For your free information (FYFI): it’s Open Access Day!

October 14, 2008 is the world’s first Open Access Day and OA itself means free online access to peer-reviewed research articles. Although we have other, slower methods, like personal homepages, emails to authors, institutional repositories to get the same article we were unable to get via closed access journals, OA is the internet-savvy solution that fits our time and science.

Let me briefly answer question 4 of the synchroblogging initiative: What do you do to support Open Access, and what can others do?

I did a lot of beta testing for free for the upcoming Google Research Datasets in this summer which will host terabytes of scientific raw data that should be in the public domain or have to have a Creative Commons license. I really liked this work.

Here’s what others said on that:

Neil Saunders:

We live in a world where people expect instant, relevant information in the top 20 hits from a Google search and that expectation is transferring to science too. I don’t care how prestigious you think your journal is, or whether you see yourself as some kind of “guardian of knowledge”. I want information, I want it now and if you can’t deliver, I’m going somewhere else.

Neil’s commenter, Stevan Harnad helps clarifying some concepts:

Compare scientific websites with a new Google Trends layer!

I always had the feeling that the Natureplex (the web division of the Nature Publishing Group headed by Timo Hannay) is ahead of most scientific journal publishing conglomerate’s similar departments. Now with the help of a new Google Trends layer that compares websites in terms of traffic this impression was confirmed again without strict numbers. I hope that more and more scientific journals gain incentives finally to experiment with new web technologies. Also a quick look to the Regions comparison on the bottom left helps you give up the history based conclusion that Science is the number 1 on the web in the US compared to Nature while Nature is so UK and Europe centric.

“Today, we add a new layer to Trends with Google Trends for Websites, a fun tool that gives you a view of how popular your favorite websites are, including your own! It also compares and ranks site visitation across geographies, and related websites and searches”

Source: Official Google Webmaster Central Blog via Webmonkey

The same comparison with Alexa:

Puzzle: Which Wired article is cited in Nature Biotechnology?

Nature Biotechnology is the (peer review) journal for me: it’s geeky, fresh and it takes into account more than just one point-of-view, that of the scientist-academist’s: technology & business are hand in hands also. (Recommending Nat Biotech makes a niche sense here while recommending Nature, which is actually the only science journal I’m reading issue by issue is hm… too obvious)

But Nature Biotech goes as far as citing even a non peer review journal – I am also pretty familiar with – called Wired.
So my puzzle is /please use your contextual knowledge first & just then your typing skills while thinking of an answer/: which Wired article is cited in a March Nature Biotech News and Views article (very good, by the way) named Synthetic genomes brought closer to life by Robert A Holt amongst strict science articles. Don’t think too high, it’s rather a reflection.

Here is a little help:

PITTCON, 2008: bioDIY questions, RFVials, and Science’s new web hirings

As a local New Orleans face (my colleagues just call me Mitoman in the lab) I had the chance to just simply walk into the grandiose PITTCON exhibiton at the Ernest N Morial Convention Center‎ and I liked it. In addition to getting answers to some strictly lab related questions concerning filters and fuges (nevermind), I satisfied my 2 major side interests: the older bioDIY and the brand new RFID.

1. I surprised every biotech vendor - some of them laughed, others were meditating a bit - with the question: ok, but what is the cheapest gadget you have for somebody who wants to set up his basic DNA private lab at his backyard?

In my coming series to help launch a grassroots biotech DIY movement I’ll put together concrete suggestions on what to buy, but according to the experts:

- the price of a new benchtop centrifuge (6-8000 x g) is $800-1200, but the manufacturer is simply not interested in individual service and recycle used machines for low-throughput hobbyist end-users

- liquid nitrogen: 24 liter tank around $5000 (you can get it lower), LN itself is not that cheap but it’s worth storing your cells in a local repository bank instead, at least an expert guy told me

- a laminar hood for sterile work with cells is also around $5000, way too much for garage biofreaks, but you can still build your own out of a household air purifier

2. Have you ever thought of tracking, reidentifying your eppendorfs and tiny PCR tubes in the lab instead of the almost impossible hand marking? Well, we are not there yet, but Baytek developed an RFID kit for glass GC or HPLC vials.

The Warda-Han-Proteomics scandal: fingerprints of plagiarism, too

We have now a well-developed and sad case example of irresponsible scientific editing and publishing: the Warda-Han advanced online paper by the academic journal Proteomics: Mitochondria, the missing link between body and soul: Proteomic prospective evidence. What started as an abstract-based hunch and question about the quality of a recent review, addressed to and amplified by the the scientific blogosphere may probably end as a piece of investigative journalism in the mainstream media with serious consequences and conclusions on scientific publishing. Right now, the real investigation takes place at the comment section of the PZ Myers post A baffling failure of peer review over at Pharyngula. The story there is quickly unfolding thanks to the smart and open-eyed (Google-savvy) contributors who figured out amongst others that Warda and Han significantly reduced their review writing efforts by borrowing many sentences from other colleagues’ papers. Here I’d like to mention and cite only 3 comments:

The fingerprints of a mighty creator in Proteomics, impact factor >5

Creationism/intelligent design is not really an issue for me as I am a biologist working with mitochondria and stem cells, also a life extension supporter, whose angle on things and projections are based on the recent advancements in science and technology. As far as I know, creationism/ID neither suggests any new experiments or heuristic solutions in my research field, nor does it help to plan&build new technologies to extend healthy lifespan. From my point of view, thinking about creationism is a waste of valuable scientific/technological processor time.

But I am not used to encounter with explicit creationism and the fingerprints of a mighty creator as an explanatory force behind a natural phenomenon in scientific peer-review journals. That’s exactly what happened to me in a recent review published online by the Wiley journal, Proteomics (ISI Impact Factor 2006: 5.735) by Mohamad Warda and Jin Han, entitled Mitochondria, the missing link between body and soul: Proteomic prospective evidence.

Last week when I wrote the post Can you tell a good article from a bad based on the abstract and the title alone? on the review I had only 10 minutes for figuring out the post between 2 experiments in the lab during lunchtime. The only thing that came into my mind reading the abstract – popped out of PubMed feeds – was that something stinks here. Now it’s Mardi Gras day and I have a couple of minutes more to address this issue and hopefully no more.

Myrmecologist and blogger Alex Wild picked one sentence from the paper in a comment, and here is the complete paragraph:

Alternatively, instead of sinking in a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption that all living cells undergo a certain degree of convergence or divergence to or from each other to meet their survival in specific habitats. Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life.

This is the closing paragraph of the section Mitochondrial integrated function disproves endosymbiotic hypothesis of mitochondrial evolution. The mitochondrial part of the well established evolutionary endosymbiotic theory claims that ATP-producing mitochondria were ancient prokariotic invaders of host prokariotic cells eventually turned out to be the common ancestors of eukaryotic cells. I always found this hypothesis one of the most fruitful scientific concepts as it constantly suggest new ideas and warns that current eukaryotic cells are the products of an evolutionary, accidental and instable alliance between the mitos and their hosts. As the endosymbiotic theory is the mainstream academic theory of mitochondrial evolution it is a challenge for scientists to attack it with counterarguments and that’s what Warda and Han are aiming for in that section. What they are doing seems like a legitimate discussion of a scientific theory but ends with the logically unacceptable jump to the fingerprints of a mighty creator as an alternative explanation.

Before I cite the section in question in full length and recommend to my readers to analyze it, I also like to suggest the detailed comment of D. Spencer saying amongst others:

If Wiley and the journal Proteomics allow this into print (it is currently only “published” online) they can kiss goodbye to any hope that Proteomics will ever again be regarded as a serious scientific publication.

Here is the complete section by Warda and Han without references that could be found in the full text:

Stat freaks, are you ready to play with the SCImago Journal & Country Rank?

Finally the Google PageRank algorithm, the core analysis tool of the current web is back to where its idea is originated from, scientific citation analysis. The recently launched SCImago Journal & Country Rank database uses an algorithm very similar to PageRank. It has a new metric: the SCImago Journal Rank (SJR). According to Nature:

A new Internet database lets users generate on-the-fly citation statistics of published research papers for free. The tool also calculates papers’ impact factors using a new algorithm similar to PageRank, the algorithm Google uses to rank web pages. The open-access database is collaborating with Elsevier, the giant Amsterdam-based science publisher, and its underlying data come from Scopus, a subscription abstracts database created by Elsevier.

The SJR also analyses the citation links between journals in a series of iterative cycles, in the same way as the Google PageRank algorithm. This means not all citations are considered equal; those coming from journals with higher SJRs are given more weight. The main difference between SJR and Google’s PageRank is that SJR uses a citation window of three years.

From now on every stat geek can compare journals to journals, countries to countries based on different metrics like citable documents, cites, self-cites or the new h-index and get a ticket to recursive heaven. Of course I started with the comparison of Nature and Science to find something very different. I couldn’t. I predict that self-cites will show a lot on how things are going on at different scientific journals and the stats will be used as serious arguments in many blog posts. But here let me share some graphs on the quick comparison of USA, UK and China in the category of Aging.

First graph: citable documents

I (scientist) desperately need a one click Reprint Request widget!

Just like other scientists, I guess, who are sending thousands of email reprint requests to other colleagues when the pdf of the paper is not available online.

Let’s vote now for the 10 Finalist Lab Websites at The Scientist!

Ladies and gentlemen of science! You can now rank the 10 finalist websites from 1 to 10 (1 being the best) at the Laboratory Website and Video Awards hosted by The Scientist. Please do not hesitate, judging is a lot of fun and this is a big issue: figuring out the parameters of the labsite of the future based on the plus and minus features of current laboratory web pages! Some comments of the judging panel were published, just scroll over the judges’ photos. Winners will be announced in December. As a member of the judging panel my comments were chosen and published by the editors too, according to the selection I was rather critical (screenshots). Quick reminder: The LaWVas awards is the one that grew out of my unofficial lab website competition idea. The winning sites as selected by the editorial team, judging panel and the readers will be announced in this December.

And 2 more:

Science’s Netwatch: Aging blog in focus

Here is another sign that the editors at Science Magazine are taking more and more attention to the web and the scientific blogosphere: Ouroboros (that is: Chris, Okie and Lev) was picked up in the Random Samples column of the current Science issue: “But research on aging is booming, and the field’s good health is on display at the blog Ouroboros, which is named for a symbol of endlessness. Three postdocs from leading aging research labs offer their takes on the latest results from conferences and the literature. The site is aimed at researchers, but it can also help beginners get up to speed.”
It seems that the editors are sharing my opinion that Ouroboros is one of the best science blogs out here and it is also worth mentioning that Chris Patil’s incentive of Ouroboros was Science Magazine’s SAGE KE.
Another remarkable thing is Chris’s approach of developing a group blog instead of building an individual brand and focusing exclusively on biogerontological peer review literature and conferences.

Flourishing lab site culture around the Laboratory Website Awards!

You can still nominate your favorite lab websites at the Laboratory Website and Video Awards or LaWVAs (pronounced like “lava) hosted by The Scientist. (Disclaimer: I am a consultant to The Scientist on the LaWVA project and a member of the judging panel.)

I’ve just checked the candidates and they are amazingly versatile ranging from little academic labs to industry heavyweights.

The winning sites as selected by the editorial team, judging panel and the readers will be announced in this December.

Nature’s history site: how to keep the tradition and identity alive

Disciplinary science has a rather short-term memory (see the reference section of peer review articles) while science publishing is relying on the long-term version, especially if it is the journal Nature, published first in 1869.

Now they launched an innovative new site dedicated solely to the history of the journal, full with multimedia snippets and short stories. Source: Nascent

As Reb Tevye says: How do we keep our balance? That I can tell you in one word: Tradition.

Wired style SENS3 conference intro or be aware of your audience

As this very site here is embedded in the blog medium, we could and should be experimental and eclectic in our style as we cannot control (just target) our audience, thank the web. Now a report on a science conference could be addressed to very different audiences, and yesterday I showed an example on how to present an unconventional science conference to the mainstream science establishment. But if I’d like to target, say, the geeky-layman Wired audience, than I should find another angle on the SENS3 conference which is not restricted to the science content but highlights the inconvenience around it. (Just take a look on how journalists at the Wired Science blog are considering to cover their subject.) Say the story would look like this:

Summary (Lead): A recent unconventional strategic conference on translational science in ageing related damages and diseases shows the benefits of mixing the traditionally homogeneous audience of science conferences with visitors from outside science in order to gain new insights, and put ageing and lifespan extension in a broader cultural context.

First paragraph: Question: Which science conference has such a variety of participants that includes hardcore life scientists from top-notch universities, entrepreneurially inclined benefactors, former IT professional turned bioinformaticians, practicing life extensionists, high school talents, fitness fanatics, lawyers, and even a Hollywood scriptwriter, or an investment banker turned biology student due to a recent cancer survival? Answer: The SENS3 conference in Cambridge.

Compare this to that:

The Laboratory Website and Video Awards by the Scientist!

Here is a classical web story told in links: a niche blogger got an idea and tries to outsource it, it is popularized by other bloggers, then goes mainstream with the help of a science journal, grows over little blogger’s head and get realized by another powerful science institution.

That’s what happened with my unofficial lab website competition idea, which was featured in Nature back in May.

Let me introduce you to the Laboratory Website and Video Awards or LaWVAs (pronounced like “lava) hosted by The Scientist. (Disclaimer: I am a consultant to The Scientist on the LaWVA project and a member of the judging panel.)

The algorithm is as follows:

1. readers nominate their favorite academic or industrial lab websites

2. editorial team will review the nominations and provide up to 30 outstanding sites to the panel of judges

3. panel of judges (e.g. Elizabeth Kerr from Apple Inc. amongst others) will then carefully review these nominations, ranking their top choices in each category (design, usability, content, community), as well as making a selection for our “Judging Panel’s Best of the Web” award.

4. Once the panel of judges has completed their review, it’s time to turn the voting back to you. The winning sites as selected by the editorial team, judging panel and the readers will be announced in this December.

Wow! Let’s make together a web-savvy laboratory culture!

Biopolis profile and cancer stem cells in current Cell Stem Cell

It is now the 3rd issue of Cell Stem Cell, which is the official journal of the International Society for Stem Cell Research (ISSCR). From the current issue:

In human pancreatic cancer a distinct subpopulation of migrating CD133⁺ CXCR4⁺ cancer stem cells turned out to be essential for tumor metastasis different from the ones responsible for tumor growth: Distinct Populations of Cancer Stem Cells Determine Tumor Growth and Metastatic Activity in Human Pancreatic Cancer

Ann Parson highlights Singapore’s Biopolis with a 3.5 billion budget for 10 years:

Biopolis, a broad and busy spectrum of largely government-funded stem cell research—everything from ES to adult cells, basic to clinical—is clear indication of a small nation eager to stay at the forefront. “One of the attractive aspects of Biopolis is that it’s the way a small island can artificially create critical mass,” Alan Colman noted. “It takes the view that there’s no way it can sustain the number and quality of scientists that you’ll find in a

The Open Aging Journal wants you to submit articles!

My gmailbox says and I see no reason not to share it: The Open Aging Journal is an Open Access online journal, which publishes research articles, reviews and letters in all areas of aging science.

The journal aims to provide the most complete and reliable source of information on current developments in the field. The emphasis will be on publishing quality articles rapidly and making them freely available to researchers worldwide. All articles are deposited in at least one major international open digital repository (such as PubMed Central). All articles are indexed by Google and Google Scholar which offers additional massive world wide web exposure.

Visiting the Nature Headquarters, part 1: the internal Nurture blog

Even those scientists, who don’t have any journalism, or out of niche discipline interests (the vast majority), would be eager to take a closer look at how Nature, the number one scientific weekly journal is made, how the articles are peer reviewed, how the column structure looks like, what are the future perspectives of Nature Publishing Group, how they are doing in the new web age, what the main problems are.

On the 10th, September I spent around 6 hours at the Nature Headquarters in London. The Macmillan building is an old Victorian house near King’s Cross at the Crinnan street.

For lunch I was happy to get the company of Nature’s Web Publishing group’s brain trust: Timo Hannay, Euan Adie, Ian Mulvany and Joanna Scott (pictures in the next post).

We started to talk about how work at NPG is organized and I asked the guys how functional the Nature email system (@nature.com addresses) is. It turned out that the mail storage capacity is poor (still in the MB range), so heroic manual delete fight is needed against full mailboxes. But instead of an efficient email system, there is an internal, email killer corporate blog called Nurture (don’t mix it with the Nurture’s magazine for Nature authors) which works perfectly well.

Ian Mulvany, Connotea experimenter, was kind enough to send me the first post of Nurture by Ben Lund (former Connotea project manager turned freelancer) from 2003 in the name of radical transparency. So here I am pleased to blog this historical first post accompanied by the current tag cloud of the Nurture blog. As Ian says retrospectively: By placing it on a blog the readership can self-select. It also allows for consumption independent from interruption.

How to iPhonize a modestly high-impact science journal?

I’ve joust found this ad in a recent Science magazine with a SciPhone in it:

Then I took a look on the journal’s website with my iPhone and here’s how it looks like through the cloudy eyes of my old MacBook:

The Gonzo Scientist on IdeaCity in Science and on the web

If you compare the Nature and the Science front pages (which is not the topic of the current post) you can notice a big difference: there are a lot of “web 2.0″ish fresh features on the Nature site while significantly fewer on the Science counterpart. Now Science came up with a new, less academic and more popculture driven (the name is telling) column, The Gonzo Scientist written and edited by John Bohannon, regular Science contributor. Bohannon writes and even audioslides (illustrations by Katrien Kolenberg) about his experience in IdeaCity.
IdeaCity is Canada’s premier geek summer camp in Toronto, and was modeled after the TED conferences. Now my synonym for the geek camp is SciFoo, but there is a big difference here: IdeaCity is free only for the 50 invited celeb speakers, while it is $3000 for the 3 days for every other visiting Idealists.

Trends in Nature’s July top ten PDF downloads: 5 stem cell papers!

Maxine Clarke over at Nature’s Nautilus blog published Nature’s July top ten PDF downloads.
July was a particularly strong month for Nature concerning pluripotency and embryonic stem cells as 5 out of the 10 top ten downloads, that is 50% of the most popular articles are tinkering with stem cell biology. The other trend: microRNAs, 2 papers. I wonder which could be the last research trend that reached that maturity and which will be the next.

Nature Clinical Practice audio articles: keeping busy doctors updated

Let’s give a chance to audio articles, a new initiative being trialed by Nature Clinical Practice. “These are FREE full-text audio versions of printed content from the March 2007 issue of Nature Clinical Practice Rheumatology. The aim of the Nature Clinical Practice journals is ‘to translate the latest findings into clinical practice’ by highlighting important original research papers so that busy doctors don’t have to read every journal associated with their specialty. The unabridged audio articles will extend this concept by enabling on-the-go doctors to make the most of their time through learning by listening, for example when commuting, exercising or driving.”

Ok, that’s the theory so far, but what is the practice behind? I listened to the demos (via iPhone on an airplane) and filled out a Surveymonkey survey.

For protocols, research and practical articles (full with numbers) it is not a good format as you cannot turn your eye back checking the earlier information (usually people are not reading scientific articles in a linear way but in circles, for instance reading abstracts firsts, than scanning figures and conclusion, then going into details in results, materials, methods, discussion and so on). Shorter, opinionated, journalistic pieces are preferred for audio content like the editorial, and viewpoints formats.

The articles are read out by natural voices, not by machines and softwares just like iSpeak It.

Make a pro buzz for your favourite stem cell papers at Nature Reports Stem Cells!

There are way too much papers and data published in the field of stem cell biology and regenerative medicine to follow and filter with traditional offline, spread of mouth tools. At the Journal Club section of Nature Reports Stem Cells, researchers have the opportunity to highlight and discuss the papers they found of utmost importance in their discipline with a user recommendation and voting system.

Highlights from Science 6/07 issue: wireless power, education, hippocampus, avatars

It was a long time ago, when I last had the opportunity to scan through a complete printed, offline Science issue. On the picture made by Anna with my iPhone (it is not named yet), I am just going to relax with Science and sync my iPhone.

Here are my suggestions to read:

Straight Talk About STEM (science, technology, engineering, and mathematics) Education (audio version of the roundtable is available)

The Power to Set You Free: One of the best-known technology magazines is Wired, capturing in one word both the attraction and the bane of the Information Age. We all want to be connected, but none of us loves the cables that connect. Of course, a rapidly expanding plethora of wireless technologies–cellular phones, WiFi, ID tags, Bluetooth, and many others–provide data connectivity. But despite improvements in battery technology and Moore’s Law, the increasing performance of portable devices still has us reaching for a power cord far more often than we would like. But now Kurs et al. report on page 83 of this issue an ingenious approach that may offer us a chance for true wireless freedom: Wireless Power Transfer via Strongly Coupled Magnetic Resonances: Using self-resonant coils in a strongly coupled regime, we experimentally demonstrated efficient nonradiative power transfer over distances up to 8 times the radius of the coils. We were able to transfer 60 watts with circa 40% efficiency over distances in excess of 2 meters.

The architecture of the scientific web, a must read/see from Timo Hannay

Natureplex boss Timo Hannay published a landmark article draft on the web opportunities for the (more and more NPG boosted) scientific web. He highlighted 3 areas: audio-video content, databases (my emphasis), social software and summarized the science webspace with an artistic figure:

Links from my reader/radar: Googlized Science Direct, Foo Camp, G Scholar as impact-o-meter

Science Direct-ly into Google by Peter Brantley, O’Reilly Radar: Elsevier has now undertaken to have the majority of its SD journals (those for which it holds or can obtain the copyrights) crawled and indexed by Google. Both Google and Google Scholar are slowly incorporating an increasing amount of this content, and these data will be appearing in search results for Google and Google Scholar.

Foo Camp Takeaways by Tim O’ Reilly, O’Reilly Radar: We held our annual Foo Camp in Sebastopol this past weekend. Foo Camp is a weekend geek campout that’s been described as “the wiki of conferences,” because there’s no program beforehand. The program is developed on the spot on Friday night by people swarming a set of big whiteboards with rooms and time blocks. (This year, courtesy of Rabble’s “foocal”, we also got an online version.) We hold Foo Camp for a number of reasons: 1. To learn about what’s next. 2. To test out new product ideas, and to find new authors, conference presenters, and possible investments. 3. To spark other people. 4. To meet new people, and to introduce our friends to each other. We meet new people, and we are always saying to each other “You’ve got to meet…” Sharing friends is one of the most satisfying kinds of sharing.

Google scholar as a measure of impact by Maxine Clarke, Nautilus: Antonio G. Valdecasas and Uta Grothkopf write: Maybe the days of the SCI are numbered, as is already the case in disciplines such as astronomy, where alternative services are used. If impact is to be used as a metric that affects people directly, then databases like Google Scholar — free, accessible to everybody, and non-discriminatory against languages other than English — could provide a tool of universal coverage for bureaucrats and evaluation committees to discover the real impact of publications and hence to be less biased in the distribution of benefits.

Scintilla, a science aggregator and recommendation engine freshly from the Natureplex

The Natureplex (Nature Web Publishing Department on the second floor of a renovated warehouse with around 25 people near at King’s Cross, London) nerds are still busy: Scintilla, a science recommendation engine was launched based on aggregating science content from RSS/Atom feeds of various websites. How could Scintilla (check what the term scintillation refers to, it is a good name) be harmonized with other products of the NPG, like Postgenomic, Connotea, Nature Network…is a future question. For me it seems that the developers would like to convince me to use Scintilla feeds (in the long run) instead of Google Reader feeds when the content is about science in general and in details. The key word is personalization and personal filtering and in that respect maybe it is worth to think of Google’s personalized search trials and web history. More info (including the mail of Euan Adie, developer): Scintilla and Scintilla brings personalization to science

Biotech Geek Blogger goes Nature Stem Cell Blogger at the Niche

In my opinion the Google of science publishing is the umbrella brand Nature Publishing Group. The best indicator of it is the growing number of freshly released beta products making NPG web initiatives a heaven for scientific early adopters. As Timo Hannay, web editor of Nature said in an interview in Spiegel: The core business of Nature is not to produce a magazine,” he says, “but to facilitate the exchange of ideas among scientists.” Indeed, Nature is technologically a step ahead of other publishers in many respects. Let’s take a look at other giant science journals’ websites. (OK, marketing blablah is over, I am not paid for this, I am just simply enthusiastic about the progress.)

I positioned myself here as the Biotech Geek Blogger with an ideal target audience of researchers and IT guys curious about BT things. A clever and fast scientist turned entrepreneur once called me a Google Biotechnologist. Now I realized a bit lately that the niche Google of my profession is called Nature.

I always wanted to participate in a professional group-blog and I had some opportunities in the past. Now I was offered to contribute freely to the Nature Stem Cell Reports‘s new blog The Niche. What could I say?

Yes. (And I won’t be the only one.) It is a huge opportunity for a rookie stem cell researcher like me and an ideal way to get in touch with the recent literature and regmed happenings, continuously process it and make it digestible to other people. The agreement is: concerning articles prepared specifically for The Niche, full blog posts will be published there, while excerpts will be published here.

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

Nature Reports Stem Cells is live from now on…for stem cell enthusiasts

No more waiting: Nature Reports Stem Cells (NRSC) launched today, and so finally there is a fully web native, scientifically high-end (naturally), freely accessible, all-in-one stem cell research hub site for everyone (especially for the researchers) to read, share, contribute and turn the acquired insights back into new experiments, policies, ethics, businesses and clinical trials.

Edited by the devoted small team Natalie DeWitt (Editor at Large), Monya Baker (News Editor) and Jessica Kolman (Editorial Assistant), based in Nature’s San Francisco office, California (where else?) NRSC has a bunch of usual and unusual ways: news, featured editor, journal club with user recommended articles and voting system, interviews, events and the really exciting and experimental Insider the paper section. From the first editorial of NRSC: “Inside the Paper posts edited discussions between authors and reviewers during peer review. Such transparency should not only deepen readers’ understandings of individual research publications, it will expose the workings of peer review itself. In the coming months, we plan to launch a Toolbox section will aggregate information on stem-cell protocols, reagents, and cell lines that would otherwise require trawling through literature or having serendipitous conversations at conferences.”

Industry and career focused stem cell report in the current Nature volume

Positively tuned (for the most part) report on stem cell science by Ricki Lewis: The hard cell Nature 447, 748-749 (June 2007) Excerpts, emphasis added by me:

research in the field is thriving globally. At least 500 companies and collaborations have sprung up, 100 of them in the past year alone…

A solid background for a researcher includes a doctorate in molecular, cell or developmental biology, as well as skills to work with specific cell or tissue types…

Forget about submitting your scientific papers written in Word 2007

Wow, I feel fresh air, although I am not sure whether the following news is a beginning of any deeper changes or not: From Science Authors Guideline: “Because of changes Microsoft has made in its recent Word release that are incompatible with our internal workflow, which was built around previous versions of the software, Science cannot at present accept any files in the new .docx format produced through Microsoft Word 2007, either for initial submission or for revision. Users of this release of Word should convert these files to a format compatible with Word 2003 or Word for Macintosh 2004 (or, for initial submission, to a PDF file) before submitting to Science.”

Tips: Undernews: SCIENCE PUBS REJECT ARTICLES WRITTEN IN WORD 2007
O’Reilly Radar: Science and Nature rejecting Word 2007 Manuscripts

One commenter in Undernews said: “This isn’t just Science and Nature. All Wiley journals now include the instructions: “[Journal] does not accept Microsoft Word 2007 documents at this time. Please use Word’s “Save As” option to save your document as an older (.doc) file type.” So don’t think it’s a singular problem — I’m sure if you visited all the science journal publications, you’d find similar instructions as well.”

What can I say: Prepare for the age of Google Office manuscripts and figures! All you need is a gmail account.

P.S. I made an attempt to coedit my ongoing first author article (desperately waiting for submission) by publishing the draft on Google Docs and adding the coauthors as collaborators, but only one coauthor (a med student) was kind enough to make one little correction this way. The rest is….well the majority of science people are living within the narrow world of Microsoft Office.

Editing my doctoral thesis on stem cells in a blog: Why not?

OK folks, after reading the official rules about how to get and manage a doctoral thesis, and after speaking with my supervisor asking for his permission, I’ve decided to edit my ongoing doctoral thesis in Pimm. Or at least the introduction of it, which is intended to be no other than a review-like summary of some current results in the stem cell biology of different tissues, organs. What will remain hidden in the first round (but can follow later): the data-heavy yet unpublished results and the discussion, conclusion session. Objectives, Materials & Methods: we shall see it. Sounds like there are complete parts of the thesis, but that’s dead wrong, at this time my doctoral thesis is in an embryonic form. Also no idea on how challenging, meaningful this project, a sub-series in Pimm, will be. What I know is that continuous experimentation with genres and frames is the essence of free blogging!
After all, what do I risk here? If someday I’d like to write a review out of the published introduction, can this cause a publishing problem? According to Maxine Clarke, Publishing Executive Editor of Nature (i.e. peer review and publishing policy expert) the status of a thesis is: “No, a doctoral thesis does not count as “previously published” and yes, you can submit work that was part of your thesis, with an appropriate citation.”

I also asked Maxine by mail and she was kind enough to enlighten me: There is no problem with you publishing your thesis in this way, so far as consideration for publication of any part of it for a Nature journal is concerned (or any NPG journal). We encourage communication between scientists via discussion of work and unpublished drafts in the form of theses, meetings, preprint servers, online scientific forums (between scientists) etc.

On CIRM’s Medical and Ethical Standards in Plos Medicine

Geoffrey P. Lomax, Zach W. Hall, Bernard Lo: Responsible Oversight of Human Stem Cell Research: The California Institute for Regenerative Medicine’s Medical and Ethical Standards

Source: Plos blog, In the May issue of PLoS Medicine

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?

Laboratory website culture and Pimm in Nature: the real digital windows

Paul Smaglik, Naturejobs editor wrote a Prospects piece in the current Nature (yeah, the big one) in his column on laboratory website culture apropos of the highly unofficial lab website competition of Pimm. Read it, think it over and build better and more professional lab websites. Oh yes, and don’t forget to allocate the resources (see the comment of Anonymous Prof).

Nature 447, 347 (May 2007) Paul Smaglik: Creating better lab websites gives potential collaborators and recruiters a clearer window into your world.

Maybe it’s the proper time to ask once again the question: Who wants to host the best laboratory website competition?

Nature Network Global Beta and social networking 2.0 for scientists

If you are busy building a professional career and want things to get done, it’s time to forget MySpace, Facebook or any other social networking 1.0 sites, that are focusing on friendship, love, spam whatever with a general membership. What you need is social networking 2.0, which is based on the special profession you’re in, or is centered around a special topic. Ning, for instance, is a tool for creating your own social network for anything specifiable.

For the business and technology (mostly IT) sector LinkedIn is a more and more frequent destination. And, at last, there is a social networking starting point for every English-speaking (natural) scientist called the Nature Network (NN), which went global in February, after 7 testing months in the local hub Boston. It is still in Beta, just like all good “web 2.0 and more” apps.

First, I was informed about the plan of Nature Network Global from a comment of Corie Lok, main editor on NN, in the comment section of a Nature Blog in January. Corie was kind enough to share with me some recent initial stats on NN: We have more than 1800 registered users. When we relaunched in mid-February, we had 400. We’ve been growing steadily since February by about 100 to 150 new users registering every week. We’re now at about 100,000 total page views across the whole website. We had about 20,000 in February.

According to the numbers, Nature Network is currently a very small but organically growing strong online community. This is exactly the most exciting period in the life cycle of every forming network, so it is a guaranteed experience and challenge to join and participate – now at least – for people like me, who are eager to test and modulate every flexible beta product.

To get the key parameters and shed light on the prospects standing before NN, I’ve made the following table, which is a comparison of NN with relative and rival professional networking site LinkedIn:

As Gavin Bell neatly summarized the core architecture and aims of NN while writing on Nature Network Boston launches: “Some of the key features of the site are the groups, which allow individual communities to have their own spaces within NNB.

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.

Free Nature Reviews Neuroscience Issue in May

From the Nautilus blog by Maxine Clarke: “Nature Reviews Neuroscience is the no. 1 monthly review journal in neuroscience, with an impact factor of 20.951. In May, online access to the entire issue is free.”

I would like to offer these articles which could be of interest for stem cell biologists:

Research Highlights

Neurogenesis: Single stress shortens survival

Cell fate: Unlocking the right combination

Stem cells: Together we are stronger

Reviews

Transcriptional regulation of vertebrate axon guidance and synapse formation

Cell cycle regulation in the postmitotic neuron: oxymoron or new biology?

Stories from my PubMed feeds: hESCs, p53, apoptosis and differentiation

Short peer-review storytelling : One big technical problem of human embryonic stem cells (hESCs) (in contrast to mouse embryonic stem cells) that hESCs normally undergo high rates of spontaneous apoptosis and differentiation, making them difficult to maintain in culture. Now we are getting to know a bit more on the molecular background of these processes. In an article in the prestigious Journal of Biological Chemistry Qin et al.’s studies reveal the important roles of p53 as a critical mediator of human embryonic stem cells survival and differentiation.

Regulation of apoptosis and differentiation by p53 in human embryonic stem cells.

J Biol Chem. 2007 Feb 23;282(8):5842-52

“Here we demonstrate that p53 protein accumulates in apoptotic hESCs induced by agents that damage DNA. However, despite the accumulation of p53, it nevertheless fails to activate the transcription of its target genes. This inability of p53 to activate its target genes has not been observed in other cell types, including mESCs. We further demonstrate that p53 induces apoptosis of hESCs through a mitochondrial pathway. Reducing p53 expression in hESCs in turn reduces both DNA damage-induced apoptosis as well as spontaneous apoptosis. Reducing p53 expression also reduces spontaneous differentiation and slows the differentiation rate of hESCs.”

Figure 2 for the pros:

Nature Publishing Editor on the idea of a public scientific multimedia site

Maxine Clarke, Publishing Executive Editor of Nature and blogger of Peer-to-Peer got interested in the problem of “supporting information” and in the idea of an open access, peer-review supporting information aggregator website. She shared with me her valuable thoughts and informations by mail, from which I now publish parts with the permission of Maxine Clarke (emphasis by me).

On the possibility of a community-approved public multimedia site (videos, audios, pictures) with open access supporting information from peer-review journals.

It would indeed be nice for authors and readers to have such a facility. If there were to be a multimedia database, accepted by the community, we’d be happy to consider making deposition mandatory. Our principle is that data described in our papers are freely available, so if there were a community-approved public multimedia site, which included annotatation and curation, we’d be happy to consider making it a condition of publication for movies etc to be deposited in it. It would need to be publisher-independent to work, so that authors could upload multimedia data wherever they’d published their paper.

The main point for us at Nature is that as a publisher we have to be confident that material published off our website is properly curated, archived and preserved. For example, when we introduced the microarray deposition policy we ensured that there was full community support for the two databases (in one of which, authors’ choice, we require deposition) before implementing the policy. So for this video idea to work, the “database” concerned would need to be publicly accessible (not commercial), curated, annotated etc.

On the status of online supporting information at Nature:

Supplementary Information on the Nature website is free, though you have to register. (Confirmed, see screenshot of a 3D supplementary animation showing that the gut-associated lymphoid tissue comprised of different subsets of haematopoietic cells, Veiga-Fernandes et al.)

On the problem and handling of online supporting information: