the geebus science & health

memories

2010-06-07T17:54:00.000-07:00

the daily dish

Spring-boarding off a series of articles by William Saletan, Jonah Lehrer reveals the true nature or remembering:

We like to think of our memories as being immutable impressions, somehow separate from the act of remembering them. But they aren't. A memory is only as real as the last time you remembered it. The more you remember something, the less accurate the memory becomes. The larger moral of the experiment is that memory is a ceaseless process, not a repository of inert information. It shows us that every time we remember anything, the neuronal structure of the memory is delicately transformed, or reconsolidated. And that is why it's so easy to convince naive subjects that they met Bugs Bunny at Disneyland.

Video above via David Craney who provides a false memory test and digs further into the research.

When in Rome

2010-02-08T17:17:00.000-08:00

HuffPo

Two cardiac-arrest-themed fast food joints on opposite sides of country are locked in a federal lawsuit over restaurant themes.

Heart Attack Grill in Chandler, Ariz. has sued Heart Stoppers Sports Grill in Delray Beach, Fla. Heart Attack's owners argue that Heart Stoppers is too similar to their own restaurant.

Both feature monstrously fatty menus, scantily-clad "nurse" waitresses, and signage with an EKG design. At both restaurants, customers over 350 lbs. eat for free. At Heart Attack Grill, customers who finish the biggest burger on the menu get wheeled out of the restaurant in a wheelchair.

According to Heart Attack's owners, the proprietors of Heart Stoppers were in talks to open a franchise of Heart Attack Grill before they opened their own restaurant in December.

Lawyers for Heart Stoppers say the restaurants are actually different. The Wall Street Journal reports:

But a lawyer for Heart Stoppers claimed the restaurants were different. "It's not the same concept," Eric Lee told Slashfood. "The Arizona restaurant's concept is high-caloric food that is bad for you and will basically kill you . . . My guys have a restaurant that is medically themed . . . My clients' restaurant seems more like an actual medical facility."
Uh, really? A medical facility? Apparently so. Heart Stoppers is, according to Slashfood, decorated with defibrillators, dialysis machines and other medical equipment, has tables that resemble wheelchairs.

hide complexity

2009-12-07T13:58:00.000-08:00

Murray, How the Leopard Gets Its Spots

Axelrod & Cohen, Harnessing Complexity: Organizational Implications of a Scientific Frontier, pp. 101-

Philip Ball, The Self-Made Tapestry

Shigeru Kondo, How Animals Get Their Skin Patterns ...

Shigeru Kondo, The reaction-diffusion system: a mechanism for autonomous pattern formation in the animal skin

Animal Hide-And-Seek jk;)

Hořava Gravity

2009-12-02T11:26:00.000-08:00

From wikipedia:

Hořava-Lifshitz gravity (or Hořava gravity) is a theory of quantum gravity proposed by Petr Hořava in 2009.^[1] It solves the problem of different concepts of time in quantum field theory and general relativity by treating the quantum concept as the more fundamental so that space and time are not equivalent (anisotropic). The relativistic concept of time with its Lorentz invariance emerges at large distances. The theory relies on the theory of foliations to produce its causal structure. It is related to topologically massive gravity and the Cotton tensor. It is a possible UV completion of general relativity. The novelty of this approach, compared to previous approaches to quantum gravity such as Loop quantum gravity, is that it uses concepts from condensed matter physicssuch as quantum critical phenomena. Hořava's initial formulation was found to have side-effects such as predicting very different results for a spherical Sun compared to a slightly non-spherical Sun, so others have modified the theory. It still has problems.^[2]

The Reference Frame 5.18.2009

SciAm 11.2009

The Reference Frame comments on the SciAm article

on Scribd ArXiv0901.3775v2

In Shift, Cancer Society Has Concerns on Screenings - NYTimes.com

2009-10-20T21:37:00.000-07:00

In Shift, Cancer Society Has Concerns on Screenings - NYTimes.com:

The American Cancer Society, which has long been a staunch defender of most cancer screening, is now saying that the benefits of detecting many cancers, especially breast and prostate, have been overstated.

"It is quietly working on a message, to put on its Web site early next year, to emphasize that screening for breast and prostate cancer and certain other cancers can come with a real risk of overtreating many small cancers while missing cancers that are deadly.

“We don’t want people to panic,” said Dr. Otis Brawley, chief medical officer of the cancer society. “But I’m admitting that American medicine has overpromised when it comes to screening. The advantages to screening have been exaggerated.”

Prostate cancer screening has long been problematic. The cancer society, which with more than two million volunteers is one of the nation’s largest voluntary health agencies, does not advocate testing for all men. And many researchers point out that the PSA prostate cancer screening test has not been shown to prevent prostate cancer deaths.

There has been much less public debate about mammograms. Studies from the 1960s to the 1980s found that they reduced the death rate from breast cancer by up to 20 percent.

The cancer society’s decision to reconsider its message about the risks as well as potential benefits of screening was spurred in part by an analysis published Wednesday in The Journal of the American Medical Association, Dr. Brawley said."

In it, researchers report a 40 percent increase in breast cancer diagnoses and a near doubling of early stage cancers, but just a 10 percent decline in cancers that have spread beyond the breast to the lymph nodes or elsewhere in the body. With prostate cancer, the situation is similar, the researchers report.

If breast and prostate cancer screening really fulfilled their promise, the researchers note, cancers that once were found late, when they were often incurable, would now be found early, when they could be cured. A large increase in early cancers would be balanced by a commensurate decline in late-stage cancers. That is what happened with screening for colon and cervical cancers. But not with breast and prostate cancer.

Still, the researchers and others say, they do not think all screening will — or should — go away. Instead, they say that when people make a decision about being screened, they should understand what is known about the risks and benefits.

For now, those risks are not emphasized in the cancer society’s mammogram message which states that a mammogram is “one of the best things a woman can do to protect her health.”

Dr. Brawley says mammograms can prevent some cancer deaths. However, he says, “If a woman says, ‘I don’t want it,’ I would not think badly of her but I would like her to get it.”

But some, like Colin Begg, a biostatistician at Memorial Sloan-Kettering Cancer Center in New York, worry that the increased discussion of screening’s risks is going to confuse the public and make people turn away from screening, mammography in particular.

“I am concerned that the complex view of a changing landscape will be distilled by the public into yet another ‘screening does not work’ headline,” Dr. Begg said. “The fact that population screening is no panacea does not mean that it is useless,” he added.

The new analysis — by Dr. Laura Esserman, a professor of surgery and radiology at the University of California, San Francisco, and director of the Carol Frank Buck Breast Care Center there, and Dr. Ian Thompson, professor and chairman of the department of urology at The University of Texas Health Science Center, San Antonio — finds that prostate cancer screening and breast cancer screening are not so different.

Both have a problem that runs counter to everything people have been told about cancer: They are finding cancers that do not need to be found because they would never spread and kill or even be noticed if left alone. That has led to a huge increase in cancer diagnoses because, without screening, those innocuous cancers would go undetected.

At the same time, both screening tests are not making much of a dent in the number of cancers that are deadly. That may be because many lethal breast cancers grow so fast they spring up between mammograms. And the deadly prostate ones have already spread at the time of cancer screening. The dilemma for breast and prostate screening is that it is not usually clear which tumors need aggressive treatment and which can be left alone. And one reason that is not clear, some say, is that studying it has not been much of a priority.

“The issue here is, as we look at cancer medicine over the last 35 or 40 years, we have always worked to treat cancer or to find cancer early,” Dr. Brawley said. “And we never sat back and actually thought, ‘Are we treating the cancers that need to be treated?’ ”

The very idea that some cancers are not dangerous and some might actually go away on their own can be hard to swallow, researchers say.

“It is so counterintuitive that it raises debate every time it comes up and every time it has been observed,” said Dr. Barnett Kramer, associate director for disease prevention at the National Institutes of Health.

It was first raised as a theoretical possibility in the 1970s, Dr. Kramer said. Then it was documented in a rare pediatric cancer, but was dismissed as something peculiar to that cancer. Then it was discovered in common cancers as well, but it is still not always accepted or appreciated, he said.

But finding those insignificant cancers is the reason the breast and prostate cancer rates soared when screening was introduced, Dr. Kramer said. And those cancers, he said, are the reason screening has the problem called overdiagnosis — labeling innocuous tumors cancer and treating them as though they could be lethal when in fact they are not dangerous.

“Overdiagnosis is pure, unadulterated harm,” he said.

Dr. Peter Albertsen, chief and program director of the urology division at the University of Connecticut Health Center, said that had not been an easy message to get across. “Politically, it’s almost unacceptable,” Dr. Albertsen said. “If you question overdiagnosis in breast cancer, you are against women. If you question overdiagnosis in prostate cancer, you are against men.”

Dr. Esserman hopes that as research continues on how to advance beyond screening, distinguishing innocuous tumors from dangerous ones, people will be more realistic about what screening can do.

“Someone may say, ‘I don’t want to be screened’ ” she said. “Another person may say, ‘Of course I want to be screened.’ Just like everything in medicine, there is no free lunch. For every intervention, there are complications and problems.”

McDensity

2009-10-18T16:09:00.000-07:00

strange maps via the daily dish

The contiguous United States, visualized by distance to the nearest McDonald's

There are over 13,000 McDonald’s restaurants in the US, or about 1 for every 23,000 Americans. But even market penetration this advanced doesn’t mean that McDonald’s is everywhere. Somewhere in South Dakota is the McFarthest Spot, the place in the US geographically most removed from the nearest McD’s (*). If you started out from this location, a few miles north of State Highway 20 (which runs latitudinally between Highways 73 in the west and 65 in the east), you’d have to drive 145 miles to get your Big Mac (if you could fly, however, it’d be only 107 miles).

Mandelbrot Interview

2009-10-05T18:20:00.000-07:00

FT.com c/o @valdiskrebs

Jonah Lehrer

2009-06-05T11:19:00.000-07:00

fora.tv

. . .. ... ..... oOo ..... ... .. . .

~35:00 metacognition

Temporal Difference Learning

Prediction Error Learning & etc.

2009.02.05 Lehrer on Colbert

The Colbert Report

Mon - Thurs 11:30pm / 10:30c

Jonah Lehrer

colbertnation.com

Colbert Report Full Episodes

Political Humor

Keyboard Cat

Barabási; Strogatz

2009-06-01T11:32:00.000-07:00

The Seed Salon
Albert-László Barabási + James Fowler

Barabási mathematically describes networks in the World Wide Web, the internet, the human body, and society at large. Fowler seeks to identify the social and biological links that define us as humans. In this video Salon, Barabási and Fowler discuss contagion and the Obama campaign, debate the natural selection of robustness, and ask: Is society turning inward?

oOo

Mathematician Steven Strogatz shows how flocks of creatures (like birds, fireflies and fish) manage to synchronize and act as a unit -- when no one's giving orders. The powerful tendency extends into the realm of objects, too.

Bugs in our Moral Code

2009-05-22T15:03:00.000-07:00

TED

Behavioral economist Dan Ariely studies the bugs in our moral code: the hidden reasons we think it's OK to cheat or steal (sometimes). Clever studies help make his point that we're predictably irrational -- and can be influenced in ways we can't grasp.

Ron Eglash on African Fractals

2009-05-21T11:10:00.000-07:00

TED

on Ron Eglash's website

on time

2009-05-13T16:44:00.000-07:00

Julian Barbour

The Nature of Time

Perimeter Institute 9.28.2008

. . .. ... ..... ... .. . .

diavlog with philosophy professor 5.1.2009

. . .. ... ..... ... .. . .

Leap Seconds 12.6.2003
- Time Scales

Mach's Principal

The End of Time

Not Probably

2009-05-11T15:06:00.000-07:00

The Daily Show With Jon Stewart

M - Th 11p / 10c

Large Hadron Collider

thedailyshow.com

Daily Show
Full Episodes

Economic Crisis

Political Humor

Rough Gardening for Bob

2009-04-29T13:16:00.000-07:00

wright / roughgarden

Roughgarden, The Genial Gene

11.5.2006 tsn Roughgarden, Dawkins, Ayala, Porco

Fractal Quantum Gravity

2009-04-01T17:41:00.000-07:00

NewScientist.com

re T.N. Palmer, Invariant Set Hypothesis (2008.12.05)

* * * *

What has been missing, [Palmer] argues, are some key ideas from an area of science that most quantum physicists have ignored: the science of fractals, those intricate patterns found in everything from fractured surfaces to oceanic flows (see What is a fractal?).

Take the mathematics of fractals into account, says Palmer, and the long-standing puzzles of quantum theory may be much easier to understand. They might even dissolve away.

It is an argument that is drawing attention from physicists around the world. "His approach is very interesting and refreshingly different," says physicist Robert Spekkens of the Perimeter Institute for Theoretical Physics in Waterloo, Canada. "He's not just trying to reinterpret the usual quantum formalism, but actually to derive it from something deeper."

* * * *

Palmer believes his work shows it is possible that Einstein and Bohr may have been emphasising different aspects of the same subtle physics. "My hypothesis is motivated by two concepts that wouldn't have been known to the founding fathers of quantum theory," he says: black holes and fractals.

Palmer's ideas begin with gravity. The force that makes apples fall and holds planets in their orbit is also the only fundamental physical process capable of destroying information. It works like this: the hot gas and plasma making up a star contain an enormous amount of information locked in the atomic states of a huge number of particles. If the star collapses under its own gravity to form a black hole, most of the atoms are sucked in, resulting in almost all of that detailed information vanishing. Instead, the black hole can be described completely using just three quantities - its mass, angular momentum and electric charge.

Many physicists accept this view, but Palmer thinks they haven't pursued its implications far enough. As a system loses information, the number of states you need to describe it diminishes. Wait long enough and you will find that the system reaches a point where no more states can be lost. In mathematical terms, this special subset of states is known as an invariant set. Once a state lies in this subset, it stays in it forever.

A simple way of thinking about it is to imagine a swinging pendulum that slows down due to friction before eventually coming to a complete standstill. Here the invariant set is the one that describes the pendulum at rest.

Because black holes destroy information, Palmer suggests that the universe has an invariant set too, though it is far more complicated than the pendulum.

Complex systems are affected by chaos, which means that their behaviour can be influenced greatly by tiny changes. According to mathematics,

the invariant set of a chaotic system is a fractal.

IEEE Spectrum: Electroporation "Knife" for Cancer

2009-02-04T23:42:00.000-08:00

IEEE Spectrum: Electroporation "Knife" for Cancer

4 February 2009—Electroporation, a technique that microbiologists have long used experimentally to temporarily punch holes in cell membranes and ferry drugs or genes into them, may yield new benefits for cancer treatment, according to medical-device firm AngioDynamics, in Queensbury, N.Y. Last month, the company showed off an electroporation device that it claims can kill cancerous tumor cells with remarkable specificity while inflicting little or no damage on surrounding structures and causing no pain for the patient.

Such claims, if they hold up, would have a tremendous impact on a cancer surgery technique called tumor ablation, in which doctors rely on either chemical treatments or an array of techniques that heat up or cool down the tumor tissue until it succumbs. Because they kill with temperature, these therapies affect all tissue indiscriminately, wiping out blood vessels along with the cancer cells and potentially causing bleeding. Electroporation, on the other hand, does not produce enough heat to disrupt nearby tissue.

“Most procedures take a soft egg and boil it,” says Stephen Kee, a radiologist at the University of California at Los Angeles Medical Center, who has been testing the device with guidance and funding from AngioDynamics. “To us, the real Achilles’ heel of ablation techniques is the destruction of blood vessels.”

When tumors abut especially large blood vessels, another problem arises for thermal ablation, says Kee. Radiologists call it the heat sink effect. The flow of blood provides convection to the area, cooling it substantially, and it becomes more difficult to maintain temperatures that thoroughly and consistently ablate the tissue. AngioDynamics’ device, the NanoKnife, might circumvent this problem all together.

The NanoKnife delivers quick bursts of energy through a set of electrodes inserted into and around the tumor. The pulses can last up to 100 microseconds and create an electrical field of up to 3000 volts per centimeter. A cell within range of the electric field will form pores in its fatty membrane, allowing ions to rush through. When electroporation is performed with a lower voltage than the NanoKnife delivers, and with single pulses instead of a train of pulses, the pores will eventually close as the electric potential of the cell stabilizes. Microbiologists have used this kind of reversible electroporation, among many other things, to transport genetic material into stem cells. When exposed to higher voltages and longer pulse duration, however, the pores in the cell membrane remain open and cause the cell to initiate a programmed suicide, known as apoptosis.

The electroporator works with both unipolar and up to six bipolar electrodes. Proper placement largely determines how successful the ablation will be, especially with the bipolar electrodes, which must be spaced correctly in order to produce a spherical electrical field. Complicating things further is the fact that the conductivity of tissue varies from organ to organ.

Mark Ortiz, the vice president of business development for AngioDynamics, says that the company is working on software that would standardize a treatment-planning protocol. He projects that medical imaging will provide information on tissue type and tumor dimension that the software will then use to automatically produce a scheme for placing electrodes and what generator settings to use.

The impact that irreversible electroporation has on blood vessels is still being researched. Studies show that they remain structurally intact, but it’s not yet clear how much damage the blood vessels endure. A study published in 2007 in Technology in Cancer Research and Treatment found that the procedure killed a large proportion of vascular smooth muscle cells—cells that line the walls of blood vessels and cause them to contract—when directly applied to the carotid artery. But the study also found that the structures that connect these cells and form the basic architecture of the vessels remained intact.

To date, the safety of the device has been shown through the experience of only a handful of patients. The NanoKnife has already been approved in the United States for use in the ablation of soft tissue, and AngioDynamics has installed prototypes in 17 medical centers around the world, 5 of which are actively using it. The device has been tested so far on 37 patients.

Ken Thomson, a radiologist at Alfred Hospital, in Melbourne, Australia, has used the NanoKnife to destroy kidney and lung tumors. He says that the patients who will benefit most from this device are those whose tumors have snuggled up next to vital blood vessels or airways. In these cases, the risks of attacking the tissue with heat are high, and electroporation provides a new alternative. Thomson has applied the technique to at least two patients whom he says would never be candidates for thermal ablation, and he has watched their tumors recede with only a Band-Aid to show for it.

“It’s just an amazing concept that you can do this,” he marvels. “There’s nothing else that will do this.”

Though electroporation provides a new alternative, doctors are having some success with thermal ablation, too. Francesco Garbagnati, the director of radiology at the National Cancer Institute of Milan, specializes in radio-frequency thermal ablation and has been using low-wattage and very thin electrodes to work on blood-vessel-rich parts of the liver. He is skeptical of electroporation. “We are having very good results around blood vessels,” he says, adding, “I don’t think [electroporation] could solve this problem.”

Daniel Tammet on Letterman

2009-01-28T11:41:00.000-08:00

Wolfram Blog : Quick-Starting Mathematica with Palettes

2009-01-21T15:39:00.000-08:00

Wolfram Blog : Quick-Starting Mathematica with Palettes

I have taught collegiate mathematics for more than 20 years and have used Mathematica for 15 or so of these years to explore, learn, and teach. For the last eight years Mathematica has been my primary tool to write all of my exams, handouts, letters, reports, papers, presentations, and even a complete electronic textbook. New features introduced recently have been revolutionary in the teaching and learning environment and make possible the creation of materials that integrate text, typeset mathematics, and interactive figures, which can be created efficiently and used effectively in ways not possible with other software tools.

For faculty and students to benefit from using Mathematica in the teaching and learning process, they must be able to use Mathematica sufficiently well to remain focused on course concepts and not become frustrated by the technology. Without question, the main challenge I face teaching new users how to use Mathematica is helping them master the task of creating syntactically correct commands, followed closely by the challenge of teaching how to use Mathematica to write rich documents that combine text, typeset mathematics, and figures.

When the use of technology gets in the way of the teaching, learning, and writing about content, which should remain the focus of academic learning, then all involved in the teaching and learning process experience frustration! If enough example commands are provided, if the ways of Mathematica are carefully explained, and if patient help is readily available, then some new users are able work their way up the learning curve and reach a point where they can focus on the subject matter and are able to comfortably use Mathematica to explore, learn, teach, and write about the concepts. Members of this group are often able to independently deepen their understanding and use of Mathematica by relying on the Wolfram Mathematica Documentation Center and other resources; but not enough new users reach this level of Mathematica knowledge and thus do not experience firsthand the marvelous capabilities of Mathematica to explore, investigate, learn, teach, and write about interesting ideas!

What can be done to support new users as they learn Mathematica? What can be done for the new user who begins using Mathematica and has no conceptual framework of the types of basic commands available in Mathematica, and who doesn’t know what their names are or what their required and optional arguments are? The new Basic Math Assistant palette in Mathematica 7 can create templates for hundreds of commands, such as the Plot example shown below, with a few clicks of the mouse. The yellow boxed placeholders can be filled in as needed and the command evaluated by clicking the Enter button on the Basic Math Assistant palette. No syntax memorization required! The basic Mathematica commands on the palette are grouped together to help a user build a mental understanding of the different types of basic commands available, including mathematical functions, algebra commands, calculus commands, matrix commands, table/list/vector commands, 2D plot commands, and 3D plot commands.

{y min,y max}]" title="Plot[function,{var,min,max},PlotRange->{y min,y max}]" width="385" height="19">

Some people master and memorize precise command syntax quickly while others do not, and whether or not they do is certainly not related to their intelligence or inquisitiveness. Why should memorization of command names and syntax be the key that unlocks the application of Mathematica to the exploration, learning, and teaching of interesting ideas? If new users have difficulty memorizing command names, required arguments, optional arguments, and syntax structures, can you imagine the frustration they would experience when using Mathematica to create a simple plot displaying the graph of the sine function as a red curve, a phase shifted sine function as a blue curve, and tick marks on the horizontal axis Π/4 units apart and 1/2 unit apart on the vertical axis for two periods of the sine function?

What can be done for the teacher who may want to create an interactive plot based on the figure above during an actual class session? Even if we assume the instructor had everything memorized and was fast at the keyboard, this sort of command is a bit too much to expect most teaching faculty to enter “on the spot” in a classroom setting. If they are teaching with an interactive whiteboard, creating such a visual would mean leaving the whiteboard and resorting to a nearby physical keyboard—not a good use of interactive whiteboard technology. Wouldn’t it be handy if the previous figure could be created quickly without needing to remember every little detail, using only a pointing device, and then made interactive with just a few more clicks? This type of command can be created completely using only a pointing device and the new Basic Math Assistant palette in Mathematica 7!

Create a template using the Basic Math Assistant palette:

{Subscript[color, 1],Subscript[color, 2]},Ticks->{Range[x start,x end,increment],Range[y start,y end,increment]}]" title="Plot[{Subscript[function, 1],Subscript[function, 2]},{var,min,max},PlotStyle->{Subscript[color, 1],Subscript[color, 2]},Ticks->{Range[x start,x end,increment],Range[y start,y end,increment]}]" width="283" height="89">

Fill in the blanks.

Fill in each yellow boxed placeholder by either typing or clicking buttons on the Basic Math Assistant palette and click the Enter button to create the figure.

{Red,Blue},Ticks->{Range[-2\[Pi],2\[Pi],\[Pi]/4],Range[-1,1,1/2]}]" title="In[1]:=Plot[{Sin[x],Sin[x-\[Pi]/4]},{x,-2\[Pi],2\[Pi]},PlotStyle->{Red,Blue},Ticks->{Range[-2\[Pi],2\[Pi],\[Pi]/4],Range[-1,1,1/2]}]" class="imageframe" width="397" height="278">

Use the Basic Math Assistant palette to create an interactive figure with the Manipulate command.

Click the Manipulate button on the palette to insert the command template Manipulate[,] into the notebook, click the Input from Above button to insert the previous Plot command in the placeholder (or recreate the Plot command right inside the Manipulate command), click Tab to go to the placeholder and select a control form from the Manipulator Control drop down menu, fill in the yellow placeholder boxes, replace Π/4 with Θ in the argument of the second sine function, and click the Enter button to create the interactive figure.

{Red,Blue},Ticks->{Range[-2\[Pi],2\[Pi],\[Pi]/4],Range[-1,1,1/2]}],{{\[Theta],\[Pi]/4},-2\[Pi],2\[Pi],\[Pi]/12}]" title="In[2]:=Manipulate[Plot[{Sin[x],Sin[x-\[Theta]]},{x,-2\[Pi],2\[Pi]},PlotStyle->{Red,Blue},Ticks->{Range[-2\[Pi],2\[Pi],\[Pi]/4],Range[-1,1,1/2]}],{{\[Theta],\[Pi]/4},-2\[Pi],2\[Pi],\[Pi]/12}]" class="imageframe" width="440" height="385">

This movie shows how to use the Basic Math Assistant palette to create the previous commands.

When I share with students and teaching colleagues that Mathematica is the only software I use to write notes, exams, handouts, lecture presentations, letters, reports, presentations, and so on, their response is often something like, “Are you crazy?” I have come to understand their surprise, because while it is certainly possible to use Mathematica in this way, it is not intuitive, or obvious, how to do what is necessary to rely on Mathematica as your primary writing tool. What can be done to assist users who want to use Mathematica for writing tasks that combine text, typeset mathematics, organization structures (sections, subsections, etc.), computations, static figures, and dynamic interactive figures? The functionality of the new Writing Assistant palette in Mathematica 7 can help you begin to write such rich documents and presentations—no third-party equation editor is required, neither is any other presentation software necessary; everything is built into Mathematica 7. These dynamic documents can be shared with anyone using Mathematica 7 or the freely available Mathematica Player, or a static PDF can be created from within Mathematica and distributed.

Some of my own students use the tools on the Writing Assistant palette to efficiently write their lecture notes during class in Mathematica and later email me their typeset calculus homework assignments—I have included a sample of a student homework assignment below sent in by a student who had been using Mathematica for less than three weeks.

The new Classroom Assistant palette in Mathematica 7 contains everything in the Basic Math Assistant and Writing Assistant palettes in addition to tools that can be used to efficiently navigate around a notebook and within an input command, and a complete onscreen keyboard for those places where no physical keyboard is available. All three palettes can be run in condensed mode to use less space on the screen.

My experiences using and teaching others Mathematica for many years convinced me of the need for a tool to help new users learn, create, and edit Mathematica commands quickly without needing to memorize names and syntax. I felt it was important to create a tool to help others create rich documents and presentations integrating text, typeset mathematics, computations, and figures. Teaching mathematics with Mathematica and an interactive whiteboard convinced me of the need for a tool that could be used to construct commands quickly without needing a physical keyboard. Working with visual thinking students and faculty, who much prefer clicking on buttons to memorizing and using keyboard commands, convinced me that a physical keyboard should be required as little as possible for common Mathematica tasks.

The three Assistant palettes were developed to provide plenty of visual reminders and functional groupings for the basic Mathematica commands. They give quick access to commonly used interface operations, they contain button tooltips galore with information about command usage, reminders, and operating-system-appropriate keyboard shortcuts, and with them a physical keyboard is optional—especially important if you are a visually oriented user, or even find yourself using Mathematica with an interactive whiteboard in a classroom setting or Tablet PC. The three new Quick-Start Assistant Palettes, accessible in Mathematica 7’s Palettes Menu, are the product of a desire to help more people experience the benefit of using Mathematica to explore, investigate, learn, teach, and write about interesting ideas.

The three Quick-Start Assistant palettes can be seen in action in the screencasts “Using the Mathematica Basic Math Assistant Palette,” “Using the Mathematica Classroom Assistant Palette,” and “Using the Mathematica Writing Assistant Palette.”

I would love to hear your thoughts, feedback, questions, and ideas about the Quick-Start Assistant palettes—write to me at wolframblog@wolfram.com.

The Many Faces of Mars: Scientific American (archiving magazine articles 7/2005)

2008-11-17T16:05:00.000-08:00

The Many Faces of Mars: Scientific American

What we have discovered is that Mars has experienced a striking diversity of processes and conditions throughout its history. The Mars we are coming to know has embraced environments ranging from bone-dry to soaking wet to blanketed with snow and ice. Simple labels no longer fi t. Rather than “warm” or “cold,” we ask: How warm? How wet? For how long? Where? The emerging answers bear on what compels so many of us to study the Red Planet: its potential for harboring life, either now or in the past.

He'll Pay for That: Scientific American (archiving magaznie articles 7/2005)

2008-11-17T16:00:00.000-08:00

He'll Pay for That: Scientific American:

"The Kavli Foundation began relatively quietly by contributing $7.5 million to a center for theoretical physics at the University of Santa Barbara in 2001 and then to an institute for particle astrophysics and cosmology at Stanford University. A year ago the foundation joined the ranks of notable small grantors by making endowments to eight more institutes at major universities. But instead of following the funding trend toward seeking nearer-term, measurable returns, the foundation pays for nondirected research in its three areas of interest: astrophysics, nanoscience and neuroscience. After Kavli finds the right people and institutions, it's hands-off. He just asks for an annual report and the occasional invitation to a lecture or event."

This Germ Could Save Your Life | Popular Science (archiving magazine articles)

2008-11-17T15:29:00.000-08:00

This Germ Could Save Your Life | Popular Science: "The trouble was that Hillman now had a true transgenic—an organism that expressed the genes of two different species. The prospect of tests in humans meant that he had to go to the FDA for approval. The FDA eventually referred his case to the National Institutes of Health’s Recombinant DNA Advisory Committee, created in 1974 in response to public concern over the safety of interspecies gene transfer. The committee, which includes ethicists and patients as well as scientists and physicians, reviews any application for a transgenic intended to be used outside a sealed laboratory.

In 2004, the committee gave Hillman the green light. Usually, this is enough for full FDA approval. But not this time. FDA regulators asked Hillman to cripple his bug to guarantee that it could be removed should it ever cause problems. “When we asked them what kind of problems, they had no idea,” he recalls. “I guess we were setting a precedent.”

The regulators saw a genetically modified bacteria that was robust enough to take over any person’s mouth, and they were worried about its unchecked spread. Their decision reflected a common criticism of GMO biotherapeutics. “The main problem . . . is that [GMOs] are usually poorly contained,” argues geneticist Joe Cummins. Recently retired from"

Training the Brain: Scientific American (archiving magazine articles 07/2005)

2008-10-28T15:37:00.000-07:00

Training the Brain: Scientific American

To medicate or not? Millions of parents must decide when their child is diagnosed with attention-deficit hyperactivity disorder (ADHD)--a decision made tougher by controversy. Studies increasingly show that while medication may calm a child's behavior, it does not improve grades, peer relationships or defiant behavior over the long term.

Consequently, researchers have focused attention on the disorder's neurobiology. Recent studies support the notion that many children with ADHD have cognitive deficits, specifically in working memory--the ability to hold in mind information that guides behavior. The cognitive problem manifests behaviorally as inattention and contributes to poor academic performance. Such research not only questions the value of medicating ADHD children, it also is redefining the disorder and leading to more meaningful treatment that includes cognitive training.

"This is really a shift in our understanding of this disorder from behavioral to biological," states Rosemary Tannock, professor of psychiatry at the University of Toronto. Tannock has shown that although stimulant medication improves working memory, the effect is small, she says, "suggesting that medication isn't going to be sufficient." So she and others, such as Susan Gathercole of the University of Durham in England, now work with schools to introduce teaching methods that train working memory. In fact, working-memory deficits may underlie several disabilities, not just ADHD, highlighting the heterogeneity of the disorder.

Ask an Astrophysicist

2008-10-28T15:32:00.000-07:00

Ask an Astrophysicist

The Microwave Magician (archiving magazine articles 12/2007)

2008-10-16T12:43:00.000-07:00

PopSci's Best of What's New 2007: "I’m not sure if I’m watching a magic trick, or an invention that will make the cigar-chomping 64-year-old next to me the richest man on the planet. Everything that goes into Frank Pringle’s recycling machine—a piece of tire, a rock, a plastic cup—turns to oil and natural gas seconds later. “I’ve been told the oil companies might try to assassinate me,” Pringle says without sarcasm.

The machine is a microwave emitter that extracts the petroleum and gas hidden inside everyday objects—or at least anything made with hydrocarbons, which, it turns out, is most of what’s around you. Every hour, the first commercial version will turn 10 tons of auto waste—tires, plastic, vinyl—into enough natural gas to produce 17 million BTUs of energy (it will use 956,000 of those BTUs to keep itself running).

Pringle created the machine about 10 years ago after he drove by a massive tire fire and thought about the energy being released. He went home and threw bits of a tire in a microwave emitter he’d been working with for another project. It turned to what looked like ash, but a few hours later, he returned and found a black puddle on the floor of the unheated workshop. Somehow, he’d struck oil.

Or rather, he had extracted it. Petroleum is composed of string"

new solar (archiving magazine articles 12/2007)

2008-10-16T12:41:00.000-07:00

PopSci's Best of What's New 2007: "Imagine a solar panel without the panel. Just a coating, thin as a layer of paint, that takes light and converts it to electricity. From there, you can picture roof shingles with solar cells built inside and window coatings that seem to suck power from the air. Consider solar-powered buildings stretching not just across sunny Southern California, but through China and India and Kenya as well, because even in those countries, going solar will be cheaper than burning coal. That’s the promise of thin-film solar cells: solar power that’s ubiquitous because it’s cheap. The basic technology has been around for decades, but this year, Silicon Valley–based Nanosolar created the manufacturing technology that could make that promise a reality.

The company produces its PowerSheet solar cells with printing-press-style machines that set down a layer of solar-absorbing nano-ink onto metal sheets as thin as aluminum foil, so the panels can be made for about a tenth of what current panels cost and at a rate of several hundred feet per minute. With backing from Google’s founders and $20 million from the U.S. Department of Energy, Nanosolar’s first commercial cells rolled off the presses this year.

Cost has always been one of solar’s biggest problems. Traditional solar cells require silicon, and silicon is an expensive commodi"

offsetting your carbon (archiving magazine articles 7/2005)

2008-10-16T12:20:00.000-07:00

Wired 13.07: START

Now they have TerraPass, a clever eco-capitalism experiment. Launched by a group of Wharton Business School classmates, the startup sells a decal that drivers can slap on their windshields. The sticker price - $79.95 for SUVs, less for greener cars - gets invested in renewable energy projects and credits. The credits are traded through local brokers on the new Chicago Climate Exchange.

TerraPass lets consumers participate in an emissions trading system the US established in 1990. (Give credit to economist Ronald Coase, who won a Nobel Prize for the idea in 1991.) Under the system, industrial operations that spew less than their share of emissions can sell a credit to companies that fail to keep gunk out of the air. In effect, the dirtier factories can pay greener operations to do the work of cutting emissions. The approach has taken off worldwide, spawning a billion-dollar market.

And it's not just for big-time polluters. Today, farmers cash in on credits by collecting and processing cow dung, which produces globe-cooking methane. Land-owners earn credits by installing wind farms on their blustery fields, which top off the power grid with carbon-free electricity.

But until now, the Chicago Climate Exchange was off-limits to all but registered traders, and the transaction cost of buying credits piecemeal from small outfits was too high. TerraPass aggregates the money plunked down by guilty - ahem, environmentally concerned - SUV drivers, allowing them to participate in the market.

YouTube Does Science, From Fruit-Fly Fight Clubs to Stem Cell Extractions (archiving magazine articles 7/2007)

2008-10-16T11:53:00.000-07:00

YouTube Does Science, From Fruit-Fly Fight Clubs to Stem Cell Extractions

WIRED MAGAZINE: ISSUE 15.07

YouTube Does Science, From Fruit-Fly Fight Clubs to Stem Cell Extractions

John Geirland 06.26.07

START

PREVIOUS: Mr. Know-It-All: Undercover GM Food, Over-the-Internet Meds

NEXT: What's Inside: Red Bull

Years behind the lab bench taught Moshe Pritsker that the trickiest part of any science experiment isn't the hypothesis, it's the method. The former Harvard researcher learned this lesson back in his student days, after carefully following the instructions on a specialized kit for isolating DNA. "Surprise," Pritsker says, "no DNA!" A colleague finally showed him how to make the kit work. And that gave Pritsker an idea: methodology porn. The Web site he cofounded, the Journal of Visualized Experiments, launched last October. Now its videos of experimental procedures and techniques — from stem-cell culture prep to hippocampal dye injection — get 300 pageviews a day. The journal's still a work in progress (nothing's gone viral yet), but just wait. "No one has published results in video before," Pritsker says. "Scientists don't know how to do it." Here are a few of the journal's faves.

Must-See Experiments

Culture of Mouse Neural Stem Cell Precursors
D. Spencer Currle, Jia Sheng Hu, Aaron Kolski-Andreaco, Edwin S. Monuki, UC Irvine.
Video Extracting a mouse uterus, removing embryos, and harvesting stem cells from the cerebral cortex.
Goal Improving stem-cell handling skills for eventual use on human cells.
Highlight Close shot demonstrating how to use bent forceps to tease out cortical tissue.

Studying Aggression in Drosophila
Sarah Certel, Edward A. Kravitz, Sibu Mundiyanapurath, Harvard Medical School.
Video Building glass arenas and staging bouts between drosophila.
Goal Figuring out how aggression is wired in the brain.
Highlight It's fruit-fly fight club — close-up lunges, blocks, and feints.

Testing Visual Sensitivity to the Speed and Direction of Motion in Lizards
Kevin L. Woo, Centre for the Integrative Study of Animal Behaviour, Macquarie University, Sydney
Video Coaxing Jacky dragons (an Australian lizard species) to take cues from moving dots.
Goal Working with lizards as a model for motion sensing.
Highlight The lizard actually completes the experiment. It's tough to motivate reptiles to stay interested in scientific work, Woo says.

A MILLION LITTLE ID TAGS - Popular Science Magazine, February 2007 (archiving magazine articles)

2008-10-16T11:43:00.000-07:00

A MILLION LITTLE ID TAGS - Popular Science Magazine, February 2007:

"Unmistakable identification keeps car thieves away from your ride.

THE THREAT: More than one million vehicles are stolen in the U.S. every year, with a total value of over $7.6 billion. And once thieves remove license plates and vehicle identification numbers, there's no way of knowing who the vehicles once belonged to.

THE SOLUTION: Datadot Technology - a startup company in Australia which has the highest rate of vehicle theft in the developed world—has devised a way to cover valuable items in identifiers as small and invisibly scattered as hairspray droplets on a bouffant. Transparent DataDots are laser-etched with an identification number unique to you and glued to every internal surface of your car, boat or laptop, The sheer number of sand-grain-size dots on treated possessions—up to 5,000—makes it all but impossible for thieves to take them off and sell the harvested parts. In contrast, existing theft-deterrent systems such as a LaJack can be hidden in only one of about 20 places, and so can be removed much more easily.

Cops determine who stolen property belongs to by using a 50x magnifier to read the dots. If a person reporting a theft mentions that the item was Data-Dotted, police departments can access a company-run international database to find out if the car has turned up elsewhere. '"

Blood Simple | Popular Science (archiving magazine articles 7/2007)

2008-10-16T11:12:00.000-07:00

Blood Simple | Popular Science

Their solution is a device that converts all blood into type O, the most coveted of the four major blood types because it can be safely transfused into nearly any patient. "Press 'start,' and the machine does everything else," says Douglas Clibourn, the CEO of ZymeQuest.

Surfing the Stars | Popular Science (archiving magazine articles 6/2007)

2008-10-16T11:08:00.000-07:00

Surfing the Stars | Popular Science

Within a decade, a dream team of astronomers and computer geeks vows to bring a world-class observatory to every desktop, giving anyone with a PC access to remote galaxies and exploding supernovae. The pledge is the result of a partnership announced last winter between a network of 19 national research institutions and engineers from the search-engine giant Google. Their collective objective is to develop potent software to process the estimated 30 terabytes of astronomy imagery (think 12 billion five-megapixel photos) that will stream nightly from the newly built Large Synoptic Survey Telescope, or LSST, slated to go online in 2013.

Set atop Cerro Pachn Mountain in Chile, the LSST will be the largest survey scope of its kind, sequentially imaging nearly 20 billion astronomical objects in the night sky twice a week at least 2,000 times over the scope's 10-year lifetime. Google's role in this $350-million project (beyond the modest $25,000 annual dues payment) is still largely undefined, but Rob Pike, Google's principal engineer for the LSST, envisions a tool set akin to Google Earth, which combines a search tool with satellite imagery. So instead of killing time flying over your ideal vacation spot onscreen, you can opt for more productive surfing, such as scanning the skies for hazardous near-Earth asteroids.

HOW IT WORKS

One thousand times as powerful as previous telescopes, the LSST will survey the entire sky every three nights using a wide-angle mirror and a three-billion-pixel digital camera. As the telescope rotates on its base, the camera's 15-second exposures take in an area 50 times as large as the full moon. Software will compile three-dimensional imagery to produce time-lapse digital "movies" of the universe.

Tumor Grenades | Popular Science (archiving magazine articles 6/2007)

2008-10-16T11:03:00.000-07:00

Tumor Grenades | Popular Science:

"Particle accelerators, the giant machines that create highly energetic beams of subatomic particles, are designed to solve the universe's grand mysteries. Now they're battling cancer. Since 1992, more than 50,000 patients have undergone proton therapy, which uses particle accelerators to precisely blast tumors with high-speed protons.

Now physicists at CERN, the European particle-physics center in Switzerland, have begun experimenting with antimatter made of rare, negatively charged twins of protons, and the results are promising. In studies involving hamster tissue, antimatter therapy has even proved to be four times as powerful as protons.

X-rays, which deliver conventional radiation therapy, burn through the body, increasing the cancer risk in healthy tissue. Protons and antimatter, by comparison, can be tuned to release most of their energy right at the tumor site, thus damaging fewer of the surrounding cells. 'I didn't experience any nausea or radiation burn,' says Florida state congressman Stan Jordan, who received proton therapy for advanced prostate cancer earlier this year at the University of Florida Proton Therapy Institute in Jacksonville. Jordan, who likened the treatment chamber to the Starship Enterprise, says the actual 'beam-me-up-Scotty' part of the therapy lasted less than two minutes.

Unfortunately, each facility costs more than $100 milli"

Tobacco Could Hold the Key to Revolutionary Gene Therapy | Wired Science from Wired.com

2008-09-03T23:00:00.000-07:00

Tobacco Could Hold the Key to Revolutionary Gene Therapy | Wired Science from Wired.com

Scientists are using a modified tobacco virus to deliver delicate gene therapies into the heart of diseased cells, with the potential to treat most cancers, viruses and genetic disorders.

The tobacco mosaic virus, which plagues the plant but is harmless to humans, is hollowed out and filled with "small interfering RNA" molecules, or siRNA, which some scientists consider to be the most significant development in medicine since the discovery of vaccines.

The virus' tubular shell provides a safe way to slip the delicate siRNA drugs into cells, serving as both a protective coating and a Trojan horse.

o0O0o

Bentley hopes that a drug company will take interest in his discovery, but he has a long way to go before it is ready for human trials. First, the team must gather more evidence that the system is an effective way to deliver medicine. It has worked with cells in a dish, but not yet been proven effective in living organisms.

Unfortunately, some scientists foresee a problem that could make the viral carrier unsuitable for long term use: Humans will eventually develop an immune response to the plant virus that would limit their effectiveness.

Did Life Evolve in Ice? | Arctic & Antarctic | DISCOVER Magazine

2008-08-26T11:53:00.000-07:00

Did Life Evolve in Ice? | Arctic & Antarctic | DISCOVER Magazine

One morning in late 1997, Stanley Miller lifted a glass vial from a cold, bubbling vat. For 25 years he had tended the vial as though it were an exotic orchid, checking it daily, adding a few pellets of dry ice as needed to keep it at –108 degrees Fahrenheit. He had told hardly a soul about it. Now he set the frozen time capsule out to thaw, ending the experiment that had lasted more than one-third of his 68 years.

Miller had filled the vial in 1972 with a mixture of ammonia and cyanide, chemicals that scientists believe existed on early Earth and may have contributed to the rise of life. He had then cooled the mix to the temperature of Jupiter’s icy moon Europa—too cold, most scientists had assumed, for much of anything to happen. Miller disagreed. Examining the vial in his laboratory at the University of California at San Diego, he was about to see who was right.

As Miller and his former student Jeffrey Bada brushed the frost from the vial that morning, they could see that something had happened. The mixture of ammonia and cyanide, normally colorless, had deepened to amber, highlighting a web of cracks in the ice. Miller nodded calmly, but Bada exclaimed in shock. It was a color that both men knew well—the color of complex polymers made up of organic molecules. Tests later confirmed Miller's and Bada’s hunch. Over a quarter-century, the frozen ammonia-cyanide blend had coalesced into the molecules of life: nucleobases, the building blocks of RNA and DNA, and amino acids, the building blocks of proteins. The vial’s contents would support a new account of how life began on Earth and would arouse both surprise and skepticism around the world.

JournalFire Blog » Blog Archive » Welcome to Journalfire

2008-08-26T11:35:00.000-07:00

JournalFire Blog » Blog Archive » Welcome to Journalfire

Welcome to Journalfire

Until recently, large media publishers controlled what we read, listened to, and watched. Now blogs, podcasts, and Youtube have put the users in control. Unfortunately science has lagged behind. Publishers still act as the primary filter of scientific information, with some top-tier journals rejecting up to 83% of submitted papers even before they are sent to peer review. Combine this with the fact that grants and faculty positions often hinge on the number of publications one has in these top journals, and the result is that a handful of people have tremendous impact on the global scientific agenda. Journalfire exists to put scientists back in control of science.

Journalfire provides a centralized location for you to share, discuss, and evaluate published journal articles. You, the scientists, are put in charge of determining what studies are significant and noteworthy.

Use Journalfire to create groups to share articles and ideas with scientists in your lab or from around the globe. Currently Journalfire links to every article in the PubMed database, with access to more databases on the horizon. When discussing articles, you decide whether the discussion is public or private, and whether or not to use your name or remain anonymous. Journalfire creates a permanent open access record of each discussion and links it directly to a specific article or group. See what articles your colleagues are discussing in their groups, and see what comments are being made about the papers that interest you most, including your own.

Journalfire provides a new way to assess scientific merit. The value of a journal article is often first assessed by the name of the journal in which it appears. Unfortunately, this is typically determined by fewer than five people. Journalfire offers a more democratic approach. By enabling you to evaluate published articles, the combined opinion of the scientific community can be used as a measure of scientific merit.

Journalfire search results take into account several criteria, including the amount of discussion an article has generated and the rating an article has received. Thus Journalfire enables you to quickly find the papers that other scientists are talking about, or papers that may have otherwise slipped through the cracks.

Journalfire was created by a group of graduate students who were frustrated with the current system of scientific discourse and publication. We believe Journalfire is a step in the right direction towards a more open and democratic scientific community. If you’d like to join us, visit journalfire.org.

By amplifying cell death signals, scientists make precancerous cells self-destruct

2008-08-18T06:18:00.000-07:00

via KurzweilAI.net

By amplifying cell death signals, scientists make precancerous cells self-destruct

When a cell begins to multiply in a dangerously abnormal way, a series of death signals trigger it to self-destruct before it turns cancerous. Now, in research to appear in the August 15 issue of Genes & Development, Rockefeller University scientists have figured out a way in mice to amplify the signals that tell these precancerous cells to die. The trick: Inactivating a protein that normally helps cells to avoid self-destruction.

Molecular Visualizations of DNA

2008-08-16T08:43:00.000-07:00

YouTube - Molecular Visualizations of DNA

more:

Drug that uses the body's cells to blast cancer | Mail Online

2008-08-14T19:46:00.000-07:00

Drug that uses the body's cells to blast cancer | Mail Online:

"Cancer patients have seen their tumours blasted into submission by a new drug which harnesses the power of their own immune cells.

The 'serial killer' treatment completely eliminated some tumours and shrunk others resistant to existing therapies.

Further successful trials could lead to blinatumomab being on the market in less than five years."

HubbleSite - NewsCenter - Three Red Spots Mix it Up on Jupiter (07/17/2008) - Release Images

2008-07-17T23:25:00.000-07:00

HubbleSite - NewsCenter - Three Red Spots Mix it Up on Jupiter (07/17/2008) - Release Images

Nanoparticle Stops Cancer From Spreading | LiveScience

2008-07-12T10:28:00.000-07:00

Nanoparticle Stops Cancer From Spreading | LiveScience

(HealthDay News) -- California researchers say they have developed molecular "smart bombs" that stop pancreatic and kidney cancer from spreading in mice while causing fewer side effects and damage to healthy surrounding tissues than traditional chemotherapy.

A team from the University of California, San Diego, designed a "nanoparticle" anti-cancer drug delivery system that zooms in on a protein marker called integrin avB3, which is found on the surface of certain tumor blood vessels. The marker is tied to the development of new blood vessels and malignant tumor growth.

While the system had little impact on primary tumors, it halted the metastasis of pancreatic and kidney cancers throughout the bodies of mice. Cancer metastasis normally is much harder to treat than the primary tumor, and it usually leads to the patient's death.

The findings were published in this week's online issue of the Proceedings of the National Academy of Sciences.

According to the report, the system works with a lower dose of chemotherapy because it attacks the cancer with such precision. In most chemo treatments, the destruction of healthy tissue is a side effect as it floods the body with cancer-killing toxins.

"We were able to establish the desired anti-cancer effect while delivering the drug at levels 15 times below what is needed when the drug is used systemically," study leader David Cheresh, vice chairman of pathology at UCSD, said in a university news release. "Even more interesting is that the metastatic lesions were more sensitive to this therapy than the primary tumor."

UCSD engineers and oncologists together designed the nanoparticle -- a microscopic particle made of lipid-based polymers -- to work with the cancer-killing drug doxorubicin.

Living the Scientific Life (Scientist, Interrupted): ScienceBlogs To Take Over The World

2008-06-30T20:14:00.000-07:00

Living the Scientific Life (Scientist, Interrupted): ScienceBlogs To Take Over The World

I have been made privy to a special 1 July 2008 press release from Seed Media Group, the parent organization for ScienceBlogs, which hosts my blog. The news is good.

In short, Seed Media Group announced that ScienceBlogs, the internet's largest science community, has experienced a phenomenal growth in readership: total visits for the first six months of 2008 has topped 14 million, an all-time high.

ScienceBlogs was launched in mid-January 2006 after inviting 14 science blogs [including my blog, Living the Scientific Life (Scientist, Interrupted)] to join their ranks. Since then, ScienceBlogs has received a total of more than 41 million visits, or "hits", and more than 107 million individual page views. According to Amazon's Kindle statistics, ScienceBlogs hosts 70% of their top-selling science blog subscriptions, and ScienceBlogs are one of Amazon's top 25 selling sites overall, along with Daily Kos, BoingBoing, and The Huffington Post (where I occasionally volunteer).

"ScienceBlogs has become a must-read destination site for the intellectually curious from around the world and we are continuously working to make it more useful and interactive for our readers," said Sarah Glasser, Vice President of Marketing for Seed Media Group.

ScienceBlogs is an international community of blog authors whose writings span the entire world of science and technology, covering fields from neuroscience to computer science. ScienceBloggers, informally known among their friends and readers as "SciBlings", comprise a group of scientists, medical doctors, educators, and journalists -- among them are 42 PhDs, 5 MDs and 2 Rhodes Scholars. More than 90 blogs have been recruited to join ScienceBlogs so far, 70 of which are written in English, and another 28 are written in German and are hosted by our sister site, ScienceBlogs.de, in partnership with Hubert Burda Media.

Seed Media Group is a global media and technology company. Their portfolio includes publishing, software, digital media, conferences, museums, and social media. Their main foci are their passion for science and their advocacy of science literacy around the world. Seed Media Group is headquartered in New York City.

Slashdot | Cancer Resistance Technique Moves To Human Trials

2008-06-29T19:00:00.000-07:00

Slashdot | Cancer Resistance Technique Moves To Human Trials

TaeKwonDood tips us to news that a new cancer resistance treatment is going into clinical trials after being quite successful at eradicating cancer in mice. Researchers discovered that certain white blood cells called granulocytes from cancer-immune mice were able to cure cancer in other mice. Now, doctors are putting out the call for healthy granulocyte donors in order to test how well it works on humans. The article quotes lead researcher Zheng Cui saying, "In mice, we've been able to eradicate even highly aggressive forms of malignancy with extremely large tumors. Hopefully, we will see the same results in humans. Our laboratory studies indicate that this cancer-fighting ability is even stronger in healthy humans."

Cancer patient cured with his own immune system

2008-06-29T18:59:00.000-07:00

KurzweilAI.net

Researchers at the Fred Hutchinson Cancer Research Center have developed a new cancer immune therapy by using large numbers of a patient's own T-cells (a special type called helper CD4 cells) to fight tumors.

The researchers collected some of these cells from the patient, cultured them, and injected five billion of them back into the patient. The treatment removed the tumors within two months.

Accidental fungus leads to promising cancer drug | Reuters

2008-06-29T18:58:00.000-07:00

Accidental fungus leads to promising cancer drug | Reuters

Tests in mice showed it worked against a range of tumors, including breast cancer, neuroblastoma, ovarian cancer, prostate cancer, brain tumors known as glioblastomas and uterine tumors.

It helped stop so-called primary tumors and also prevented their spread, Ofra Benny of Children's Hospital Boston and Harvard Medical School and colleagues reported.

"Using the oral route of administration, it first reaches the liver, making it especially efficient in preventing the development of liver metastasis in mice," they wrote in their report. "Liver metastasis is very common in many tumor types and is often associated with a poor prognosis and survival rate," they added.

Self-Similarity

2008-06-27T16:01:00.000-07:00

Google Health

2008-06-17T21:49:00.000-07:00

Google Health

Google Health allows you to store and manage all of your health information in one central place. And it's completely free. All you need to get started is a Google username and password.

Google believes that you own your medical records and should have easy access to them. The way we see it, it's your information; why shouldn't you control it?

Keep your doctors up-to-date
Stop filling out the same paperwork every time you see a new doctor
Avoid getting the same lab tests done over and over again because your doctor cannot get copies of your latest results
Don't lose your medical records because of a move, change in jobs or health insurance

With Google Health, you manage your health information — not your health insurance plan or your employer. You can access your information anywhere, at any time.

It's safe and secure

We believe that your health information belongs to you, and you should decide how much you share and whom you share it with. We will never sell your data. We store your information securely and privately. Check out our privacy policy to learn more.

You are in control — you choose what you want to share and what you want to keep private.

Features

With Google Health, you can:

	Build online health profiles You can enter your health conditions, medications, allergies, and lab results into your Google Health profile and you can name the profile anything you want. You can even create multiple profiles for family members or others you care for.
	Import medical records from hospitals and pharmacies Choose from a list of Google Health partners to see if your hospital or pharmacy can send copies of your medical records or prescriptions to your Google Health profile. This way, you can save an accurate history of your medical conditions, medications, and test results all in one place.
	Learn about health issues and find helpful resources Review trusted information on diseases and conditions and learn about possible medication interactions and other topics to talk your doctors about.
	Search for doctors and hospitals You can search for a doctor's name or location, find a doctor's website, get directions to a doctor's office, and save a doctor's information to your medical contacts list.
	Connect to online health services Browse the online health services directory to find services that are integrated with Google Health that can help you better manage your health needs.

The Loom : A New Step In Evolution

2008-06-02T20:21:00.000-07:00

The Loom : A New Step In Evolution: "One of the most important experiments in evolution is going on right now in a laboratory in Michigan State University. A dozen flasks full of E. coli are sloshing around on a gently rocking table. The bacteria in those flasks has been evolving since 1988--for over 44,000 generations. And because they've been so carefully observed all that time, they've revealed some important lessons about how evolution works."

APOD: 2008 May 23 - Jupiter s Three Red Spots

2008-05-23T07:43:00.000-07:00

APOD: 2008 May 23 - Jupiter s Three Red Spots

NASA - Artist's representation of binary galaxy 3C321 eating a nearby galaxy

2008-05-12T15:53:00.000-07:00

NASA - NASA Announces Discove ry of Assault by a Black Hole

The one galaxy appears to be eating the second galaxy.

YouTube - Charlie Rose: August 23, 2002

2008-04-23T11:04:00.000-07:00

YouTube - Charlie Rose: August 23, 2002

The interview with Stephan Wolfram from 8/23/2002 is interesting and starts at about 14:25.

That said, it is also interesting to see the latter half of the Jim Lehrer interview (which is just prior to Wolfram's segment) to hear how he and Charlie Rose discussed Iraq and the issues of the day (8/23/2002).

Wolfram's snowflake cellular automaton

2008-04-23T09:58:00.000-07:00

YouTube - Wolfram's snowflake cellular automaton

Coupled Cellular Automaton:

Artificial life and multiagent systems:

Copy That

2008-04-17T21:53:00.000-07:00

Copy That (pay):

"Identical twins may look alike, but their DNA is not the same as long thought, a new study finds. Moreover, each twin grows more genetically distinct over time. Aside from maybe giving forensic investigators a way to tell which twin committed a crime, these recent findings highlight just how changeable human genomes might really be, twins or not.

Identical, or monozygotic, twins result when a fertilized egg, or zygote, splits in two. Because they derive from the same cell, such twins are generally assumed to be physically identical except for features shaped by environmental factors, such as fingerprints, and by womb conditions."

code 1599 is cool

2008-04-14T14:08:00.001-07:00

Code 1599:

Cancer Therapy Without Side Effects Nearing Trials

2008-04-13T16:33:00.000-07:00

Cancer Therapy Without Side Effects Nearing Trials

A promising new cancer treatment that may one day replace radiation and chemotherapy is edging closer to human trials.

Kanzius RF therapy attaches microscopic nanoparticles to cancer cells and then "cooks" tumors inside the body with harmless radio waves.

Based on technology developed by Pennsylvania inventor John Kanzius, a retired radio and TV engineer, the treatment has proven 100 percent effective at killing cancer cells while leaving neighboring healthy cells unharmed. It is currently being tested at M.D. Anderson Cancer Center in Houston.

“I don’t want to give people false hope,” said Dr. Steve Curley, the professor leading the tests, “but this has the potential to treat a wide variety of cancers.”

Modern cancer treatments like radiation and chemotherapy have proven remarkably effective at treating many cancers, especially in combination, but are plagued with toxic side effects. These treatments kill healthy cells as well as cancerous ones.

Kanzius RF therapy is noninvasive, and uses nontoxic radio waves combined with gold or carbon nanoparticles, which have a long history of medical use.

Stephen Wolfram: A New Kind of Science Free Online Version

2008-03-28T21:46:00.000-07:00

Stephen Wolfram: A New Kind of Science | Online - Table of Contents

Wolfram...a new kind of physics

2008-03-28T21:20:00.000-07:00

Bloggingheads.tv - diavlogs

I put this here for the first 30 seconds from the ding-a-link. At about 1:30 in, however, they get a bit into the why other scientists ignored him. Then he self-exemplifies why.

Wolfram on Committee work: "... it's not my way ... there's some kind of cognitive disconnect in that way of making progress in things ..."

YouTube - INCREDIBLE TORNADO VIDEO!! May 4, 2007 - Ellis Co., OK

2008-03-23T20:11:00.000-07:00

YouTube - INCREDIBLE TORNADO VIDEO!! May 4, 2007 - Ellis Co., OK

Google Sky

2008-03-16T07:33:00.000-07:00

Google Sky

Slashdot | Large Sheets of Carbon Nanotubes Produced

2008-03-02T11:49:00.000-08:00

Slashdot | Large Sheets of Carbon Nanotubes Produced

StCredZero brings news that scientists have developed sheets of nanotubes that measure up to three feet by six feet, and they promise "slabs 100 square feet in area as soon as this summer." The developers see uses for the sheets in electromagnetic shields and airplane construction, and according to the Next Big Future blog, the sheets could also impact the development of solar sails.

"The sheets, which the company can produce on its single machine at a rate of one per day, are composed of a series of nanotubes each about a millimeter long, overlapping each other randomly to form a thin mat. The tensile strength of the mat ranges from 200 to 500 megapascals--a measure of how tough it is to break. A sheet of aluminum of equivalent thickness, for comparison, has a strength of 500 megapascals. If Nanocomp takes further steps to align the nanotubes, the strength jumps to 1,200 megapascals."

When the world's great scientific thinkers change their minds

2008-02-13T08:58:00.000-08:00

Edge: Cover Story - Publico Sunday Magazine
by Ana Gerschenfeld

One hundred and sixty-five eminent thinkers, researchers, and communicators, at the annual request of the edge.org website, answered the following question: 'What Have You Changed Your Mind About? Why?'

From particle physics to evolutionary theory, to the atomic bomb, to global warming, to the battle of the sexes, to the equality of human beings, to God and the paranormal, and to the dogmatism of scientists themselves, dozens of the big thinkers in the world explained online, at the start of 2008, what the most important things that they’ve change their minds about during their lives are.

more

Dawkins & Ventner: Life, A Gene-centric View

2008-02-06T12:38:00.000-08:00

Edge 235

Link: sevenload.com

First Google Health Screenshots

2008-02-03T14:49:00.000-08:00

First Google Health Screenshots

Google Health, codename “Weaver”, is Google’s planned health information storage program. Google’s Vice President of Engineering Adam Bosworth lobbies for the program for quite a while now. Adam said the current US health care system is challenged when it comes to “supporting caregivers and communicating between different medical organizations.” Adam went on to say that people “need the medical information that is out there and available to be organized and made accessible to all ... Health information should be easier to access and organize, especially in ways that make it as simple as possible to find the information that is most relevant to a specific patient’s needs.” Adam adds that this – making information accessible – happens to be along Google’s mission.

Slashdot | Carbon Nanotubes Can Exist Safely Inside the Body, Help Treat Cancer

2008-01-31T22:34:00.000-08:00

Slashdot | Carbon Nanotubes Can Exist Safely Inside the Body, Help Treat Cancer

"A team of scientists at Stanford University has tracked the movement of carbon nanotubes through the digestive systems of mice. They've determined that the nanotubes do not exhibit any toxicity in the mice, and are safely expelled after delivering their payload. As a result, the study paves the way toward future applications of nanotubes in the treatment of illnesses. Previous research by the same team demonstrated that nanotubes can be used to fight cancer. The nanotubes do this in two ways. One method involves shining laser light on the nanotubes, which generates heat to destroy cancer cells. Another method involves attaching medicine to the nanotubes, which are able to accurately 'find' cancerous cells without impacting healthy cells."

APOD: 2007 December 1 - M74: The Perfect Spiral

2007-12-01T08:51:00.000-08:00

APOD: 2007 December 1 - M74: The Perfect Spiral

New Age Thinking: Alternative Ways of Measuring Age, Their Relationship to Labor Force Participation, Goverment Policies and GDP

2007-11-05T11:36:00.000-08:00

New Age Thinking: Alternative Ways of Measuring Age, Their Relationship to Labor Force Participation, Goverment Policies and GDP

The current practice of measuring age as years-since-birth, both in common practice and in the law, rather than alternative measures reflecting a person's stage in the lifecycle distorts important behavior such as retirement, saving, and the discussion of dependency ratios. Two alternative measures of age are explored: mortality risk and remaining life expectancy. With these alternative measures, the huge wave of elderly forecast for the first half of this century doesn't look like a huge wave at all.

APOD: 2007 November 2 - Three Nebulae in Narrow Band

2007-11-02T07:37:00.000-07:00

APOD: 2007 November 2 - Three Nebulae in Narrow Band

Relax And Think Like A Rat | Learning | DISCOVER Magazine

2007-10-31T16:41:00.000-07:00

Relax And Think Like A Rat | Learning | DISCOVER Magazine

Don't feel guilty about the breaks you've been sneaking at work—they could be helping you learn. Neuroscientists at MIT find that rats take a similar pause after exploring an unfamiliar maze. During that break, the animals' brains repeatedly review a backward version of the route they just took, most likely cementing memories of the steps needed to reach the goal.

David Foster and his team zero in on this process by placing tiny wires into the rats' brains and then eavesdropping on individual cells. The neurons that light up during the experiments lie in a region known to form short-term memories. But as those cells play the memory again and again—10 times faster than the original experience—the rest of the brain has lots of opportunities to absorb the information and to place it into long-term storage. "This implies that it's not just during an experience that learning occurs," Foster says. "If we're right, the period after the experience is just as important, maybe more important."

The results may explain previous studies showing that people and animals learn best when given breaks between tasks—and provide a persuasive new justification for office daydreaming.

A Better Energizer | Gadgets | DISCOVER Magazine

2007-10-31T16:37:00.000-07:00

A Better Energizer | Gadgets | DISCOVER Magazine

If you've ever had a cell phone suddenly die on you, you know that batteries are the weak link in mobile electronics. That's why MIT electrical engineer Joel Schindall thinks the time is ripe for capacitors. "They are better than batteries in almost every way, except in the amount of energy they store," he says. Schindall and his research group have licked that limitation.

Unlike batteries, which produce voltage from a chemical reaction, capacitors store electricity between a pair of metal plates. The larger the area of the plates, and the smaller the space between them, the more energy a capacitor can hold. Schindall's group had a radical idea: Cover the plates with millions of microscopic filaments known as carbon nanotubes. The tiny tubes vastly expand the surface area, creating a perfect sponge for electricity. "Now we can expect to store an amount of energy that is comparable to what batteries store," he says.

A capacitor-powered cell phone could be charged in minutes or seconds instead of hours. And since capacitors can be reused indefinitely, environmental waste from discarded batteries would become a thing of the past. Schindall says battery-free bliss may be less than five years away.

Whatever Happened to Cold Fusion? | Elements | DISCOVER Magazine

2007-10-30T21:17:00.000-07:00

Whatever Happened to Cold Fusion? | Elements | DISCOVER Magazine

The scientists who continue to work in the field claim that their experiments show minute, unexplained outputs of energy. Within the year, Hagelstein says, he plans to begin conducting cold fusion research at MIT, an institution that once held a ceremonial wake in cold fusion's honor. He aims to show that novel physical processes can trigger fusion without a significant input of heat. Hagelstein insists that those beyond the inner circle don't know the whole story. "People working in the field believe cold fusion is real and that the issue is settled," he says.

A Vaccine for Your In-Box | Computers | DISCOVER Magazine

2007-10-30T21:13:00.000-07:00

A Vaccine for Your In-Box | Computers | DISCOVER Magazine

Shir notes that viruses typically propagate by sending themselves to addresses harvested from Outlook or other similar e-mail programs. He counters this strategy by seeding networks with "honeypot" computers, designed to draw out any active viruses. Each of these computers has a normal-looking e-mail address, but as soon as a virus activates its e-mail system, the computer records the virus's characteristics. It then sends other networked machines a description of the virus's code so that the other computers can block the virus, much as antibodies learn to stop real viruses.

This approach has a leg up on programs like Norton AntiVirus, which require each computer to download a list of virus descriptions compiled by the company that sells the software. "Current antivirus schemes are focused on cleaning the specific computer on which they were installed," Shir says. "Our goal is to immunize the entire network." He says the strategy requires only a modest investment. Simulations show that placing one honeypot among every 250 computers in a network produces such a quick reaction that no virus can infect more than 1 percent of them. Shir hopes to release a commercial version of the software within the next few years.

Autism: It’s Not Just in the Head | Nutrition | DISCOVER Magazine

2007-10-30T21:02:00.000-07:00

Autism: It’s Not Just in the Head | Nutrition | DISCOVER Magazine:

"“What we’ve got here is a far more comprehensive set of characteristics for autism,” says Herbert, “one that can include behavior, cognition, sensorimotor, gut, immune, brain, and endocrine abnormalities. These are ongoing problems, and they’re not confined just to the brain. I can’t think of it as a coincidence anymore that so many autistic kids have a history of food and airborne allergies, or 20 or 30 ear infections, or eczema, or chronic diarrhea.”"

Resistant Bacteria: Go Kill Yourselves

2007-10-30T20:30:00.000-07:00

Resistant Bacteria: Go Kill Yourselves:

"Researchers at the Hebrew University of Jerusalem have discovered a protein they call 'extracellular death factor' (EDF). Bacteria use EDF to regulate their colonies by inducing suicide in some cells. The protein could be used to create a new class of antibiotics that would effectively treat bacterial species that have grown resistant to conventional antibiotics."

Emerging Technology | Computers | DISCOVER Magazine

2007-10-30T16:00:00.000-07:00

Emerging Technology | Computers | DISCOVER Magazine

December, 2005:

When Katrina struck New Orleans on Monday, August 29, similar notices began to appear online—on craigslist, on Yahoo, on the Red Cross Web site. But that information was too scattered to be useful. The queries were everywhere—on dozens of sites. So it was almost impossible to report that someone had been located and be guaranteed that the information would reach the people who needed it. On Saturday, September 3, as the catastrophe worsened, a handful of tech-savvy volunteers led by David Geilhufe started gathering data from these sites by "screen scraping," an automated process that involves grabbing the relevant information for each person—name, location, age, and description—and depositing it in a single database. Geilhufe and his team concocted a standardized method of organizing the data, which they called PeopleFinder Interchange Format.

Still, there were thousands of missing-person notices online the next day that hadn't been converted into the PeopleFinder format because they were not machine readable. Typically these messages were quite simple: for example, "I'm looking for my uncle John who lived in the Ninth Ward—Sarah Bowen." That requires a human to parse the syntax. So that morning two well-regarded online figures—Jon Lebkowsky and Ethan Zuckerman—decided to team up to coordinate a volunteer effort, with Lebkowsky recruiting people to scan through all the online posts and Zuckerman dealing out chunks of data to be analyzed.

By the next morning, PeopleFinder had attracted the attention of a few widely read bloggers. They spread the word to their readers about the need for volunteers. By the end of the day, thousands were volunteering. The group was briefly hamstrung by the database's being overloaded with activity. But by Tuesday night 50,000 entries had been processed, and the number continued to rise dramatically in the days that followed. Meanwhile, people looking for relatives or friends could visit www. katrinalist.net, where the PeopleFinder team provided a search tool that made it possible to enter a name, a zip code, or an address and get a list of names matching the query within seconds.

PeopleFinder was the kind of data-management effort that could have taken a year to execute at great expense if a corporation or a government agency had been in charge of it. The PeopleFinder group managed to pull it off in four days for zero dollars.

"The goal was not to overengineer our tools for the data-entry effort," Zuckerman says, "but to build something very quickly that would let people lend a hand. The solution we came up with was adequate to let 3,000 people participate. And 3,000 people, lightly coordinated, can do impressive things." Zuckerman is reluctant to compare the speed of PeopleFinder with the slow government response to Katrina. "We weren't pulling people from toxic waters," he says. But he does think that the decentralized nature of PeopleFinder has advantages: "One of the reasons PeopleFinder was deployed so quickly is that we had no one to answer to. When no one is approving your work, it's an invitation to solve problems in whatever way you want. I suspect there are many folks involved with the government response who wished they'd had that much flexibility and freedom."

There were other decentralized responses to Katrina. Barely 48 hours after the hurricane hit, two Web designers in Utah launched a site called www. katrinahousing.org to connect evacuees with people all across the country who had a spare bedroom or a guest cottage or even a foldout couch. Two weeks later, 5,000 people had found temporary homes through the site.

Of course, it's impossible to benefit from services like Katrinahousing and Katrinalist if you don't have Internet access. Most of the region affected by Katrina couldn't make a landline phone call after the storm hit, much less log on to the Web. But groups set out to remedy that problem by creating improvised wireless networks in damaged areas, distributing computers and "voice over IP" phones to storm victims and first responders, and establishing low-power FM radio stations in places like the Astrodome. According to the Champaign-Urbana Community Wireless Network home page, the groups involved in the project shipped 2,600 pounds of equipment to the region within days.

The people at the forefront of these efforts had no professional disaster experience. All they had was technical expertise and access to a vast network of people willing to volunteer time, provide shelter, or donate equipment.

Grassroots efforts can replace certain government tasks when disaster strikes.

Killing Cancer With Red-Hot Nanotubes | Nanotechnology | DISCOVER Magazine

2007-10-30T15:34:00.000-07:00

Killing Cancer With Red-Hot Nanotubes | Nanotechnology | DISCOVER Magazine

If a silver bullet that kills cancer is ever developed, the man holding the gun might be physical chemist Hongjie Dai of Stanford University. Dai's research team is testing a cancer killer that does not harm healthy cells and acts without drugs or chemotherapy. "It should work for all cancers," says Dai, "because the mechanism is so simple."

Carbon nanotubes (green) take
aim at cancer cell nuclei (red).

Dai's team coats carbon nanotubes—hollow cylinders of carbon only a few atoms wide—in folic acid, a molecule that binds with certain types of cancers, including breast cancer. Once the cancer cells absorb the carbon, the researchers fire a near-infrared laser at the cells for two minutes. The beam passes harmlessly through living tissue, but the nanotubes get so hot they roast nearly all of the cancer cells after one exposure.

Last year, researchers at Rice University developed a similar treatment that uses a near-infrared laser to heat nanoshells—microscopic glass beads coated in gold that are too large to be absorbed by healthy cells but small enough to sneak inside tumors through their blood vessels. The Houston-based company Nanospectra has licensed the treatment, and company president Don Payne expects to begin testing it on cancer patients within a year.

Discover Dialogue: Harvard Clinician John Abramson | Health Policy | DISCOVER Magazine

2007-10-30T15:31:00.000-07:00

Discover Dialogue: Harvard Clinician John Abramson | Health Policy | DISCOVER Magazine

November, 2005:

John Abramson is a clinical instructor of primary care at Harvard Medical School. He began his career in Appalachia, serving in the National Health Service Corps. In 1982 he became a family physician in Hamilton, Massachusetts, and practiced there for 20 years. He was selected by his peers three times as one of the best family doctors in the state. After researching his book, Overdosed America, he says health care in the United States is becoming less effective than in other industrialized countries while becoming much more expensive.

Interview:

Enemy Anemones Wage All-Out War | LiveScience

2007-10-30T15:26:00.000-07:00

Enemy Anemones Wage All-Out War | LiveScience

When the tide is out, sea anemones sit quiet and still. It's a totally different scene once the tide rolls back in, as neighboring colonies of polyps wage all-out war.

Each colony is an "army," with the troops divided up into scout, warrior, and reproductive rankings, new research shows.

Large colonies of the sea anemone Anthopleura elegantissima claim turf on tidal boulders, which they vehemently defend.

As the tide starts to cover the colonies, "scouts" move to the border and look for empty space to claim. The "warrior" anemones – which are larger and well-armed with stinging cells – provide backup by inflating their arms and slapping at enemies, sometimes from four rows back off the front lines.

Meanwhile, in the center of the colony, poorly armed anemones concentrate on reproduction, making sure there are enough "troops" to maintain the colony.

And they coordinate all these complex behaviors without a single brain among them.

Warring colonies form boundary zones – which can stay in place for years – between the two armies. Anemones that contact soldiers from another colony will fight, whacking each other with special tentacles that stick stinging cells on their enemies.

The research was conducted by David Ayre of the University of Wollongong, Australia and Rick Grosberg from University California, Davis. They had previously studied one-on-one fights between sea anemones, but this study was the first to observe two entire colonies duking it out.

Rankings in the colony appear to depend on a combination of signals from enemy stings and the colony's genetics, say the researchers. Different colonies react differently to similar signals. This causes colonies to organize their troops in different ways.

Sea anemones – named after a terrestrial flower – are water-dwelling, filter feeding animals. As members of the phylum Cnidaria, they are closely related to coral and jellyfish. Sea anemones have a foot which most species use to anchor themselves in sand or attach to rocks. Other species use their foot to attach to kelp, but some are free-swimming.

The new findings, announced today, were detailed in the June issue of the journal Animal Behaviour.

Energy | Alternative Energy | DISCOVER Magazine

2007-10-30T15:23:00.000-07:00

Energy | Alternative Energy | DISCOVER Magazine

October, 2005:

In organisms that run the gamut from microbes to magnolias, photosynthesis creates biomass. Water (H2O) plus carbon dioxide (CO2) plus light energy (solar radiation) produces carbohydrates plus oxygen. Normally, no hydrogenase (a natural enzyme that promotes the formation of gaseous hydrogen) is involved in the process. But with microbes, it is possible to intervene genetically in ways that encourage the activation of hydrogenase enzymes. The end result is an altered photosynthetic process that produces less oxygen and more hydrogen.

Researchers at the National Renewable Energy Laboratory in Golden, Colorado, have already succeeded in converting solar energy directly and continuously into hydrogen by manipulating photosynthesis in Chlamydomonas reinhardtii, a common species of green algae. Biologist Michael Seibert and his colleagues found they could activate hydrogenase during photosynthesis by withholding sulfate. “This is a neat little system that shows that you can get an alga to produce hydrogen for days. In fact, we’ve now done it for about six months, continuously,” says Seibert.

Ramping up the efficiency and scale of the photosynthesis-to-hydrogen process to industrial production will be a challenge. But strange as it may seem, visions of pond scum may soon be dancing in energy analysts’ heads. Seibert offers this scenario: “Imagine if 200 million passenger vehicles in this country were fuel-cell driven—and that may be something that happens—and we could get this process working at a 10 percent conversion efficiency. Then it would take an area of bioreactors—hydrogen-impermeable covered ponds, essentially—equivalent to a square plot about 100 miles on each side in, say, New Mexico or Arizona to produce all the hydrogen needed to run those 200 million vehicles.”

Tissue Engineering | Biotechnology | DISCOVER Magazine

2007-10-30T15:20:00.000-07:00

Tissue Engineering | Biotechnology | DISCOVER Magazine

To improve those odds, tissue engineers are trying to harness the power of stem cells by designing three-dimensional plastic molds, called scaffolds or matrices, that resemble organs or body parts. When a soup of nutrients and stem cells is squirted over a matrix, stem cells may grow into a hunk of tissue that can later be transplanted into a waiting patient. Somehow, the matrix imparts critical organizing information to the cells.

Researchers have successfully created simple tissues such as skin, cartilage, and bone. More complex structures—an ear and teeth—have also been grown. But the hope is that a complex organ, like a kidney or a heart, can be built.

Customized hearts, arteries, or valves would be a boon because substitutes leave much to be desired. Prosthetic devices can’t grow with young patients. Donor valves, whether from cadavers or pigs, fail after 10 to 15 years and sentence the recipient to a lifetime of immunosuppressive drugs to combat rejection. A heart, artery, or valve built from a patient’s own cells may never be rejected.

In what are among the earliest clinical trials, German researchers have created hybrid replacement valves. They started by removing valves from donor cadavers. Then they stripped the valves of rejection-provoking cells, leaving only an elastin-and-collagen matrix, and seeded the valves with stem cells taken from a vein in the leg or arm. The stem cells knit themselves into this donor matrix and, when the valve was transplanted, functioned well for more than three years. Critics of the protocol say it’s not ideal, because donor heart valves are still in short supply. So researchers are hammering away on two fronts: nailing down how stem cells work—and constructing better matrices.

Oceanography | Robots | DISCOVER Magazine

2007-10-30T15:17:00.000-07:00

Oceanography | Robots | DISCOVER Magazine

October, 2005:

Starting next year a global project called Neptune, for North East Pacific Time-series Undersea Networked Experiments, will lay wire-and-fiber-optic cable over a 200,000-square-mile region of the seismically active Juan de Fuca tectonic plate off the northwest coast of the United States. The cables will deliver tens of kilowatts of power so that scientists can plug sensors into the network, sending back real-time data on composition, bacteria, and more. Self-guided robotic devices will eventually be deployed to observe sudden events, such as volcanic eruptions, and then head to underwater bases for recharging. Unlike manned ocean voyages, which are inherently limited to a small crew of scientists, the network will be wired to the Internet, so researchers anywhere in the world can log on. McNutt’s group is building a test site for the American contribution to Neptune.

Nanotechnology | Nanotechnology | DISCOVER Magazine

2007-10-30T14:03:00.000-07:00

Nanotechnology | Nanotechnology | DISCOVER Magazine

October, 2005:

How do the basic components of living systems construct themselves in such stunning variety, yet with such unerring precision and with so little energy? Scientists are gradually beginning to discover—and exploit—the rules of autonomous self-organization. Many researchers believe that sort of kinder, gentler dynamic self-assembly will soon be widely available, as scientists learn to nanoengineer more chemicals that can combine only in certain specific orientations, like Lego blocks. Some of the most dramatic accomplishments to date employ self-assembling artificial materials to promote complex biological repair.

Science Education | Physics & Math | DISCOVER Magazine

2007-10-30T14:00:00.000-07:00

Science Education | Physics & Math | DISCOVER Magazine

October, 2005:

My early physics education was very strange,” says theoretical physicist Lee Smolin. Strange, but effective. In the early 1970s, Smolin’s mentors at Hampshire College in Amherst, Massachusetts, flipped the usual order of courses, teaching quantum mechanics to freshmen and classic Newtonian regimes to upperclassmen. Smolin, a researcher at the Perimeter Institute for Theoretical Physics in Waterloo, Ontario, and a major contributor to loop quantum gravity theory, worries that the best and brightest students are turning to other disciplines because basic physics curricula are stodgy.

ooOoOoo

DEAN KAMEN, founder of DEKA Research and Development Corporation in Manchester, New Hampshire, and inventor of the Segway Human Transporter, has made it a personal mission to shore up the sagging interest of American teens in science and engineering. In 1992 he founded First—For Inspiration and Recognition of Science and Technology—which runs an annual nationwide robotics competition that provided 74,000 high school students this year with creative motivation and hands-on engineering experience.

What gave you the idea that the span from ages 7 to 17 is a crucial decade when it comes to exposing kids to science and engineering?

K: I looked at my own life and the lives of people I know. Very few people I know get into their twenties, never mind their thirties and beyond, and decide, “I have never done math or science, but I think I will become an engineer or a scientist or a physicist.” Most people, by the time they graduate from high school, have constructed the boundary conditions for what their career options will or will not be.

So the idea is not necessarily to pound more knowledge into kids’ heads during that decade but rather to stretch those boundary conditions?

K: Right. If a kid can come away from a science or engineering program in that decade and think, “I like this, I can do this, this is an option as a career,” then he or she can go on from there and take steps to get the necessary college education.

What if kids don’t?

K: Then we will slide, as other cultures in the world have, into being a second-rate, has-been society. That is a very real risk unless we do something quickly.

Is there an increasing chance that each new generation will be left further behind?

K: Absolutely. A generation or two ago, you could open the hood of a car and, without much training, simply see how it operated. Even a radio—you could see if the tube was lit or not. But now the train is picking up speed. If you don’t grab on, you will be left behind as this thing called technology goes whizzing faster and faster into the future. Take a half-dozen Nobel laureates in medicine in the 1980s: The work that won them the prize is now routinely done in high school biology labs. And there is more competition. This generation of American high school kids will be competing with nearly a billion people of their same generation, people who are hungry for knowledge, passionate and determined to pull themselves up the economic ladder.

Most education in the United States is government funded. Your program runs on corporate donations. What can government learn from you?

K: If our whole program were government funded, there would be strings attached, and it would suffer. But, frankly, it is expensive to run this, so there is a way government funding can help, and it’s a win-win-win situation. Now NASA, as a government agency, needs more scientists, engineers, and roboticists. So well over 100 of our teams are funded directly by NASA this year, and they are fantastic sponsors. This could expand. Let the big science and technology organizations in government—the federal labs, all the places that need technological people—become part of First the same way corporate sponsors do: by adopting high schools and supporting teams.

Does it have to be just with First?

K: No, it’s not a zero-sum game. There is no such thing as a bad program if it gets kids to be more effective at making career choices and becoming responsible citizens. The more we get our program to succeed, the more the other programs it spawns will succeed.

The Brain | Biotechnology | DISCOVER Magazine

2007-10-30T13:52:00.000-07:00

The Brain | Biotechnology | DISCOVER Magazine

October, 2005:

Theodore Berger, a professor of engineering at the University of Southern California, is ready for the era of the bionic brain. He has spent 30 years developing computer chips that can link with neurons in an effort to compensate for memory loss. The chips that can do it exist. Most of the software exists. The challenge is to make a reliable, long-term connection between the hardware and the wetware—one that is unaffected by corrosion, scar tissue, or the shifting and dying of cells in the brain. “That’s the big showstopper,” Berger says.

He is part of a growing movement of researchers struggling to perfect neural prostheses, devices that employ electrodes to receive signals from and transmit them to the brain. Cyberkinetics, a company cofounded by neuroscientist John Donoghue at Brown University, has begun clinical trials on an implant that can transmit signals from a paralyzed person’s motor cortex to a computer or to a prosthetic limb. Several groups, including one led by Ali Rezai of the Cleveland Clinic Center for Neurological Restoration, have tentatively shown that stimulation of the thalamus can relieve chronic pain, obsessive-compulsive disorder, and depression. Similar devices may be able to treat blindness, epilepsy, and Parkinson’s disease. All these applications will depend on solving the connection problem.

Nutrition | Nutrition | DISCOVER Magazine

2007-10-30T13:50:00.000-07:00

Nutrition | Nutrition | DISCOVER Magazine

October, 2005:

Determining the effect of different nutrients on each gene variant is tricky and revolutionary because it would enable people to optimize their diet according to their particular genetics. Jim Kaput, a nutritional genomics researcher at the University of California at Davis and the University of Illinois at Chicago, notes that a percentage of the population has a polymorphic version of the GPDH gene, responsible for making an enzyme that helps cells convert sugar to energy.

Your Brain on Video Games | Mental Health | DISCOVER Magazine

2007-10-30T13:42:00.000-07:00

Your Brain on Video Games | Mental Health | DISCOVER Magazine

July, 2005:

Gee’s epiphany led him to the forefront of a wave of research into how video games affect cognition. Bolstered by the results of recent laboratory experiments, Gee and other researchers have dared to suggest that gaming might be mentally enriching. These scholars are the first to admit that games can be addictive, and indeed part of their research explores how games connect to the reward circuits of the human brain. But they are now beginning to recognize the cognitive benefits of playing video games: pattern recognition, system thinking, even patience. Lurking in this research is the idea that gaming can exercise the mind the way physical activity exercises the body: It may be addictive because it’s challenging.

Earth Without People | Extinction | DISCOVER Magazine

2007-10-30T13:39:00.000-07:00

Earth Without People | Extinction | DISCOVER Magazine

February, 2005:

Given the mounting toll of fouled oceans, overheated air, missing topsoil, and mass extinctions, we might sometimes wonder what our planet would be like if humans suddenly disappeared. Would Superfund sites revert to Gardens of Eden? Would the seas again fill with fish? Would our concrete cities crumble to dust from the force of tree roots, water, and weeds? How long would it take for our traces to vanish? And if we could answer such questions, would we be more in awe of the changes we have wrought, or of nature’s resilience?

Worrying About Killer Flu | Infectious Diseases | DISCOVER Magazine

2007-10-30T13:37:00.000-07:00

Worrying About Killer Flu | Infectious Diseases | DISCOVER Magazine

February, 2005:

Although any new pandemic would be costly and dangerous, there are good reasons to think that avian flu would be unlikely to morph into a strain that is both virulent and highly transmissible among humans. As Ewald has pointed out, the 1918 flu may have developed its unique virulence, and its unique focus on young adults, precisely because of the terrible conditions in wartime Europe. The disease first appeared as a relatively mild outbreak in the United States in the spring of 1918. A far deadlier form incubated among soldiers on the Western Front. It stalked the trenches, the hospitals stacked with wounded, sick, and dying soldiers, the trucks that carted sick and wounded from one crowded hospital to another, the trains on which the immobilized sick lay face-to-face with the helpless wounded, and the boats that returned ill soldiers to the United States.

Only comparable conditions, Ewald says, would allow the development of a highly virulent and transmissible human flu. As the conditions that created the 1918 flu abated, so did the virulence of the disease and its specificity for healthy people in the prime of life. But it did not disappear. For decades after 1918, H1N1 wandered around the planet, a commonplace flu, no more virulent than any ordinary strain, a killer of the very old and the very young. It spread the way human flu strains always do—coughs and sneezes. Precisely because people have to be healthy enough to walk around and cough into other people’s faces, ordinary human flu strains must be relatively mild to spread. Lethal flu requires the sort of conditions found in the animal markets of Guangdong or the trenches of World War I.

The Chandra X-ray Observatory Center :: Gateway to the Universe of X-ray Astronomy!

2007-10-30T13:35:00.000-07:00

The Chandra X-ray Observatory Center :: Gateway to the Universe of X-ray Astronomy!

from P.42 February, 2005:

The Chandra X-ray Observatory Center:

This vast online resource contains Chandra images, scientific explorations and related links.

Testing Darwin | Computers | DISCOVER Magazine

2007-10-30T13:26:00.000-07:00

Testing Darwin | Computers | DISCOVER Magazine

February, 2005:

quotes from the article:

The Avida team makes their software freely available on the Internet, and creationists have downloaded it over and over again in hopes of finding a fatal flaw. While they’ve uncovered a few minor glitches, Ofria says they have yet to find anything serious. “We literally have an army of thousands of unpaid bug testers,” he says. “What more could you want?”

00O0O00

Bringing diversity into Avida has brought more bad news for those who think complexity cannot evolve. Ofria decided to run the complexity experiment over again, this time with a limit on the supply of numbers. “It just floored me,” he says. “I went back and checked this so many ways.” In the original experiment, the organisms evolved the equals routine in 23 out of 50 trials. But when the experiment was run with a limited supply of numbers, all the trials produced organisms that could carry out the equals routine. What’s more, they needed only a fifth of the time to do it.

00O0O00

Human society depends on countless acts of cooperation and personal sacrifice. But that doesn’t make us unique. Consider Myxococcus xanthus, a species of bacteria that Lenski and his colleagues study. Myxococcus travels in giant swarms 100,000 strong, hunting down E. coli and other bacteria like wolves chasing moose. They kill their prey by spitting out antibiotics; then they spit out digestive enzymes that make the E. coli burst open. The swarm then feasts together on the remains. If the Myxococcus swarm senses that they’ve run out of prey to hunt, they gather together to form a stalk. The bacteria at the very top of the stalk turn into spores, which can be carried away by wind or water to another spot where they can start a new pack. Meanwhile, the individuals that formed the stalk die.

This sort of cooperation poses a major puzzle because it could be undermined by the evolution of cheaters. Some bacteria might feast on the prey killed by their swarm mates and avoid wasting their own energy making antibiotics or enzymes. Others might evolve ways of ensuring that they always end up becoming spores and never get left behind in the dead stalk. Such cheaters are not theoretical: Lenski and his colleagues have evolved them in their lab.

The Avida team is now trying to address the mystery of cooperation by creating new commands that will let organisms exchange packages of information. “Once we get them to communicate, can we get them to work together to solve a problem?” asks Ofria. “You can set up an information economy, where one organism can pay another one to do a computation for it.”

If digital organisms cooperate, Ofria thinks it may be possible to get them working together to solve real-world computing problems in the same way Myxococcus swarms attack their prey. “I think we’ll be able to solve much more complex problems, because we won’t have to know how to break them down. The organisms will have to figure it out for themselves,” says Ofria. “We could really change the face of a lot of computing.”

ooOoO00

Ofria has been finding that digital organisms have a way of outwitting him as well. Not long ago, he decided to see what would happen if he stopped digital organisms from adapting. Whenever an organism mutated, he would run it through a special test to see whether the mutation was beneficial. If it was, he killed the organism off. “You’d think that would turn off any further adaptation,” he says. Instead, the digital organisms kept evolving. They learned to process information in new ways and were able to replicate faster. It took a while for Ofria to realize that they had tricked him. They had evolved a way to tell when Ofria was testing them by looking at the numbers he fed them. As soon as they recognized they were being tested, they stopped processing numbers. “If it was a test environment, they said, ‘Let’s play dead,’ ” says Ofria. “There’s this thing coming to kill them, and so they avoid it and go on with their lives.”

ooOoOoo

More: http://devolab.cse.msu.edu/

The Evolutionary Origin of Complex Features: R.E. Lenski, C. Ofria, R.T. Pennock, and C. Adami in Nature (2003), pages 139-145.

As the World Warms | Global Warming | DISCOVER Magazine

2007-10-30T11:59:00.000-07:00

As the World Warms | Global Warming | DISCOVER Magazine

February, 2005:

Hardly a day goes by, it seems, without fresh evidence of climate change. New reports—from Greenland to Antarctica—show rising temperatures at both poles and changing conditions in what were once stable, icebound areas. A sampling:

• Data from NASA, European, and Canadian satellites show a continuing impact from the collapse of the Larsen B ice shelf in early 2002. Nearby glaciers along the Antarctic Peninsula are now flowing into the open ocean three to eight times faster than when they were buttressed by the ice shelf, contributing significantly to rising sea levels. Additionally, NASA satellites found that some glaciers in the area have thinned by up to 125 feet.

• Populations of krill have declined by 80 percent in the Southern Ocean in the last 30 years. An international team of oceanographers attributed the drop to a loss of winter sea ice that supports the algae on which young krill feed. Krill, small shrimplike creatures, form a cornerstone of the southwest Atlantic food web.

• NASA satellites confirm that the rate of ice flow into the ocean from Greenland’s Jakobshavn Isbrae glacier—the continent’s fastest moving—has doubled between 1997 and 2003, increasing the rate of sea level rise by 4 percent.

• Temperatures are going up twice as fast in the Arctic as in the rest of the world, according to an impact statement by the Arctic Council, a consortium of 14 countries and six organizations of indigenous peoples. Further, the group reports that polar snow cover declined 10 percent in 30 years, and the thaw of permafrost will likely creep hundreds of miles northward within this century. The council also predicts that by the end of the century the famously ice-locked Northwest Passage through the Arctic Ocean will become open water in summer.

93: Broccoli Kicks Cancer | Nutrition | DISCOVER Magazine

2007-10-30T11:51:00.000-07:00

93: Broccoli Kicks Cancer | Nutrition | DISCOVER Magazine

January, 2005:

Vegetables pack a roundhouse punch against cancer, according to a September report by nutritional scientist Keith Singletary of the University of Illinois at Urbana-Champaign. Studies had shown that substances in some vegetables help prevent mutations that turn normal cells cancerous. Now Singletary’s research reveals a phytonutrient in vegetables can also kill breast cells that are already cancerous.

Singletary added sulforaphane, a chemical in broccoli, kale, brussels sprouts, and other cruciferous vegetables, to cultures of human breast cancer cells. Within hours, the cells stopped dividing. Sulforaphane seems to work by interrupting the tiny microtubules that normally pull pairs of chromosomes apart when cells divide. Without the tubules, malignant cells can’t multiply. And sulforaphane seems to leave normal cells untouched.

Singletary warns that what happens in the test tube may not be what happens in the body. “We need to better understand the effects of this compound at levels that are physiologically relevant,” he adds. “But what we can say is that this is more evidence that including plant foods in our diets is generally a good idea.”

78: Dietary Study Jolts Scientists | Nutrition | DISCOVER Magazine

2007-10-30T11:49:00.000-07:00

78: Dietary Study Jolts Scientists | Nutrition | DISCOVER Magazine

January, 2005:

Even jaded nutritionists, long inured to the public’s atrocious dining habits, were taken aback by the study. “The dose really does make the poison,” says epidemiologist Gladys Block, the study’s lead author. “We knew people ate a lot of this stuff. But that much?”

Not only do these foods fuel the nation’s obesity epidemic, says Block, they are displacing the nutrient-rich fruits and vegetables necessary to fend off disease. The result, Block says, is an unappetizing paradox: a nation of people simultaneously overfed and undernourished.

Under pressure from food manufacturers, health officials have hesitated to demonize particular foods as junk and instead proffer general advice about good nutrition. Block says it’s time to tell Americans to eat more foods that matter—and to say aloud that, nutritionally speaking, some foods do not.

40: Security Scanner Sees Through Ship Containers | Weapons & Security | DISCOVER Magazine

2007-10-30T11:47:00.000-07:00

40: Security Scanner Sees Through Ship Containers | Weapons & Security | DISCOVER Magazine

January, 2005:

Scientists at Lawrence Livermore National Laboratory in California began testing a device in May that can quickly detect concealed nuclear materials. The invention could plug a gaping hole in American security: the unexamined 6 million ship containers that enter U.S. ports every year.

Physically searching every container would cause shipping to grind to a halt. Today’s scanners—just big X-ray devices—would miss a terrorist’s nuclear bomb or a lump of enriched plutonium if it were shielded in a simple steel box. The Livermore scanner is not so easily fooled. It bombards a suspect cargo with neutrons. If the neutrons hit fissile material, gamma rays are produced that can be instantly picked up by low-cost detectors. The technique, called active neutron interrogation, readily penetrates most shielding, although it does have an Achilles’ heel. “Lead is transparent to neutrons, but hydrocarbons like agricultural products are tougher,” says Dennis Slaughter, one of the scanner’s originators.

Researchers say that the neutrons emitted by the scanner would pose no threat to operators, to cargo, or even to human stowaways. Livermore physicist Adam Bernstein, leader of detector design, says he and his team are close to their goal: detecting as little as a few pounds of plutonium while taking less than a minute to scan each container and creating no more than one in 1,000 false alarms. Bernstein expects to have a full-size prototype ready to start sniffing cargo containers within a couple of years.

79: Bald Men: This Mouse Is for You | Genetics | DISCOVER Magazine

2007-10-30T11:45:00.000-07:00

79: Bald Men: This Mouse Is for You | Genetics | DISCOVER Magazine:

January, 2005:

"Earlier work hinted that skin follicles harbor stem cells kept in reserve to replace epidermal cells when they die. “The critical question was whether there really is a cell that can do it all—epidermis, hair, sebaceous glands,” says Fuchs. “And now we know that we really have a bona fide stem cell.” That means curing baldness could just be the beginning. “Maybe these stem cells could do other things,” says Fuchs. “Maybe they could make corneas for the treatment of blindness.”"

34: Prostate Cancer Test Questioned | Cancer | DISCOVER Magazine

2007-10-30T11:43:00.000-07:00

34: Prostate Cancer Test Questioned | Cancer | DISCOVER Magazine

January, 2005:

Back in 1987, Stamey was among the first to suggest that the level of PSA, a protein normally produced by the prostate gland, might be useful in detecting prostate cancer. But based on an analysis of more than 1,300 prostates removed over the past 20 years, Stamey reported in the October issue of the Journal of Urology that the PSA test is currently predictive of cancer in only 2 percent of cases. Because of the increase in screening and detection of prostate cancer over the past two decades, he now says a higher PSA level may most often reflect a harmless age-related increase in prostate size.

When doctors follow up a high PSA level with a biopsy, they often find cancer. But this is only because most men have some degree of prostate cancer. Studies have shown that 80 percent or more of men over age 70 die with—but not from—prostate cancer. As counterintuitive as it seems, detecting prostate cancer is not always in the patient’s best interest. Once cancer is diagnosed, most men opt for treating it either with radiation or removal of the prostate. In many cases, that leads to impotence, urinary incontinence, and other unpleasant side effects.

Turning Point | Global Warming | DISCOVER Magazine

2007-10-30T11:40:00.000-07:00

1: Turning Point | Global Warming | DISCOVER Magazine:

January, 2005:

"Evidence of global warming became so overwhelming in 2004 that now the question is: What can we do about it?"

When our grandchildren write the history of global warming—how we discovered and debated it, and what we finally did about it—the stinkbugs that ate Maggs’s tomatoes may not loom large. Nor will the blue mussels that showed up this past year off Spitsbergen, Norway, at 78 degrees north latitude. Nor even the catastrophic failure of Scottish seabirds to breed, which some researchers attributed to a dearth of plankton in the warming waters of the North Sea. But our descendants may well decide that it was the long string of such close-to-home observations—the early springs, the shifting ranges of plants and animals, the mortal heat waves—that, more than any climatological data, convinced people that something needed to be done about global warming. And maybe, just maybe, those future historians will decide that 2004 was the turning point.

Circulation Booster | Heart Disease | DISCOVER Magazine

2007-10-30T11:38:00.000-07:00

Circulation Booster | Heart Disease | DISCOVER Magazine

January 2005:

Painful blockages of arteries in the legs—called peripheral arterial obstructive disease, or PAOD—are less familiar than the ones that cut off blood flow to the heart, but they can be just as dangerous. Serious cases can lead to gangrene, kidney damage, stroke, and even death, but arterial bypass surgery or amputation rarely alleviates the condition. Now cardiologist Brian Annex of Duke University Medical Center has found a promising experimental treatment that might cure the disease with little more than an injection.

Annex and his colleagues focused on a gene that induces the body to grow new blood vessels around a blocked artery, a process called angiogenesis. The researchers injected this gene into rabbits with simulated PAOD. Soon the rabbits began producing proteins that triggered angiogenesis in the animals’ legs and halted the process of cell death that leads to gangrene. A few previous studies on animals have induced vessel growth with gene therapy, but this one provides a template for the next stage in the research: clinical trials on humans. One set of clinical trials is already under way at the National Institutes of Health, and another is in the works at Duke University.

Eight million to 12 million people in this country have PAOD; among the 250,000 with the severe form, up to 40 percent die within a year. “We’d love to improve on that,” Annex says.

Genetics: Stephen Fodor | Genetics | DISCOVER Magazine

2007-10-30T11:35:00.000-07:00

Genetics: Stephen Fodor | Genetics | DISCOVER Magazine:

November, 2004:

"In the late 1980s, long before the human genome had been sequenced, Stephen Fodor and a few scientist pals in Silicon Valley dreamed of putting the entire human genome on a single glass test chip the size of a thumbnail. Late last year, Affymetrix—the company that Fodor founded and heads as CEO—announced the creation of the whole-genome chip. Researchers and doctors can use it to scan the entire library of human genes and, in a single semiautomated experiment, zoom out and spot the interactive activity of many far-flung bits of DNA in a particular type of cancer, for example, then track the tumor’s response to treatment. Last spring the company created a slightly different tool that promises to be at least as transformative: two tiny glass grids, each containing 50,000 SNPs (pronounced “snips”), or single nucleotide polymorphisms, which can be thought of as all the slightly different spellings of many genetic “words.” Because geneticists use SNPs as markers throughout the genome, this new tool can tease out the link from a particular pattern of widely spaced genes to such complex diseases as autism, diabetes, and cancer. Fodor’s big idea—to wed crisp computer-chip technology to gooey biology—started it all."

Neuroscience: John Donoghue | Machine-Brain Connections | DISCOVER Magazine

2007-10-30T11:32:00.000-07:00

Neuroscience: John Donoghue | Machine-Brain Connections | DISCOVER Magazine

November, 2004:

John Donoghue is building a brain decoder that could transform the lives of people paralyzed by injury or disease. Those who have lost the ability to move their limbs often have perfectly intact brains, so Donoghue hopes to implant a chip that can monitor their brain activity and convert their intentions into computer commands. In its current version, the chip’s 100 hair-thin electrodes listen to neurons firing in an area that controls arm movement and translate the activity into electronic signals. A program then decodes the brain signals into commands that direct a cursor on a computer screen. Donoghue hopes the chip can eventually control appliances or even robotic limbs. “We’re effectively rewiring the nervous system—not biologically but with real wires,” says Donoghue. So far, more than 20 monkeys have been equipped with the implanted chip, and four of them have successfully willed a cursor to follow a moving target. Now Cyberkinetics, the company Donoghue cofounded to develop the device they call BrainGate, is preparing to test it in five paralyzed humans. “People with these kinds of injuries are perfectly capable of leading full and productive lives,” says Donoghue. “They just can’t get their signals out.”

This Is Your Ancestor | Human Evolution | DISCOVER Magazine

2007-10-30T11:29:00.000-07:00

This Is Your Ancestor | Human Evolution | DISCOVER Magazine

November, 2004:

The sponge is the earliest, most primitive multicelled animal, Sogin says. Some scientists believe the ability to grow different cell types started animals on the evolutionary road to becoming humans. With just a few kinds of cells, only loosely connected, the sponge manages to produce a variety of asymmetrical shapes, from cups and fans to tubes and piecrust shapes. Sponges survive handsomely on their own and can even shelter other sea creatures: Scientists found a large sponge in the Gulf of Mexico hosting 16,000 snapping shrimp and 1,000 other aquatic animals. The sponge’s cells, its calcium carbonate or glasslike silica spicules, and the mass of collagen that forms its visible body all create a network of tunnels and chambers, with little flailing hairs called cilia on the walls that wave the water through and filter out plankton and waste. No matter how large the sponge, it can eat only what its individual cells can absorb.

Sponges are also the earliest sexual reproducers; most are hermaphroditic, producing both eggs and sperm, which they release into the water. The sperm drift along until they find their way into the tunnels and caves of another sponge. But the sponge has other reproductive options. If you push one through a sieve, breaking free its individual cells, these cells will drift until they find each other, then stick together and create an exact genetic duplicate of the parent. If wounded, a sponge doesn’t need to grow new tissue; it simply moves old cells into the wound to close it. These techniques have helped sponges survive at least 500 million years. A few have remarkable capabilities. One, living in a Mediterranean underwater cave, traps small crustaceans with the sharp, glassy spikes jutting from its body, then surrounds them with its cells and digests them.

Biologist Calhoun Bond, then at the University of North Carolina at Chapel Hill, found in 1986 that sponges don’t just sit still—many actually move. Using time-lapse microscopy, he filmed freshwater sponges slowly crawling across the bottom of their containers. He found that larger, saltwater sponges do the same by extruding flat paddlelike extensions of their bodies and pulling themselves along, often climbing the sides of their glass tanks in labs. One sponge, a lavender beauty called Heliclona loosanoffi, moved four millimeters a day.

Cancer's Master Genes | Cancer | DISCOVER Magazine

2007-10-30T11:20:00.000-07:00

Cancer's Master Genes | Cancer | DISCOVER Magazine

November, 2004:

The idea that everybody’s genes are pretty much the same, a central conceit of the Human Genome Project, may need some revising. A group of researchers has accidentally discovered that our DNA contains substantial areas of repeated genes—and the location and number of these genetic echoes vary considerably from person to person.

Biologist Michael Wigler of Cold Spring Harbor Laboratory, who led the study, started out studying genes in cancer cells but soon realized he was seeing unexpected patterns in the healthy cells he examined for reference. Although he does not know exactly what the large-scale repeats mean, he suspects that the number of genes a person is carrying may be just as important as the codes those genes contain. “More copies probably means more expression of whatever that gene is coding for,” he says. Several of the repeated regions involve genes regulating appetite and body weight; others occur in regions associated with breast cancer, leukemia, and nerve development, leading Wigler and his teammates to speculate that differences in these copied genes could help explain why some people are particularly susceptible to obesity, cancer, or neurological diseases.

If the disparities are so large, why has nobody found them before? Part of the answer is simply that the most commonly used DNA probes tell whether or not a given sequence is present, not how many times it appears in an individual cell. As a result, researchers have tended to focus on point variations, such as the mutation or deletion of a single DNA letter within a gene. “People have known isolated cases where this sort of multiple copying existed,” Wigler says. “But everyone assumed that these were just anomalies, and so it wasn’t something anyone was looking for.”

We're Not So Alike After All | Genetics | DISCOVER Magazine

2007-10-30T11:18:00.000-07:00

We're Not So Alike After All | Genetics | DISCOVER Magazine

November, 2004:

The idea that everybody’s genes are pretty much the same, a central conceit of the Human Genome Project, may need some revising. A group of researchers has accidentally discovered that our DNA contains substantial areas of repeated genes—and the location and number of these genetic echoes vary considerably from person to person.

Biologist Michael Wigler of Cold Spring Harbor Laboratory, who led the study, started out studying genes in cancer cells but soon realized he was seeing unexpected patterns in the healthy cells he examined for reference. Although he does not know exactly what the large-scale repeats mean, he suspects that the number of genes a person is carrying may be just as important as the codes those genes contain. “More copies probably means more expression of whatever that gene is coding for,” he says. Several of the repeated regions involve genes regulating appetite and body weight; others occur in regions associated with breast cancer, leukemia, and nerve development, leading Wigler and his teammates to speculate that differences in these copied genes could help explain why some people are particularly susceptible to obesity, cancer, or neurological diseases.

If the disparities are so large, why has nobody found them before? Part of the answer is simply that the most commonly used DNA probes tell whether or not a given sequence is present, not how many times it appears in an individual cell. As a result, researchers have tended to focus on point variations, such as the mutation or deletion of a single DNA letter within a gene. “People have known isolated cases where this sort of multiple copying existed,” Wigler says. “But everyone assumed that these were just anomalies, and so it wasn’t something anyone was looking for.”