that remained free of complications into adulthood. (Scientific American is part of Nature Publishing Group).

[. . .]

But wading into this type of approach is also fraught with ethical issues. Marcy Darnovsky, executive director of the Center for Genetics and Society, fears that this reproductive approach could soon lead to tampering with other traits, such as intelligence or sports ability. “Life is full of slippery slopes and we need brakes,” she says. “This is described as saving lives but it is not aimed at people who are sick,” she adds. The FDA advisory committee does not plan to consider ethical issues at this meeting. Instead it will focus on the scientific aspects of future clinical trial considerations, including long-term risk of carryover of abnormal mtDNA, the potential benefits and harm to mothers and future children, and the need for multigenerational follow-up in any trials (because female children could pass on mitochondrial disease to future offspring). “Our job will be purely to air the issue and bring it out into the open,” says Evan Snyder, chair of the committee and director of the Stem Cell and Regenerative Biology Program at Sanford–Burnham Medical Research Institute in La Jolla, Calif. “We’re not going to come out at the end of the meeting and say we are advocating for clinical trials or any particular technique. This is educational,” he says.

Written by Randy McDonald

February 27, 2014 at 8:47 pm

[LINK] “Does Free Will Exist? Ancient Quasars May Hold the Clue”

The title of Jason Major’s Universe Today article is fantastic.

[R]esearchers at MIT were trying to determine how to get past a more recent conundrum in physics: Bell’s Theorem. Proposed by Irish physicist John Bell in 1964, the principle attempts to come to terms with the behavior of “entangled” quantum particles separated by great distances but somehow affected simultaneously and instantaneously by the measurement of one or the other — previously referred to by Einstein as “spooky action at a distance.”

The problem with such spookiness in the quantum universe is that it seems to violate some very basic tenets of what we know about the macroscopic universe, such as information traveling faster than light. (A big no-no in physics.)

Then again, testing against Bell’s Theorem has resulted in its own weirdness (even as quantum research goes.) While some of the intrinsic “loopholes” in Bell’s Theorem have been sealed up, one odd suggestion remains on the table: what if a quantum-induced absence of free will (i.e., hidden variables) is conspiring to affect how researchers calibrate their detectors and collect data, somehow steering them toward a conclusion biased against classical physics?

“It sounds creepy, but people realized that’s a logical possibility that hasn’t been closed yet,” said David Kaiser, Germeshausen Professor of the History of Science and senior lecturer in the Department of Physics at MIT in Cambridge, Mass. “Before we make the leap to say the equations of quantum theory tell us the world is inescapably crazy and bizarre, have we closed every conceivable logical loophole, even if they may not seem plausible in the world we know today?”

So in order to clear the air of any possible predestination by entangled interlopers, Kaiser and MIT postdoc Andrew Friedman, along with Jason Gallicchio of the University of Chicago, propose to look into the distant, early Universe for sufficiently unprejudiced parties: ancient quasars that have never, ever been in contact.

There is a news release that goes into the final technical detail. Quasars as calibrators of reality? Why not?

Written by Randy McDonald

February 27, 2014 at 5:00 am

[BLOG] Some Saturday links

  • BlogTO’s Derek Flack shares pictures of Toronto in the 1970s.
  • James Bow thinks, in response to discussion at Toronto city council, that the position of head of the TTC should be put up to a general election.
  • Centauri Dreams notes the ESA’s new PLATO planet-hunter telescope, positioned at the Earth-Sun L2 point, and features a guest post from J. N. Nielsen talking of the means by which life will be dispersed.
  • City of Brass’ Aziz Poonawalla is unsurprised by the recent finding that the NYPD’s spying on Muslims was legal.
  • Discover‘s D-Brief notes a very odd pulsar.
  • The Dragon’s Tales links to a paper wondering if the products of Europa’s geysers–including signs of life?–could be sampled by spacecraft.
  • Eastern Approaches notes Ukraine’s agony.
  • Geocurrents notes, in light of Spain’s recent law granting Sephardic Jews the right to gain Spanish citizenship, the vexed question of what Sephardim are.
  • Lawyers, Guns and Money notes a study chroniclingly state-by-state startling post-1979 increases in inequality in the US. (I fear a similar study from Canada.)
  • Marginal Revolution notes that Ukraine will see the next big financial crisis.
  • The Signal notes the exceptional fragility of the ageing rewritable CDs used to store WNYC’s radio programs.
  • Torontoist noted that Doug Ford won’t be running in the next provincial election as a candidate.
  • Understanding Society’s Daniel Little argues that narrative history should seek to explain underlying patterns to be useful.
  • Window on Eurasia speculates that Kazakhstan could lead the integration of the Turkic world.

[LINK] On termites as models for construction robots

Wired’s Nadia Blake pointed towards the latest development in applied swarm intelligence.

Termites normally inspire thoughts of insect invasions, obnoxiously colored house-tents, or the Orkin man. But for a group of scientists at Harvard University, the cooperative insects inspired a whole new army of robots, described in Science.

These robots, each about the size of your head, follow a minimal set of rules when building a structure. Instead of detailed plans, they rely on environmental cues to accomplish their task — a minimalist strategy that’s based on a principle called “stigmergy.” Conceived in 1959 by a French biologist, the term describes how termite colonies cooperate and self-organize to build massive, intricate mounds. In some places, these mounds can be 8 feet tall; they’re also air-conditioned by a network of internal tunnels, and are often oriented along the Earth’s north-south magnetic axis.

But unlike humans, termites don’t follow blueprints or plans while constructing their homes. All they know is what the finished product is supposed to be, and what to pay attention to along the way. As each termite scoops up mudballs and deposits them in various places, it leaves a trail of chemical cues for other builders. Based on these cues, the other termites modify their building behaviors and deposit their own mudballs where the stuff is needed. Boom. Termite mound.

The fleet of Harvard robots follows this strategy, too. Their minimal programming includes the ability to move forward, backward, and rotate; they can also climb, sense, pick up and deposit bricks. Where they lay those bricks depends on what the other bots are doing and what the final structure is supposed to be.

Meeri Kim’s Washington Post article goes into much more detail.

“Around here, you hear about termites destroying buildings,” said Justin Werfel, a Harvard University computer scientist and author of a study in the current issue of the journal Science. “But in Africa and Australia, they are known for building enormous, complicated mounds of soil.”

[. . .]

Each termite is an organism of fairly low complexity, but, using stigmergy, a colony can build a highly complex structure. So the team started with this simple framework: Each robot must have its own basic brain and sensors, and be programmed with certain “traffic rules” it must obey.

The sensors enable them to see bricks and robots next to them, and the traffic rules depend on the final structure. They prevent robots from placing bricks in places where they might easily collapse, or constructing a scenario in which a brick would have to be squished in between two others.

Each robot, about eight inches long, consists of internal metal gears and hardware as well as 3-D printed parts. The bricks themselves are also made in a way that helps the robots climb and align them better.

“In our system, each robot doesn’t know what others are doing or how many others there are — and it doesn’t matter,” Werfel said.

The main difference from the real-life insect is that termites don’t have a desired end product. Rather, there is a random component involved; given the same starting place, a colony will build a slightly different structure every time. But for constructing a house, for instance, the robots would need to follow a specific blueprint. So Werfel created the option for a user to input a picture of a predefined structure, and the robots will go to town on building it.

The paper in question is here.

Written by Randy McDonald

February 19, 2014 at 4:55 am

[LINK] “How Supernova 2014J Will Help Determine the Extragalactic Distance Scale and Impact Cosmology”

Universe Today’s Ian Steer has a nice article explaining how Supernova 2014J, a Type 1A supernova in the nearby M82 galaxy (only ten million light-years away!), will help astronomers better understand the universe.

“Being the nearest supernova of this kind, SN 2014J will help us to better calibrate the expansion of the Universe,” said Adam Riess, co-leader of the Supernova H0 for Equation of State (SHOES) project, and co-winner of the 2011 Nobel Prize in Physics.

[. . .]

Measuring ever more accurately our Universe’s exact expansion rate has been the Holy Grail of cosmology since Hubble’s discovery of expansion in 1929. Type Ia are perfect for probing cosmological scale distances, because these stellar explosions occur only when white dwarf stars exceed a certain critical mass, equivalent to 1.4 solar masses.

As a result, most type Ia supernova explode with roughly the same intrinsic or absolute magnitude. They therefore provide a unique kind of “standard candle,” by which any type Ia supernova observed to be one hundred times fainter than another can be understood to be exactly ten times farther than the other. In practice, subtle differences between actual type Ia supernovae, amounting to around ten percent on average in their net effect on distance estimates, are accounted for. Technically, therefore, type Ia supernova provide “standardizable candles.”

Normal type Ia supernovae are well understood. Within just days of its discovery, Robert Quimby of the Kavli Institute for the Physics and Mathematics of the Universe at the University of Tokyo was able to predict the peak apparent magnitude of m_V = 10.5 and time of peak brightness of February 2 for SN 2014J, more than a week prior to their occurrence. As observations now available show, as summarized in the light-curve available thanks to the American Association of Variable Star Observers, Quimby’s prediction based on the light-curves of other similar type Ia supernova, was spot on.

Written by Randy McDonald

February 13, 2014 at 1:13 am

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