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Cat vision

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Nikolay Lamm blogs:

[These photos] hypothesize what human and cat vision looks like. Human vision is up top and cat vision is below.

  • Cats have a visual field of 200 degrees compared to humans 180 degrees.
  • Peripheral vision for humans is 20 degrees each side. This is represented by the blurriness.
  • Peripheral vision for cats is 30 degrees each side. This is represented by the blurriness.
  • Cats can see 6-8 times better in dim light than humans due the high number of rods and because of their elliptical pupil, large cornea and tapetum.
  • Our retinas have many more cones than cats, especially in the area of the fovea (which is all cones and no rods). This gives us fantastic day vision with lots of vibrant colors and excellent, detailed resolution. Dogs and cats have many more rods, which enhances their ability to see in dim light and during the night. They have no fovea, but an “area centralis” that, though has more cones than other areas of the retina, still has more rods than cones. The increase in rods also enhances their “refresh rate”, so that they can pick up movements much faster (very helpful when dealing with small animals that change direction very quickly during a chase). These differences also help them to have great night vision, an excellent ability to pick up and follow quick movements, but at the cost of less vibrant color, with less detailed resolution. Interestingly, this also means that humans have the ability to see very slowly moving objects at speeds 10 times slower than cats (that is to say that we can see very slow things move that would not appear to be moving to a cat).

Written by Arhopala Bazaloides

October 18, 2013 at 5:10 pm

The grammar of art

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Nature reviews an exhibition based on a cognitive scientists’ study of dancers:

As with any scientific project, Kirsh began studying Random Dance by characterizing the different phenomena he saw “like a botanist”, he says. “I go out with six or seven high-definition video cameras, I put them around the studio floor and collect everything from the moment he introduces a dancer to the premiere weeks later.” He and a trained team of students then deciphered the different techniques for instruction and practice that they saw in the videos, in much the same way that primatologists characterize behaviour.

One phenomenon that caught Kirsh’s attention was ‘marking’, in which dancers in rehearsal elaborate only the basics of a dance movement. “It’s a lower-energy version; they won’t stretch as far; they won’t have the emotional force in it. It’s a way to avoid injury and because you can’t dance for five hours after two hours of exercises warming up,” Kirsh says.

But as he discovered when conducting a controlled experiment, there is more to it. He showed dancers a new routine, gave them time to learn the moves, and divided them into three groups to practise again. One group performed the full movements, a second marked them, and a third lay down and imagined themselves performing the dance. To Kirsh’s surprise, the dancers who marked the routine executed it most faithfully later. “Nobody predicted this,” he says. “This is the hint at a theory of practising, and now it’s open to study this much more carefully to understand how people focus on aspects of what they’re practising.” The experiment, he feels, is evidence of physical activity influencing thought.

On the basis of his work with Random Dance, Kirsh has published research papers on interaction design, McGregor’s creative process and a phenomenon that he calls distributed memory, in which dancers remember dozens of complicated movements through physical cues from other dancers. McGregor, too, has gained from their collaboration. When he instructs dancers and other young choreographers, he now uses terms that Kirsh devised, such as ‘sonifications’ — sounds that choreographers make to guide how a dancer shapes a move, such as “yah ooh ehh”. Kirsh notes, “Now that the term has been named, the phenomenon is clear.”

This reminded me of the studies by the pioneering Indian computer scientist R. Narasimhan on oral notations in Indian tradition: of the art of Kollam, and of tabla bols. I had heard a detailed exposition by him on the syntax of bols in a colloquium in the mid 1980s. The only surviving printed record seems to be in a booklet called Characterizing Literacy: A Study of Western and Indian Literacy Experiences by R. Narasimhan, published by Sage. His discussion of the usage of bols by players of the tabla seem to be equivalent to the notion of “sonification”, and predates it by a few decades.

Written by Arhopala Bazaloides

October 15, 2013 at 7:04 pm

2013 Nobel Prize in Chemistry

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There is a press release from the Nobel Foundation on the prize in chemistry:

Chemists used to create models of molecules using plastic balls and sticks. Today, the modelling is carried out in computers. In the 1970s, Martin Karplus, Michael Levitt and Arieh Warshel laid the foundation for the powerful programs that are used to understand and predict chemical processes. Computer models mirroring real life have become crucial for most advances made in chemistry today.

Chemical reactions occur at lightning speed. In a fraction of a millisecond, electrons jump from one atomic nucleus to the other. Classical chemistry has a hard time keeping up; it is virtually impossible to experimentally map every little step in a chemical process. Aided by the methods now awarded with the Nobel Prize in Chemistry, scientists let computers unveil chemical processes, such as a catalyst’s purification of exhaust fumes or the photosynthesis in green leaves.

The work of Karplus, Levitt and Warshel is ground-breaking in that they managed to make Newton’s classical physics work side-by-side with the fundamentally different quantum physics. Previously, chemists had to choose to use either or. The strength of classical physics was that calculations were simple and could be used to model really large molecules. Its weakness, it offered no way to simulate chemical reactions. For that purpose, chemists instead had to use quantum physics. But such calculations required enormous computing power and could therefore only be carried out for small molecules.

Martin Karplus, U.S. and Austrian citizen. Born 1930 in Vienna, Austria. Ph.D. 1953 from California Institute of Technology, CA, USA. Professeur Conventionné, Université de Strasbourg, France and Theodore William Richards Professor of Chemistry, Emeritus, Harvard University, Cambridge, MA, USA.

Michael Levitt, U.S., Brittish and Israeli citizen. Born 1947 in Pretoria, South Africa. Ph.D. 1971 from University of Cambridge, UK. Robert W. and Vivian K. Cahill Professor in Cancer Research, Stanford University School of Medicine, Stanford, CA, USA.

Arieh Warshel, U.S. and Israeli citizen. Born 1940 in Kibbutz Sde-Nahum, Israel. Ph.D. 1969 from Weizmann Institute of Science, Rehovot, Israel. Distinguished Professor, University of Southern California, Los Angeles, CA, USA.

Prizes in 2013: Physiology and medicine, Physics, Chemistry, literature, Peace, and Economics.

Written by Arhopala Bazaloides

October 9, 2013 at 10:18 am

2013 Nobel prize in Physics

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Francois Englert (left) and Peter Higgs (right) in CERN on July 4, 2012 at the announcement of the discovery of the Higgs particle

A press release from the Nobel Foundation confirmed everyone’s guess:

François Englert and Peter W. Higgs are jointly awarded the Nobel Prize in Physics 2013 for the theory of how particles acquire mass. In 1964, they proposed the theory independently of each other (Englert together with his now deceased colleague Robert Brout). In 2012, their ideas were confirmed by the discovery of a so called Higgs particle at the CERN laboratory outside Geneva in Switzerland..

The awarded theory is a central part of the Standard Model of particle physics that describes how the world is constructed. According to the Standard Model, everything, from flowers and people to stars and planets, consists of just a few building blocks: matter particles. These particles are governed by forces mediated by force particles that make sure everything works as it should.

The entire Standard Model also rests on the existence of a special kind of particle: the Higgs particle. This particle originates from an invisible field that fills up all space. Even when the universe seems empty this field is there. Without it, we would not exist, because it is from contact with the field that particles acquire mass. The theory proposed by Englert and Higgs describes this process.

On 4 July 2012, at the CERN laboratory for particle physics, the theory was confirmed by the discovery of a Higgs particle. CERN’s particle collider, LHC (Large Hadron Collider), is probably the largest and the most complex machine ever constructed by humans. Two research groups of some 3,000 scientists each, ATLAS and CMS, managed to extract the Higgs particle from billions of particle collisions in the LHC.

François Englert, Belgian citizen. Born 1932 in Etterbeek, Belgium. Ph.D. 1959 from Université Libre de Bruxelles, Brussels, Belgium. Professor Emeritus at Université Libre de Bruxelles, Brussels, Belgium.

Peter W. Higgs, UK citizen. Born 1929 in Newcastle upon Tyne, UK. Ph.D. 1954 from King’s College, University of London, UK. Professor emeritus at University of Edinburgh, UK.

One hears that Prof. Higgs had made up his mind to be untraceable today. BBC reports:

Professor Higgs is renowned for shying away from the limelight, and he could not be located for interview in the immediate aftermath of the announcement.

“He’s gone on holiday without a phone to avoid the media storm,” his Edinburgh University physics colleague Alan Walker told UK media, adding that Higgs had also been unwell.

But the university released a prepared statement from Higgs, who is emeritus professor of theoretical physics:

“I am overwhelmed to receive this award and thank the Royal Swedish Academy.

“I would also like to congratulate all those who have contributed to the discovery of this new particle and to thank my family, friends and colleagues for their support.

“I hope this recognition of fundamental science will help raise awareness of the value of blue-sky research.”

Francois Englert said he was “very happy” to win the award, speaking at the ceremony via phone link.

“At first I thought I didn’t have it [the prize] because I didn’t see the announcement,” he told the committee, after their news conference was delayed by more than an hour.

Here are the links to the paper Broken Symmetry and the Mass of Gauge Vector Mesons by F. Englert and R. Brout and Broken Symmetries and the Masses of Gauge Bosons by Peter W. Higgs. The papers are available without subscriptions.

There is indignance on the far side of the Atlantic. Physical Review Letters reported:

“It’s unfortunate that the Nobel Prize is limited to only two recipients,” said R. Sekhar Chivukula (2010 chair of the APS Sakurai Prize Selection Committee), “because failing to recognize the work of Guralnik, Hagen and Kibble is a significant oversight. I’m glad that the APS could award a prestigious prize in a way that makes clear just how important they all were in establishing the foundations of contemporary particle physics.”

The 2010 Sakurai Prize cites Guralnik, Hagen, Kibble, Brout, Englert, and Higgs for “elucidation of the properties of spontaneous symmetry breaking in four-dimensional relativistic gauge theory and of the mechanism for the consistent generation of vector boson masses.”

Interestingly, this citation is carefully crafted to exclude P. W. Anderson by referring to four-dimensional relativistic gauge theory. Peter Higgs in his paper says: “This phenomenon is just the relativistic analog of the plasmon phenomenon to which Anderson has drawn attention”. It is unfortunate that the Nobel prize is not given to seven people. It is the nature of science that the process of discovery is diffuse. It is also the nature of myths and prizes that the story of discoveries is simplified.

Prizes in 2013: Physiology and medicine, Physics, Chemistry, literature, Peace, and Economics.

Written by Arhopala Bazaloides

October 8, 2013 at 12:23 pm

Science shutdown

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The Guardian ran a FAQ on the US government shutdown for non-Americans:

Will the shutdown mean the entire US government grinds to a halt?

No, it’s not an anarchist’s (or libertarian’s?) dream. Essential services, such as social security and Medicare payments, will continue.
The US military service will keep operating, and Obama signed emergency legislation on Monday night to keep paying staff. But hundreds of thousands of workers at non-essential services, from Pentagon employees to rangers in national parks, will be told to take an unpaid holiday.

Nature runs news of under-appreciated effects of the US shutdown:

Siddharth Hegde, a PhD student at the Max Planck Institute for Astronomy in Heidelberg, Germany, had lined up a trip to NASA’s Ames Research Center near San Francisco, California. Hegde is an astronomer who models atmospheres on extrasolar planets, and he was planning to study the optical properties of extremophiles — organisms that thrive in extreme environments — during his sojourn.

But then the US government shutdown hit. Hegde, who had carefully nurtured and grown his extremophiles, had to pack up his things and walk out of the Ames lab. Without someone there to oversee the cells and feed them regularly, the extremophile cultures are now dying. (The seed cultures, gathered from hostile environments such as the Atacama and Mojave deserts, remain safe in deep freeze.)

“To go from seed culture to see them grow takes some time,” says Hegde. “Some of these organisms were taking a long time to grow, and if all of these die then I have to start again and wait another month.”

Time is precious because Hegde, an Indian citizen, has a three-month US visa. When that expires at the end of November, he will have to go back to Germany and re-apply if he wants to return — even as other work there requires his attention. “It’s not a question of money right now,” he says. “It’s time. There is no substitute for time.”

Elsewhere, Nature reports:

The [National Science Foundation] has kept its three Antarctic research stations open during the initial days of the shutdown, which began on 1 October, under rules designed to protect human lives and US government property. But Lockheed Martin, the contractor that runs the NSF’s Antarctic operations, has told researchers that it will run out of money by mid-October.

At that point, the company would be forced to evacuate all but a skeleton staff from McMurdo, Amundsen–Scott and Palmer stations. And that would spell the end to this year’s research season, which normally runs from October to February.

Yet another report in Nature says that scientists are not even allowed to talk about their work:

Researchers from the National Institutes of Health (NIH) who were in San Francisco, California, attending a meeting on cytokines found their trips unexpectedly cut short when the government began shutting down at midnight on 1 October. As soon as the news broke, NIH officials told the travelling researchers to come back immediately “by any means necessary”.

The organizers quickly rescheduled the meeting so that all the NIH employees could give their talks before the agency officially shut down. “They told us giving a talk after that was a federal crime,” says one NIH immunologist who asked that her name not be used, as she is not authorized to speak to the press.

A possible consequence is nicely summarized here:

“The knock-on effects — undermining confidence in public funding of research and ceding scientific priority to other nations — are hugely deleterious,” says Ian Holmes, a computational biologist at the University of California, Berkeley.

Written by Arhopala Bazaloides

October 8, 2013 at 4:03 am

2013 Nobel prize in Physiology and Medicine

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A press release from the Nobel foundation announces:

The 2013 Nobel Prize honours three scientists who have solved the mystery of how the cell organizes its transport system. Each cell is a factory that produces and exports molecules. For instance, insulin is manufactured and released into the blood and chemical signals called neurotransmitters are sent from one nerve cell to another. These molecules are transported around the cell in small packages called vesicles. The three Nobel Laureates have discovered the molecular principles that govern how this cargo is delivered to the right place at the right time in the cell.

Randy Schekman discovered a set of genes that were required for vesicle traffic. James Rothman unravelled protein machinery that allows vesicles to fuse with their targets to permit transfer of cargo. Thomas Südhof revealed how signals instruct vesicles to release their cargo with precision.

Through their discoveries, Rothman, Schekman and Südhof have revealed the exquisitely precise control system for the transport and delivery of cellular cargo. Disturbances in this system have deleterious effects and contribute to conditions such as neurological diseases, diabetes, and immunological disorders.

James E. Rothman was born 1950 in Haverhill, Massachusetts, USA. He received his PhD from Harvard Medical School in 1976, was a postdoctoral fellow at Massachusetts Institute of Technology, and moved in 1978 to Stanford University in California, where he started his research on the vesicles of the cell. Rothman has also worked at Princeton University, Memorial Sloan-Kettering Cancer Institute and Columbia University. In 2008, he joined the faculty of Yale University in New Haven, Connecticut, USA, where he is currently Professor and Chairman in the Department of Cell Biology.

Randy W. Schekman was born 1948 in St Paul, Minnesota, USA, studied at the University of California in Los Angeles and at Stanford University, where he obtained his PhD in 1974 under the supervision of Arthur Kornberg (Nobel Prize 1959) and in the same department that Rothman joined a few years later. In 1976, Schekman joined the faculty of the University of California at Berkeley, where he is currently Professor in the Department of Molecular and Cell biology. Schekman is also an investigator of Howard Hughes Medical Institute.

Thomas C. Südhof was born in 1955 in Göttingen, Germany. He studied at the Georg-August-Universität in Göttingen, where he received an MD in 1982 and a Doctorate in neurochemistry the same year. In 1983, he moved to the University of Texas Southwestern Medical Center in Dallas, Texas, USA, as a postdoctoral fellow with Michael Brown and Joseph Goldstein (who shared the 1985 Nobel Prize in Physiology or Medicine). Südhof became an investigator of Howard Hughes Medical Institute in 1991 and was appointed Professor of Molecular and Cellular Physiology at Stanford University in 2008.

Prizes in 2013: Physiology and medicine, Physics, Chemistry, literature, Peace, and Economics.

Written by Arhopala Bazaloides

October 7, 2013 at 1:57 pm

Planet earth: not long to live

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Only about 1750000000 years of life left on earth, according to a paper by Andrew Rushby and friends in the journal Astrobiology:

The HZ [habitable zone] lifetime for Earth ranges between 6.29 and 7.79×109 years (Gyr). The 7 exoplanets fall in a range between 1 and 54.72 Gyr, while the 27 Kepler candidate planets’ HZ lifetimes range between 0.43 and 18.8 Gyr. Our results show that exoplanet HD 85512b is no longer within the HZ, assuming it has an Earth analog atmosphere. The HZ lifetime should be considered in future models of planetary habitability as setting an upper limit on the lifetime of any potential exoplanetary biosphere, and also for identifying planets of high astrobiological potential for continued observational or modeling campaigns.

A news item in Nature explains:

Earth will be able to host life for just another 1.75 billion years or so, according to a study published on 18 September in Astrobiology. The method used to make the calculation can also identify planets outside the Solar System with long ‘habitable periods’, which might be the best places to look for life.

The habitable zone around a star is the area in which an orbiting planet can support liquid water, the perfect solvent for the chemical reactions at the heart of life. Too far from a star and a planet’s water turns to permanent ice and its carbon dioxide condenses; too close, and the heat turns water into vapour that escapes into space.

Habitable zones are not static. The luminosity of a typical star increases as its composition and chemical reactions evolve over billions of years, pushing the habitable zone outward. Researchers reported in March that Earth is closer to the inner edge of the Sun’s habitable zone than previously thought.

The inner edge of the Sun’s habitable zone is moving outwards at a rate of about 1 metre per year. The latest model predicts a total habitable zone lifetime for Earth of 6.3 billion–7.8 billion years, suggesting that life on the planet is already about 70% of the way through its run. Other planets — especially those that form near the outer boundary of a star’s habitable zone or orbit long-lived, low-mass stars — may have habitable-zone lifetimes of 42 billion years or longer.

Written by Arhopala Bazaloides

September 23, 2013 at 4:29 am

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