Biocurious

/ a biophysics blog

Dead tree scrolls

Posted 1 July 2009 by PhilipJ under

I have long wondered who, exactly, still reads the dead tree copies of journals. I don’t know a soul who wanders over to a library to get the latest journal articles. The library is now where you go for only those journal articles that have (annoyingly) not yet found their way into a digital format that is Internet-accessible. I also don’t know many people who have subscriptions to dead tree copies of most journals. I’ll see the odd Science and Nature sitting around the coffee tables in various departments, but I don’t know many who prefer to read their favourite journals that way. Besides, Science and Nature are filled with enough news articles and op-eds that they really are science magazines with a more general appeal. Something like the Journal of the American Chemical Society? Definitely not.

Which is why I was quite happy to hear that the American Chemical Society is gradually moving to an entirely online distribution method. As per Nature News,

In 2010, ACS members will no longer be able to buy print subscriptions of journals, and the publications division will monitor print renewals from institutional subscribers. In general, Susan King [senior vice-president of the ACS’s journals publishing division] foresees a “move beyond print to an electronic-only scientific publishing environment”.

Not only is printing a dead tree version of a journal an incredible waste of money (which is obviously the real reason for the change by the ACS), it’s also an incredible waste of paper. Most journal articles are not interesting to most people. Online browsing of Tables of Contents and only printing out the articles you find interesting is a much better (from every perspective!) way of reading the scientific literature.

Of course, there will be a few dissenters. In this week’s Nature, Francois Diederich argues for the print editions of journals. As member of the German chemical society and a senior editor for Angewandte Chemie, he claims “there is a risk that the quality of these prestigious journals [Angewandte, JACS, etc] could gradually decline to the standard of many of today’s web-only journals.”

I’m having a lot of trouble coming up with a rational reason why this might be the case. How does the application of ink to paper by people and machines unrelated to the actual writing, editing, and production of the articles have anything to do with the quality of the science presented in a journal? In fact, abandoning the inconvenient medium of paper will allow for more informative Materials and Methods sections and (hopefully) a reduction in Supplemental Information. A return to well-described and documented methodology is one of the distinct advantages of moving to paperless scientific publishing.

I suspect the reason Diederich is so opposed to the idea is more his initial claim of convenience: “[printed journals] provide distinct advantages in letting me browse their content (during breakfast at home, for example) and readily take in information, without the lengthy opening of individual web pages, article by article.”

In an age of wireless Internet connections and mobile computing, this is not a compelling argument for the continual waste of both money and trees.

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Baby spider nests

Posted 5 June 2009 by PhilipJ under

I’m back in Newfoundland for a vacation, and while mowing the lawn came across a bunch of baby spiders in a nest, that looked something like this:

baby spiders
(hat tip to Boby Dimitrov on Flickr)

It was quite a windy day, but when I crouched down to look at them, even the slightest breeze from my own breath caused them to disperse out from their tight bunch, much like these spiders are doing:

baby spiders dispersing
(hat tip to gardnergrout, on Flickr)

Being biocurious, I have been wondering, what’s the difference between a breeze and my own breath that the baby spiders ignore the former and run at the feel of the latter?

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Obama to National Academy of Sciences: Long Term Investment in Basic Science Will Help Meet Generational Challenges

Posted 27 April 2009 by Andre under

The text from Obama’s speech to the National Academy of Sciences has been released by the Office of the Press Secretary. He says a lot of promising things about research funding including going forward with the Advanced Research Projects Agency for Energy (ARPA-E), doubling the budget of the NSF, DOE, and NIST, and increasing funding for the NIH. On the political side, he is announcing the members of the President’s Council of Advisors on Science and Technology (PCAST) that he promises to work closely with because to “undermine scientific integrity is to undermine our democracy.” Obama also discussed plans for a program to encourage states to improve their K-12 science education by competing for $5 billion in federal funds as part of the Secretary of Education’s “Race to the Top” program.

These announcements are more evidence that Obama recognizes the importance of basic research in solving some of humanity’s most pressing problems. He also understands the critical role that government funding plays in basic research and that the outcomes of this research are inherently unpredictable:

The fact is, an investigation into a particular physical, chemical, or biological process might not pay off for a year, or a decade, or at all. And when it does, the rewards are often broadly shared, enjoyed by those who bore its costs but also by those who did not.

That’s why the private sector under-invests in basic science – and why the public sector must invest in this kind of research. Because while the risks may be large, so are the rewards for our economy and our society.

No one can predict what new applications will be born of basic research: new treatments in our hospitals; new sources of efficient energy; new building materials; new kinds of crops more resistant to heat and drought.

Finally, it’s always nice to see one’s field mentioned explicitly by the higher-ups. In the discussion of restoring science to its rightful place, Obama states that in “biomedicine, for example, this will include harnessing the historic convergence between life sciences and physical sciences that is underway today.”

In the end, this is still just a speech, but we already have evidence that Obama is serious about science given his appointment of Steven Chu as energy secretary and the boost to science in the stimulus package. I’m hopeful that he will follow through on these promises and that he will get the support he needs in congress.

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Nano Nano Naaaano

Posted 9 March 2009 by Andre under

What a wonderful surprise…


The Nano Song from nanomonster on Vimeo.

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Nature Network Pub Night: January 26th

Posted 22 January 2009 by PhilipJ under

There’s a Nature Network pub night in Toronto this coming Monday, and the topic is blogging! From Eva:

Have you ever thought that you’d like to start a blog, but wondered how to combine blogging with your work?

Toronto tech blogger (and “Accordion Guy”) Joey DeVilla will give a talk about how he successfully incorporated blogging in his life and work.

We’ll also look at the newest edition of Open Laboratory, a book collecting the best posts from science weblogs in the past year, and get a report from the ScienceOnline09 conference (held January 16-18 in North Carolina) to see some of the ways blogs are used in science.

Date: Monday January 26th 2009
Location: Fionn MacCool’s (181 University at Adelaide)
Time: 6 PM onwards (talks start at 7)
Contact: Eva Amsen eva@easternblot.net

As a scientist blogger living in Toronto, there’s no way this can be passed up. See you on Monday!

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Hot off the Press: Fluorescent timers

Posted 20 January 2009 by PhilipJ under &

While we’re waiting for the most exciting future biophysics tool to get built, there are all kinds of practical improvements to current-generation microscopy that would still be exciting and useful. We’ve talked a lot about increasing the spatial resolution of optical microscopy, but it would also be useful to have tools for temporal measurements of dynamics in a living cell. Many cellular processes occur on temporal scales of many hours, and being able to track such processes with current-generation optical microscopes would still give exciting information about intracellular trafficking and dynamics. To do this, a tagging system that would give temporal information as well as spatial information is necessary.

A paper in the February issue of Nature Chemical Biology discusses just such a technique. Subach et al’s Monomeric fluorescent timers that change color from blue to red report on cellular trafficking introduces a new fluorescent timer system based on directed evolution of mCherry, a protein that fluoresces in the red. By carrying out mutagenesis on selected amino acids that interact with the chromophore of the GFP-like protein, it was possible to generate variants of the protein that had differing maturation rates for the chromophore (leading to different fluorescence intensities over time), as well as a temporal shift in the fluorescence spectrum from blue to red. Different mutants resulted in fast-, medium-, and slow-fluorescent timer molecules where the maturation rate of the fluorescence change varied as their namesake.

An example of the maturation of the slow-FT reporter fused to a protein in mammalian cells is shown in the figure below. This shows the ratio of blue to red fluorescence as a function of time in vivo, where even in the complex environment of the cell, the temporal properties of the fluorescent timers remain intact.

fluorescent timer colours

This system of fluorescent reporters was then used to study the dynamics of lysosome-associated membrane protein 2A, a protein that must reach lysosomes either via the Golgi complex directly, or via endocytosis from the plasma membrane. The medium-FT molecules had an ideal timescale to study the LAMP-2A intracellular dynamics, and the figure below shows the result of expressing a LAMP-2A-medium-FT fusion protein in mammalian cells.

FTs in the cell

Careful analysis of the localization and colours of fluorescence made it possible to conclude that a primarily indirect pathway for LAMP-2A trafficking is taken, based on the blue-to-red ratios both near the plasma membranes and in the Golgi. While the details of this specific experiment are complex, the above figure shows that this is a very powerful new technique to study both localization and temporal dynamics in vivo, and a range of fluorescent timer mutants with fast to slow dynamics should give the ability to study a wide range of intracellular processes. Indeed, the authors point out a number of interesting things to study in their conclusion:

FT proteins will also allow for identification of recycling events among compartments, temporal tracking of molecules before and after a particular cellular event (without the need for additional labeling or artificial photoswitching) and timing of particular intracellular post-translational modifications traceable by fluorescent procedures such as ubiquitination and farnesylation.

The optical microscope has a lot of science left to do.

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