Funny Journal Content

1. A candidate for the funniest journal title/paper graphic…
Here’s a cute paper: rolling a single molecular at the atomic scale. The authors look at C₄₄H₂₄, a molecule possessing two triptyene ‘wheels’ (with three ‘paddles’, each) and thus two intramolecular degrees of freedom when adsorbed on a metal surface (the independent rotation of each wheel), and push it along with an STM tip. Interestingly, the STM current is a good indicater of what kind of motion the molecule is undergoing (‘rolling’ versus ‘hopping’). What I find most amusing is that the molecule was previously used to construct a ‘molecular wheelbarrow’, a result which was published in Tetrahedron Letters – probably the funniest journal title I’ve come across – and includes the following priceless graphic:

2. Can a biologist fix a radio? Or, what one scientist learned while studying apoptosis
Speaking of funny papers, this paper by Yuri Lazebnick (via Structure+Strangeness) is great. Here’s an excerpt, dealing with the question of how would a biologist fix a radio, knowing only that it is a box meant to play music?

How would we begin? First, we would secure funds to obtain a large supply of identical functioning radios in order to dissect and compare them to the one that is broken. We would eventually find how to open the radios and will find objects of various shape, color, and size. We would describe and classify them into families according to their appearance. We would describe a family of square metal objects, a family of round brightly colored objects with two legs, round-shaped objects with three legs and so on. Because the objects would vary in color, we will investigate whether changing the colors affects the radio’s performance. Although changing the colors would have only attenuating effects (the music is still playing but a trained ear of some people can discern some distortion), this approach will produce many publications and result in a lively debate.

3. Formation of a nematic fluid at high fields in Sr₃Ru₂O₇:
I had quite a lengthy post on electronic liquid crystals in 2-dimensional electron gases (e.g. GaAs/AlGaAs heterostructures) a while back, and briefly noted that:

Scientists in Europe have measured a large magnetoresistive anisotropy in the correlated electron oxide strontium ruthenate (Sr₃Ru₂O₇) near the ‘metamagnetic quantum critical point’, indicating the formation of a new quantum nematic phase. This is strikingly similar to the tranport anisotropy in 2DEGs I’ve been talking about… in particular, both show strong sensitivity to disorder – and the authors claim that the formation of this phase is tuned by the divergence in the quasiparticle effective mass near this critical point. One can only wonder what other kinds of systems could yield such behavior as well.

This European work is now one of the feature papers for the online Journal Club for Condensed Matter Physics, with a far more in-depth (yet very readable) commentary by Catherine Kallin of McMaster University in Canada.

Neural Networks III

Last week I wrote the second post in my ongoing series of posts on Computational Neuroscience, based on a class I’m taking on the subject. I take notes on my computer in class anyway, so what I post here is a modified version of those and hence a reasonably good course chronicle.

While a lot of the development can be very technical, I’m trying to make these posts accessible to most people with a general interest in biophysics, neural networks or computational neuroscience. This means that I have to gloss over a lot of interesting details, including a lot of fun derivations, but that’s ok – for one thing, I don’t know how to easily incorporate equations into these posts (nor do I have the time to). However, I do provide references to more detailed papers when I feel the need.

Last week’s subject was Mikhail Bongard’s problems of pattern recognition, Herrnstein’s discovery that pigeons were particularly adept at solving them, more perceptrons and the credit assignment problem, and how backpropagation provided a means of solving it. The week before, I introduced McCulloch-Pitts neurons and perceptrons, particularly the perceptron convergence theorem and linearly separable problems. This week builds on the past two weeks: we’ll be looking at NETtalk, the Ising Model and Hopfield Networks, and Attractor Dynamics.

Pseudo-book review: Edward Tufte

(from ‘The Visual Display of Quantitative Information’, Edward Tufte)

Perhaps best known in some circles for his scathing critique of Microsoft Powerpoint, Edward Tufte is the Leonardo da Vinci of data, as the New York Times put it, and his self-published books (the newly released Beautiful Evidence or the all-time classic The Visual Display of Quantitative Information) are quite elegant.

Tufte isn’t just about making things look pretty – the epilogue of the latter book (excerpted above) says it best: “what is to be sought in designs for the display of information is the clear portrayal of complexity… that is, the revelation of the complex.” There are more books, too, but those are the two that I came across recently, and the thing is, he really means it. This man is in the business of taking data, getting rid of everything extraneous, superfluous, and distracting, presenting it in the most honest and unassuming form possible, and doing it in as accessible and user-friendly a way as possible. And you know what? Among other things, this is the business of science, too – to take good data, and force it reveal its secrets. Although Tufte comes from a social sciences background, I think his work is invaluable to any experimentalist, at the very least.

Book Review: The New Physics

The New Physics For the Twenty-First Century
Gordon Fraser, Editor (Cambridge University Press, 2006)

Gordon Watts had a post a few days ago on undergraduate physics curricula, noting that:

The biggest complaint I hear over and over is that we aren’t teaching enough modern physics to our students. By modern I don’t mean quantum mechanics (which is typically called modern physics), but, rather, I mean recent discoveries. Dark matter/energy. Applications in condensed matter. Materials. Basically, the stuff we do for research, or did perhaps 20 years ago (and so is well established at this point). I think everyone agrees with this basic idea.

Here at Penn, we have a new class that is offered every two years that attempts to fill this need that goes under the rather dull name of “Intro to Research” (I took it as a sophomore). The idea is simple: professors from the department give two or three 1.5 hour lectures on their research, going into a significant amount of depth along the way. The goal is to expose undergraduates to what ‘real’ physics is – an idea I consider not only good, but essential, if only because some students need to be shown that ‘real’ physics research isn’t all just dry, pointless derivations or stuffy textbooks. Real physics is exciting, and that point often gets lost amidst weekly problem sets. Grading is done using homework assignments based on the lectures, and a presentation/paper that students have to prepare on another topic of their choosing that researchers are working on.

Ideas in Condensed Matter Physics

Doug Natelson has a post soliciting suggestions for the most powerful idea in condensed matter physics, putting out the Hohenberg-Kohn-Sham theorem/method underlying DFT as being a good candidate. Others have suggested Bloch’s theorem, Anderson’s paper on localization, Laughlin’s paper on the Fractional Quantum Hall Effect, Onsager’s solution of the 2D Ising model, Landau’s papers on Fermi liquids, BCS theory, “and whatever the most appropriate Bethe ansatz paper is”.

I need to learn way more condensed matter physics in order to say anything constructive, although I do feel that another on the list could be Philip Anderson’s “More is Different: Broken symmetry and the nature of the hierarchichal structure of science“, which arguably set the tone for the principle (paradigm?) of emergence in complex systems (and perhaps unwillingly led to a good deal of philosophy and/or pseudoscience, too). Perhaps one of the most-quoted passages from the paper – that I’ve seen, at any rate – is the following:

The ability to reduce everything to simple fundamental laws does not imply the ability to start from those laws and reconstruct the universe… The constructionist hypothesis breaks down when confronted with the twin difficulties of scale and complexity. At each level of complexity entirely new properties appear. Psychology is not applied biology, nor is biology applied chemistry. We can now see that the whole becomes not merely more, but very different from the sum of its parts.

Anyway, the post reminded me of a paper I came across a long time ago in Rev. Mod. Phys. by W. Kohn (of Hohenberg-Kohn-Sham, as mentioned above) in 1999 that basically attempts to document the evolution of condensed matter physics. Here’s an excerpt:

It is perhaps interesting to look at the history of condensed matter physics from the viewpoint of T. S. Kuhn… [who] sees scientific history as a succession of (1) periods of ‘‘normal’’ science, governed by serviceable scientific paradigms, followed by (2) transitional, troubled periods in which existing paradigms are found to be seriously wanting, which in turn lead to (3) ‘‘scientific revolutions,’’ i.e., the establishment of new paradigms, which may or may not be accompanied by the rejection of the old ones.

Such a linear view seems applicable to the whole field of CMP for some of the broadest revolutions, which directly or indirectly affected a large fraction of the field:

• x-ray diagnostics yielding crystal structures (1910s);
• achievement of low temperatures allowing the observation of calmed condensed matter (1900s);
• quantum mechanics, (1920s);
• the band-structure paradigm (1920s, 1930s);
• nuclear and electron spin magnetic-resonance diagnostics (1940s and 50s);
• neutron elastic and inelastic diagnostics (1950s);
• many-body electron theories (beginning in the 1930s, with major revolutionary steps in the 1950s and 60s);
• electronic computer-assisted theory and experiments (1960s-);
• soft matter (1960s-);
• and nanoscience (1980s-).

I like it – clearly this is very broad, but it’s a very good summary of how the field has evolved into what it is today.