The Niche: The Stem Cell Blog hosted by Nature Stem Cell Reports

How many fine niche stem cell blogs do you know? 4-3-2-1? How many with an attractive, easy to remember name? 0? Good, short, actual and proper blog names are rare. Let me introduce you The Niche which intends to become THE Stem Cell Blog in the niche of the niches. It is the newest Nature blog hosted by the also newly launched Nature Reports Stem Cells “to provide an informal forum for debate and commentary on stem cell research and its wider implications for ethics, policy, business, and medicine.”

Here is the RSS feed for the posts: http://blogs.nature.com/reports/theniche/atom.xml

also don’t forget to subscribe to the comments: http://blogs.nature.com/reports/theniche/index.rdf

Cell’s Superhero Cover: the role of comics in science popularization

I’ve just realized how cool is Cell magazine May 4 issue’s cover (the one with the Scientist Enter the Blogosphere report by Laura Bonetta) with the S-nitrosothiol superhero T-shirt. This substance may have some therapeutic utility in diseases such as heart failure and asthma.

Illustration: Cell and me this morning.

Cartoons are terrific education tools, let’s consider howtoons for instance. Howtoons are cartoons showing kids of all ages “How To” build things. What about cartoons for scientists?

Looking for user friendly, attractive peer review article titles….

These two titles are freshly out of my feed readers: B-type natriuretic peptide inhibited angiotensin II-stimulated cholesterol biosynthesis, cholesterol transfer and steroidogenesis in primary human adrenocortical cells. and

In vivo expression of human ATP:cob(I)alamin adenosyltransferase (ATR) using recombinant adeno-associated virus (rAAV) serotypes 2 and 8.

How user friendly these titles are? Let’s examine me: Theoretically I have some (limited) background knowledge on these topics as they are covered by my Google Reader with some properly chosen search terms. For the first trial I see only familiar characters in a weird arrangement without any intelligence flash in my mind, for the second some mental forms are beginning to take shape, for the third a little more context enter, but instead of a fourth title trial I skip to the abstract in case I’m interested in what follows based on the previous title impressions. But I’d truly appreciate if I could capture at least half of the title at first. And the titles above are not the worst at all. After reading the steroidogenesis-one many times, it became my friend. But people would like to put less energy into conceiving a simple title and more to understand and apply the new results. A good title is about the proper filtering of the proper reader and vice versa.

Yes, there must be some good policies on titles of peer review articles. In case of the steroid paper, the Instructions to Authors for Endocrinology says on title requirements: Full title (a concise statement of the article’s major contents)

PNAS has a longer title guide for instance, this paragraph is from an older version of PNAS Information for Authors: Title: Titles should be simple, informative, and comprehensible for a broad scientific audience. Authors should avoid nonstandard abbreviations and colonic phrases. Titles may not be phrased as questions. Titles are limited to three lines or 135 characters including spaces.

Towards Universal Online Laboratory Notebooks - in theory

Maxine Clarke, Nature’s blogactive and web-oriented Publishing Executive Editor blogged on has an interesting and opinionated editorial on Share your lab notes in Nature 447, 1-2 (3 May 2007). also available at Nautilus.

Her The line of argument is: The use of electronic laboratory notebooks should be supported by all concerned since they “contain data that flow automatically from lab instruments and can be read by all lab members”. This availability to other collaborators should compel the keeping of better records. Most importantly: “If each notebook is allocated a unique identifying code — a permanent alphanumeric string containing information about provenance, creation dates and digital location — it can be cited in journals as a confirmation that the data are safely stored, ultimately available and sharable (with due regard for the rights of the researchers involved). It also confirms that the original data can be retrieved in the case of errors or accusations of fraud.” This way, Clarke the editorial goes on, both “the rigour and transparency of publicly funded research will be improved”.

And she the author of the editorial is absolutely right. But there are many, geographically distant interlab collaborations too, not just intralab projects in the vicinity of 2 rooms on the same floor. Let’s put these ideas into context to see them live.

I’d like to step further a little bit as Clarke the author of the editorial misses to consider the current technological situation: all these nice aims, the standardization (unique URL to every lab notebook), the universal, collaborative sharing of digital notebooks could obviously be realizable by web-based applications (Google Docs, collaborative wikis) rather than Office-like desktop softwares and restricted local networks.

Or more dynamically: can you imagine individual experiments as blog posts, and a lab notebook as a project blog? After all, every experiment has a principal investigator, and all the other participators could be interpreted as commenters. Or this is not the case (we need a group blog in case when the FACS measurement at the end of my cell culture experiment is implemented and recorded by another scientist), and more democratic wikis are the real solutions? Who knows it yet? But the direction is clear. Webtop apps.

Nature Medicine 2.0 alarms by its editor in chief

Oops, the folks at Nature Publishing Group are more and more watching us, the people of the second-generation Internet, you know the two point oh. Recently, the editor chief of Nature Medicine (impact factor 28.878 in 2005), Juan Carlos Lopez wrote and editorial and even a blog post concerning “what is the Web 2.0–driven scientific publishing world going to look like?” The editorial is a static monologue by form, but at the end of it, there is an outgoing link to the dynamic blog post. And a post is successful, when it becomes a dialogue and that success is fulfilled only through comments.

In the traditional academic environment an editor in chief of a peer-review journal like Nat. Med. is in a position of enormous power from a point of view of an experimental scientist interested in submitting a paper. But this time it is not the case, the emphasis is on the survival of the traditional brand based and peer review model: “One idea is that the community will increasingly do without high-profile journals to decide what an important paper is and what it is not. If many scientists get together to discuss papers in social-networking sites, they may provide visibility to papers published in obscure journals and deprecate articles from more visible titles. If this becomes the case, and if high-profile journals make enough editorial mistakes while selecting the papers we publish, then the value of those publications will indeed go down.” In a fractionated tribal niche world, like the current web “is there room for journals like Nature Medicine?”

Nature News on JoVE: is JoVE really the YouTube for life scientists?

Nature News has an article of the new Journal of Visual Experiments website, whereof Pimm had a story one week ago with the help of Moshe Pritsker, founder of the site. The title of the Nature News post: YouTube for test tubes, which sounds good really, but is problematic a little bit. In a way the YouTube analogy is true, the biologists can now upload their protocol videos on the site, and can watch it freely, and there is the exciting DIY possibility, but on the other hand JoVE is not YouTube at all: there is a strict submission process with clear policies to go through, which excludes junk, and you cannot embed the videos freely. The first aim of JoVE is to be useful for people in the lab, which is a scientific purpose. Entertainment is just after that. Good luck for any bioDIYers.