Complex networks, robustness, and attacks

László Barabási’s office is down the hall from my own, and he’s an amazing scientist who works on the statistical mechanics of complex networks. I’ve never heard him speak before yesterday, but at yesterday’s talk he gave a great introduction to complex random and scale-free networks.

In this field, a network is any particular graph that connects nodes with links. The nodes could be power-transmission stations, airports, or web pages, and the links could be power lines, airline routes, or web links. This is a field with implications to everything from biology (proteins and their interactions are a network) to homeland security (terrorists and their cell phone communications are a network).

Yesterday, after hearing László speak about his research, I went and looked up this review article in Reviews of Modern Physics. Some of the conclusions scare me. Some kinds of networks (like the internet) are robust under random node removal, but are fragile under a coordinated “attack” which disables a few highly-connected nodes. We can use this property to our advantage; arrest a Mohammed Atta and a terrorist network may fall to pieces, or find a biochemically important node in HIV transmission and we might be able to stop the disease from propagating. It also points out ways we are vulnerable; if O’Hare airport is attacked, the transportation system in the US may suffer immensely.

The paper is a very interesting read, and is well worth the time spent reading it.

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The Guardian’s Bad Science Column

The weekly Bad Science column in the Guardian looks like fun. The latest one is about strange ideas on dietary supplements being used as anti-bacterial agents, but my favorite by far is the request for the most stupid thing anyone has ever said to you about science at a party.

For me, the stupidest science-comments-at-a-party seem to revolve around Hydrogen-powered vehicles (and usually devolve into long discussions about 6000 psi liquid-H2 tanks and the energy source to make the H2 in the first place.)

There’s another category of mathematics comments that are even funnier. In all seriousness, I once had someone tell me that a particular student was " on the inflection point of the exponential curve of her career". The person who uttered this remark is someone for whom I have enormous respect (even if they don’t understand inflection points), so no names will be mentioned. What’s the most insane mathematics someone has ever expounded to you at a party?

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Darwin’s Dangerous Idea

This paragraph is from Daniel Dennett’s 1995 book, Darwin’s Dangerous Idea: Evolution and the Meanings of Life:

"Now if you want to reason about faith, and offer a reasoned (and reason-responsive) defense of faith as an extra category of belief worthy of special consideration, I’m eager to play. I certainly grant the existence of the phenomenom of faith; what I want to see is a reasoned ground for taking faith as a way of getting to the truth, and not, say, just as a way people comfort themselves and each other (a worthy function that I do take seriously). But you must not expect me to go along with your defense of faith as a path to truth if at any point you appeal to the very dispensation you are supposedly trying to justify. Before you appeal to faith when reason has you backed into a corner, think about whether you really want to abandon reason when reason is on your side. You are sightseeing with a loved one in a foreign land, and your loved one is brutally murdered in front of your eyes. At the trial it turns out that in this land friends of the accused may be called as witnesses for the defense, testifying about their faith in his innocence. You watch the parade of his moist-eyed friends, obviously sincere, proudly proclaiming their undying faith in the innocence of the man you saw commit the terrible deed. The judge listens intently and respectfully, obviously more moved by this outpouring than by all the evidence presented by the prosecution. Is this not a nightmare? Would you be willing to live in such a land? Or would you be willing to be operated on by a surgeon you tells you that whenever a little voice in him tells him to disregard his medical training, he listens to the little voice? I know it passes in polite company to let people have it both ways, and under most circumstances I wholeheartedly cooperate with this benign agreement. But we’re seriously trying to get at the truth here, and if you think that this common but unspoken understanding about faith is anything better than socially useful obfuscation to avoid mutual embarrassment and loss of face, you have either seen much more deeply into the issue that any philosopher ever has (for none has ever come up with a good defense of this) or you are kidding yourself. (The ball is now in your court.)"

I bring this wonderful paragraph up because it speaks directly to the issue of Intelligent Design and whether it should be taught or even mentioned in science classes. The proponents of ID are trying to breach the "benign agreement" that keeps faith and reason in separate social spheres. Honest scientists shy away from problems and questions for which we cannot design falsifiable experiments. This means that there are questions that science refuses to answer (and rightly so). In return, we have come to expect that those for whom faith is important will not claim their faith as a path to truth about the physical world. The proponents of Intelligent Design are making a claim about the way the physical world operates, and they are now facing pushback as a result.

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Raining Perseids

The August 6th Astronomy Picture of the Day shows a large number of superimposed 30-second exposures of the Perseid meteor shower. The perseid shower peaked last Friday, but this is a great picture.

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Breaking Visual CAPTCHA

I just ran across this wonderful article by Mori and Malik on a technique to break the EZ-Gimpy visual CAPTCHA images that attempt to distinguish between human and automated blog commenters. (Comment, memberlist, trackback and forum spam are a huge problem for sites like ours, and automated Turing tests like visual CAPTCHA are a promising way to avoid them). Mori and Malik propose a cool lettershape-matching algorithm based on log-polar histogram plots of edge-detected objects found within the image. They further refine their letter detection by tying the strings of possible letter choices together in an attempt to form dictionary words. Their algorithm does better than I was able to do on some of the overlaid word images.

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Kung Fu Science

Kung Fu Science, the physics of Kung Fu!

When I first heard about the site, I thought that physical combat would be an odd way to settle scientific disputes, although it would make comment-response sections in the journals a much more entertaining read. A little more thought had me even more amused: “My Taylor Expansion Claw technique is the best!” “I will beat you with my Angry Contour Integration Style!”

The site is actually an Institute of Physics production that is part of the Einstein Year .

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A History of Science on Stamps

I just ran across this wonderful Science Stamp exhibit. It is a real time-wasting collection (the best kind) but I’m struck by how few science and mathematics stamps the US has produced, and how many scientists have been placed on the stamps of places like Mauritania, San Marino, and Guyana.

There’s also this site devoted to mathematicians on stamps, which has links to some equally wonderful physics collections. My favorite stamp of the whole bunch is this Danish stamp depicting Neils Bohr and his wife on a three-legged bench.

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Online article submission systems

So we just submitted a new article to Biophys. J. I’ve done online article submission through five different sites now; the ACS paragon system is probably the nicest of the bunch and the Biophysical Journal system, well, it needs some work. There’s the hidden bibtex and latex style sheets that you can only see after you register (we found this out after wasting two hours rolling our own bst file). There’s the fiddly formatting that must be done before the manuscript gets assigned to an editor. You are also made to enter (by hand) suggested reviewer information that they probably already have on file.

Don’t get me wrong. I love the journal. The online submission system needs some work, however.

In related news, the Biophysical Society is one of the signatories of the DC Principles for Free Access to Science which appears to be an attempt by small not-for-profit publishers to find a middle ground between the closed access preferred by the for-profit publishers and the completely open access preferred by many scientists. I’ve said before that journals add tremendous value to science and I understand that the added value costs money. I’m also a taxpayer and I’d like to see the fruits of taxpayer-funded research become publicly accessible in a reasonable period of time. Perhaps the DC principles group is on to something.

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The Light Bulb Problem

Found another fun web comic called Bug Bash. The June 13th strip brings up a silly interview technique: ask the candidate a thought problem that tells you nothing about the candidate other than his/her ability to rehearse the answers to silly thought problems. Yes, the light bulb problem can be solved with a little bit of thought, but does it tell you if a technical person is the right person to tackle a large multi-month complicated development project? I don’t think so.

When prospective graduate students come by my office to talk about joining my group, I usually ask them to tell me about their previous research projects. I can tell a lot about their background and ambition from their ability to answer this kind of open-ended question. A few pointed queries can break out of any rehearsed descriptions and let you know exactly how deeply and broadly prepared they are.

We’re facing a challenge now on how to design the graduate placement exams for the coming fall semester. Although this isn’t really an interview (the students are already attending graduate school), we want questions that will tell us about the students’ backgrounds and exactly what they know about basic physical chemistry. What are the best and worst placement exam questions you’ve seen?

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Software Carpentry

Geoff Davis pointed me to the Software Carpentry site, which looks like an intensive web-based course on good software development practices for scientists and engineers. It has been assembled by Greg Wilson and covers topics like Version Control, Automated Builds, Object-Oriented Programming, Unit Tests, XML, Coding Style, and many more. It uses Python examples to illustrate many points.

This course looks like one of the most useful resources for scientists who are creating computational tools but don’t know what’s out there to help them build and debug their tools. I’ve learned a lot from Greg’s course in about a half hour, so it is probably worth a longer look.

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