Depth-First: Tag publication

Extreme Data Visualization

Rich Apodaca — Fri, 13 Jun 2008 11:08:00 -0400

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.

NIH Hears Publisher Feedback on Open Access Mandate

Rich Apodaca — Fri, 21 Mar 2008 18:17:00 -0400

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.

Rethinking Chemistry Publications: Nature Protocols Makes the Experimental Section a First-Class Citizen

Rich Apodaca — Mon, 10 Sep 2007 09:35:00 -0400

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:

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

Thinking of Starting an Anonymous Science Blog? Five Reasons to Think Again

Rich Apodaca — Fri, 17 Aug 2007 11:29:00 -0400

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.

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.
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.
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?
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.
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

Editable and Searchable 2D Molecular Images

Rich Apodaca — Mon, 30 Jul 2007 08:01:00 -0400

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.

Go West, Young Man: Does Open Access Really Matter in the Long Run?

Rich Apodaca — Mon, 16 Jul 2007 09:31:00 -0400

Making a name for yourself in science is no easy job. Aside from the technical challenge of doing noteworthy science while working under constraints, there's the compounding challenge of making your work known to influential colleagues. Excellent work done in a vacuum is lost to science, only to be "rediscovered" by those more willing or capable of self-promotion. Look around at the most successful scientists in your field, and you'll find that they are both extraordinarily adept at doing noteworthy science and in promoting their work.

Scientists have been using the scientific publication system for hundreds of years as a channel for promoting their work. For a variety of reasons, this system is now breaking down before our eyes. There are many reasons - consider these:

The printed page doesn't matter anymore. Old-guard scientific publishers have been able to prosper by acting as gatekeepers of a precious resource: the printed page. The arrival of immediate, ultra-cheap, ubiquitous, interactive, and persistent communication through the Internet means that printed journals are increasingly viewed as wasteful and irrelevant.
Printed journals have priced themselves out of the marketplace. How many printed journals has your library dropped over the last year? Does your "library" even carry current printed journals anymore?
Electronic Information wants to be free. Few things are more frustrating than knowing the answer to your question exists on a server somewhere, but you are forbidden from accessing it. Yes, you can pay $15-$30 for each article you need or get multiple subscriptions costing thousands per year, but is that any way to spend your budget?
The minimum publishable unit is shrinking. Scientists have legitimate interests in maximizing the number of papers they publish, in minimizing their size, and in decreasing their interval. Submissions to top-tier journals continue to increase. New journals are started to catch the overflow, placing additional strain on the system's ability to find readers and "qualified" reviewers, and driving up production costs in the process.
Too much information. How many scientific papers have you actually read, from start to finish, in the last month? How many important, relevant papers in your field could you have completely read in the last month? How many of them did you find through an automatic notification system? How many papers have you used solely for one specific piece of information they contain? How many of these papers did you find through a database of some kind?

Open Access has become a hot topic, mainly in response to the points above. Although well-intended, the debate assumes that scientific publication in the Internet age will continue to work essentially the same way it always has - with scientists submitting manuscripts to publishers who act as editors, distributors, and in many cases quality-assurance agencies.

But what if it doesn't end up working out that way?

The reason that the existing scientific publication system has flourished for hundreds of years is that it solved the fundamental problems of two key groups: (1) scientists who wanted to be informed of new developments; and (2) scientists who wanted to promote their work and careers.

If you accept this premise, then nothing prevents entirely new publication models from replacing the existing ones - provided that they solve the basic problem scientists face. If anything, the Internet is replete with examples of powerful old-guard gatekeepers of all stripes being first undermined as they denied that their business models were failing, then lashing out at everything but the root cause of their problems, and finally being driven into oblivion.

Why should old-guard scientific publishers be immune to this process?

Some scientists are discovering value in bypassing scientific publishers altogether. In chemistry, the best-known example is Jean-Claude Bradley and his group at Drexel. As Bradley's group is joined by others willing to experiment in this area, they will uncover a variety of problems that need to be addressed. Some of the most significant (at this point) include:

tools to create content
services that host and archive that content indefinitely
peer-review mechanisms that fully leverage the power of collaboration over the Internet
utilities for finding and promoting the work

These are the new high-payoff areas in scientific publication. Like all high-payoff areas, this one starts out looking dangerous or insignificant to most people.

This is not to say that that the Internet eliminates the need for gatekeepers. Instead, it creates tremendous opportunities for new gatekeepers. Google, eBay, and Wikipedia are gatekeepers. Facebook and YouTube are also gatekeepers. By all accounts, these services have done phenomenally well and will continue to flourish for some time. Significantly, each service addresses the basic need of information consumers to be informed and information producers to have their message heard. These systems have found powerful mechanisms for quality control that in many cases put the current practice of scientific peer-review to shame. And in no case will you find a business model requiring pay-per-view.

Google, eBay, Wikipedia, Facebook, YouTube, and hundreds of other gatekeepers thrive because each has found a new precious resource to allocate, not by trying to extract every last drop of value from the old ones. Both scientific publishers and Open Access proponents would be wise to consider their example.

Image Credit: Seamus Murray

Scientific Publication and the Seven Deadly Sins

Rich Apodaca — Mon, 14 May 2007 09:07:00 -0400

Why do scientists publish? There is a myth - common among non-scientists - that scientists publish their work mainly out of an altruistic desire to make the world a better place. Sharing their work helps science move faster and that's a Good Thing. This is, of course, an important factor for most scientists. At least it's hard to imagine any scientist seriously thinking that they want their work to be used to make the world worse off.

The problem with the altruism myth is that it obscures many of the deeper reasons that scientists publish.

Recently, I attended a talk given by Max Levchin, co-founder of PayPal, on the subject of product design. In it, he advised those seeking to create a successful startup to build products designed to enable users to commit one or more of the Seven Deadly Sins.

His reasoning was simplicity itself. The Seven Deadly Sins were those activities so universal, that people needed to be threatened with all kinds of bad things if they did them. Looking at it from a detached, secular perspective, most people seem hard-wired to want to commit one or more of the Seven Deadly Sins - repeatedly and without encouragement. Looking at it from a product designer perspective, cha-ching!

Levchin went on to observe that people can commit every one of the Seven Deadly Sins on the Web - except for gluttony. Thus, the popularity of the Internet as a venue for doing business.

It may seem a little odd at first, but can this reasoning be applied to scientific publication? How many of the Seven Deadly sins does publishing satisfy? Does this offer any insight into the deeper reasons scientists publish their work?

Below, I offer some ideas on the Seven Deadly Sins as they apply to scientific publication:

Greed The flip-side of "Publish or Perish" is "Publish and Prosper". We're not talking about directly profiting from scientific publication (only scientific publishers do that). No, we're talking about using a publication record to build a reputation. It's that reputation that in turn leads to funded grant proposals, scheduled job interviews, lucrative offers from recruiters, raises, bonuses, and promotions. If science is a business, then publications are it's currency.
Envy Don't get left out. Few things are more jarring than to suddenly realize that your publication record is far below average.
Pride Finish a job well-done. Doing science the right way is hard work. It can involve both skilled experimental technique and ingenious insights. Why not cap off that achievement by letting the world know how it was done and how you got there first?
Wrath Stick it to someone who deserves it. Or, just tear to pieces an idea that's plain wrong. Scientists as dispassionate observers? Not always.
Gluttony Anything worth doing is worth doing to excess. Remember Dr. Soandso who publishes way too many (perhaps low-quality) papers? The rise in popularity of the Communication shows he's not alone. Who could blame him or anyone else, given what's at stake?
Sloth N/A. Actually, it takes the mighty pull of the other sins on this list to overcome the mental barrier to drafting a manuscript and getting it publication-ready.
Lust Depends on how you define it. See "Gluttony" and "Greed".

Depending on definitions, at least five of the Seven Deadly Sins factor into scientists' motivations for publishing. Notice that despite the term "Sin", not all of these motivations are malevolent. Scientists should take pride in their work, they need to feed themselves and their families, nobody likes to be left behind, sometimes it really is better to write three Communications than one long paper, and some things are worth getting mad about.

Why does any of this matter? For the simple reason that information technology and economics are in the process of rendering obsolete existing models of scientific publication. To build the systems of the future, it's essential to understand the motivations of those using the current one.