The new science of metagenomics, where the DNA of entire communities of microbes -- most of them previously unknown -- is studied simultaneously, promises to revolutionize understanding of the microbial world, says a new National Research Council report. It calls for a Global Metagenomics Initiative to drive advances in the field.

See a Scientific American-level article, Metagonemics: The Science of Biological Diversity.

Also: Focus on Metagenomics from Nature:

Metagenomics has emerged as a powerful tool that can be used to analyze microbial communities regardless of the ability of member organisms to be cultured in the laboratory. Metagenomics is based on the genomic analysis of microbial DNA that is extracted directly from communities in environmental samples. This technology — genomics on a huge scale — enables a survey of the different microorganisms present in a specific environment, such as water or soil, to be carried out. By integrating the information gleaned with information about biological functions within the community, the structure of microbial communities can potentially be probed. Metagenomics could also unlock the massive uncultured microbial diversity present in the environment to provide new molecules for therapeutic and biotechnological applications.

See also this conference, Metagenomics 2006, for a selection of presentations (with video) on the subject. For example, see "Cyber metagenomics":

The explosion of both genomic and environmental data requires that their union in environmental metagenomics utilize the latest in emerging capabilities of cyberinfrastructure. Recent developments such as the emergence of the National LambdaRail, service-oriented software architectures, and commodity clusters for scalable computing, storage, and visualization have made a new approach to these data-intensive science projects possible. The California Institute for Telecommunications and Information Technology (Calit2) has been building teams in these areas for the last six years.

Earlier this year, the Gordon and Betty Moore Foundation funded Calit2 to bring into being a Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA). This project is a partnership with J. Craig Venter Institute in Rockville, MD, UCSD’s Center for Earth Observations and Applications (centered at the Scripps Institution of Oceanography), the San Diego Supercomputer Center, and a number of key UCSD centers. This talk will explore the cyberinfrastructure underpinnings at Calit2 that enable and extend the implementation of the vision behind CAMERA and other metagenomics cyberinfrastructure.

Metagenomics Will Transform Modern Microbiology

We asked 100 writers and thinkers to answer the following question: Left and right defined the 20th century. What's next? The pessimism of their responses is striking: almost nobody expects the world to get better in the coming decades, and many think it will get worse

The big question

George Johnson reviews Hofstadter's new book -- first announced here almost a year ago.

To get into a properly loopy mind-set for Douglas R. Hofstadter's new book on consciousness, I plugged a Webcam into my desktop computer and pointed it at the screen. In the first instant, an image of the screen appeared on the screen and then the screen inside the screen. Cycling round and round, the video signal rapidly gave rise to a long corridor leading toward a patch of shimmering blue, beckoning like the light at the end of death's tunnel.

Giving the camera a twist, I watched as the regress of rectangles took on a spiraling shape spinning fibonaccily deeper into nowhere. Somewhere along the way a spot of red--a glint of sunlight, I later realized--became caught in the swirl, which slowly congealed into a planet of red continents and blue seas. Zooming in closer, I explored a surface that was erupting with yellow, orange and green volcanoes. Like Homer Simpson putting a fork inside the microwave, I feared for a moment that I had ruptured the very fabric of space and time.

Johnson doesn't really do much to review the book. He describes it as a "condensed" GEB, and it's clearly personal. Are there other reviews now? Yes!

Publishers Weekly gives it a Starred Review:

Hofstadter —— who won a Pulitzer for his 1979 book, Gödel, Escher, Bach —— blends a surprising array of disciplines and styles in his continuing rumination on the nature of consciousness. Eschewing the study of biological processes as inadequate to the task, he argues that the phenomenon of self-awareness is best explained by an abstract model based on symbols and self-referential "loops," which, as they accumulate experiences, create high-level consciousness. Theories aside, it's impossible not to experience this book as a tender, remarkably personal and poignant effort to understand the death of his wife from cancer in 1993 —— and to grasp how consciousness mediates our otherwise ineffable relationships. In the end, Hofstadter's view is deeply philosophical rather than scientific. It's hopeful and romantic as well, as his model allows one consciousness to create and maintain within itself true representations of the essence of another. The book is all Hofstadter —— part theory, some of it difficult; part affecting memoir; part inventive thought experiment —— presented for the most part with an incorrigible playfulness. And whatever readers' reaction to the underlying arguments for this unique view of consciousness, they will find the model provocative and heroically humane.

Booklist also gives it a starred review:

For more than 25 years, Hofstadter has been explaining the mystery of human consciousness through a bold fusion of mathematical logic and cognitive science. Yet for all of the acclaim... [ Read More (0.1k in body) ]

Scientific American: A New Journey into Hofstadter's Mind

If you don't already own this book, the new edition is a good reason to check it out.

Updated for the first time, the classic book on why cooperation is not only natural but also the best survival strategy

The Evolution of Cooperation addresses a simple yet age-old question: If living things evolve through competition, how can cooperation ever emerge? Despite the abundant evidence of cooperation all around us, there existed no purely naturalistic answer to this question until 1979, when Robert Axelrod famously ran a computer tournament featuring a standard game-theory exercise called The Prisoner's Dilemma. To everyone's surprise, the program that won the tournament, named Tit for Tat, was not only the simplest but the most "cooperative" entrant. This unexpected victory proved that cooperation--one might even say altruism--is mathematically possible and therefore needs no hidden hand or divine agent to create and sustain it. A great roadblock to the understanding of all sorts of behavior was at last removed. The updated edition includes an extensive new chapter on cooperation in cancer cells and among terrorist organizations.

The Evolution of Cooperation, by Robert Axelrod (Updated!)

Publishers Weekly concludes: "This superb tale of scientific discovery is required reading for everyone interested in the nature of human morality."

In a world supposedly governed by ruthless survival of the fittest, why do we see acts of goodness in both animals and humans? This problem plagued Charles Darwin in the 1850s as he developed his theory of evolution through natural selection. Indeed, Darwin worried that the goodness he observed in nature could be the Achilles heel of his theory. Ever since then, scientists and other thinkers have engaged in a fierce debate about the origins of goodness that has dragged politics, philosophy, and religion into what remains a major question for evolutionary biology.

The Altruism Equation traces the history of this debate from Darwin to the present through an extraordinary cast of characters-from the Russian prince Petr Kropotkin, who wanted to base society on altruism, to the brilliant biologist George Price, who fell into poverty and succumbed to suicide as he obsessed over the problem. In a final surprising turn, William Hamilton, the scientist who came up with the equation that reduced altruism to the cold language of natural selection, desperately hoped that his theory did not apply to humans.

Hamilton's Rule, which states that relatives are worth helping in direct proportion to their blood relatedness, is as fundamental to evolutionary biology as Newton's laws of motion are to physics. But even today, decades after its formulation, Hamilton's Rule is still hotly debated among those who cannot accept that goodness can be explained by a simple mathematical formula. For the first time, Lee Alan Dugatkin brings to life the people, the issues, and the passions that have surrounded the altruism debate. Readers will be swept along by this fast-paced tale of history, biography, and scientific discovery.

Read the first chapter online:

This book is about one of Darwin’s problems. It began as a small difficulty with honeybees. At first glance, it did not seem like the sort of complication that could sink a theory that many have characterized as the most important one that biology has ever produced. But it turned into a problem that troubled biologists, fascinated naturalists, engaged popular writers and the general public, and even worked its way into political discourse for the next 145 years.

...

The Altruism Equation: Seven Scientists Search for the Origins of Goodness

Marc Siegel is a doctor, so he talks about disease, but the logic is universal.

America has its killer bugs, but Americans don't, as a rule, express great concern about them: Pneumonia, which killed 63,000 Americans in 2000, draws little public comment. Until 2003, when the flu deaths of 20 U.S. children early in the season were widely publicized, Americans didn't worry much about influenza either, despite the tens of thousands of deaths attributed to that disease each year.

In comparison, relatively minor threats are widely feared.

We live temperature-controlled, largely disease-controlled lives.

And yet, we worry more than ever before. The natural dangers are no longer there, but the response mechanisms are turned on much of the time. We implode, turning our adaptive fear mechanism into a maladaptive panicked response.

One wonders if Turner will be sued for the medical expenses of Boston-area residents who suffered traumatic stress at the hands of the Mooninites.

At a time in history when true scourges are quite rare, the population is controlled by fear. Rather than enjoy the safety that our technological advances have provided us, we feel uncertain.

Worry about the wrong things puts us at greater risk of the diseases that should be concerning us in the first place.

For more recent coverage specifically on the ATHF case:

In the statute, "hoax device" is defined as an object that someone could "reasonably" believe to be an "infernal machine" intended to cause death, injury, or property damage by "fire or explosion." Assistant Attorney General John Grossman argues that the devices resembled bombs, and that this constitutes intent. The men face up to five years in prison if convicted.

However, Dr. Marc Siegel, an associate professor at the NYU School of Medicine and author of "False Alarm: The Truth About the Epidemic of Fear," warns that the word "reasonably" may be close to meaningless in this context.

While the "hoax device" argument might not hold up in court, TBS is still open to a civil case ...

"We need to realize that emotion is running amok here. The risk of terrorism is not zero, so it makes sense that we have a system in place for reacting to perceived threats. However, this kind of event makes it necessary to assess if we over-react routinely," Siegel says, "and what it costs us psychologically and financially." For one thing, he adds, "you can put a lot more effort into identifying the risk before you shut down the city."

Boston Mayor Thomas Menino isn't deterred.

In 2005, Siegel's book on fear, False Alarm: The Truth about the Epidemic of Fear, was adapted for... [ Read More (0.2k in body) ]

The Irony of Fear

The Royal Society recently provided access to an archive of papers published in the scientific academy's prestigious journal. Some 25 thousand scholarly works date from 1665 to the present day. Many notable scientific advancements are included in the archive, including, for example, Watson and Crick's discovery of DNA. This interesting data set was ripe for some visual tinkering. The database I used was put together by Brian Amento and Mike Yang of AT&T Labs.

The Author Distribution visualization displays papers chronologically. Paper titles radiate downward from the vertical midpoint at a 45 degree angle. Within a single year, papers are sorted alphabetically. The year a volume was published is shown, centered among it's respective block of papers. The size varies linearly by the number of number of papers published during that year's volume. Authors are shown radiating upwards from the vertical midpoint at a 45 degree angle. Their positions are computed by calculating the average position of the papers they authored. The size of the author's name reflects how prolific they were (linear relationship). Essentially, author names are "centered" above the time period they were active.

It's really interesting to explore these images! For example, the first section (1665-1710) has Edmond Halley (of Halley Comet fame), Isaac Newton, Antony van Leeuwenhoek (inventor of the microscope) and other famous scholars.

The Word Distribution visualization has the same visual characteristics as the author distribution (above). However, instead of authors, this visualization explores the distribution of words in publication titles. Word size is determined with a square root function, which helps dampen extremely common words (i.e. 'the' and 'of'). Only words used three or more times are shown. It's interesting to see how words evolve and fields like photography and electronics emerge.

Chris Harrison - Visualizing the Royal Society Archive

Almost two decades after the appearance of most of the classical texts on the subject, this book's fresh introduction to Graph Theory offers a reassessment of what are the theory's main fields, methods and results today. Viewed as a branch of pure mathematics, the theory of finite graphs is developed as a coherent subject in its own right, with its own unifying questions and methods. The book thus seeks to complement, not replace, the existing more algorithmic treatments of the subject.

This book can be used at various different levels. It contains all the standard basic material to be taught in a first undergraduate course, complete with detailed proofs and numerous illustrations. To help with the planning of such a course, it includes precise information on the logical dependence of results, including forward referencing.

Intended Audience:

For a graduate course, the book offers proofs of several more advanced results, most of which thus appear in a book for the first time. These proofs are described with as much care and detail as their simpler counterparts, often with an informal discussion of their underlying ideas complementing their rigorous step-by-step account.

To the professional mathematician, finally, the book affords an overview of graph theory as it stands today: with its typical questions and methods, its classic results, and some of those developments that have made this subject such an exciting area in recent years.

Graph Theory, Third Edition, by Reinhard Diestel

Some say that one of the main differences between science and philosophy is that science makes progress while philosophers go round in circles endlessly discussing the same questions.

Is Philosophy Progressive?

Five years ago, Steven Pinker ignited an academic firestorm with the best-selling book The Blank Slate: The Modern Denial of Human Nature, which argued that innate behavioural differences exist among individuals and between men and women.

The 52-year-old cognitive scientist is again challenging conventional wisdom with The Stuff of Thought, a book about language due out in September. He'll deliver a lecture in Toronto on the topic Wednesday, as part of 15th anniversary celebrations for the Canadian Institute for Advanced Research.

You know it's big when the book tour starts nine months in advance. He'll be at UCSB on February 2. He was in Toronto last night.

See also:

10 questions for Steven Pinker
How Steven Pinker Works

Of thought and metaphor