The image is from Edward H. Adelson at MIT, and you can find my original source here. More details (proof, etc) on Adelson’s site here, which includes this explanation:

The visual system needs to determine the color of objects in the world. In this case the problem is to determine the gray shade of the checks on the floor. Just measuring the light coming from a surface (the luminance) is not enough: a cast shadow will dim a surface, so that a white surface in shadow may be reflecting less light than a black surface in full light. The visual system uses several tricks to determine where the shadows are and how to compensate for them, in order to determine the shade of gray “paint” that belongs to the surface.

The first trick is based on local contrast. In shadow or not, a check that is lighter than its neighboring checks is probably lighter than average, and vice versa. In the figure, the light check in shadow is surrounded by darker checks. Thus, even though the check is physically dark, it is light when compared to its neighbors. The dark checks outside the shadow, conversely, are surrounded by lighter checks, so they look dark by comparison.

A second trick is based on the fact that shadows often have soft edges, while paint boundaries (like the checks) often have sharp edges. The visual system tends to ignore gradual changes in light level, so that it can determine the color of the surfaces without being misled by shadows. In this figure, the shadow looks like a shadow, both because it is fuzzy and because the shadow casting object is visible.

The “paintness” of the checks is aided by the form of the “X-junctions” formed by 4 abutting checks. This type of junction is usually a signal that all the edges should be interpreted as changes in surface color rather than in terms of shadows or lighting.

As with many so-called illusions, this effect really demonstrates the success rather than the failure of the visual system. The visual system is not very good at being a physical light meter, but that is not its purpose. The important task is to break the image information down into meaningful components, and thereby perceive the nature of the objects in view.

(Like the earlier illusion post, this one’s also from my mother-in-law, who should apparently be writing this blog instead of its current—woefully negligent—author.)

Last week, Woods Hole researchers reported a 22-mile-long underwater plume that they mapped out in the Gulf of Mexico in June — a finding indicating that much more oil may lie deep underwater and be degrading so slowly that it might affect the ecosystem for some time. Also last week, University of Georgia researchers estimated up to 80 percent of the spill may still be at large, with University of South Florida researchers finding poisoned plankton between 900 feet and 3,300 feet deep. This differed from the Aug. 4 proclamation by Administrator Jane Lubchenco of the National Oceanic and Atmospheric Administration that three-quarters of the oil was “completely gone’’ or dispersed and the remaining quarter was “degrading rapidly.’’

But then comes the Lawrence Berkeley National Laboratory, which this week said a previously unclassified species of microbes is wolfing down the oil with amazing speed. This means that all the scientists could be right, with massive plumes being decimated these past two months by an unexpected cleanup crew from the deep.

This is often the case for anything remotely complex: the opacity of the research process to the general public, the communication skills of various institutions, the differing perspective between what the public cares about (whose fault is it? how bad is it?) versus the interests of the researchers, and so on.

It’s a basic issue around communicating complex ideas, and therefore affects visualization too — it’s rare that there’s a single answer.

On a more subjective note, I don’t know if I agree with the premise of the editorial is that it’s on the government to sort out the mess for the public. It’s certainly a role of the government, though the sniping at the Obama administration makes the editorial writer sound one who is equally likely to bemoan government spending, size, etc. But I could write an equally (perhaps more) compelling editorial making the point that it’s actually the role of newspapers like the Globe to sort out newsworthy issues that concern the public. But sadly, the Globe, or at least the front page of boston.com, has been overly obsessed with more click-ready topics like the Craigslist killer (or any other rapist, murderer, or stomach-turning story involving children du jour) and playing “gotcha” with spending and taxes for universities and public officials. What a bunch of ghouls.

(Thanks to my mother-in-law for the article link.)

More from Kokichi Sugihara (including an explanation of how this works) can be found here.

(thanks to my mother-in-law, who sent the link)

From the explanation:

The picture clearly shows the path of the sun through the sky over the last six months. I believe you can see we didn’t have a great summer by the broken lines at the top. More sun shone in the month of October.

The post also links to a description of how to make your own.

Dear colleagues,

We invite you to participate in the first EMBO Workshop on Visualizing Biological Data (VizBi) 3 – 5 March 2010 at the EMBL’s new Advanced Training Centre in Heidelberg, Germany.

The goal of the workshop is to bring together, for the first time, researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). We have assembled an authoritative list of 29 invited speakers who will present an exciting program, reviewing the state-of-the-art and perspectives in each of these areas. The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data.

The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a ‘fastforward’ presentation about their work (limited to 30 seconds and 1 slide).

To apply to join the workshop, please go to http://vizbi.org and submit an abstract and image related to your work. Submissions close on 16 November 2009. Since places are limited, participants will be selected based on the relevance of their work to the goals of the workshop.

Notifications of acceptance will be sent within three weeks after the close of submissions.

We plan to award a prize for the submitted image that best conveys a strong scientific message in a visually compelling manner.

Please forward this announcement to anyone who may be interested. We hope to see you in Heidelberg next spring!

Seán O’Donoghue, EMBL
Jim Procter, University of Dundee
Nils Gehlenborg, European Bioinformatics Institute
Reinhard Schneider, EMBL

If you have any questions about the registration process please contact:

Adela Valceanu

Conference Officer
European Molecular Biology Laboratory
Meyerhofstr. 1
D-69117 Heidelberg
Tel: +49-6221-387 8625
Fax: +49-6221-387 8158
Email: valceanu@embl.de

For full event listings please visit our website or sign up for our newsletter.

Which also reminds me, I oughta finish cooking a few back-burner genetics projects before they go bad…

To quote myself, because it looks important:

We often think of scientific ideas, such as Darwin’s theory of evolution, as fixed notions that are accepted as finished. In fact, Darwin’s On the Origin of Species evolved over the course of several editions he wrote, edited, and updated during his lifetime. The first English edition was approximately 150,000 words and the sixth is a much larger 190,000 words. In the changes are refinements and shifts in ideas — whether increasing the weight of a statement, adding details, or even a change in the idea itself.

The idea that we can actually see change over time in a person’s thinking is fascinating. Darwin scholars are of course familiar with this story, but here we can view it directly, both on a macro-level as it animates, or word-by-word as we examine pieces of the text more closely.

This is hopefully the first of multiple pieces working with this data. Having worked with it since last December, I’ve been developing a larger application that deals with the information in a more sophisticated way, but that’s continually set aside because of other obligations. This simpler piece was developed for Emily King’s “Quick Quick Slow” exhibition opening next week at Experimenta Design in Portugal. As is often the case, many months were spent to try to create something monolithic, then in a very short time, an offshoot of all that work is developed that makes use of that infrastructure.

Oddly enough, I first became interested in this because of a discussion with a friend a few years ago, who had begun to wonder whether Darwin had stolen most of his better ideas from Alfred Russel Wallace, but gained the notoriety and credit because of his social status. (This appealed to the paranoid creator in me.) She cited the first edition of Darwin’s text as incoherent, and that it gradually improved over time. Interestingly (and happily, I suppose), the process of working on this piece has instead shown the opposite, and I have far greater appreciation for Darwin’s ideas than I had in the past.

Specter’s defection is only relevant (if it’s relevant at all) until the next election cycle, so it’s frustrating to see something that could affect us for five to fifty years pre-empted by what talking heads are more comfortable bloviating about. It’s a reminder that with all the progress we’ve made on how quickly we can distribute news, and the increase in the number of outlets by which it’s available, the quality and thoughtfulness of the product has only been further undermined.

Update, a few hours later: it’s a battle of the readers! now Jamie Alessio passed along a high quality video of the the President’s speech from the White House channel on YouTube. Here’s the embedded version:

I believe it is not in our American character to follow – but to lead. And it is time for us to lead once again. I am here today to set this goal: we will devote more than three percent of our GDP to research and development. We will not just meet, but we will exceed the level achieved at the height of the Space Race, through policies that invest in basic and applied research, create new incentives for private innovation, promote breakthroughs in energy and medicine, and improve education in math and science. This represents the largest commitment to scientific research and innovation in American history.

I’m not much for patriotism rah-rah but it’s hard not to get fired up about this. I found the rest of his speech remarkable as well, listing specific technologies that emerged from basic research, too often overlooked:

The Apollo program itself produced technologies that have improved kidney dialysis and water purification systems; sensors to test for hazardous gasses; energy-saving building materials; and fire-resistant fabrics used by firefighters and soldiers.

And the announcement of a new agency along the lines of DARPA:

And today, I am also announcing that for the first time, we are funding an initiative – recommended by this organization – called the Advanced Research Projects Agency for Energy, or ARPA-E.

This is based on the Defense Advanced Research Projects Agency, known as DARPA, which was created during the Eisenhower administration in response to Sputnik. It has been charged throughout its history with conducting high-risk, high-reward research. The precursor to the internet, known as ARPANET, stealth technology, and the Global Positioning System all owe a debt to the work of DARPA.

The speech, nearly 5000 words in total (did our former President spill that many words for science during eight years in office?) continues with more policy regarding research, investment, and education–all very exciting to read. But perhaps my most favorite line of all, when he said to the members of the National Academy of Sciences in attendance:

And so today I want to challenge you to use your love and knowledge of science to spark the same sense of wonder and excitement in a new generation.

Our forty-fourth president:

That we are in the midst of crisis is now well understood. Our nation is at war, against a far-reaching network of violence and hatred. Our economy is badly weakened, a consequence of greed and irresponsibility on the part of some, but also our collective failure to make hard choices and prepare the nation for a new age. Homes have been lost; jobs shed; businesses shuttered. Our health care is too costly; our schools fail too many; and each day brings further evidence that the ways we use energy strengthen our adversaries and threaten our planet.

These are the indicators of crisis, subject to data and statistics. Less measurable but no less profound is a sapping of confidence across our land – a nagging fear that America’s decline is inevitable, and that the next generation must lower its sights.

For the politically-oriented math geek in me, his mention of statistics stood out: we now have a president who can actually bring himself to reference numbers and facts. I searched for other mentions of “statistics” in previous inaugural speeches and found just a single, though oddly relevant, quote from William Howard Taft in 1909:

The progress which the negro has made in the last fifty years, from slavery, when its statistics are reviewed, is marvelous, and it furnishes every reason to hope that in the next twenty-five years a still greater improvement in his condition as a productive member of society, on the farm, and in the shop, and in other occupations may come.

Progress indeed. (And what’s the term for that? A surprising coincidence? Irony? Is there a proper term for such a connection? Perhaps a thirteen letter German word along the lines of schadenfreude?)

And it’s such a relief to see the return of science:

For everywhere we look, there is work to be done. The state of the economy calls for action, bold and swift, and we will act – not only to create new jobs, but to lay a new foundation for growth. We will build the roads and bridges, the electric grids and digital lines that feed our commerce and bind us together. We will restore science to its rightful place, and wield technology’s wonders to raise health care’s quality and lower its cost. We will harness the sun and the winds and the soil to fuel our cars and run our factories. And we will transform our schools and colleges and universities to meet the demands of a new age. All this we can do. And all this we will do.

And how a swarm reacts to a falcon attack, via Burak Arikan:

For myself and all you designers out there just getting their heads around particle simulations, this is just a reminder: nature is better than you.