I’ve recently written two pieces on scientists and social networks over at my other blogging gig, and thought they might be of interest to readers here:

Scientists Still Not Joining Social Networks

and

NIH Funds a Social Network for Scientists–Is It Likely to Succeed?

Some recent articles discussing computer software designed for use by biologists (I can’t personally vouch for any of these programs, but thought they might be of interest to readers of CSH Protocols):

Even Better Free Molecular Biology Software: Serial Cloner–the always valuable Bitesize Bio website has a review of Serial Cloner, a cross platform program for molecular biologists:

“It is very intuitive and is packed with features; from basics like constructing importing sequences, constructing plasmid maps and restriction mapping, through more complex things like sequence alignment, Gateway cloning and siRNA design.”

One of the commenters on the article also suggests PlasmaDNA.

iPhone apps every biologist needs: article from The Scientist, detailing 10 apps of interest. While many look useful, I’m not sure how many of them have added appeal on a mobile device (as opposed to use on a laptop or desktop computer). How often do you need to consult the periodic table while you’re on-the-go?

Also, I may be a luddite, but in my lab days, you wouldn’t even take a lab manual to the bench, you’d photocopy the protocol you were going to use because you didn’t want the expensive manual exposed to harsh chemicals and other contaminants. Are people really using expensive and fragile items like the iPhone at the lab bench? Do you set your iPhone down next to the phenol, just behind the HCl? Can you use it while wearing gloves? Wouldn’t you worry about all the E. coli contaminating your gloves from the plasmid preps you’re doing? Do you really want to smear that all over the device you’ll be holding next to your face?

9/12/09–Edited to add–Here’s another list, of 50 Useful iPhone Apps for Science Students & Teachers.

Although many feel that RSS is dead, I still find it to be a highly useful tool for finding new interesting reading material. As such, we’re happy to announce some new functionality in Cold Spring Harbor Protocols involving our RSS feeds that send out alerts when new articles are published. Previously you could only sign up for RSS feeds for article types–protocols, emerging model organisms, etc. Now you can sign up for notice of new material by subject area. This will let you see when new protocols are available in your specific subject area, whether it’s Genome Analysis, Imaging Development or Plant Cell Culture. For those more reliant on e-mail than RSS feeds, remember you can sign up for a wide variety of alerts by table of contents, subject, citation, keyword or author.

Time to catch up on some interesting links:

The End Of Free
Last week’s posting at the Scholarly Kitchen, discussing the idea of using free content as a marketing tool, and how some uses are reaching the end of their usefulness. I have a new blog entry there that will be out on Monday discussing Microsoft’s Bing and Google’s Wave.

Teen Practices
Very interesting set of observations of how teenagers use technology. Twitter and e-mail are boring things that old people use. Once again proving the idea that different tools are appropriate at different stages of one’s life and social development. This study backs it up with more numbers.

Landmark study: DRM truly does make pirates out of us all
A few weeks back, I wrote about the Kindle’s DRM:

By providing a product that suffers the limitations of lock-in and prevents users from doing the things they’re used to doing with books, Amazon is encouraging potentially honest customers to become copyright infringers.

This study offers further evidence for such behavior, and argues against DRM.

If Research Papers Had A Comments Section
A cautionary tale, in cartoon form.

Another Blogger Leaves the Seed Blogs
Some dissension in the ranks over at ScienceBlogs. Like we’re seeing at the Nature Networks, these clubhouses are hitting some rough waters.

For Wired, a Revival Lacks Ads
Interesting article on Wired Magazine’s struggles. It notes that Chris Anderson of “Long Tail” fame seems to make around $35-50,000 per lecture he gives to businesses. Ironic in that the concepts he champions seem to be failing at the actual business he runs.

And it wouldn’t be right to end one of these without some Web 2.0 cynicism/snark. So I’ll offer up Conan O’Brien’s painfully accurate Twitter Tracker, and this lovely Social Media Venn Diagram t-shirt.

More interesting articles from the last week or so……

The Comment Is King
A look at comments left on articles in The Washington Post and Slate, which does not bode well for those of us interested in creating commenting systems for science articles.

Will Wolfram make bioinformatics obsolete?
Interesting piece on the potential for Wolfram Alpha to be used as a much easier interface for bioinformatics questions.

Clay Shirky Debunks the WSJ’s “Bloggers For Hire” Feature
The increasingly ubiquitous Clay Shirky does a detailed analysis of Mark Penn’s Wall Street Journal article claiming that there are hordes of people who make their living blogging. Shirky’s pretty much shreds the poorly researched nonsense to pieces.

Too much free
Seth Godin notes that giving away your book or e-book (or whatever) for free is losing its novelty value as a marketing technique.

Wikipedia hoax points to limits of journalists’ research
Two good points made here. 1) Wikipedia is completely untrustworthy, and 2) newspapers continue to hasten their own doom by lowering the quality of journalism they perform.

Kindle wrap-up
New Kindle was announced this week, bigger, even more absurdly expensive, still black and white (which makes it a non-starter for textbooks). Hard to understand why students who are pretty much required to have laptops these days would want an extra big bulky device to lug around as well.
The Kindle Lets Amazon Make a Lot From the Few
Speculation on the Kindle’s business model. Steve Jobs was right, not enough people read to make lots of money selling a device, but Amazon thinks that small group of people will buy lots and lots of e-books, which is where the profit lies.
Publishers Nurture Rivals to Kindle
Meanwhile, publishers are unhappy with Amazon, looking to avoid turning control of their industry over to one company and repeating the mistake the music industry made in ceding control to Apple.

Google book settlement has librarians worried
Librarians weigh in on the increasingly problematic Google Book Settlement.

The Extreme Google Brain
Google’s lead designer left the company recently, and caused a stir with his revelations of how anti-design the company seems to be. This analysis looks at the extreme personality types that thrive in places like Google, and I couldn’t resist this vicious and hilarious description:

My impression of “Googlers,” which I concede is based on little direct knowledge and is prejudicial on its face, is one of undersocialized, uncultured, pampered, arrogant faux-savants who have cultivated an arrested adolescence that the Google working environment further nurtures. Their computer-programming skills, the sole skills valued by the company, camouflage the flaws of their neuroanatomy. Their brains are beautifully suited to the genteel eugenics program that is the Google hiring process but are broken for real-world use.

A bit of a follow-up to last week’s posting on Twitter, which seemed to come out as part of a society-wide post-Oprah/Ashton Twitter backlash.

When assessing something like Twitter, I think it’s important to remember that it’s just a tool, and as David Pogue has written, it is whatever you make of it. My objection is not so much with the tool itself, but to the way it’s being used, or at least the way so many are advising that I use it. I do understand that there is a power in Twitter, in both its immediacy and its accessibility. And that it can be a very valuable tool when used in a correct context. Cameron Neylon gives a great example of a specific situation where Twitter was very handy. He describes an ad hoc group put together to discuss a webcast meeting that led to the organization of a new meeting on the subject. Twitter worked well because people could contact one another in real-time, and more importantly, a widespread group was able to find one another to connect. It’s interesting to note that Neylon and his group needed to move beyond Twitter to other tools better suited for their efforts. While the 140 character limit is often pitched as a “feature” of Twitter, in reality, it’s a drawback to serious conversation and the communication of information. It either leads to shallow discussions or to kludgy workarounds like sending shortened URLs of webpages where you’ve written out what you actually want to say.

The issue isn’t with using something like Twitter in that sort of situation, where it’s appropriate and useful. The issue is with the idea that we’re all supposed to subscribe to one another’s tweets and spend chunks of our day reading through the gibberish that makes up so much of Twitter’s traffic. The telephone is also a useful tool, but no one is suggesting you leave the speakerphone on in your office all day to listen to the idle conversations of strangers. The stereotype so often used to deride Twitter is someone sending out messages about what they are having for breakfast. Jason Kottke attempts to defend the banality in so much of Twitter by noting that people are inherently banal, so trivial and meaningless conversations are to be expected. The problem I have with this is understanding why I would deliberately subject myself to even more banality than I face in my real life. Yes, we all generate and tolerate a good deal of smalltalk in our lives. But do we want to commit extra time to collecting more of it? Is it somehow more meaningful if it comes from a famous or respected person? Am I supposed to get off on the frisson of knowing what Ashton Kutcher is watching on tv?

Like most working professionals, I am limited in my time and attention, and need to spend both judiciously. While serendipity can lead to interesting new directions, it’s a highly inefficient process and directed methods are always going to be preferred where possible. So Twitter strikes me as a tool that can prove useful in a directed manner in specific situations. It’s the idea of using it for sorting haystacks for needles that strikes me as uninteresting.

Haven’t done one of these for a while, so here’s a few recent bookmarks of interest:

Kindle Failings Serve as Early Warning
I’ve got a new gig, well, sort of. I’ve been invited to join the crew at the Scholarly Kitchen, so I’ll be posting there occasionally when I have something relevant to say. My first post was a summary of who I am and what I’ve written about over here. This is my first original post over there, on worries about DRM and how we’re conditioning e-book buyers to act like illegal music downloaders.

America’s Newest Profession: Bloggers for Hire
The Wall Street Journal’s Mark Penn writes a laughably implausible article on how all us bloggers are getting rich. Makes me want to load up the truck and move to Beverly. The comments on his article set him straight, as have other bloggers.

Ford Bets the Fiesta on Social Networking
Ford gives 100 “millenials” a car and makes them Twitter, Facebook, YouTube and Flickr about their experiences. Do companies really expect efforts like this to work? If only they’d read this article first, This is how Social Media really works:

So maybe instead of getting your company on twitter, paying marketers to mention you are on twitter, and paying people to blog about your company, forget all that and just make awesome stuff that gets people excited about your products, hire people that represent the company well, and when your stuff is so awesome that friends share it with other friends, you may not even need “social media marketing” after all.

And finishing up with some follow-up to my recent Twitter rant, we have Maureen Dowd calling Twitter, “a toy for bored celebrities and high-school girls” (found via The Intersection), web-strategist Jeremiah Owyang predicting that alpha-geek early adopters will move on to the next thing as Twitter enters the mainstream, and best of all, the genius of Keith Starky Explains Twitter an in-depth analysis of what Twitterers are really saying with the medium.

This week saw some interesting criticisms of Twitter, which helped reinforce some of my own biases against bothering with it. Science blogger Sheril Kirshenbaum weighed in on her oath to never use Twitter:

Welcome to generation ADD….Privacy is so last millenium.
Well call me old fashioned, but I draw the line at Twitter. Yes folks, the rumors are true. Physioprof and I have made a pact. We will never ever Twitter. It’s time to slow things down a notch. We want to enjoy a few moments disconnected. No electricity required, batteries not included.

Elsewhere, Clay Shirky has an introspective piece about the fallout from Amazon’s recent glitch where “adult”material was removed from their ranking systems, which led to widespread furor in the Twittersphere that discrimination was afoot:

Though the #amazonfail event is important for several reasons, I can’t write about it dispassionately, because I was an enthusiastic participant in its use on Sunday. I was wrong, because I believed things that weren’t true…Those are good conversations to have, we need to have them, but they are not conversations that would enrage thousands of people in the space of a few hours and kick off calls for boycotts and worse.”

Twitter is essentially a public Instant Messaging (IM) system, one where your messages can be read by anyone interested, and you can join in the conversation anyone else is having. For me, that’s the main reason I find the concept unappealing–I’ve never been a big fan of IM. I tried to give it a go back in the days of AOL/IM and found it incredibly annoying. Even with a limited group of contacts, the constant chiming from my desktop was so distracting and interruptive that I found it difficult to get anything done. Twitter strikes me as the same thing multiplied by several powers of ten. I screen my calls as well, by the way.

I know, I know, I’m missing out and I’m an old fogey stuck in the past. So be it. We each have our own time constraints and workflows. I do understand the appeal of chatting online with strangers. I used to be a huge user of usenet back in the day, and enjoyed being a part of the community discussing my favorite basketball team or whatever tv show/music I was listening to at the time. But that was back when I was very early in my graduate career, was still working my way into a research project, and had time to kill. As we get older and gain responsibilities, both career and family, time for such things gets smaller and smaller. As I progressed through graduate school and got closer and closer to my degree, my time spent in newsgroups grew smaller and smaller until I abandoned them altogether. And that’s something that worries me about most of these Web 2.0 mediums (media?) for science–that they’re going to be dominated and used mostly by those with the most time on their hands, and subsequently the least interesting things to say. Here’s a good example of someone reaching the tipping point, realizing where blogging stands in his list of priorities and considering letting it go.

Kirshenbaum makes good points about both the banality of much of what’s posted, and the exhibitionism and odd willingness to give up all sense of privacy by many users. I’ve written about boundaries before, they’re important, and you won’t find me going on about my private life or family in this blog. I don’t have a Facebook or Myspace page. It’s really none of your business. The linked Wired article in that previous blog posting should give you a sense of how easy it is to connect geo-tagged information to the real world, and I expect we’ll see some unpleasant incidents in the near future that begin to change attitudes towards being so open.

There’s also a certain laziness that Twitter seems to breed. While one constantly reads about the incredible discipline needed to edit posts to 140 characters, no one seems to mention the massive quantity of those disciplined 140 character messages that are generated. Merlin Mann describes it as “raging id”. I don’t really have the time nor the desire to read an unchecked stream of consciousness from most people. Several of the bloggers whose writing I enjoy are spending more time on Twitter than on their blogs as of late (John Hodgman for one, Neil Gaiman for another). While both are superb writers, neither generates anything I’m interested in reading via Twitter. I do understand why we’re seeing this shift, it’s easier to just spew out a thought off the top of your head than to sit and spend an hour (or hours) fully fleshing out an idea. Which is why I think it’s a lazy medium (I’m not alone in this). Even famous and talented folks just aren’t all that exciting and clever if you’re being hit with a splatter of every single thought they have. If you want my valuable attention, then you need to do a little work Edit it down, keep the good bits, and develop those ideas further. The raw material is just blather, and frankly, I don’t have a lot of time to listen to other people blathering. You’re just not that interesting.

The other noted advantage of Twitter is the “timeliness”. You can find rave after rave about how we learned about the plane landing in the Hudson or the Mumbai crisis from Twitter before the news networks had full reports on what was happening. So what. Unless you had a relative on that plane or staying in that hotel, would it have affected your life if you had to wait a few hours before knowing the story there? Kirshenbaum calls this “Generation ADD” (I prefer “Generation Now”). I guess this rampant voyeurism is the counterbalance to the rampant exhibitionism mentioned above. Shirky’s article points out how this immediacy can lead to sweeping mob movements based on incorrect and incomplete information. Amazon has apparently suffered from a threatened boycott and massive amounts of negative publicity based on false assumptions.

Even those heavily invested in Twitter advise that you shouldn’t try to read everything, that you should take time off. I’ve been told repeatedly that the key to managing information flow in this day and age is the use of powerful filters, perhaps the most powerful being that you don’t have to join in and use every technology simply because it exists. Usenet, in its time, was highly influential and great fun. But no, you’re not suffering now because you didn’t use it. Something else came along and replaced it, and something then replaced that. If you have the time and interest to join in, well, good for you. It’s an investment I can’t make and it’s good to know I’m not alone in this.

I’ll leave you with this funny, but impressively accurate list of Why Twitter is Evil.

What at first seemed to be an odd April Fool’s joke turned out to be real–the Journal of Visual Explanations (JOVE) has gone from an open access publishing model to a closed access subscription model. No official statement was made, but on Noah Gray’s blog, JOVE’s Moishe Pritsker made the following statement:

“We (JoVE) are changing our model, and from now will provide our content under subscription. Until now it was all for free.

The reason is simple: we have to survive. To cover costs of our operations, to break even, we have to charge $6,000 per video article. This is to cover costs of the video-production and technological infrastructure for video-publication, which are higher than in traditional text-only publishing. Academic labs cannot pay $6,000 per article, and therefore we have to find other sources to cover the costs.

As much as I would like to continue to provide our content for free, JoVE has to survive. I believe the world would be a better place having a video-publication under subscription than not having a video-publication at all.”

More details can be found on this Friendfeed thread:

“…we are indeed closing access. Not an April Fool’s joke. We’ve been trying to get universities to subscribe to us, but nobody seems to be taking us seriously and, given our situation, being free is just not sustainable.”

I can’t say I’m terribly surprised. JOVE set themselves a monumental task, trying to break ground with a new type of science publishing AND at the same time trying to do so with an unproven business model. Doing both together was perhaps a bit too ambitious. I can think of several reasons why open access wasn’t going to cut it for them:
1) their insistence on high production values–the only journals I know that are sustainable/profitable using an author-pays open access model are those that emphasize high quantities of publication and minimal editorial oversight and support. By striving for high production values, JOVE added significant editorial overhead and costs.
2) A large number of JOVE’s publications are demonstrations of techniques. As the editor of a methods journal, I’m painfully aware of the “second-class citizen” attitude most scientists take toward writing up methods. Obviously data papers are the bread and butter of the working scientist–that’s where they’re going to advance their careers. Methods papers are a nice addendum, but they are not a priority. It’s hard to get scientists to write up methods, and much of my time is spent trying to commission articles. At CSH Protocols, we go so far as to pay our authors a royalty as an incentive for writing up methods for publication with us. I find it hard to believe that there will be very many willing to not only spend the time to put together a video of a method, but willing to pay JOVE’s costs to do so.

And so the economic realities seem to have hit home. I wish the best to JOVE, the folks I’ve met from the journal are all smart, nice people and their experiment is an intriguing one. I worry though, that so much of their support and hype came from the small but very vocal group of open access proponents so prevalent online. This shift in business models may not be taken very well by that community.

There’s been a rash lately of articles and blog entries pleading with scientists to enter the blogosphere. One disturbing aspect of this has been how many of them have been written by various aspects of the Nature Publishing Group. Three recent articles (here, here and here) all make the case that scientists should start writing blogs because science journalism is on the wane, and that science blogs can fill the void left behind for educating the general public about science. Coincidentally, Nature just happens to run one of the biggest centers for science blogging. Does their desire to have this venture grow and succeed have any influence whatsoever on their opinions about the need for scientists to take on this extra workload? From Nature’s own ethical guidelines:

“In the interests of transparency and to help readers to form their own judgements of potential bias, Nature journals require the authors of most articles to declare any competing financial interests in relation to the work described…”

Interesting how that applies to authors but apparently not to their own editorials.

Now, as to the meat of the subject matter presented–are science blogs going to replace science journalism? I have my doubts, which I’ll explain below. The whole thing reminded me of Clay Shirky’s recent article, Newspapers and Thinking the Unthinkable. While I’ve strongly disagreed with Shirky in the past, I thought this was a perceptive piece, and I particularly liked the open-endedness of his argument. Essentially what Shirky says is that things break quickly, then it takes a while for something new to develop to replace those things. There’s not an immediate fix on the horizon for our disappearing newspapers. I like that instead of the usual vague cliches most Web 2.0-proponents spout for suggestions on how to proceed, Shirky leaves the question up in the air and doesn’t try to pretend there’s an obvious answer:

“No one experiment is going to replace what we are now losing with the demise of news on paper, but over time, the collection of new experiments that do work might give us the journalism we need.”

The one caveat I’d add is that the article assumes that good journalism is something our society values enough to preserve, which may be more of an open question. Sometimes things don’t get fixed after a revolution, they get worse. Time will tell.

That said, some thoughts on why science blogging is a poor substitute for science journalism:

1) Journalism is a real profession that requires training and a difficult to master skill set when done properly, as I discussed in this posting. Scientists, and science bloggers are not trained in that skill set. One can certainly make the argument that what passes for science journalism these days is far from ideal, but replacing it with something equally flawed does not strike me as an improvement.

2) Aside from the obvious problems with newspapers’ economic models, the reason journalism is on the wane is the dropping quality. Newspapers have systematically tried to cut costs over recent years, placing economic pressures on reporters. This has resulted in much of what passes for journalism becoming regurgitation of press releases (see Churnalism). Given that many science blog entries are just links to other articles, isn’t this much the same thing? Furthermore, if the nature of so many blogs (often including this one) is to provide links and commentary on original published works, what are bloggers going to write about if those original stories no longer exist? Do away with published news articles about science and you do away with a huge chunk of the subject matter of the science blogosphere.

3) The other big problem with the current state of journalism is the substitution of opinion for factual reporting. As noted here:

“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.”

I can’t think of a single blog that I’ve ever read that wasn’t opinionated. Blogs are more like the editorial page of a newspaper than the front page.

4) As Larry Moran recently pointed out, most scientists are never going to blog. Reading and writing blogs appeals to a limited percentage of people in general, scientists being no different. Start with the subset of scientists deeply interested in communication, education and outreach, and then remove those who don’t enjoy the blogging process and you’re left with science bloggers. Factor in Jakob Nielsen’s 90-9-1 rule (online content is created by 1% of users, 9% occasionally contribute a little, 90% never contribute) and you’re talking about a tiny fraction of scientists. Does this give a balanced view of science? Anyone who regularly reads science blogs can quickly point out some of the general biases and viewpoints held by most of the blogosphere. Remember also that those doing really interesting research, the people you’d most like to hear from, are the least likely to blog. They’re too busy doing that research.

5) The world of science blogging is filled with navel-gazing. I think this is one of the main reasons you don’t see the mainstream of scientists writing or reading science blogs. The vast majority of blog articles I see are either about blogging (or other online communication tools) or about what other bloggers are doing/blogging about. Another big chunk is about life as a scientist. Then there’s a small percentage of posts about actual science. All this is great for building community and feeling a part of a connected group, but I’m not sure how interested the general science reading public is going to be in these cliques.

Phew. I seem to have quite a few rants in me as of late. Bottom line, let’s all keep blogging. It’s fun (at least for those of us who are into it) and no doubt it serves a solid educational purpose and opens lines of communication between scientists and between scientists and non-scientists. But I don’t expect it to become a required activity for most scientists. And let’s be honest about what it really is. The majority of these enjoyable personal diaries and spaces for voicing our opinions are a far cry from well-researched, well-written professional journalism. And I’m with Shirky on this one. New business models and new forms of communication will emerge to continue the process of journalism. We just haven’t seen them yet.

Edited to add–the one point I forgot to add. It’s interesting that the tools that were originally being sold to us as a means for scientists to interact, to troubleshoot techniques and experiments, to find collaborations, are now being pitched as a means for scientists to educate the general public. I always thought the original plans were a bit far-fetched (if every graduate student starts posting daily blog entries about their experiments, who’s going to read them all, let alone offer advice?), and it goes to show you that no matter what your intentions when you create a tool, users often find it better suited for something else. Which I guess explains why a tool created to help college students know their fellow students is now used by grandparents to show pictures of children to their former high school classmates.