Reading William Gunn’s recent blog posting, Could this be the Science Social Networking killer app? got me thinking more about the many online scientific reference list repositories like Connotea, CiteULike and 2Collab, and why they are failing to catch on. William is suggesting a Pandora-like system of expert reviewers tagging papers to set up a recommendation system. I’m not sure this would be really helpful–what you get from a scientific paper is very different from what you get from listening to a song, and their interconnectedness works in very different ways. And it brings to mind the failings of organizing your references by tags.

If you’ve ever dealt with any of these social bookmarking sites, you know how incredibly tedious they are to use. Even for journals like CSH Protocols, where we have buttons on every article to add it directly to these sites, you still end up jumping through hoops, filling out forms, writing summaries, adding tags. You’re on the spot at that moment to come up with a list of tags that will remind you about the content of that paper. As your worldview changes over time, and with it your research priorities, you’re probably going to want to revisit many papers and add additional tags. Even with all this time-consuming work, you still may not have added an appropriate tag to let you find what you want to find at a given moment. Did you add a tag for every method used in the paper? Every conclusion, every subject referenced? That band on the gel in figure 3 that you’re ignoring today might be very important to you tomorrow. How are you going to tag the paper in case you need to find it again?

It’s more work than it’s worth, particularly given the ability to do full-text searches on your collection of articles through programs like Papers (out for the iPhone this week, by the way). Why tag every single aspect of a paper when you can just do a quick search? Even Google Scholar and PubMed strike me as much easier tools to use for these purposes than social bookmarking sites. It’s why Apple, Microsoft and Google have spent so much time and money on desktop search applications over the last few years. Investing efforts in organizational schemes is pointless when you can call up the file you need via a quick search. Sure, with Papers or the search engines, you lose the social aspects of things, the use of the network as a discovery tool. Then again, your hard work adding tags isn’t helping you discover new papers, it’s helping other people. You have to hope that others are tagging papers as relentlessly as you and that they’re tagging the aspects of papers that fit your interests.

The tedium of tagging versus the relative ease of searching brought to mind this recent article from John Gruber on the Daring Fireball site, Untitled Document Syndrome. Gruber talks about friction, the number of tedious steps involved in so many programs:

“There’s the stuff you want to do, and there’s the stuff you have to do before you can do what you want to do. People have a natural tendency to skip the have to do stuff to get right to the want to do stuff if they can get away with it. Friction is resistance.”

His example is writing a Word document. How often do you find yourself starting a new document, and writing for a long while without actually saving it? Saving changes to an already saved document is trivial, a keystroke away, but a new document means you have to go through that dialogue box, figure out where you’re saving it, come up with a title, etc.

“The obvious problem with Untitled Document Syndrome is in the rare cases where you lose data because you never saved it. The non-obvious problem is that the mental friction posed by the Save dialog often keeps you from ever even creating or saving small items of data in the first place.”

Gruber talks about the different approach taken by programs like Apple’s iLife suite, where you just dump in music, video or photos, and you don’t have to worry about naming them, or deciding where to store them. The program does it for you. It’s no surprise then, that programs like Papers or Yojimbo, which are based on the same iLife-style interface, are so much easier to use for organizing your scientific research list. Given the time demands faced by scientists, it’s no wonder I’ve heard rave after rave about Papers, but never really receive much more than a shrug when discussing online reference sites with folks at the bench.

One other caveat–if you are going to invest your time in tagging, be sure to regularly extract your account’s information and back it up. Sites may disappear at the drop of a hat. Some of the science paper bookmarking sites are clearly unaware of the Napster and Grokster court decisions and their willingness to become redistributors of copyrighted material places them only a lawsuit away from the abyss. And even with those backups, uploading them to the next site is never as clean as you’d like it to be. Be prepared to repeat a lot of your efforts.

February’s issue of Cold Spring Harbor Protocols contains a Topic Introduction on the subject of Photoactivation by Graham Ellis-Davies from Drexel University:

“Specific molecular interactions control cellular function. The photorelease of caged compounds (nucleotides, neurotransmitters, peptides, second messengers, proteins, etc.) can be used to control these interactions in living cells. Caged compounds are biological effector molecules whose active functionality has been chemically masked with a photoremovable protecting group. Illumination produces a concentration jump from the caged molecule. This article discusses the basic principles underlying photoactivation, the properties of caging chromophores and commercially available caged compounds, and practical considerations for their effective use.”

Our collection of protocols includes a wide variety of applications using photoactivation including the following:
Design, Synthesis, and Characterization of Caged Compounds
Introduction of Caged Peptide/Protein into Cells Using Microinjection
Introduction of Caged Peptide/Protein into Cells Using Bead Loading
Photoactivation-Based Labeling and In Vivo Tracking of RNA Molecules in the Nucleus
Inorganic Caged Compounds: Uncaging with Visible Light
Chemical Two-Photon Uncaging
Infrared-Guided Laser Stimulation of Neurons in Brain Slices
Photoactivation Cell Labeling for Cell Tracing in Avian Development

So much fodder, so little time:

Ma.gnolia suffers catastrophic data loss
Further evidence that “cloud” computing may not be the best approach for storing your precious research data. Remember, if you’re keeping any information in an online repository, it’s not enough just knowing that you can get your information out, you actually have to regularly do so and back it up.

False Fact On Wikipedia Proves Itself
Slashdot thread on the circular nature of Wikipedia. Someone posts something, another source sees it on Wikipedia and repeats it, Wikipedia confirms the fact by citing that source.

Twitter? It’s What You Make It
David Pogue weighs in on Twitter. His basic point is that while yes, it often is “a teenage time-killer”, there are useful things you can do with it. His suggestions for what’s useful though, are:

“I pass on jokes. I share little thoughts that don’t merit a full blog or article post. I follow links and track buddies….And I query the multitudes. Last week, I was writing a script for a TV segment, and needed a great example of “an arty movie that a teenage baby sitter wouldn’t be caught dead watching.” My followers instantly shot back a huge assortment of hilarious responses. (“Gandhi.” “My Dinner with André.” “The Red Balloon.”). Other people plug their blogs, or commiserate, or break news…”

So, he’s basically using it as a teenage time-killer, as a “lazy-web” way to get others to do his work and thinking for him, and for self-promotion. I can see the second use here as being a time-saver. But the question is, can you get anyone to follow you and respond to you queries if you don’t engage in the teenage jibber-jabber types of activities? Do you have to do the time-wasters to build an audience who might help you save time?

Time Demonstrates Non-Understanding of Social Media
Speaking of the sometimes overwhelming self-promotion that goes on under the guise of Web 2.0, here’s an amusing blog posting with the typical defensiveness aimed at anyone who questions the incredible value of jibber-jabbering away all day on a social network. As a colleague pointed out upon reading this:

“I think what people fail to realize is that no-one reads anybody else’s lists – like most blogs. The popularity of this sort of thing is ‘the doing it’. There is of course a whole ‘nother discussion as to why one would want to do something like that.”

Which makes me ask, if everyone is using these sorts of tools to “promote their personal brand”, is anyone actually reading anyone else’s promotion? Is Web 2.0 a room full of people with megaphones, each shouting, “Look at me!”?

Time to Hang Up the Pajamas
Fake Steve Jobs (Real Dan Lyons) notes that no, you’re not going to get rich blogging.

who is on twitter
Very amusing, my favorites being:

people who are involved in “social networking” and optimizing the power of re-Tweeting and “computers”
and
people who are concerned about the collapse of the publishing industry

Why aren’t we on Facebook?
The Onion, as usual, nails it. Count me in as part of that 22%.

With the advent of Google Latitude and the new geo-tagging features of digital cameras and cel phones, we’re beginning to see a new era where one’s online presence meets one’s real-world presence. The question must be asked though–how much information do you really want to share? As pointed out in this article about establishing a “location-aware lifestyle”, there are some inherent worries. The author’s wife points out that he’s announced on his blog that he’ll be out of town for two weeks, and that on Flickr, he’s posted many photos taken in his apartment that show all his fancy, expensive electronic equipment, along with geo-tags showing the exact location of said apartment. As a proof of concept, he watches a woman take a picture in the park on an iPhone, then goes to Flickr later that day, searches by location and finds the photo, and from there easily finds that woman’s home address. A friend recently let me know that she’d been contacted by her former stalker from 20 years ago, who found her through someone else’s web page that had her contact information listed. Needless to say, she was not pleased.

There’s a fine line between arranging easy meet-ups with your network and “Hey! Who’s that creepy guy hanging around in the bushes in front of my house?”

Finally, someone else has come right out and said it–the general expectation that e-books should only cost “a dollar or two” is unrealistic, and will be a major barrier to their adoption. Bob Miller from Harper Studio weighs in here:

“Whether a book is printed on paper and bound or formatted for download as an e-book, publishers still have all the costs leading up to that stage. We still pay for the author advance, the editing, the copyediting, the proofreading, the cover and interior design, the illustrations, the sales kit, the marketing efforts, the publicity, and the staff that needs to coordinate all of the details that make books possible in these stages. The costs are primarily in these previous stages; the difference between physical and electronic production is minimal. In fact, the paper/printing/binding of most books costs about $2.00…so if we were to follow the actual costs in establishing pricing, a $26.00 “physical” book would translate to a $24.00 e-book”

And in the comments, he discusses Amazon’s pricing scheme (currently selling e-books at a loss), and the actual costs of shipping:

“the cost of shipping a physical book is usually about 20-25 cents per copy”

The common mistake appears to be, at least in my experience, that people start with the assumption that an e-book costs nothing to make–you’ve already paid for everything with the print version, and converting those files to an e-book costs nothing or very little. But every e-book copy you sell means one less print copy you’re going to sell, so the total cost of production has to be amortized out over both the e-book and the print version. It’s a big mistake John Siracusa makes here, which puts a big hole in his argument.

The book-buying public does not seem willing to accept that e-books cost a few dollars less than a regular book to produce, and does not seem willing to buy them at that price. Which is yet another reason we’re seeing slow uptake of this type of technology.

Our series highlighting new and lesser-known laboratory model organisms continues in February, with two sets of articles detailing the use of moss and choanoflagellates.

The moss Physcomitrella patens has been used in laboratory research for more than 80 years, but the last 15 have seen a resurgence in moss research. P. patens can easily be grown in the lab, and spends most of its life in a haploid state that allows many of the approaches used in yeast and microbes to be applied. Methods for RNAi have been worked out, the genome has been sequenced and assembled, physical and genetic maps are available, and more than 250,000 expressed sequence tags (ESTs) are known. Ralph Quatrano and colleagues have contributed an overview of the use of P. patens as a laboratory organism to February’s issue of Cold Spring Harbor Protocols along with protocols for culture, isolation of protoplasts, somatic hybridization, chemical and UV mutagenesis, transformation via direct DNA uptake, T-DNA mutagenesis, and biolistic delivery systems, and isolation of DNA, RNA and proteins.

Choanoflagellates are a varied group of protozoa that are the closest living relative to the metazoa, and their study is leading to new insights into metazoan ancestry and origins. Barry Leadbeater and colleagues have written up a series of articles highlighting the use of Monosiga brevicollis as a representative species, as it has recently had its genome sequenced, and is readily grown and manipulated in the laboratory (protocols included are generally transferable to most choanoflagellate species). The set of articles includes an overview of choanoflagellates, and protocols for isolation from field samples and culture of choanoflagellates, long-term storage, visualization of actin and beta-tubulin, purification of total RNA, and preps for rapid DNA isolation, high molecular weight DNA isolation and separation of choanoflagellate and bacterial genomic DNA.

These articles on Emerging Model Organisms are being collected in a series of lab manuals, the first of which is currently available here (now on sale 25% off!).

One of our featured articles for February comes from S.P. Dinesh-Kumar and colleagues at Yale University and is an update to a method first published a few years ago in our RNAi manual (now marked way down to a bargain price in both hardcover and paperback). RNAi has become a commonly-used tool for the down-regulation of genes in plants. The most effective means of accomplishing this gene silencing is through the use of viral vectors, with the Tobacco Rattle Virus (TRV) providing the most robust results. Virus-Induced Gene Silencing as a Tool for Delivery of dsRNA into Plants outlines a simple procedure for introducing TRV-based vectors into plants such as Arabidopsis, Nicotiana benthamiana and tomato.

Like all of our featured articles, access to this protocol is free for both subscribers and non-subscribers alike.

February’s issue of CSH Protocols has just posted, and one of our featured articles this month is The OP9-DL1 System: Generation of T-Lymphocytes from Embryonic or Hematopoietic Stem Cells In Vitro, from Juan Carlos Zúñiga-Pflücker’s laboratory at the University of Toronto. By using OP9-DL1 cells as a support system, researchers can study the differentiation of embryonic stem cells into mature components of the immune system. The article contains a series of protocols describing the establishment, maintenance, and storage of OP9 and OP9-DL1 cells; the co-culture of these cells with embryonic stem cells or hematopoietic stem cells from fetal liver or bone marrow; and the in vitro differentiation of the stem cells into lymphocytes. The OP9-DL1 system has been useful in addressing questions about the cellular and molecular regulation of T-lymphocyte lineage commitment, pre-T cell receptor signaling (Beta-selection), functional characteristics of progenitor T cells, and maturation of functional CD8 T cells.

Like all of our featured articles, this set of protocols is freely available to subscribers and non-subscribers.

As a quick follow-up to this posting, a colleague sent along a review of a new book called Flat Earth News by Nick Davies, which rightly points out that the “death of journalism” isn’t a murder, it’s a murder-suicide. Yes, readers are abandoning print newspapers and magazines, preferring to get their information online (with an assumption that such things are free). At the same time, this abandonment is being driven by a decline in quality of the old media, as the owners seek to cut costs and increase profits. From the review:

“The most basic function of journalism, in Davies’s view, is to check facts. Journalists don’t just pass on what they’re told without making an effort to check it first. At least, in theory they don’t. In practice, contemporary journalism has been corrupted by an endemic failure to verify facts and stories in a manner so fundamental that it almost defies belief. The consequences of that are pervasive and systemic…Journalists report much less than they used to, and much less than they should, as the papers have switched over to a reliance on columnists and opinion…Stories need to be cheap, meaning ‘quick to cover’, ‘safe to publish’; they need to ‘select safe facts’ preferably from official sources; they need to ‘avoid the electric fence’, sources of guaranteed trouble such as the libel laws and the Israel lobby; to be based on ‘safe ideas’ and contradict no loved prevailing wisdoms; to avoid complicated or context-rich problems; and always to ‘give both sides of the story’ (‘balance means never having to say you’re sorry – because you haven’t said anything’). And conversely, there are active pressures to pursue stories that tell people what they want to hear, to give them lots of celebrity and TV-based coverage, and to subscribe to every moral panic.”

I do strongly believe that people are still willing to pay for quality, but as this review points out, that’s not what’s being offered by most of our media outlets. The book looks interesting, definitely worth a read.