Plausible Accuracy

I was thinking last night: “Why don’t I hear more about Open Access?  Why do I have to hunt down information (in the form of subscribing to blog feeds etc) rather than have the information come to me?”.  I have this feeling that more scientist would rally behind the Open Access cause if they simply knew (more) about it.

In a moment of insight that had me reaching for my aluminum foil hat, I realized that one of the primary ways scientists get their information about the community is via publications from various societies.  For example around our group room you will always find a few copies of the recent issues of Chemical & Engineering News, the weekly publication of the American Chemical Society.  Well, the ACS is inextricably tied up with “Big Publishing”.  They rely strongly on the current subscription models to support the activities of the society, and no doubt see Open Access as a threat to their fundamental business model.  Indeed, C&EN has in the past published very anti-Open Access editorials.

I don’t actually believe that information wants to be free. I don’t think information gives a damn. I think cheapskates want information to be free.

-Rudy Baum, C&EN editor-in-chief

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MITworld has posted a (76 minute) video of a seminar on Open Access.  The speakers are John Wilbanks, the vice president of ScienceCommons; and Anna Gould, the head of the Libraries for Science & Engineering at MIT.

I think that Wilbanks is more or less dead on in his description of the issues in finding scientific data online today — the Google Search doesn’t do the job for finding data.  You will find a pile of papers that may have the data you’re looking for buried within, but you really just want the extracted bit of information.

He goes on to point out that the copyrights enforced by the journal electronic subscriptions explicitly forbid actually doing any sort of digital indexing of the content.  In other words you aren’t allowed to set up a search function based on journal text, let alone set up databases to extract data and allow for new combinations and cross-referencing.

He goes on to talk about some really exciting ideas.  Of course a fair bit of time is spent on the Creative Commons-based copyrights for scholarly publications, which I am all for.  He also describes attempting to set up a “transactional system” for repositories of scientific materials.

You don’t email Stallman to get the Gnu code

To me, this would fundamentally alter the practice of science. Most of science takes place in isolated labs, with perhaps some limited academic discussions between similar workers and maybe the occasional plasmid sent from one lab to another.  The Science Commons project iBridge, however, streamlines the process and sets up something that looks almost like a store for scientific materials.  Presumably these requests would go to the central repositories who would fulfill the request.  I haven’t gotten a chance to investigate iBridge very much yet, but I’ll try to follow up on this in a later post.

He finishes up by talking about generalizing code to automate some scientific queries that are currently repetitive and manual tasks.  It might sound dull, but he demonstrates some relatively simple code that can do data extraction from open access data.  As the other tools of the Science Commons are developed, this will become even more powerful and will allow for much more complex and interesting data extraction, indexing, and recombination.

Gould goes on to focus more specifically things that people are doing today to develop new ways to look at scientific data.  One in particular that I like is SciVee, where the paper authors can submit a video highlighting the results of their papers.  She also mentions sort of a research library “union” being developed at CERN, called SCOAP3.

Overall it’s a very engrossing talk, and has sort of set my head spinning with ideas.  If you get time, I’d recommend watching it (although at over an hour I understand that finding the time might be tough).

via Open Access News

You would think that potential employers would value honesty in their incoming candidates.  From my experience in the past several months of job hunting, however, this wouldn’t seem to be the case.  There is almost no faster way to be culled from the pool of applicants than to simply be forthright and straightforward about your own strengths and weaknesses.

Take a look at any interview advice column.  Every single one that I’ve read focuses on that odious concept of “spin”.  You should minimize talking about your weaknesses.  Always follow them up with how you overcome them or a strength that balances them.  Gloss over any rough patches.  It’s mild dishonesty in my opinion, and I don’t like it.

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Cory Doctorow is fairly well known as a champion against DRM and strict copyright regulations.  He’s one of the contributors to the massively popular blog BoingBoing, and also a (science?) fiction writer.

I’ve read all of his work (I think), but the story which has had the most lasting effect on me was his first, Down and Out in the Magic Kingdom (just an aside here: Doctorow releases all his work under a Creative Commons license, so if you click that last link and look at the top of the page you will see a “Download for Free” link.  This is indeed the full novel if you’d like to read it for yourself).  (more…)

Most of my posts lately have been Internet: Serious Business(tm).  Lest my reader think that all I do is sit in my darkened spire all day contemplating biochemistry and Open Access, I wanted to mix it up a bit and talk about a couple of hobbies I was able to enjoy this weekend: drinking wine and playing computer games.

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My RSS reader spit out an article from Science with the interesting title “COMPUTER SCIENCE: Science 2.0″, written by Dr. Schneiderman from the University of Maryland.  Before I could even switch Firefox tabs to check it out, however, I came across two good writeups of the article in Nobel Intent and Wired Science.  This wouldn’t be the blogosphere if I didn’t chime in with my own opinion…

Let me just start out by saying that attempting to lump the entire process of science prior to this as “Science 1.0″ and the “new” form of science he is  advocating as the ever-so tired “Science 2.0″ is immediately off-putting.  It’s true that it’s difficult to come up with a pithy term for leveraging web/network technologies for scientific research, but “Science 2.0″ is neither original, accurate, or descriptive.  It doesn’t help that, in the end, Dr. Schneiderman is more or less talking about applying the fields of psychology and sociology to web communities, rather than introducing a new and innovative research methodology.

Both of the commentaries by Nobel Intent and Wired pick up on this lack of clarity in the Science perspective.  In particular the comment thread at Wired is… lively.  I think that commenter Ania summed up my thoughts well:

What would have been nice (especially in Nature [sic]) would be an article on how the power of the web is being used to change research… such as changing the way we design and begin our experiments (usually with a bioinformatic study of whatever gene we are going to look at, a literature search through pubmed or another database). There are an incredible number of things we can do over the internet which help science each and every day, not withstanding being able to look up the genomes of sequenced animals, being able to do a blast search ( a search which compared nucleotides of sequences… ) of two genes or sequences in about 20 seconds (depending on if the americans are awake yet).

Schneiderman B, Science 7 March 2008: Vol. 319. no. 5868, pp. 1349 - 1350 DOI: 10.1126/science.1153539

I had this masterful plan to write about today’s seminar from Dr. Tobias (UC Irvine), including a review of the professor’s work, direct quotes from lunch with him, and notes from his talk at the end of the day.

Unfortunately weather has kept the speaker away, so instead I think I’ll just review a recent paper!

Fortunately for us, Dr. Tobias was a co-author on a recent paper in Science discussing specific ion effects in solution.  The paper is a minireview of recent literature that goes against the conventional wisdom of what salts are doing in solution.  The seminal work on salt’s action in a solution was done in the late 1800’s by Franz Hofmeister.  The common thought is that adding salts to a solution causes widespread changes in the structure of water (water’s rapidly shifting morass of hydrogen bonds is what keeps it liquid rather than gas at room temperature - adding salt is thought to influence this network on a large scale).

Computational chemistry experiments, however, have indicated that salt effects are more local, and only influence water molecules nearby the ions of the salt.  Other biophysical measurements also seem to call the long-range bulk model of salt effects into question.  Experiments also indicate that certain ions may concentrate at the interface between two solvents (or at the air/solvent interface), while others stay away from the interface.

This work is interesting, both from purely theoretical as well as practical standpoints.  Theoretically, it demonstrates that the simplistic view of salts based on the Hofmeister series smooths over some details which may be minor but significant.  This has practical applications in the field of crystallography, where scientists often use solvents with varying salts and salt concentrations to carefully induce their proteins to crystallize.  This crystallization process is poorly understood, and it’s almost certain that these sorts of specific ion effects are at least partially involved.

Tobias, D.J., Hemminger, J.C. (2008). CHEMISTRY: Getting Specific About Specific Ion Effects. Science, 319(5867), 1197-1198. DOI: 10.1126/science.1152799

The Scientist magazine has released their annual survey of the best places to work as a postdoc.  It’s an interesting list, as usual, with a lot of the typical candidates near the top.  I find it interesting that the best places tend to be smaller, less well-known institutes rather than the large research behemoths that most people have heard of.

Part of me feels like they should name this list “Greener Grass Grows Here” or “Places You Won’t Be Working in 2008″, because while I’m sure these might be fantastic for the people who are already post-docs there, it  doesn’t mean that they are hiring, or that you will be able to land a job there.

The other issue, of course, is that “quality of employment” is not a factor that you hear budding scientists talk too much about.  We have been conditioned to deal with long hours at little pay with no benefits - it’s called graduate school.  Most people when applying for postdocs are following the science, not a particular working environment.

Well, regardless it’s always interesting to see what the more progressive institutions are doing as far as benefits and perks for their post-docs.   Most of the time professors just want to hook their new post-docs up to the data milking machine and work them until they collapse.  A big part of me thinks that the standard term for a post-doc fellowship has held steady near two years simply for medical purposes.

This is the story of a scientific ethics incident. The names have been obscured, but the events are true. I know because I was part of the lab group it involves.

I’ll be telling this story in 3 parts, which I’ll link here when they are written.

Part One | Part Two | Part Three

Part Three: “What do we do now?”

The bombshell had dropped.  Dr. C’s students now knew that, within several months, their lab would no longer exist.  They still didn’t know why, and no one who knew was talking.   In addition to trying to make sense of what had caused this sequence of events, the lab members were now also thrown headfirst into a very practical concern: salvaging their careers as best they could.  In the end, the justification for the firing of Dr. C would be an ancillary issue.

For about a week or so, no one did much of anything in Dr. C’s lab.  They sent overtures to Dr. C in the form of letters and emails, which were met with little to no response.  The word was that Dr. C was distraught and angry, and couldn’t face the students.   Quickly they realized that they couldn’t wait for an explanation; it was time to go into damage control mode and recover as best as they could.

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This is the story of a scientific ethics incident. The names have been obscured, but the events are true. I know because I was part of the lab group it involves.

I’ll be telling this story in 3 parts, which I’ll link here when they are written.

Part One | Part Two | Part Three

Part Two: “There will be a meeting”

Months had passed since the computer incident of Part One.  Things in Dr. C’s lab had returned more or less to normal, with the day-to-day drudgery typical of research pushing aside any misgivings about what was going on outside of the lab.  There hadn’t been any further incidents to raise suspicion, so it was a case of “out of sight, out of mind” for those working in the lab.
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