It turns out that there is a striking similarity between how the human brain determines what is going on in the outside world and the job of scientists. Good science involves formulating a hypothesis and testing whether this hypothesis is compatible with the scientist’s observations. Researchers in the Max Planck Institute for Brain Research in Frankfurt together with the University of Glasgow have shown that this is what the brain does as well. A study shows that it takes less effort for the brain to register predictable as compared to unpredictable images.

Alink and colleagues based this conclusion on the characteristics of responses in the primary visual cortex. It is known that the primary visual cortex is critical for vision and that responses in this brain area create a map of what we are currently looking at. Alink and colleagues, however, for the first time show that images induce smaller responses in this area when they are predictable. The implication of this finding is that the brain does not just sit and wait for visual signals to arrive. Instead, it actively tries to predict these signals and when it is right it is rewarded by being able to respond more efficiently. If it is wrong, massive responses are required to find out why it is wrong and to come up with better predictions.

Tom Henderson, aka Mathpunk on Twitter, is a mathematics lecturer at Portland State University and an improve comedian with the group The Light Finger Five. He edits mathpunk.net and is co-host of the podcast Math for Primates (with scientist and professional weightlifter graduate student and competitive weigh lifter Nick Horton). He received the Pandora Award (Bronze) from Chris DiBona, Open Source Program Manager for Google, for his participation in the game Superstruct.

Klint Finley: What does it mean to be a (or, rather THE) “mathpunk”?

Tom Henderson: Ha! Okay. When I was maybe 20 years old, my high school girlfriend was telling me about a punk band called “Green Dave.” I told her that I found punk to be totally unimpressive, because it was a musical genre that, near as I could tell, was founded upon not knowing how to play your instrument.

She set me straight. The point of punk, she said, was that ANYone could get the experience of being in a band, of performing in front of peers, of expressing yourself, without there being a prerequisite to participate.

This blew my mind, and it was that conversation that turned me from a nascent douchebag into a self-aware poser.

Later, a girlfriend who had honest-to-god Southern California punk credibility — this was the time that The Offspring was getting radio play so, what, she was probably most deep in the hardcore scene? — got me interested in the music, and explained to me that punks could be astronomers or Shakespeare devotees with no clash. (Pardon the pun.)

So, these things are tucked into my brain. Later, I move to Portland. I move to Portland with the extensive plan of “take math classes until head blows up, or degree achieved.”

This is the first serious long-term plan I’ve ever had. I figure, Shit, I’m a guy with long term plans now? I need to re-roll my character sheet. I start with appearance (self-aware poser), and ramp up the mathematical angle, to cobble together a philosophy of punk rock mathematics.

Read the rest of this entry »

Outlaw Biology was a DIY biology symposium held January 29-30 at UCLA. Here’s a list of workshops that may or may not have occurred:

1. Bioweathermap, Jason Bobe. With field-trips to the UCLA Arboretum and Hammer Museum (in cooperation with Machine Project

2. Learn to Design a DNA-based nanostructure using cadnano software, Philip Lukeman

3. Paint colorful microbes – luminescent, fluorescent, and pigmented – on do-it-yourself solid media. With a little time and luck, we’ll preserve the painted results in epoxy, like microbiological paintings in amber, Mackenzie Cowell

4. SKDB: Learn to use software tools for open source manufacturing and bioengineering, Bryan Bishop and Ben Lipkowitz

5. Use of Acinetobacter calcoaceticus strain ADP1 as a DIY bioengineering platform, David Metzgar

6. Ars Synthetica: Have an informed, ethical, and open dialogue on the emerging field of synthetic biology, Gaymon Bennett

7. Extract DNA from Strawberries, CSG Staff

8. Lactobacillus Plasmid Recovery and Visualization for fun and profit, Meredith L. Patterson

9. DIY Webcam Microscopy. Join us for a worldwide webcam hacking event and make your own 100x USB microscope for less than $10. We’ll provide the webcams and a live internet feed from other workshop locations across the world, from Bangalore to Australia. Find out more at diybio.org/ucam

10. Velolab, See the first Bicyclized Mobile Biology lab, Sam Starr

11. Learn about FBI Outreach: Promoting Responsible Research & Career Opportunities, Special Agent Edward You

12. Learn about LavaAmp: The Personal Thermal Cycler, Guido Núñez-Mujica and Joseph P. Jackson III

13. The HOX Gene Zodiac project. Learn about homeobox genes, body plans and the Chinese Zodiac, Victoria Vesna

Learn more at their web site.

(via Grinding)

Despite Fears of a Post-9/11 Drop, Most Science, Engineering Post-Grads Have Stayed

Most foreigners who came to the U.S. to earn doctorate degrees in science and engineering stayed on after graduation—at least until the recession began—refuting predictions that post-9/11 restrictions on immigrants or expanding opportunities in China and India would send more of them home.

Newly released data revealed that 62% of foreigners holding temporary visas who earned Ph.D.s in science and engineering at U.S. universities in 2002 were still in the U.S. in 2007, the latest year for which figures are available. Of those who graduated in 1997, 60% were still in the U.S. in 2007, according to the data compiled by the U.S. Energy Department’s Oak Ridge Institute for Science and Education for the National Science Foundation.

Foreigners account for about 40% of all science and engineering Ph.D. holders working in the U.S., and a larger fraction in engineering, math and computer fields. “Our ability to continue to attract and keep foreign scientists and engineers is critical to…increase investment in science and technology,” Oak Ridge analyst Michael Finn said.

Wall Street Journal: U.S. Keeps Foreign Ph.D.s

(via Beerken’s Blog)

the emerging science of human-microbe symbiosis has an even greater implication. “Human beings are not really individuals; they’re communities of organisms,” says McFall-Ngai. It’s not just that our bodies serve as a habitat for other organisms; it’s also that we function with them as a collective. As the profound interrelationship between humans and microbes becomes more apparent, the distinction between host and hosted has become both less clear and less important?—?together we operate as a constantly evolving man-microbe kibbutz. Which raises a startling implication: If being Homo sapiens through and through implied a certain authority over our corporeal selves, we are now forced to relinquish some of that control to our inner-dwelling microbes. Ironically, the human ingenuity that drives us to understand more about ourselves is revealing that we’re much less “human” than we once thought.

Seed: The Body Politic

(Thanks Social Fiction)

See also:

The BacterioSphere

Networks, Bacteria, and the Illusion of Control

There’s an interesting article in Wired about how scientists deal with data that conflicts with their expectations and whether biases in how the brain deals with contradictory information might influence scientific reasoning.

The piece is based on the work of Kevin Dunbar who combines the sociology of science with the cognitive neuroscience of scientific reasoning.

In other words, he’s trying to understand what scientists actually do to make their discoveries (rather than what they say they do, or what they say they should do) and whether there are specific features of the way the brain handles reasoning that might encourage these practices.

One of his main findings is that when experimental results appear that can’t be explained, they’re often discounted as being useless. The researchers might say that the experiment was designed badly, the equipment faulty, and so on.

Mind Hacks: Dealing with data of the damned

The Wired article in question is also worth reading.

Prof Roger Wotton, from University College London, found that flight would be impossible for angels portrayed with arms and bird-like feathered wings.

“Even a cursory examination of the evidence in representational arts shows that angels and cherubs cannot take off and cannot use powered flight,” said Prof Wotton. “And even if they used gliding flight, they would need to be exposed to very high wind velocities at take off – such high winds that they would be blown away and have no need for wings.

“Interestingly, the artist Giotto showed one angel with a rigid ‘mono-wing’ which could be an adaptation for gliding flight. But if they do just glide, how are the wings folded, unfolded and held rigid?”

Telegraph: Angels can’t fly, scientist says

(via Swadeshine)

In 2009, researchers at the California Academy of Sciences added 94 new relatives to our family tree. The new species include 65 arthropods, 14 plants, eight fishes, five sea slugs, one coral, and one fossil mammal. They were described by two dozen Academy scientists along with several dozen international collaborators.

Proving that there are still plenty of places to explore and things to discover on Earth, the scientists made their finds over four continents and two oceans, climbed to the tops of mountains and descended to the bottom of the sea, looked in their owns backyards (Yosemite National Park) and on the other side of the world (Yunnan Province, China). Their results, published in 29 different scientific papers, add to the record of life on Earth and will inform future studies on biodiversity, evolution, and conservation.

PhysOrg: Nearly 100 new species described by California Academy of Sciences in 2009

(via Social Physicist)

Sometimes mutating is bad for you:

Scientists have unlocked the entire genetic code of two of the most common cancers – skin and lung – a move they say could revolutionise cancer care.

Not only will the cancer maps pave the way for blood tests to spot tumours far earlier, they will also yield new drug targets, says the Wellcome Trust team. [...]

The lung cancer DNA code had more than 23,000 errors largely triggered by cigarette smoke exposure.

From this, the experts estimate a typical smoker acquires one new mutation for every 15 cigarettes they smoke.

Although many of these mutations will be harmless, some will trigger cancer.

BBC: Scientists crack ‘entire genetic code’ of cancer

(via Social Physicist)

When doctors disagree with each other, they usually couch their criticisms in careful, measured language. In the past few months, however, open conflict has broken out among the upper echelons of US psychiatry. The focus of discord is a volume called the Diagnostic and Statistical Manual of Mental Disorders, or DSM, which psychiatrists turn to when diagnosing the distressed individuals who turn up at their offices seeking help. Regularly referred to as the profession’s bible, the DSM is in the midst of a major rewrite, and feelings are running high.

Two eminent retired psychiatrists are warning that the revision process is fatally flawed. They say the new manual, to be known as DSM-V, will extend definitions of mental illnesses so broadly that tens of millions of people will be given unnecessary and risky drugs. Leaders of the American Psychiatric Association (APA), which publishes the manual, have shot back, accusing the pair of being motivated by their own financial interests – a charge they deny. The row is set to come to a head next month when the proposed changes will be published online. For a profession that exists to soothe human troubles, it’s incendiary stuff. [...]

Some of the most acrimonious arguments stem from worries about the pharmaceutical industry’s influence over psychiatry. This has led to the spotlight being turned on the financial ties of those in charge of revising the manual, and has made any diagnostic changes that could expand the use of drugs especially controversial. “I think the DSM represents a lightning rod for all kinds of groups,” says David Kupfer of the University of Pittsburgh, Pennsylvania, who heads the task force appointed by the APA to produce the revised manual.

New Scientist: Psychiatry’s civil war

(via HipGnosis23)

Invetech, an innovator in new product development and custom automation for the biomedical, industrial and consumer markets, today announced that it has delivered the world’s first production model 3D bio-printer to Organovo, developers of the proprietary NovoGen bioprinting technology. Organovo will supply the units to research institutions investigating human tissue repair and organ replacement.

Dr. Fred Davis, president of Invetech, which has offices in San Diego and Melbourne, said, “Building human organs cell-by-cell was considered science fiction not that long ago. Through this clever combination of technology and science we have helped Organovo develop an instrument that will improve people’s lives, making the regenerative medicine that Organovo provides accessible to people around the world.”

R&D Magazine: First commercial 3-D bio-printer makes human tissue and organs

(Thanks James K!)

Underwater footage reveals that the creatures scoop up halved coconut shells before scampering away with them so they can later use them as shelters.

Writing in the journal Current Biology, the team says it is the first example of tool use in octopuses.

One of the researchers, Dr Julian Finn from Australia’s Museum Victoria, told BBC News: “I almost drowned laughing when I saw this the first time.”

He added: “I could tell it was going to do something, but I didn’t expect this – I didn’t expect it would pick up the shell and run away with it.”

BBC: Octopus snatches coconut and runs

(Thanks Cat Vincent)

Today, Alex Feigel at the Soreq Nuclear Research Center, a government lab in Yavne Israel, suggests an entirely new way to modify the momentum of the quantum vacuum and how this can be exploited to generate propulsion.

Feigel’s approach combines two well-established ideas. The first is the Lorentz force experienced by a charged particle in electric and magnetic fields that are crossed. The second is the magnetoelectric effect–the phenomenon in which an external magnetic field induces a polarised internal electric field in certain materials and vice versa.

Technology Review: A Blueprint for a Quantum Propulsion Machine

(via HiggsBoson23)

The site, which straddles 30,000 square meters of ocean floor off the southern Peloponnese, is believed to have been consumed by the sea around 1000 BC. Although discovered by a British oceanographer some 40 years ago, it was only this year that marine archaeologists, aided by digital technology, were able to properly survey the ruins.

What they found surpassed all expectations. Thanks to shifting sands and the settlement’s enclosure in a protected bay, the exploration revealed a world of buildings, courtyards, main streets, rock-cut tombs and religious structures. In addition, the seabed was replete with thousands of shards of pottery.

Guardian: Lost Greek city that may have inspired Atlantis myth gives up secrets

(via Paul Bingman)

There are many speculative locations of Atlantis.

I have previously linked to the Collina-Girard’s theory (See: Spartel Bank hypothesis on Wikipedia) and Robert Sarmast’s theory (see Near Cyprus hypothesis on Wikipedia).

This seems more legitimate than these others.

(*sigh*, Mac would have loved to have read about this… I found that Cyprus theory link on his blog…)

Wired: 35 Years of the World’s Best Microscope Photography

Spending on science in the developing world grew at three times the rate of that of richer countries between 2002 and 2007, according to figures released yesterday (6 October) by the UNESCO Institute for Statistics (UIS).

And the number of researchers in developing countries jumped from 1.8 million to 2.7 million over the same period.

SciDev: Poor countries spending more on science

(via Beerkens)

Get ready for chaos:

Two sunspots are visible on our star’s face for the first time in more than a year, possibly ending an unexpected lull in solar activity.

Solar flares rise and fall on an 11-year cycle, so scientists thought sunspot activity would pick up some time in 2008. It didn’t. And this year has been quiet, too. No sunspots have been visible on the sun for 80 percent of the days this year.

Sunspot activity is correlated with the total amount of energy we receive from the sun. If the sun’s activity were to change remarkably, it would have an influence on global climate. So, in the context of climate change, the fact that the current solar minimum has been the longest and deepest in more than a century has been of special interest.

Wired Science: The Sun Gets Its Spots (Back)

See also: Telluro-magnetic conspiracy toward the Sun

Engineering studies, or lessons on how products are designed and built, have the potential to bolster student engagement and understanding in math and science, despite the topic’s relatively modest and undefined presence in the nation’s schools.

That’s the conclusion, outlined in a study unveiled today, of an expert committee charged with evaluating the status of engineering lessons in K-12 schools and judging their effectiveness.

Education Week: Panel Urges Engineering Be Added to Curriculum

(via Appropedia)

Christopher Wall, who was born with his heart on the outside of his chest, recently celebrated his 34th birthday. Amazing.

Boy Born With Heart Outside Body Defies Odds

(via What a Wonderful Place to Be)

High-throughput sequencing has turned biologists into voracious genome readers, enabling them to scan millions of DNA letters, or bases, per hour. When revising a genome, however, they struggle, suffering from serious writer’s block, exacerbated by outdated cell programming technology. Labs get bogged down with particular DNA sentences, tinkering at times with subsections of a single gene ad nauseam before moving along to the next one.

A team has finally overcome this obstacle by developing a new cell programming method called Multiplex Automated Genome Engineering (MAGE). Published online in Nature on July 26, the platform promises to give biotechnology, in particular synthetic biology, a powerful boost.

Led by a pair of researchers in the lab of Harvard Medical School Professor of Genetics George Church, the team rapidly refined the design of a bacterium by editing multiple genes in parallel instead of targeting one gene at a time. They transformed self-serving E. coli cells into efficient factories that produce a desired compound, accomplishing in just three days a feat that would take most biotech companies months or years.

PhysOrg: Researchers rapidly turn bacteria into biotech factories

(Thanks Nova)

US researchers have created ‘bacterial computers’ with the potential to solve complicated mathematics problems. The findings of the research demonstrate that computing in living cells is feasible, opening the door to a number of applications. The second-generation bacterial computers illustrate the feasibility of extending the approach to other computationally challenging math problems. [...]

The Hamiltonian Path Problem asks whether there is a route in a network from a beginning node to an ending node, visiting each node exactly once. The student and faculty researchers modified the genetic circuitry of the bacteria to enable them to find a Hamiltonian path in a three-node graph. Bacteria that successfully solved the problem reported their success by fluorescing both red and green, resulting in yellow colonies.

Science Daily: ‘Bacterial Computers’: Genetically Engineered Bacteria Have Potential To Solve Complicated Mathematical Problems

(via OVO)

The labs listed below are WWW-based engineering/science experiments developed for beginning science and engineering students. The objective of the course and the virtual laboratory is to introduce students to experimentation, problem solving, data gathering, and scientific interpretation early in their careers–perhaps as high school seniors or college freshmen. Ordinarily this exposure would be offered to students in their junior or senior year in a design lab.

The experiments which follow are written in JAVA and are fully interactive. As such, they require that the student access them using the Web browser Microsoft Internet Explorer 3.0 (or later) operating within a 32-bit operating system (e.g., Windows 95, Windows NT, Unix) and with a display capability of at least 256 colors. (Netscape 3.01 (or later) may also be used with these modules. But, within some operating systems, this browser introduces idiosyncracies in the modules’ operation. Earlier versions of Netscape, including 3.0, will not work.) Further, within these experiments are MPEG movie sequences which may require additional software–an MPEG viewer, e.g., VMPEGWIN which is available as demonstration shareware (sufficient for these experiments). This is a project under development. Expect modifications ( and additions and removals).

Johns Hopkins University: Virtual Laboratory

Wired’s overview of contemporary mad scientists:

Daryl Bem – Precognition
Edward Kelly – Disembodied consciousness (“Remote Viewing”?)
Eric Lerner – Origin of the cosmos
Rollin McCraty – Atmospheric effects on physiology
Garret Moddel – Telekinesis
Peter Sturrock – UFOs

Wired: The Truth Is Out There, and the Nation’s Maddest Scientists Are After It

When you’re on a diet, deciding to skip your favorite calorie-laden foods and eat something healthier takes a whole lot of self-control–an ability that seems to come easier to some of us than others. Now, scientists from the California Institute of Technology (Caltech) have uncovered differences in the brains of people who are able to exercise self-control versus those who find it almost impossible.

The key? While everyone uses the same single area of the brain to make these sorts of value-laden decisions, a second brain region modulates the activity of the first region in people with good self-control, allowing them to weigh more abstract factors–healthiness, for example–in addition to basic desires such as taste to make a better overall choice.

These findings not only provide insight into the interplay between self-control and decisionmaking in dieters, but may explain how we make any number of decisions that require some degree of willpower. [...]

The next step, the researchers say, is to come up with ways to engage the DLPFC in the decisions made by people with poor self-control under normal conditions. For instance, Hare says, it might be possible to kick the DLPFC into gear by making the health qualities of foods more salient for people, rather than asking them to make the effort to judge a food’s health benefits on their own. “If we highlight the fact that ice cream is unhealthy just before we offer it,” he notes, “maybe we can reduce its value in advance, give the person a head start to making a better decision.”

Science Daily: Mechanisms Of Self-control Pinpointed In Brain

(via OVO)

“Taking a hint from the text comparison methods used to detect plagiarism in books, college papers and computer programs, University of California, Berkeley, researchers have developed an improved method for comparing whole genome sequences. With nearly a thousand genomes partly or fully sequenced, scientists are jumping on comparative genomics as a way to construct evolutionary trees, trace disease susceptibility in populations, and even track down people’s ancestry.

To date, the most common techniques have relied on comparing a limited number of highly conserved genes – no more than a couple dozen – in organisms that have all these genes in common. The new method can be used to compare even distantly related organisms or organisms with genomes of vastly different sizes and diversity, and can compare the entire genome, not just a selected small fraction of the gene-containing portion known to code for proteins, which in the human genome is only 1 percent of the DNA.

The technique produces groupings of organisms largely consistent with current groupings, but with some interesting discrepancies, according to Sung-Hou Kim, professor of chemistry at UC Berkeley and faculty researcher at Lawrence Berkeley National Laboratory. However, the relative positions of the groups in the family tree – that is, how recently these groups evolved – are quite different from those based on conventional gene alignment methods.The computational results have surprised scientists in being able to classify some bacteria and viruses that until now were enigmatic. The technique, which employs feature frequency profiles (FFP), is described in a paper to appear this week in the early online edition of the journal Proceedings of the National Academy of Sciences.”

(via UC Berkley News. Thanks Josh!)