Using what is without question the most unusual (innovative) data visualization technique I've ever seen, Postgenomic has created Pubmed Faceoff. The idea is simple: humans have evolved highly sophisticated face recognition abilities; why not exploit this ability in the visualization of multidimensional datasets? The technique, known as Chernoff Faces, has been around for awhile now, although the idea of using photorealistic faces seems to be an innovation of the Postgenomic team.

The service itself is actually quite usable, if a bit slow. Only newer papers in PubMed are covered, but that's still enough to get a feel for what's possible.

One feature I'd like to see: depict scientific subjects using faces. For example, just looking at the pathetic crowd I got by typing the keyword "schizophrenia" into the search box seems to suggest that field has some problems. A few stars, but apparently a lot of junk.

Another idea: click on any face and get a page containing all of the papers with that face. In other words, show me all of the papers getting more than the expected number of citations. Or show me all of the papers published in "crap journals" getting no citations. Average citation count seems much less interesting for some reason.

Credit: Thanks to Scholarship 2.0 for the lead.

The NIH heard public comments yesterday on its plans for implementing PL 110-161 Section 218, a new law that grants the agency broad powers to intervene in the scientific publication system.

Scientific publishers were out in force. According to The Scientist, Jack Ochs of the American Chemical Society (ACS) was first in line to offer comments:

He started out by saying that a brief meeting was no substitute for the formal comments on rulemaking process like the one the NIH held when they were implementing the voluntary submission program in 2005. He was the first of several to call a halt to implementing the mandate so the details could be worked out.

A lot is riding on the outcome. The new law requires NIH grant recipients to deposit peer-reviewed manuscripts of their publications into PubMed Central, in apparent opposition to the policies of many leading scientific publishers - including the ACS.

NIH has given its grant recipients until April 7 before compliance will become mandatory. It remains unclear what steps, if any, ACS will take to enable authors to comply.

Unless ACS policy changes, NIH grant recipients face the possibility of losing one of the most prestigious publication options in chemistry.

Also see Peter Suber's comments.

Experimental procedures are strange beasts. Loathed (at least temporarily) by those who must prepare them yet central to science, the lowly experimental section is mostly forgotten in the daily struggle of publish or perish. Abstracts, discussions, and conclusions will probably be useless 20 years from now, at least in chemistry. In contrast, the experimental section (and the tables based on them) may well live forever.

It was from this perspective that I was fascinated to learn about Nature Protocols from thescepticalchymist. From the website:

Nature Protocols is an online resource for protocols, including authoritative, peer-reviewed 'Nature Protocols' and an interactive 'Protocols Network'. The two create a dynamic forum for scientists to upload and comment on protocols.

Experimental protocols may be poised to make a comeback in the world of scientific publication. Specifically two chemistry protocols caught my eye:

• Partial reduction of electron-deficient pyrroles

• Synthesis of pyrimidines by direct condensation of amides and nitriles

Unlike most publications in which the experimental section is treated as an afterthought, in Nature Protocols, the experimental section occupies center-stage. Richly annotated and hyperlinked descriptions are complimented by full-color images. Videos have also begun to appear.

Many modern chemistry journals have either abandoned the experimental section altogether or simply downplay it to the point of making it far less useful than it could be. This might have made sense when paper was the primary means of distributing scientific content. With digital storage capacity now routinely measured in terabytes and long-tail scientific economics in full force, this position makes little sense today. The information-delivery platform has changed forever; to what degree will this change the nature of what gets communicated?

image credit: Donohoe and Thomas, Nature Protocols

You can find them in nearly every scientific discipline: the anonymous science blog. For a variety of reasons, their authors have decided not to reveal their identities, as is their right. Styles range from the absolutely analytical to the cynically sarcastic.

I have nothing against anonymous science blogs. Some of the most interesting writing I've seen has been posted to them. But I do have some reasons why you might want to think twice before starting one.

1. If you're writing about anything remotely interesting, you will be identified sooner or later. Have you ever attended a scientific meeting and noticed how many perfect strangers you meet who know someone you know? Scientific disciplines are very small worlds. Not only that, but Google is a frighteningly powerful tool to find obscure information. If one of your colleagues stumbles onto your blog, chances are excellent they will be able to identify you if they're determined.

2. Owning your content keeps you sane. Have you ever noticed how otherwise considerate people can be very inconsiderate drivers? There's something about anonymity that brings out the worst in people. Connecting your name with what you write forces you to carefully consider what you're doing. And that's a good thing. You're going to be identified anyway (see above), so you might as well write like it from the start.

3. Consider your motive. What's the real reason you're writing under a pseudonym? Is it to be able to vent without consequence? To avoid upsetting your boss? Wanting to avoid colleague reactions or embarrassment? Uncertainty as to whether you're "allowed?" Do you worry about writing something that a future employer might not like, thus endangering you chances of getting a job? Going back to Point 1 above, you will be identified eventually. When that happens, will you be prepared to face the music?

4. Your current employer has rights. If you're working in industry, you've signed an agreement that gives your employer rights to your ideas and inventions. If you're in academics, your advisor probably doesn't want you disclosing the details of cutting-edge research. The immediacy and reach of blogging will turn scientific publication on its head; these are merely previews of the issues that lie ahead. When in doubt, ask before blogging.

5. It's a new form of scientific publication. Would you want to be an anonymous author on your scientific publications? Of course not. Every scientist is a businessperson, whether they like the idea or not. The business model is simple: trade your scientific reputation for money in the form of grants, salaries, bonuses, and job opportunities. Publication is the currency of scientific business. Blog-like scientific writing is simply its newest incarnation.

Own your content. The career you help (or save) may be your own.

image credit: flyzipper

Word processing replaced the typewriter for the simple reason that documents could be prepared and edited so much more quickly. If Web authoring replaces conventional word processors, it will be for the simple reason that Web documents can be found, distributed, reprocessed, and combined with other content so much more effectively. The peculiar nature of chemical structure information complicates chemistry's transition to Web authoring. This article, the first in a series, discusses some of the challenges that lie ahead.

State of the Art: Word/ChemDraw

Microsoft Word allows 2D molecular graphics, typically created with ChemDraw, to be embedded in documents and later edited. Those images can then be copied into Power Point presentations and reused in a variety of other Windows-specific products. This practice has become so widespread throughout industry and academics, that few chemists even think about the technology that many of them rely on several times a week.

Chemical Structures are Peculiar

A 2D molecular image, like the one depicting fluoxetine at the top of this article, is a peculiar beast. On one level, it's a picture that anybody can look at. But on another level, it's a type of object for which manipulation by humans and computers is extremely useful. The combination of Microsoft Word and ChemDraw lets chemists conveniently manage the dual nature of chemical structures.

Live Molecular Images

Why would anybody want to create editable and searchable 2D molecular graphics such as JPGs, PNGs, and SVGs? Alas, technology has a way of moving on just when we're getting comfortable with it (an especially difficult concept for typewriter manufacturers who went bust during the 1980s, and the dedicated word processor manufacturers who followed).

Consider the number of Word and PowerPoint documents you read last week compared to the number of Web pages. Chances are the ratio is at least 1:10. The trend shows no signs of reversing itself.

Although Web authoring tools have been very slow to reach the average user, the blogging explosion has led to rapid evolution in the field. As tools like WordPress, Movable Type, and even Wikipedia race to satisfy the needs of power authors, the average user will rather unexpectedly discover that they have access to perfectly capable tools that let them abandon their over-engineered (and expensive) word processors to experiment with Web publishing.

The Wikipedia Chemisty/Structure Drawing Workgroup hints at what lies ahead for chemistry. Two tools, GChemPaint and ACD ChemSketch, now enable molecular structure information to be embedded in images.

As chemistry turns to the Web as its primary publication medium, chemists will need the same ability to deal with chemical structures offered by their current tools of choice. In articles to follow, I'll discuss some ways this could happen.