Biocurious

/ a biophysics blog

Science Rendezvous 2008

Posted 8 May 2008 by PhilipJ under

If you find yourself in Toronto this Saturday, May 10, you should check out the wide variety of events going on under the Science Rendezvous umbrella, everything from science demos at universities or malls to lectures by one of Canada’s own Nobel laureates, John Polanyi.

I’ll be presenting optics demos with the Institute for Optical Sciences in the McLennan Physics building at the St. George campus of the University of Toronto, and there will be all kinds of other interesting things happening in the immediate vicinity of the physics and chemistry buildings — click here to see them all.

If you need any further convincing, you can see some of the neat experiments we’ll be demonstrating in this video – my Ph.D. advisor’s enthusiasm is catching.

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Robotic Beast of Burden

Posted 23 March 2008 by Andre under

Here’s a great video of “Big Dog,” a quadruped robot that walks up and down hills and shows some very impressive balance:

Big Dog was made by Boston Dynamics with funding from DARPA. Its balance looks very life-like but what really surprised me was how much empathy I felt for the thing when it was kicked or when it almost fell on the ice. Apparently I will be of no use to the human race during the eventual take over by cute biomimetic robots.

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Airplanes, conveyor belts, mythbusters

Posted 28 January 2008 by PhilipJ under

After the airplane and conveyor belt internet hysteria, it looks like the guys on Mythbusters will do the experiment. January 30th, 9pm.

For anyone who missed it the first time around, the problem is such:

“A plane is standing on a runway that can move (some sort of band conveyer). The plane moves in one direction, while the conveyer moves in the opposite direction. This conveyer has a control system that tracks the plane speed and tunes the speed of the conveyer to be exactly the same (but in the opposite direction). Can the plane take off?”

Update — physics is saved! (the plane takes off.)

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It's like powering gym lights with treadmills...

Posted 14 November 2007 by Andre under &

You know those squiggly words you need to decipher to post comments on some blogs or to create new accounts at some sites? These can be annoying, but I hate spam as much as the next person so I don’t mind going through the slight extra effort. Now, that little extra effort can be harnessed to do good! Sean at Cosmic Variance describes a talk he attended by the inventor of the method. Basically, by flipping the problem on its head Luis von Ahn realized that all the work people are doing deciphering words could actually be applied to deciphering scanned texts that computers are having trouble with. Genius!

I love these kinds of ideas and it reminds me of one of these projects for taking advantage of large numbers of otherwise idle computers: using Playstation 3s to predict protein structures. A lot of console gaming systems are networked these days, so researchers can use them to simulate proteins when they’re not being used to simulate gun fights.

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Scientists still can't write good

Posted 11 November 2007 by PhilipJ under &

One of the first entries written for this blog over two years ago was on the sad state of writing in the sciences, and, not surprisingly, little has changed. The September issue of Nature Physics went so far as to include a guideline for writing papers (open access, PDF), largely because “so many papers deserve to be better written than they are”. I couldn’t agree more, but I have ended up frustrated with this editorial, and I’ll explain why.

According to Nature Physics, your paper’s title must be succinct and informative, but should also tempt a reader to at least look at the first paragraph. That first paragraph should set the stage for the “story” of your paper, and why that story should be told to begin with. The story of the paper should then underlie the rest of the article’s structure, and overly technical details should be left to the Methods or Supplemental Information sections.

You should explain, not hype! Avoid cliches “like the plague”, and refrain from unnecessary use of adjectives. Be quantitative in lieu of using superlative prefixes (femtosecond instead of ultrashort, and I doubt you really are studying a quantum nanobiological effect).

This is all sound advice, but vanity journals have really only themselves to blame for the overhyping and the near-ubiquitous quantum-, nano-, and bio-fication of (novel!, which they somehow forgot to mention) scientific results.

Furthermore, pushing aside the actual science into the all-too-brief Methods and Supplemental Information sections is rarely helpful. Methods are never complete enough to reproduce an experiment, and in the case of Supplemental Information (which is relegated to an extra file to download)*, often replete with errors. Real science is technical, and I thought that journals like Nature introduced the Editor’s Summaries and News and Views features so that the basic results of a paper could be read and understood by everyone. We either need to find better ways to incorporate those bothersome, technical details (which are the heart of science, in my opinion) into our science papers, or give Methods and Supplemental Information sections their due with proper editing and sufficient detail. Currently, science articles fail at both.

The best advice given in the editorial, however, is on the final paragraph of a paper:

It is commonly advised that a paper should begin by stating what will be said, continue by saying what is to be said, and then conclude by summarizing what has been said. This is bad advice that recommends lazy composition. Conclusions are not mandatory, and those that merely summarize the preceding results and discussion are unnecessary (and, for publication in Nature Physics, will be edited out). Rather, the concluding paragraphs should offer something new to the reader.

They go on to quote Jonathan Shewchuk:

“Here’s a simple test: if somebody reads your conclusions before reading the rest of your paper, will they fully understand them? If the answer is ‘yes’, there’s probably something wrong. A good conclusion says things that become significant after the paper has been read. A good conclusion gives perspective to sights that haven’t yet been seen at the introduction. A conclusion is about the implications of what the reader has learned.”

This in particular is something I will strive to follow in my own writing, and is by far the best advice of the day. Abstracts already play the role of brief accounts of the paper, conclusions shouldn’t be another repetition.

Unfortunately, the editorial didn’t link to what it considers to be some prime examples of well written science, a real shame given that being able to write a good science paper will only come to a new author after reading lots of well written science papers. If anyone has any examples of particularly well written papers, please share them in the comments!

* I’d like to know the relative number of downloads a supplemental information file gets compared to its parent article!

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STIX Fonts

Posted 6 November 2007 by PhilipJ under

I’m on a bit of a typography kick recently (this past weekend I went on the second type and tile tour of Toronto’s subway system), so when I saw this (on Slashdot of all places!) a few days ago, I got interested:

The mission of the Scientific and Technical Information Exchange (STIX) font creation project is the preparation of a comprehensive set of fonts that serve the scientific and engineering community in the process from manuscript creation through final publication, both in electronic and print formats. Toward this purpose, the STIX fonts will be made available, under royalty-free license, to anyone, including publishers, software developers, scientists, students, and the general public.

The STIX mission will be fully realized when:
- Fully hinted PostScript Type 1 and TrueType font sets have been created
- All characters/glyphs have been incorporated into Unicode representation or comparable representation and browsers include program logic to fully utilize the STIX font set in the electronic representation of scholarly scientific documents

By making the fonts freely available, the STIX project hopes to encourage the development of applications that make use of these fonts. In particular, the STIX project will create a TeX implementation that TeX users can install and configure with minimal effort.

The STIX project is a joint effort by the APS, ACS, AIP, IEEE, AMS, and everyone’s favorite for-profit publisher, Elsevier.

The fonts have been released as a public beta (though lacking a TeX implementation), which you can download here. It is a serif font, with a not-unpleasant appearance, though there is also nothing to really grab you and stand out. This is quite possibly the purpose, though. Here’s how the alphabet and numbers look:

Your thoughts? I would personally despise it if all the big publishers unified on a single font, but I don’t expect that to happen, and so the more choice the better.

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