The Brachistochrone Challenge

Saturday, August 30th, 2014

If you want to roll a ball down a slope, what shape of slope will get the ball from point A to point B in the least time? This is the so-called brachistochrone challenge.

At first you might naively assume that a straight line would get the ball to its destination in the least time, because the shortest distance between two point is a straight line, but the ball is not moving at a constant speed.

In fact, because it needs to get rolling, the ball will travel down a concave ramp much faster than down a convex ramp. But which concave curve?

Brachistochrone Challenge

The winning curve is an inverted cycloid, the curve traced by a point on the rim of a circular wheel as the wheel rolls along a straight line.

Cycloid

(Hat tip to Charles.)

Flatley’s Law

Friday, August 29th, 2014

Over the past 13 years, the cost of sequencing DNA has dropped from $100 million per human genome to only $1,000:

The only thing more extraordinary than the growth rate of the sequencing revolution is that the beneficiary is a single company, Illumina of San Diego, and most of the credit for the rate of change can be laid at the feet of one entrepreneur, Chief Executive Jay Flatley. Thanks largely to Flatley’s leadership, Illumina emerged as the dominant maker of DNA sequencers eight years ago and has maintained 80% market share despite an assault by several well-funded competitors.

Since 2008 Illumina’s sales and profit have both increased 147%, to $1.42 billion and $125 million, respectively, as the stock increased 617% and the company’s market capitalization reached $23 billion.

Shock Waves Damage Eyes

Thursday, August 28th, 2014

One of the defining pieces of a modern soldier’s kit is a pair of sunglasses, because those shades offer protection not only against the sun but against ballistic fragments. Fragments aren’t the only danger though. It turns out that shock waves alone can damage eyes:

A new study by the University of Texas San Antonio and U.S. Army Institute of Surgical Research has found that blast waves themselves — not just the dirt and debris propelled by the blast — can cause significant and permanent damage to the eyes.

In an experiment that had the scientists blasting away at pig eyes with a high-powered air cannon, researchers learned the shock wave alone can damage portions of the eye, including the sclera — the white part — the retina, the optic nerve and more.

Among the most commonly seen injuries in the blasted porcine eyeballs was retinal detachment.

“Detachment is more common to older adults. But two clinicians on our team, an Army optometrist and ophthalmologist, told us this was something they were seeing in troops and couldn’t explain. That gave us the idea to look for this sort of damage in this study,” said Mathew Reilly, assistant professor of biomedical engineering at UTSA.

DoD data shows that ocular injuries account for 13 percent of all battlefield injuries and roughly 80 percent of eye injuries in combat are associated with blasts.

Scientist Shamans

Wednesday, August 27th, 2014

Frank Herbert based the Bene Gesserit “witches” of Dune in part on the scientific wizards of Isaac Asimov’s Foundation trilogy.

Herbert’s judgment on them is implicit in the way he has reversed the roles played by such scientists in Dune.

Asimov’s trilogy is set in a crumbling galactic empire, in which a “psychohistorian” named Han Seldon has analyzed with mathematical precision the forces acting upon masses of people and can predict nearly exactly what will happen hundreds and even thousands of years in the future. Seldon has set up a foundation to act in accordance with the statistical laws of psychohistory and take the necessary steps to bring about a new order from the ruins of the old. In Seldon’s vision, the Foundation will enable the rebuilding of galactic civilization in 1,000 years instead of the 10,000 years of turmoil that would otherwise be required.

The trilogy chronicles the successes of the Foundation and the complete accuracy of the long-dead Seldon’s scientific predictions, until a freak mutant is born. An empathetic superman, called “the Mule” because he is sterile, he was completely unexpected by Seldon, whose science could predict only mass dynamics and not the truly exceptional individual. The Mule shatters the Foundation’s precious new civilization in his own hungry grab for power, and is stopped only by a mysterious “second foundation” established by Seldon to study the science of the mind and to prepare for such unforeseen emergencies as the material science of the first foundation could not handle.

Herbert questioned the assumptions about science that he saw at work in Asimov’s trilogy. In a recent essay, he wrote:

History… is manipulated for larger ends and for the greater good as determined by a scientific aristocracy. It is assumed, then, that the scientist-shamans know best which course humankind should take…. While surprises may appear in these stories (e.g., the Mule mutant), it is assumed that no surprise will be too great or too unexpected to overcome the firm grasp of science upon human destiny. This is essentially the assumption that science can produce a surprise-free future for humankind.

Dune is clearly a commentary on the Foundation trilogy. Herbert has taken a look at the same imaginative situation that provoked Asimov’s classic — the decay of a galactic empire — and restated it in a way that draws on different assumptions and suggests radically different conclusions. The twist he has introduced into Dune is that the Mule, not the Foundation, is his hero.

The Bene Gesserit are clearly parallel to the “scientist-shamans” of the Foundation. Their science of prediction and control is biological rather than statistical, but their intentions are similar to those of Asimov’s psychohistorians. In a crumbling empire, they seek to grasp the reins of change. The Sisterhood sees the need for genetic redistribution — which ultimately motivates the jihad — and has tried to control that redistribution by means of their breeding program. The Kwisatz Haderach, the capstone of their plan, is not its only goal. Their overall intention is to manage the future of the race. Paul, like the Mule, is the unexpected betrayal of their planned future.

The irony is that Paul is not a freak but an inevitable product of the Bene Gesserit’s own schemes. Although he has come a generation early in the plan due to Jessica’s willfulness in bearing a son instead of a daughter, the real surprise is not his early birth but the paradox of the Sisterhood’s achievement: the planned instrument of perfect control, the Kwisatz Haderach, was designed to see further than his creators, He could not help but know the emptiness of their dreams. The universe cannot be managed; the vitality of the human race lies in its random generation of new possibilities. The only real surety is that surprises will occur. In contrast to the Foundation trilogy’s exaltation of rationality’s march to predicted victory, Dune proclaims the power and primacy of the unconscious and the unexpected in human affairs. Paul’s wild ride on the jihad, not the careful Bene Gesserit gene manipulation, provides the answer to the Empire’s needs.

Even though Dune so clearly undercuts the assumptions about science applauded in the Foundation trilogy, such antirationalism was the culmination of a long struggle. Early on, Herbert saw that the same assumptions pervaded much of science fiction, including his own. In order to embody his visions of the future, he needed to untangle himself from their hold.

Knickebein

Monday, August 25th, 2014

A couple years ago Gregory Cochran mentioned The Wizard War, R. V. Jones’ account of his time leading scientific intelligence for Britain during the war, because it had some interesting examples of thick and thin problems — but mostly because it’s so damn much fun.

I bought a copy, under the original British title, Most Secret War — “most secret” is the British equivalent of “top secret” — and recently read and enjoyed it.

The classically thin problem that Cochran cites involves the German two-beam navigation system (Knickebein). From page 97 of my copy:

It may help here if I explain what a Lorenz beam is, for this is what we expected to find. If one arranges a number of aerial units (‘dipoles’, which look like the simplest type of television aerial) side by side, as in a fence and about the same distance apart as they are long, and feeds the radio energy to them in a suitable manner they will generate the beam which emerges broadside to the fence; and, paradoxically perhaps, the longer the ‘fence’ the sharper the beam. But without a fence of prohibitive length, the beam would not be nearly sharp enough to define a target one mile wide at two hundred miles range. The clever trick in the Lorenz system was to transmit two fairly blunt beams, pointing in slightly different directions but overlapping one another in a relatively narrow region which now in effect becomes the ‘beam’ along which the aircraft are intended to fly.

Knickebein Principle of the Lorenz Beam Diagram

The two overlapping beams are most simply generated by two aerial systems pointing in slightly different directions and mounted together on a single turntable. The actual radio transmitter is switched from one of these aerials to the other and back again in a repetitive sequence, so that one aerial transmits for a short time followed by a longer interval, giving a ‘dot’ to anyone who listens to it on a suitable radio receiver, while the other transmits for a long time followed by a short interval, giving a ‘dash’. Anyone so placed as to receive the two aerials at the same strength would hear the one transmit a dot immediately followed by the other transmitting a dash, so that he would think that he was listening to a single aerial transmitting continuously. As he moved sideways into the zone in which one beam, say the ‘dot’ beam, was stronger than the other, he would being to hear the dots coming up above the continuous note, and vice versa with the dashes. By listening for the predominance of dots or dashes he would know the direction in which he would have to steer to bring himself back into the narrow ‘equi-signal’ zone. This zone can be as narrow as one hundredth or even one thousandth of the width of the ‘dot’ or ‘dash’ beam alone.  The aerials are therefore set on the turntable in such a direction that the equi-signal zone passes over the target.  To warn the pilot that he is approaching the target, a similar beam system would be set up from one site well to the side of the director beam, and this second system would transmit a marker beam to cross the director a few kilometres before the target.

Creating History Is Hard

Thursday, August 14th, 2014

I still haven’t played Dwarf Fortress, but its world-building process intrigues me:

Adams has, over the years, developed an intricate process to simulate eons of complex geologic time, a way of stacking fractal layers and blending them with algorithms to give life to each world.

The first layer plots the annual rainfall of each map location. Then a separate fractal simulates the deposition of mineral elements throughout the underground strata, giving the land itself a kind of texture. A temperature fractal is generated and rough biomes emerge as contiguous tiles on the map that contain a subset of closely related flora and fauna.

The order here is important, because in the next step — drainage — Dwarf Fortress begins to simulate the complex forces of erosion. Only after the biomes have been created can the rivers run, slashing deep valleys as they flow toward unnamed oceans. When they finally meet the sea a salinity algorithm kicks in to define the areas for swampy river deltas, alluvial islands and mangrove swamps.

[...]

In his research for the game Adams learned that in the real world when warm, wet air travels up the side of a mountain it loses moisture. Rain precipitates out creating areas like rain forests and snow capped peaks. On the other side of the mountain deserts form in areas that are called “rain shadows.”

[...]

After the map has been locked into place, the game assigns a kind of energy to each region, ranging from good to evil on a scale of one to 20. It then uses the positive and negative energy of each area to generate place names — The Ocean of Muting sit along the edge of The Jungles of Mire near the Ivory Hills — and on and on creating hundreds of uniquely named regions.

But these are just the names as translated for the player. Adams says that each area of the map has been named by one of four cultures. Human, dwarven, elvish and goblin languages are actually programmed into the game.

Ayn Rand in the Happy Lab

Thursday, August 14th, 2014

Sonya Lyubomirsky ran an experiment where participants were given a task and then received a performance rating — and were told another participant’s performance rating, too. But — suprise! — the performance ratings weren’t related to their actual performance.

Their reaction depended on how happy they already were, before the experiment:

To analyze the data, I divided my participants into those who, before performing, reported being very happy and those who reported being relatively unhappy. When I examined the “before” and “after” data of my very happy participants, I found that those who learned that they had performed very poorly reported feeling less positive, less confident, and more sad after the study was over. Their reaction to ostensible failure was perfectly natural and not at all surprising. By contrast, the very happy participants who learned that they had performed extremely well (a 6 out of 7) subsequently felt better on all dimensions, and, notably, learning that someone did even better did not dilute the pleasure of their ostensible success.

Things turn Randian, Bryan Caplan says, when they looked at the unhappy participants, who resembled Randian villains:

The results for my unhappiest participants, however, were dramatic. Their reactions, it appears, were governed more by the reviews they had given their peers than by their own feedback. Indeed, the study paints a stark and quite unpleasant portrait of an unhappy person. My unhappiest volunteers reported feeling happier and more secure when they received a poor evaluation (but heard that their peer did even worse) than when they had received an excellent evaluation (but heard that their peer did even better). It appears that unhappy individuals have bought into the sardonic maxim attributed to Gore Vidal: “For true happiness, it is not enough to be successful oneself… One’s friends must fail.”

Learning Without Questioning

Wednesday, August 13th, 2014

Kenya Kura of Japan explains why Asians aren’t more successful in science, citing two factors:

1. Low curiosity, which is expressed by lower Openness to experience (-.59 SD) as shown in various cross-cultural personality comparisons.

2. Collectivism, which is captured by various individualism-collectivism indices such as the Hofstede individualism index (IDV), or Hofstede and Triandis individualism index (about -2 SD). The genetic underpinnings for these traits, such as DRD4, 5HTTLPR, and OPRM1 have also become increasingly apparent.

To integrate these psychological traits, a “q” factor is constructed by factor analysis on measures of Openness and Collectivism, which are then correlated with variables measuring academic achievements and also student assessments. It is found that IQ scores coupled with “q” factor scores neatly predict racial scientific achievements and also world-wide student assessments.

(Hat tip to Mangan.)

How Tests Make Us Smarter

Tuesday, August 12th, 2014

Henry L. Roediger III reviews how tests make us smarter:

One insight that we and other researchers have uncovered is that tests serve students best when they’re integrated into the regular business of learning and the stakes are not make-or-break, as in standardized testing. That means, among other things, testing new learning within the context of regular classes and study routines.

Students in classes with a regimen of regular low- or no-stakes quizzing carry their learning forward through the term, like compounded interest, and they come to embrace the regimen, even if they are skeptical at first. A little studying suffices at exam time — no cramming required.

Moreover, retrieving knowledge from memory is more beneficial when practice sessions are spaced out so that some forgetting occurs before you try to retrieve again. The added effort required to recall the information makes learning stronger. It also helps when retrieval practice is mixed up — whether you’re practicing hitting different kinds of baseball pitches or solving different solid geometry problems in a random sequence, you are better able later to discriminate what kind of pitch or geometry problem you’re facing and find the correct solution.

Surprisingly, researchers have also found that the most common study strategies — like underlining, highlighting and rereading — create illusions of mastery but are largely wasted effort, because they do not involve practice in accessing or applying what the students know.

When my colleagues and I took our research out of the lab and into a Columbia, Ill., middle school class, we found that students earned an average grade of A- on material that had been presented in class once and subsequently quizzed three times, compared with a C+ on material that had been presented in the same way and reviewed three times but not quizzed. The benefit of quizzing remained in a follow-up test eight months later.

Savory-Flavored Carbs and Fat

Tuesday, August 12th, 2014

The main driver of the obesity epidemic has been increased intake, rather than decreased energy expenditure, Stephen J. Simpson and David Raubenheimer say:

The obesity problem is best understood not as the result of the overconsumption of a single macronutrient, but from a skewing of the proportion of each macronutrient in our diet — notably the dwindling quantity of protein in processed food products. The paucity of protein relative to fats and carbohydrates in processed foods drives the overconsumption of total energy as our bodies seek to maintain a target level of protein intake.

[...]

Many processed food products are protein-poor but are engineered to taste like protein. Many people therefore eat far too much fat and carbohydrate in their attempt to ingest enough protein. In this way, engineered foods subvert the appetite control systems that should be helping to balance the consumption of macronutrients. The results are striking. In the United States, the typical diet saw a 0.8% decline in protein concentration between 1971 and 2006. During this same period, the consumption of calories from carbohydrates and fats increased by 8%, a trend reflected in the rising prevalence of obesity, but protein intake remained almost unchanged.

The substitution of carbohydrates and fats for protein is driven by economics. Food manufacturers have a financial incentive to replace protein with cheaper forms of calories, and to manipulate the sensory qualities of foods to disguise their lower protein content. This leads to savoury-flavoured food that makes us think we’re eating protein when in reality it is loaded with carbohydrates and fats.

Magic Mushrooms Inspired Dune

Friday, August 8th, 2014

Frank Herbert’s Dune included one element that particularly endeared it to the counterculture — the spice, melange, which granted its users prescience. It turns out that magic mushrooms were the inspiration for the spice, according to mycologist Paul Stamets’ Mycelium Running:

Frank Herbert, the well-known author of the Dune books, told me his technique for using spores. When I met him in the early 1980s, Frank enjoyed collecting mushrooms on his property near Port Townsend, Washington. An avid mushroom collector, he felt that throwing his less-than-perfcct wild chanterelles into the garbage or compost didn’t make sense. Instead, he would put a few weathered chanterelles in a 5-gallon bucket of water, add some salt, and then, after 1 or 2 clavs, pour this spore-mass slurry on the ground at the base of newly planted firs. When he told me chanterelles were glowing from trees not even 10 years old, I couldn’t believe it. No one had previously reported chanterelles arising near such young trees, nor had anyone reported them growing as a result of using this method.” Of course, it did work for frank, who was simply following nature’s lead.

Frank’s discovery has now been confirmed in the mushroom industry. It is now known that it’s possible to grow many mushrooms using spore slurries from elder mushrooms. Many variables come into play, but in a sense this method is just a variation of what happens when it rains. Water dilutes spores from mushrooms and carries them to new environments. Our responsibility is to make that path easier. Such is the way of nature.

Frank went on to tell me that much of the premise of Dune — the magic spice (spores) that allowed the bending of space (tripping), the giant worms (maggots digesting mushrooms), the eyes of the Freman (the cerulean blue of Psilocybe mushrooms), the mysticism of the female spiritual warriors, the Bene Gesserits (influenced by tales of Maria Sabina and the sacred mushroom cults of Mexico) — came from his perception of the fungal life cycle, and his imagination was stimulated through his experiences with the use of magic mushrooms.

Air Waveguides

Wednesday, August 6th, 2014

Lasers lose intensity and focus with increasing distance as photons naturally spread apart and interact with atoms and molecules in the air.

Fibre optics solves this problem by beaming the light through glass cores with a high refractive index, which is good for transmitting light.

The core is surrounded by material with a lower refractive index that reflects light back in to the core, preventing the beam from losing focus or intensity.

Fibre optics, however, are limited in the amount of power they can carry and the need for a physical structure to support them.

Air waveguides may get around some of these limitations:

Milchberg and colleagues’ made the equivalent of an optical fibre out of thin air by generating a laser with its light split into a ring of multiple beams forming a pipe.

They used very short and powerful pulses from the laser to heat the air molecules along the beam extremely quickly.

Such rapid heating produced sound waves that took about a microsecond to converge to the centre of the pipe, creating a high-density area surrounded by a low-density area left behind in the wake of the laser beams.

“A microsecond is a long time compared to how far light propagates, so the light is gone and a microsecond later those sound waves collide in the centre, enhancing the air density there,” says Milchberg.

The lower density region of air surrounding the centre of the air waveguide had a lower refractive index, keeping the light focused.

“Any structure [even air] which has a higher density will have a higher index of refraction and thereby act like an optical fibre,” says Milchberg.

Cheap and compact medical testing

Wednesday, August 6th, 2014

Researchers have developed a cheap and compact electrochemical detector for medical testing:

The device, already in field trials in India, costs about $25 to produce, weighs just two ounces, and is about the size of a pack of cigarettes. It was modeled after the latest generation of inexpensive glucose monitoring devices, which are in widespread use, but whose function is limited to testing blood sugar. In addition to conducting the tests, the new device can send data over the lower-tech cellphones common in the developing world to distant physicians, who can text instructions back to researchers, government officials tracking outbreaks, and others.

[...]

He focused on an electrochemical detector, which measures the voltage or current generated in liquids for characteristic signatures of the liquid’s contents. For example, by applying a small amount of electricity to a drop of blood mixed with a reagent, the device can gauge glucose levels. The same goes for heavy metals in water, malaria antigens in blood, and sodium in urine.

[...]

They created software that converted the data to audible tones so it could be sent — after plugging the device into the phone’s headphone and microphone jack — just as if it were someone’s voice. The data is then sent over the phone’s audio network to a physician, database, or other recipient.

How America Fell in Love with Vitamins

Tuesday, August 5th, 2014

Brian Alexander tells the story of how America fell in love with vitamins and fortified foods, how public universities were transformed into money-making patent mills serving corporations, and how a clever young man, an electrical engineer from Cincinnati born with an ample supply of ambition and drive, became an unlikely celebrity and was hailed as a genius — all because of vitamin D:

In the beginning, fame was the prize in vitamin research, not money. This is why most of the early research on vitamins took place in universities: Scientists were freed from the demands of commerce. Patenting a discovery was taboo. The ethos demanded science for the sake of science, and for the public good.

But business soon developed a simple formula: If a little bit of vitamin in food was good, more had to be better. The only way to get lots more in one gulp was with a pill, or by finding some way to add more of it to food. Vitamin D, the scourge of rickets, was an especially good candidate for commercialization because most food didn’t have it at all.

With the cultures of business and academia circling each other, it didn’t take long for someone to break the taboo. The big leap came in 1922 when Frederick Banting and Charles Best at the University of Toronto announced that they had treated diabetes with a purified cow pancreas extract called insulin. The two scientists quickly patented their process and gave the rights to the university — which then licensed Eli Lilly and Company to produce insulin for the U.S. and Latin American markets in return for a 5 percent royalty on net sales. Lilly would go on to dominate the insulin market for the next 50 years and grow into a pharmaceutical powerhouse, and the university reaped millions.

For American scientists, it was a eureka moment: Suddenly, universities — and select researchers — could get rich. George Sperti would eventually be one of those lucky researchers. But so would the man who ultimately outplayed him in the arena of science and commerce, relegating Sperti to a curious, if still famous, footnote.

Though he had a nice-guy reputation among his lab employees, Harry Steenbock zealously guarded his turf. You had to if you worked in the vitamin field. An agricultural biochemist at the University of Wisconsin, he had reason to envy the Toronto scientists. His first push to patent a vitamin discovery had been pooh-poohed by the university. He never forgot the slight.

In 1924 Steenbock published a paper in the Journal of Biological Chemistry detailing an experiment that involved exposing rat food to light from a quartz-mercury vapor lamp. Rats who ate the irradiated food did not get rickets; control rats did. Somehow, and he wasn’t sure exactly how, the light had activated anti-rachitic properties in the food. Recognizing the potential, Steenbock included an addendum to the paper: “To protect the interest of the public in the possible commercial use of these and other findings soon to be published, applications for Letters of Patent…have been filed with the United States Patent Office.”

It was a bold move, and in some corners of the medical-industrial complex, an outrage. Children were suffering and Steenbock was patenting a possible preventive? The British Drug Houses, a trade group, tried to shame him, declaring in a letter: “As you know, extremely important contributions to this discovery were made by workers in this country who refused to seek any patent protection for their work.”

Steenbock shrugged off the criticism. He foresaw big commercial possibilities for vitamin D. With the help of a tough-minded Chicago patent attorney and Wisconsin alum named George Haight, he set up an independent, private, nonprofit business group called the Wisconsin Alumni Research Foundation (WARF). Though not part of the university, its aim was to fund University of Wisconsin research by licensing intellectual property created by university scientists. For the time being, that meant Steenbock, who remained intimately involved in WARF’s vitamin D deals.

Quaker Oats was the first; WARF made a secret agreement with the company in 1926. Quaker could experiment with what was being branded as the “Steenbock Process” for small yearly royalties. If the company commercialized a product, it would pay WARF an annual fee of up to $60,000 (almost $800,000 in today’s dollars) once sales began.

The Spy Who Loved Frogs

Monday, August 4th, 2014

Herpetologist Edward Taylor led the life of an old-school, adventuring naturalist:

As [Rafe] Brown made his career studying biodiversity in the Philippines over the next two decades, he could not escape Taylor’s long shadow. The elder herpetologist had logged 23 years in the field over his lifetime, collecting more than 75,000 specimens around the world, and naming hundreds of new species.

There is a darker side to Taylor’s legacy, however. He was a racist curmudgeon beset by paranoia — possibly a result of his mysterious double life as a spy for the US government. He had amassed no shortage of enemies by the time he died in 1978. An obituary noted that he was, to many, “a veritable ogre — and woe to anyone who incurred his wrath”. More damaging, perhaps, were the attacks on his scientific reputation. After the loss of his collection in the Philippines, many of the species he had named were declared invalid or duplicates. The standards of taxonomy had advanced beyond Taylor’s quaint descriptions, and without the specimens to refer to, his evidence seemed flimsy.