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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Status Update

Posted 29 June 2009 by Andre under

PhD Dissertation Comic

PhD Dissertation Comic

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Molecule of the Month: Vaults

Posted 6 June 2009 by PhilipJ under

Vaults

Our cells are filled with compartments, each performing a specific function. Some of these compartments, such as mitochondria and lysozomes, are very large and enclose many different molecular machines. Other intracellular compartments are smaller, such as the transport vesicles that shuttle proteins from site to site inside the cell. Most of these compartments, including mitochondria, lysozomes and transport vesicles, are surrounded by membranes. However, in special cases, cells build smaller compartments surrounded by a protein shell. In our own cells, vaults are a spectacular example of these protein-enclosed compartments.

Vaults are composed of many copies of the major vault protein, which assembles to form a hollow football-shaped shell. The one shown here is from rat liver cells (PDB entries 2zuo, 2zv4, and 2zv5) and contains 78 copies of the protein. Inside cells, the vault also encloses a few other molecules, which were not seen in the crystal structure because they don’t have a symmetrical structure inside the vault. These molecules include several small RNA molecules, a protein that binds to RNA, and an enzyme that adds nucleotides to proteins.

Read more by David Goodsell at the RCSB PDB here.

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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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Molecule of the Month: Influenza Neuraminidase

Posted 13 May 2009 by PhilipJ under

influenza neuraminidaseInfluenza virus is continually changing and every decade or so, a dangerous new strain appears and poses a threat to public health. This year, there has been an outbreak of a new strain of H1N1 flu, more commonly known as swine flu. The H1N1 designation refers to the two molecules that cover the surface of the virus: hemagglutinin and neuraminidase. Together, these two molecules control the infectivity of the virus. Hemagglutinin plays the starring role as the virus approaches a cell, binding to polysaccharide chains on the cell surface and then injecting the viral genome into the cell. Neuraminidase, on the other hand, plays its major role after the virus leaves an infected cell. It ensures that the virus doesn’t get stuck on the cell surface by clipping off the ends of these polysaccharide chains.

Neuraminidase, shown here at the top from PDB entry 1nn2, is composed of four identical subunits arranged in a square. It is normally attached to the virus surface through a long protein stalk (not shown). The active sites are in a deep depression on the upper surface. They bind to polysaccharide chains and clip off the sugars at the end. The surface of neuraminidase is decorated with several polysaccharide chains (seen extending upwards and downwards in this structure) that are similar to the polysaccharide chains that decorate our own cell surface proteins.

As with hemagglutinin, neuraminidase comes in a variety of subtypes named N1-N9. These subtypes are defined by their interaction with antibodies: all of the variants within a given subtype will be neutralized by a similar set of antibodies. These subtypes are one of the causes of the continual effectiveness of influenza. Some of the subtypes promote infection in people, others promote infection in birds, and others target pigs and other mammals. As viruses spread and infect different organisms, they can mix and match different subtypes, randomly building new combinations and occasionally coming up with particularly lethal combinations.

To read more about this timely molecule of the month, click here for the rest by David Goodsell at the RCSB PDB.

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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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