Monday, August 06, 2007

Readings, 5 August 2007

I'm trying a new approach to this, so we have a bumper crop of readings this week. Don't count on as much every time, but have fun with the current list.

The text following each item is quoted material, except for editorial comments, which are in color.

General and physical science

Open Access and the Progress of Science
The power to transform research communication may be at each scientist's fingertips.

Open access publishing seems very important to me. It's quite frustrating – for both the writer and the reader – to present an overview of some important scientific research, yet have the actual research publication be inaccessible to most readers, and at best accessible to a few only by jumping through hoops. This is especially frustrating in the case of research that may have personal importance to certain readers, as with health and medical issues. It's also a major barrier to raising the scientific literacy of the public when there is no practical way for the public to gain a better understanding of a subject – by going to the original research papers – than provided by the mass media.

The chemistry of space grows more complex
The chemistry of outer space continues to amaze astronomers. After several decades of doubt, they know that chemical processes around and between stars produce complex molecules including precursors of organic life. But recent discoveries with a new observing technique show they have barely glimpsed what's really going on.

Space station's future in doubt
NASA has only a slim margin of error for completing construction of the international space station before the space shuttle is retired -- and more concerns about supplying it after that date....

And even if no unforeseen scheduling issues arise, experts said NASA faces problems dealing with changes to its work force as the agency moves to a future moon-Mars exploration program. And there is a shortage of science being done on the space station, conceived as a 200-mile-high floating laboratory.

In order to support real scientific research, NASA should be provided with a little of the hundreds of billions of $$ now being squandered on military boondoggles. Failing that, it would be a blessing if funding for real science came from savings that would result if the space station were simply abandoned, or at least mothballed for a few years. For comments regarding better use by NASA of its budget, see this and this.

The Great Global Warming Swindle Swindle
With all those other endangered species going extinct it's nice to know there's still a handful of global warming skeptics kicking around. ABC Science Online's Bernie Hobbs looks at the facts behind the vitriol in the film that's got everyone looking up the word 'polemic'.

Nice exposé of a propaganda film put out by global warming skeptics.

Self Assembly
Hofstadter's new book, deeply thought-provoking though it is, is less engaging than either Gödel, Escher, Bach or Le Ton Beau de Marot. Yet I Am a Strange Loop carries the high hopes of its author, not just those of its readers. Hofstadter feels that his first book, despite its massive popularity, has been widely misunderstood. Its fundamental message seems not to have been noticed: "It sometimes feels as if I had shouted a deeply cherished message out into an empty chasm and nobody heard me." This new volume is his attempt to set the record straight.

The core intellectual claim, then, is much the same as that of Gödel, Escher, Bach: namely, that a proper understanding of Gödel's proof helps us to see that life, mind and self are all constituted not by biochemistry but by the higher-level patterns that biochemistry makes possible. In particular, human selves are abstract self-referential (reflexively looping) patterns that arise spontaneously out of the meaningless base of neural activity.

Margaret Boden's review of Douglas Hofstadter's new book is brief, but should not be missed.

Do Loops Explain Consciousness? Review of I Am a Strange Loop
Another review of Hofstadter's book, by no less than Martin Gardner, who opines on its place in the philosophy of consciousness.


Poincaré, Perelman and proof
This is a review of Donal O'Shea's The Poincaré Conjecture: In Search of the Shape of the Universe. Both author and reviewer (Nigel Hitchin) are professional mathematicians, so the indications are this book is a must-have if you're even vaguely interested in the subject. The review itself nicely summarizes both the technical issues and the personal story of Grigori Perelman, who proved the Poincaré conjecture.

GEOMETRY AND THE IMAGINATION: Pricey Proof Keeps Gaining Support
No report on advances in topology is complete these days without an update on Russian mathematician Grigory Perelman's proof of Thurston's Geometrization Conjecture and its million-dollar corollary, the Poincaré conjecture (Science, 22 December 2006, p. 1848). After poring over Perelman's papers for 4 years, topologists are confident of the result, says John Morgan of Columbia University, who gave an overview of the proof at the Thurston conference.

There were other interesting results presented at the conference in honor of William Thurston. You can access accounts of these results here (subscription required for full access).

Tom Lehrer's Derivative Ditties
Should you be not old enough for the name Tom Lehrer even to ring a bell for you, Ivars Peterson offers a summary of the mathematician-songwriter's work having special appeal to the mathematically inclined. Such as "New Math". Somehow, he neglects to mention "Lobachevsky". Or perhaps you'd just like to know of a catchy little tune that's a hilarious send-up of Catholicism: "The Vatican Rag". (Needs to be heard sung to be really appreciated.) And for chemistry devotees there's "The Elements".


Building an Immersive Web
Early virtual worlds such as ­Second Life demonstrate that highly visual, 3-D online environments hold the potential to transform the way humans interact not only with computers but with each other .... Hyped as they are, these immersive environments address two fundamental aspects of being human: our visual and social natures.

A Smarter Web
New technologies will make online search more intelligent--and may even lead to a "Web 3.0."

This longish article may be for you if you have ever puzzled over questions like "What comes after Web 2.0?" or "What the heck is this 'Semantic Web' thing?"

At last, semiconductor industry begins embracing nano
Even though the conservative semiconductor industry, with its extreme performance and manufacturing demands, has done much of its manufacturing in nanoscale dimensions for years, it hasn’t yet had much use for the unique properties of nanoparticles, fullerenes, nanowires, quantum dots, etc.-the technologies usually considered “true” nanotech. Nor have the nanoscale patterning processes developed by the chip makers been of much use to the rest of the nanotechnology world.

But the old ways are starting to change.

A bot's life
Robotic designs based upon natural organisms are as diverse as the animal world itself. There are devices in the works that mimic caterpillars, spiders, dogs and octopuses. Their goals and purposes are equally varied, from new medical treatments to space labor to being a soldier's best friend.

Life sciences

What Do Mirror Neurons Mean?
The discovery of mirror neurons in the frontal lobes of macaques and their implications for human brain evolution is one of the most important findings of neuroscience in the last decade. Mirror neurons are active when the monkeys perform certain tasks, but they also fire when the monkeys watch someone else perform the same specific task. There is evidence that a similar observation/action matching system exists in humans.

This is a symposium comprising several papers on mirror neurons published in the last three years. I wrote about the subject here and here. These papers are technical but worth a look.

Genetic Engineers Who Don’t Just Tinker
FORGET genetic engineering. The new idea is synthetic biology, an effort by engineers to rewire the genetic circuitry of living organisms.

The ambitious undertaking includes genetic engineering, the now routine insertion of one or two genes into a bacterium or crop plant. But synthetic biologists aim to rearrange genes on a much wider scale, that of a genome, or an organism’s entire genetic code. Their plans include microbes modified to generate cheap petroleum out of plant waste, and, further down the line, designing whole organisms from scratch.

Can Adult Stem Cells Do It All?
Scientists may have turned mouse skin cells into embryolike stem cells, but prior claims for the power of adult cells have yet to stand the test of time.

Don't believe everything you read by opponents of embryonic stem cell research, such as the supposed power of adult stem cells to do whatever ESCs can.

An Elegant Molecular Dance
Her team's strategy is to spy on biological machines in action, watching as individual molecules fold, interact with one another, and do their work. They use sensitive optical imaging techniques to collect extraordinarily detailed pictures of this activity—watching, for example, as a single molecule of RNA folds into its functional shape or a tiny polio virus invades a mammalian cell. Combining those images with findings from their experiments in molecular biology and biochemistry, the scientists are revealing how the structural dynamics and movements of molecules drive biological processes. ...

One of the lab's most recent successes, however, is developing a precise portrait of the molecular dance that creates telomerase, a complex of molecules that protects the ends of chromosomes during DNA replication. Michael Stone, a postdoctoral fellow in Zhuang's lab, led the study published in the March 22 issue of Nature. The enzyme is essential for rapidly dividing cells, such as those in a developing embryo, but is usually shut off in healthy adult human cells. Upregulating the enzyme's activity allows adult cells to achieve a dangerous immortality. The enzyme is inappropriately active in the vast majority of human cancers, making it a potential target for new cancer therapies. ...

With experiments like these, Zhuang says biophysicists and biologists are steadily moving their field toward the kind of fundamental and quantitative ways of explaining the world that first attracted her to science.

Arresting developments
Dr Harel has been working on a computer model of C. elegans. He hopes this will reveal exactly how pluripotent stem cells—those capable of becoming any sort of mature cell—decide which speciality they will take on. He thinks that a true understanding of the processes involved will be demonstrated only when it is possible to build a simulation that does exactly—but artificially—what happens in nature.

There are interesting ideas in this short piece, the nature of which you would never guess from the dreadfully useless title. For example, the idea of computer modeling of entire, albeit simple, organisms. Inevitably, with the ever-increasing power of supercomputers, it will be possible before long to model more complex animals, like, say, jellyfish. This will enable zoologists who study such critters to gauge the quality of their understanding by observing how lifelike their computer models are.

Brain Boosters
Two days from now I'm planning to further tweak my mind by taking a brain-boost pill. Called Provigil, it differs from its predecessors in that it is believed to home in on a section of the brain that helps govern alertness and memory. The pill is manufactured by ­Cephalon of Frazer, PA, and its active ingredient is called modafinil. The drug's targeted delivery is supposed to prevent the side effects of stimulants that diffuse throughout the brain and rev up everything.

In addition to the Provigil the writer discusses electrical stimulation devices for the brain, which supposedly enhance performance, however slightly. Personally, I find caffeine works pretty well, and abundant evidence that's pretty well-known to all suggests I'm hardly alone. But did you know that the caffeine, plus exercise, may lower risk of skin cancer too?

Health and medicine

Gene therapy trial on hold
As the US Food and Drug Administration prepares to investigate the death of a patient in a phase I/II gene therapy trial for inflammatory arthritis, researchers in the field say the treatment's delivery vector, an adeno-associated virus (AAV), was unlikely to be the culprit.

It will be very good news if these researchers are correct, as a number of mainstream media accounts are portraying this gene therapy trial problem as yet another black eye for the whole concept of gene therapy.

Obesity: A Link to Rare Gene Variations
Sometimes, the rarest of the rare can still have an impact. A multi-institutional team of scientists led by Berkeley Lab geneticist Len Pennacchio has found that extremely uncommon gene variations likely contribute to obesity.

How and why — and to what extent — remain a mystery, but the research adds another clue to the problem of obesity, which is reaching epidemic proportions in developed nations. Overeating and lack of exercise loom as the chief culprits. But heredity and gene defects are implicated too, and now scientists have a better understanding of their role.

AIDS Abated: Genome scans illuminate immune control of HIV
Some people who contract HIV, the virus that causes AIDS, maintain low amounts of the virus in their bodies for years. These long-term nonprogressors—so called because a decade or more can pass before they develop full-blown AIDS—have attracted great attention from researchers.

Now, using powerful, whole-genome scans, researchers have identified three genetic variations that partially explain why some HIV-infected people develop AIDS quickly while others keep it at bay.

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