hide complexity

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

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

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

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

FT.com c/o @valdiskrebs

Jonah Lehrer

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

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

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

TED




on Ron Eglash's website

on time

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

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

wright / roughgarden

Roughgarden, The Genial Gene

11.5.2006 tsn Roughgarden, Dawkins, Ayala, Porco

Fractal Quantum Gravity

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

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

Wolfram Blog : Quick-Starting Mathematica with Palettes

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.