March’s issue of Cold Spring Harbor Protocols includes a set of three articles detailing common methods for DNA isolation from plants:

Quick Miniprep for Plant DNA Isolation gives a rapid method, good when processing large numbers of samples where high purity of the resulting DNA is not needed.

Dellaporta Miniprep for Plant DNA Isolation is quick and inexpensive and results in a higher quality end product. Because it yields enough DNA to test a large number of markers, it’s recommended in cases when many markers will be tested on the same samples.

Cetyltrimethyl Ammonium Bromide (CTAB) DNA Miniprep for Plant DNA Isolation is useful for isolation of DNA from tissues containing high amounts of polysaccharides. The presence of polysaccharides can inhibit PCR reactions. Under high salt conditions, CTAB binds the polysaccharides and takes them out of solution.

These articles join a previously published protocol for plant DNA purification, from C. Eduardo Vallejos, An Expedient and Versatile Protocol for Extracting High-Quality DNA from Plant Leaves. This method results in DNA that has virtually no protein or phenolic contaminants, is RNA-free, contains high-molecular-weight fragments according to CHEF electrophoresis, and is fully digestible by restriction enzymes.

As I explained last year, Cold Spring Harbor Protocols is something of an experiment as a publishing business model. Because some of our articles come from our lab manuals, where we owe authors and editors royalties, we chose to extend those royalty payments to authors of new, original articles. Writing up methods is usually not a priority for most scientists, they’re more focused on data-driven papers. We wanted to provide a nice incentive for authors to 1) write up their methods and 2) publish them with us, rather than other journals who don’t offer such incentives. We’re not talking about huge amounts of money, but as I recall from my graduate student days, every little bit helps. If I could have published a paper AND gotten some cash for a night on the town, I would have been thrilled.

The way it works is that each year we set aside a percentage of our subscription revenue for the journal. This total amount continues to grow as the journal’s subscription base continues to grow–and we’re happy to report that CSH Protocols is seeing a lot of uptake by the scientific community. That sum is then divided among all authors based on the usage of individual articles. Original articles generated a range from around $3 (for an article published right at the end of the year, with little time to accumulate readership) to one of our most-read articles, which will result in a payment of $367 for the author (our top original paper author wrote a set of two papers and will receive just over $600).

So, if you wrote an article for us that was published in 2008, you should expect to see a check in the mail in the next few weeks. We hope that this revenue sharing is a nice bonus for the hard work you put into your article and that this serves as an incentive to write up more methods for publication. And if you haven’t yet published with us, what are you waiting for?

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.

So many bat puns, so hard to choose just one for the headline…

March’s issue of Cold Spring Harbor Protocols includes two sets of Emerging Model Organism articles with protocols. The first set, on Darwin’s Finches, is covered here. The second set is on the Short-Tailed Fruit Bat (Carollia perspicillata), and a bat embryo is featured on our cover. There are at least 1,116 species of bats, comprising >20% of all living mammalian species. Their abundance and diversity suggests that further study would give us a more balanced and comprehensive view of mammalian biology.
The Short-Tailed Fruit Bat Carollia perspicillata: A Model for Studies in Reproduction and Development is contributed by Richard Behringer, Chris Cretekos and John Rasweiler. This group has done some fascinating recent work using the bat as a comparative model for limb development, asking why a mouse makes a front leg where a bat makes a wing. Interesting morphological features like wings are just one reason among many to study bats as the authors point out:

Among the interesting features of the early embryogenesis of Carollia are development to the blastocyst stage and shedding of the zona pellucida in the oviducts, formation of reticulated endoderm during implantation (as in humans), development of an unusually large inner cell mass (ICM), disposition of endoderm and Reichert’s membrane around all or nearly all of the ICM, extensive apoptosis of epiblast cells during amniogenesis, and formation of a planar embryo at the primitive-streak stage (in contrast to the cup-shaped embryo of rodents) (Badwaik et al. 1997). Carollia is also unusual among mammals in that it sometimes takes embryos into prolonged periods of delay (diapause) after implantation, at the primitive-streak stage, which can last from weeks to months. This delay period occurs seasonally in the wild, but in response to stress in captivity (Rasweiler and Badwaik 1997), and is associated with major alterations in trophoblastic differentiation and placental development (Badwaik and Rasweiler 2001). The endocrine control of the delay remains to be elucidated.

Along with a general primer on the use of bats in the lab, Behringer and colleagues have also supplied protocols for feeding, generating timed pregnancies, collection of bats from the wild, collection of embryos, fixation and storage of embryos, staining of cartilage and bone, whole-mount in situ hybridization and whole-mount immunohistochemistry (the latter two providing my title on methods for visualizing bat signals, for which I apologize).

Time to close some open tabs and clear out a few recent bookmarks of interest in the world of science, publishing and Web 2.0.

Social Media is Here to Stay… Now What?
Insightful essay on social networking from a researcher at Microsoft. Many interesting concepts herein, I particularly like her contrast of youth vs. adult behaviors on social networks. It once again points out that the recurrent meme that “once the kids who grew up on myspace reach adulthood, the whole world will work like myspace” is absurd. People change as they age, their behaviors change, and the things they want to do on social networking sites change (see Why Facebook Is For Old Fogies for some concrete examples) . Which is why all the “myspace for scientists” sites are so misguided. Scientists aren’t teenagers learning socialization skills (though a good many scientists could probably use additional training). They are professionals, with very different needs from other communities.
I also like her take home message:

“Specific genres of social media may come and go, but these underlying properties are here to stay. We won’t turn the clock back on these. Social network sites may end up being a fad from the first decade of the 21st century, but new forms of technology will continue to leverage social network as we go forward. If we get away from thinking about the specific technologies and focus on the properties and dynamics, we can see how change is unfolding before our eyes. One of the key challenges is learning how to adapt to an environment in which these properties and dynamics play a key role.”

What I’ve Learned from Hacker News
The editor of an online community news site writes on some of the lessons learned. Of particular interest is the “Fluff Principle”:

“…on a user-voted news site, the links that are easiest to judge will take over unless you take specific measures to prevent it.”

He goes on to discuss the valuable role that editors play in maintaining the quality of the material presented.

In Praise of the Sales Force
Along similar lines, Cory Doctorow’s latest column celebrates the things he gets from his publisher that can not be provided by going it alone on the internet. The first comment left on the article is something many would-be self-publishers fail to think about:

“I am always looking for good ways to talk to authors about why *not* to self-publish: the publishing industry exists for a reason – you don’t make better books and better money by “cutting out the middleman”, you just take all the work on yourself, and do it without their experience, expertise, or, as you write, distribution network. Let alone their budget.”

Typos and Value
Keeping with that theme, more on the value of editorial oversight.

“In the realm of communication, especially the communication of research years in the making, we need to spend time preserving signal and eliminating noise.”

Lines of communication
Nature Methods editorial pleading with scientists to start blogging. Could the subtext here be that they’ve spent an awful lot of money on the Nature Network and are disappointed to only have around 50 regular bloggers and no real uptake by the mainstream of scientists?

End of Free Access
Surprised this one didn’t receive more notice in the open-access-leaning science blogosphere. The Journal of Clinical Investigation (JCI), which went to free access for all articles in 1996 is now switching to a subscription-access only business model, as open access was not sustainable for their journal.

Visits to Gmail surpass YouTube
Another common meme as of late has been the “death of e-mail”, with pundits opining over the new technologies, Twitter, Seesmic, etc. Yet the numbers show consistent growth and heavy usage of e-mail. Google, always a company to watch for future trends, recently announced Google Voice, a way to move your phone and text messaging communication to e-mail. Perhaps the obituary of e-mail is a bit premature.

And we’ll close this set with a bit of humor:
A spectacular new e-book interface device can be seen here, a flow chart for deciding whether you should send all your friends that clever picture of a cat with a misspelled caption that you saw online is here, and a quick primer on who joins which social network is here.

With all the celebration of the 200th anniversary of Charles Darwin’s birth this year, we thought it might be interesting to take a modern look at one of his model organisms: the Galapagos finches first described during his voyage on The Beagle in 1835. Today, these birds continue to be an important source of information on speciation, niche partitioning, morphological adaptation and species ecology. In the March issue of Cold Spring Harbor Protocols, Harvard University’s Arhat Abzhanov has written a primer on Darwin’s Finches: Analysis of Beak Morphological Changes During Evolution, which gives detailed background information on the use of the finch as a model system. He has also provided protocols for collection of embryos, in situ hybridization and microarray analysis.

Regulating Protein Stability in Mammalian Cells Using Small Molecules, by Thomas Wandless and colleagues is featured in this month’s issue of Cold Spring Harbor Protocols. This technique provides a rapid, reversible, and tunable method for studying the activity of a protein of interest in cells. The protein is attached to a destabilization domain, and the resulting fusion proteins are unstable and degraded, except in the presence of small ligands. The speed of small-molecule binding makes it an attractive alternative to studying gene function using RNA interference (RNAi). Wandless’ group also provides a second protocol, A General Method for Conditional Regulation of Protein Stability in Living Animals.

Like all of our featured articles, Regulating Protein Stability in Mammalian Cells Using Small Molecules is freely available to subscribers and non-subscribers alike.

Are there times when science shouldn’t be a conversation? When sitting quietly and listening is more important than joining in discussion?

As a self-confessed grumpy old man who is still eluded by the allure of Twitter, I was thrilled to recently see that I’m not alone, and patron saint Jon Stewart is thinking along the same lines. After the recent O’Reilly TOC conference, there were scores of articles talking about twittering during presentations, Joe Wikert for one noting, “I found myself listening to a speaker in one session while also reading the tweets from the others running simultaneously.” Which brings up the obvious question Stewart asks:

“Why aren’t you paying attention? There’s a reason they don’t allow cel phones in seventh grade classrooms.”

Is it really possible to pay detailed attention to a speaker while you’re simultaneously typing and reading and having a conversation with others? I find it incredibly annoying when sitting in a seminar with a colleague who won’t stop commenting or talking long enough for me to take in what the speaker is saying. There’s usually a reason why a particular person is asked to speak on a particular subject. Do we owe them the courtesy of listening to what they have to say, or are we evolving into such an ego-centric society that we must constantly force ourselves into the spotlight? Must everything be a conversation where every voice is heard, or are there some situations where it’s okay to let one person have the floor? Colin Robinson notes:

In an increasingly self-centered society a premium is placed on being heard rather than listening, being seen rather than watching, and on being read rather than reading.

I’m all for asking questions and debating a speaker’s results, but can’t you wait until they’re actually presented before doing so? If you’re going to spend the talk having a conversation with friends and checking your e-mail why even attend at all? Here’s an interesting look at a criminal law class where the professor banned laptops from the classroom. 71% felt it improved their concentration in class, 52% said it made the time in class more interesting, and 54% felt it increased their overall enjoyment of the class. Perhaps there’s merit in focus and attention after all.

Is what you have to say really so important that I can’t wait until the talk is over to hear it? Are your pithy thoughts more important than the speaker’s? Are your comments even relevant if you’re not listening to what’s being said? If we’re having a conversation instead of listening, why are we even here, shouldn’t we be in the bar doing this?

Are tools like Twitter really an improvement, or do they just pander to our increasingly short attention spans, our laziness (more on this in my next rant) and our need to be the center of attention at all times?

The March issue of Cold Spring Harbor Protocols has posted, and one of our featured articles looks at long-range chromosomal interactions and the proteins that mediate them. Stephen Baylin and colleagues from Johns Hopkins University contribute a method for the Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein Mediated Genome Architecture. 6C technology combines multiple techniques to identify the proteins that bridge distant genomic regions, while simultaneously identifying physical proximities. The method is also useful for determining if a candidate protein might mediate long-range interactions, both in cis and in trans in the nucleus. The 6C assay advances our understanding of chromatin folding and provides an important tool to examine the role of specific proteins in nuclear organization.

Like all our featured articles, this method is freely accessible for subscribers and non-subscribers alike.