Nature Personal Genomics Very Special

The newest Nature issue concentrates on personal genomics and its consequences via many types of articles some of them with free access.

I only read 1 piece so far by Erika Check Hayden, who has the exclusive freedom at Nature to always pick the best stories and write on any of them, but being a heavy 23andMe user I was instantly reminded again on the program Promethease with which I can extend the interpretation of my data with an approximately 2 hour run.

According to two commercial gene-testing services — 23andMe and deCODEme — US Army medic Timothy Richard Gall of Fort Belvoir, Virginia, has a higher-than-average risk of basal cell carcinoma, type 2 diabetes and psoriasis. But much more enlightening than these results, which cost Gall more than $1,400, was a free online program called Promethease that he used to further analyse the data. By offering more in-depth information and interpreting of more of his genetic variants, Promethease “gives a much more realistic view of the usefulness of the information”, Gall says. Start-ups and services such as Promethease are now developing ways to improve the limited value of information provided by personal genomics companies for consumers and scientists alike.

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:

Science Blogging 2008 in London by Nature Network

Looks like this August is the center of my science related social life in 2008: starting with the bottom-up BioBarCamp unconference in Palo Alto followed by the top-down Sci Foo Camp unconference in Mountain View and now The Science Blogging Conference in London on the 30th. This conference is an interesting mix: on one hand it is organized solely by Nature Publishing Group and held at The Royal Institution of Great Britain (“the oldest independent research body in the world”), on the other hand it is about science blogging (one of the newest independent research body of the world) which today is affordable for almost everybody in the world with a broadband connection and already has an increasing equalizing effect on how science is done and how science is communicated. Secondly, although it started as conference with a schedule in advance the organizers later included 3 parallel unconference sessions that will be proposed at the beginning of the conf. I hope that later even the strictest, hardcore scientific conferences will include unconference sessions thereby introducing a random, surprising and entertaining element into the regularities of academic life.

What I am most interested in on The Science Blogging is the people, the bloggers behind and their case stories of successful or failed actions, communications, instigations via their blog posts.

From the programme I’d like to highlight

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:

Meet Dr. Google Health: Roni Zeiger, right out of Stanford!

Roni F. Zeiger, MD (watch his presentation), Google Health product manager, whose PubMed profile (if he really is the very same person) gives us a very strong reason why he was hired by Google for this job (he joined Google in 2006).

The 38-year-old, who still sees patients some evenings and weekends at a nearby clinic, said: “At Google, I can use my expertise and knowledge to potentially help millions of people each day.”

Fortunately all of his 3 papers are freely accessible out of which 2 are particularly interesting and related to Google (Health). Here I just copy the abstracts and probably get back to the papers after I digested them.

Zeiger RF, Stave CD, Schmitzberger F, Fagan LM. Modeling the relationship between search terms in clinical queries. AMIA Annu Symp Proc. 2005; 2005: 1167.

We designed hedges for clinical queries sent to MEDLINE and Google in an attempt to explicitly model the relationship, such as treatment or diagnosis, between search terms. A pilot evaluation suggested that mean average precision (MAP) improved for a precomputed diagnostic query but not for a precomputed treatment query. An important limitation to this approach is that target resources do not explicitly model these relationships.

Roni F Zeiger Toward Continuous Medical Education J Gen Intern Med. 2005 January; 20(1):91–94.

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.

Let’s compile a Biotech for IT folks book and publish it!

IT people are the dominant high tech tribe today and especially on the web. But biotechnology (BT) is the next infotech so no wonder that the IT crowd is growingly curious about everything biotagged on the one hand, while they are usually not too savvy in DNA-RNA-protein-organelle-cell-tissue-organ-organism related matters on the other hand. Check for instance Tim O’ Reilly at Nature: science meets bored tech-savvyness to find new things.

And what can biotech bloggers do in order to meet the growing demands: well here is a little conversation from my twitter channel in the last 20 minutes:

New JoVE helps old Wiley to publish video articles on Current Protocols

A partnership between the Journal of Visualized Experiments and big science publisher Wiley-Blackwell: the JoVE guys will give the technology, the art of making video experiments and Wiley provides the established network, audience on its Current Protocols site.

I wonder what will be the access status of those videos: current JoVE videos are freely available, while Current Protocols has pricey subscription rates (see screenshot).

Links: Alla Katsnelson, The Scientist: Online methods videos go mainstream:

“Rumors of JoVE’s deal with Wiley-Blackwell and other mainstream science publishers have been circulating in the blogosphere since late January. Moshe Pritsker, CEO of JoVE, told The Scientist this week that he had also signed similar deals with Annual Reviews and Springer Protocols.“

Visual journal partners with Wiley

Update from Moshe Pritsker, JoVE chief: The protocols will be co-published, that is freely available on JoVE.

Thanks, Moshe, that’s good news.

‘The horror of closed-access publishing’ according to Jonathan Eisen

Jonathan Eisen is the new Academic Editor-in-Chief of PLoS Biology and wants to build a world in which Open Access and “top tier” can go hand-in-hand:

So I accepted the invitation and became an Academic Editor. But I confess that I was not yet a true convert to OA or to PLoS Biology. So I decided to do what any good scientist should do in such a situation—I planned a publishing experiment. I’d had many papers in Science and Nature before. And so I convinced my collaborators on a high-profile paper to submit it to PLoS Biology, to see how this new high-profile OA journal would compare.

But then, while finalizing the paper, a two-month-long medical nightmare ensued that eventually ended in the stillbirth of my first child. While my wife and I struggled with medical mistakes and negligence, we felt the need to take charge and figure out for ourselves what the right medical care should be. And this is when I experienced the horror of closed-access publishing. For unlike my colleagues at major research universities that have subscriptions to all journals, I worked at a 300-person nonprofit research institute with a small library. So there I was—a scientist and a taxpayer—desperate to read the results of work that I helped pay for and work that might give me more knowledge than possessed by our doctors.

Nature’s Great Beyond on the Warda-Han-Proteomics-Creator paper

Peer review, ‘a mighty creator’ and an almighty row

However the paper was only retracted for “a substantial overlap of the content of this article with previously published articles in other journals.”, not for the strange “mighty creator” line. Peer review isn’t perfect but you’d hope it would catch something like this.

Warda speaks: “We say the truth, I not burrow any sentences from others.”

The Warda-Han-Proteomics saga continues and finds its way to the show/entertainment business. We’ve already listened to Han, now it’s time for Warda to speak, which he did in an email to James Randerson over at the Guardian Science blog, which makes think (indeed ‘rethink’ as W suggests) that the Warda-Han pair is probably the Laurel and Hardy of the science showbiz.

Screenshot of the day: Warda-Han-Still-Missing-Link paper retracted!

First of all: thanks to the commenters/scientists (the online flash mobbers) for being the most efficient part of the science blogosphere! Although the paper was retracted from the online version of Proteomics, you can still make historical screenshots on the PubMed version.

Blogosphere links in chronological order:

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

CNN, USA Today and the terraniche media on niche science video sites

What do you think about the distinction of mainstream – niche on the web? Isn’t it the case that ‘mainstream media’ is just a niche after all, and not necessarily the most important?

We have a very nice case study now on how ideas, memes, actions, movements in the science/tech arena are spreading throughout the web: science video sites like JoVE, Labaction, SciVee were first embraced by the more and more muscular science blogosphere followed by a broader science/tech media coverage like Wired, The Scientist and finally reached CNN, USA Today today via the same Associated Press story by Alicia Chang (I am looking forward to a presidential debate on how to make and publish good science videos online):

CNN: Scientists make videos for the Web

USA Today: Niche sites spread science on the Web

Seattle Times: Video-sharing Web sites let scientists show off experiments, make science more accessible

From the story:

Researchers who are uploading their experiments and lectures online are discovering filmmaking is more art than science. If the narrators are boring or the image is shaky, viewers will quickly learn to click elsewhere…

“We need to show our experiments, and ‘show’ in our age means video,” Pritsker said.

Some experts say the biggest advantage to science videos is making research more accessible to nonscientists. There’s no guarantee that video can’t be manipulated, but the medium also may force scientists to think twice before committing fraud.

“It’s one thing to put your name on a fake paper and it’s another to make a fake video that your friends and family could watch,” said John B. Horrigan, associate director for research at the Pew Internet & American Life Project.

Last year, Horrigan authored a study that found more than half the people who seek science information online want to hear it from the original source.

Translating the experiments to video won’t be without challenges. Chief among them is attracting enough Web traffic to make the sites profitable.

Thanks for the tip, Moshe.

Science videos on Pimm:

Wired on the emerging science video websites: see one, do one, teach one

LabAction.com: new player on the science video niche market

Biological Video Protocols on JoVE: Online Journal of Visualized Experiments

Science: video protocols can help to share the tacit dimension

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.

Unofficial and hypercritical peer review of a paper on p53′s role in hESC regulation

Once I wrote shortly about the following peer review paper which was popped out of my PubMed feeds to draw some attention to it: Han Qin, Tianxin Yu, Tingting Qing, Yanxia Liu, Yang Zhao, Jun Cai, Jian Li, Zhihua Song, Xiuxia Qu, Peng Zhou, Jiong Wu, Mingxiao Ding, Hongkui Deng
Regulation of apoptosis and differentiation by p53 in human embryonic stem cells.
J Biol Chem. 2007 Feb 23;282(8):5842-52 doi:10.1074/jbc.M610464200

Now I got a very thorough comment on this paper by an author nicknamed “wolf” which systematically goes through the paper and gives a highly critical peer review of it. So I just publish the comments and next ask the authors (the first or the last) of the criticized paper and give them the possibility to defend their experiments and statements. My role here is the role of the blog”publisher”.

Comments re Qin paper p53 and hESC apoptosis by “wolf”:

This paper starts with making a fundamental mistake in not determining the kinetics of UV induced apoptosis and therefore missing the modulation of p53 target genes.
Subsequently they attempt to explain the absence of this by using transient transfections and analysing the cells at timepoints when half of the cells (mainly the undiff cells) are already dead and then interpret the data of the differentiated transfected (more resistant) hESC as if they were undiff hESC. The paper then desperately tries to come up with explanations for their own contradictory results). The data set further lacks controls (lentiviral mock transduced cells, no isotype controls etc), uses the wrong assays (such as PI staining to assess apoptosis, morphological assessment of differentiation by surface area) and lacks insight into the mechanisms controlling apoptosis (no cyt c release, no idea how p53 by itself might trigger mitochondrial apoptosis, etc).

Specifically;

Materials and Methods

Page 2: The authors use mainly one line of late passage hESC (p42-p68) grown in KSOR, which are highly CD30 positive leading to alterations in apoptosis regulation. We use three hESC lines at passages before p12 only.

Page 3: endoderm differentiation occurs in 4 days after Activin addition ? This is very quick with >80 % of hESC expressing sox17 after 100 ng/ml activin ?

Page 3: In immunostaining no antibody controls were used instead of isotype control with identical concentrations. We use isotype controls for all our immunos.

What is your (science) blogging writing style, Maxine Clarke?

I met Maxine online first when she commented my post on the The problem of online “supporting information” in peer-review articles and then interviewed her on Nature policies concerning the same problem. Then I met Maxine offline in London and learnt a lot on how every issue of Nature is born and other insights I hope I can share with my readers here later. The following is Maxine’s answer to my stylish question and I would also like to offer her culture rich personal bookblog, Petrona.

My professional blogs (Nautilus, Peer to Peer and From the Blogosphere) are addressed to a particular group of people: scientists who read, review and publish, or would like to publish, in our journals. Therefore, the style I try to achieve is helpful, informative and stimulating, yet not didactic or dull. I aim to highlight the benefits of publishing at Nature Publishing Group and provide assistance to those wishing to do so, in a way that is not too directly promotional, but which is constructive to authors and interesting to them and other readers, as well as encouraging their feedback. Therefore I write about news concerning journal policies and format, as well as announcements of new journals, projects, conferences and online tools of interest to authors and reviewers. I also highlight when journal content is free for some reason, because this means that the authors of those articles are achieving greater “reach” for their articles (as well as making it possible for more people to read them, by my announcement). I also highlight news from the wider world of science communication, for example about quality indicators (citations tools and impact factors, for example), ethics, peer-review and so on, in the hope of stimulating community discussion of these issues, as this can help us decide on our journals’ evolution. Finally, I blog to provide an approachable forum for potential authors to ask questions about our publication policies, and to have them answered quickly in a way that can also benefit others, as they can see the responses.

Next blogterviewee is the number one scientific aging blogger, Chris Patil of Ouroboros.

Earlier:

Deepak Singh

me

Blogrunner Science vs. Scienceblogs vs. Postgenomic?

Alien vs. Predator like stupid question for the weekend: Which do you think is the best source when it is about interesting and quality science content: the Techmeme clone Blogrunner (here it’s the science channel of Blogrunner), that is the newly launched automated online news service and blogs aggregator by the New York Times or Scienceblogs or Postgenomic? Which model is the best?

And what do you think about the tons of Eurekalert Press Releases on Blogrunner? Do you like to read press releases?

Tim O’ Reilly at Nature: science meets bored tech-savvyness to find new things

As a biotech geek blogger and occasionally Make contributor, who stands at the intersection of science and technology with a (life) science bias, it is more and more exciting to see how the attractive brands of the 2 sides are building the bridge and creating a shared channel. So far, the biggest manifestation of this shared channel was the SciFoo Camp, organized by Nature and O’Reilly, hosted by Google. Now Tim O’Reilly, a native of Cork, Ireland turned Californian tech publisher visited the Nature Headquarters and talked about his angle on the web and tech publishing (giving me an incentive to finish the story of my earlier visit at Nature at September). You can read the informal account of Timo Hannay on the meeting at Nascent (picture: my shot on Tim and Timo summarizing the SciFoo experience at the Googleplex).

One thing seems more visible to me: Tim is bored about his original business and industry and is looking for some new which he seems to find in…. science (see Craig Venter and Tim O’Reilly chat: when 2 worlds meet).

The computer industry was a very exciting place, and then it became boring, because it became consolidated. ..There is going to be a lot of consolidation, the man will take over (he might be idealistic like google), it is going to get a lot more boring. The interesting question is what will happen when google’s growth slows down?
But you have to have a belief in people’s ability to find new things. There are going to be a lot new areas coming out of science, one thing we can do is to help to birth the future.

or: What happens when folks from synthetic biology meet hedge fund hackers meet roboticists and makers?

Tim’s boreness is really good (not the burned out part) for scientists like me. For instance, one of my ideas (an idea briefly communicated to Phil Torrone at the Austin Maker Faire) is to collect enough bioDIY projects like the “Make stem cells from the placenta at home” together, that is enough to set up an exclusive “sciencey” BioMaker Faire.

BioMed Search relaunched

BioMed Search, the Google-like BioMedical Image Search Engine is alive after a long off period as it was relaunched about 1 month ago.

Current informal science communication in the lab (say in lab meetings or in journal clubs) is centered around interpreting figures. BioMed Search catches somehow the essence of this communication with indexing the images, figures, diagrams, tables of about 1 million images from peer review articles. The primary source is Highwire press and Biomed Central – informed me Alex Ksikes, sole creator of BioMed Search.

I wouldn’t be surprised if one day Google (whose Scholar does not have a special figure search engine) bought this pretty useful service.

Looking forward to further updates.

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.

Unpublished SENS3 conference report for mainstream scientists!

Recently I wrote a meeting report on the SENS3 conference for a very prestigious science journal, but finally it did not go through the filters. I knew that the chance for publication is small as the journal rarely publish such meeting reports and as it was in many respects an unconventional science conference. The standards were really high and the genre itself is strictly restricted: no more than 900 words and only 1-2 conference topic could be covered focusing on new data. On the whole it was a really good science writing experience for me. I finally realized how challenging it is to introduce the concept of robust scientific life extension for the mainstream science audience although it is not impossible at all.

But if a man has an interactive blog with a quality readership even an officially unpublished text could be useful, so please read my draft in its final form and think about it. Links of the video versions of the referred presentations and references are included, a perpetual advantage of the web comparing to offline publication. I’d like to say thanks for the folks who helped me with the draft: Aubrey de Grey, Michael Rae, Mark Hamalainen from within the SENS camp, Matthew Oki O’ Connor and Chris Patil, fellow scientists-bloggers and first of all, Anna.

Subject scrapline: Biotechnology

Title: Translating ageing

Summary: A recent unconventional strategic conference on translational science in ageing related damages helps to put some puzzle pieces together.

Changes in the adult tissue stem cells or in the mitochondria are two main processes under constant investigation amongst researchers curious about the ins and outs of the ageing process. At the SENS3 conference in Cambridge scientists and laymen shared their results and ideas, respectively.＊

Despite its mixed population with a scientist majority, the conference resembled a mainstream life science conference due to its topic sessions focusing on the different types of lifelong, ageing accumulated damages. SENS decodes as Strategies for Engineered Negligible Senescence, which aims to suggest a panel of interventions on how to robustly extend the mean and maximum human life span and claims to identify the adequately exhaustive list of main age-related pathologies ranging from cell depletion to mitochondrial mutations. SENS is by definition a flexible enough umbrella term to include other coming life extension technologies and concepts under its brand. Also, it is an engineering project compiled by main organizer Aubrey de Grey, a computer scientist turned theoretical biologist with a grand mission and hypotheses yet to be experimentally tested. The presentations were mainly reviewing the progress in the related branches, with enough new data to keep the experts interested.

Stem cells exhausted

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.

Wired on the emerging science video websites: see one, do one, teach one

Wired has a nice piece on Video Sites Help Scientists Show Instead of Tell by Alexis Madrigal focusing on the high-end, non-youtubish, let’s-build-the-pro-network-of-video-geeks-in-the-labs-out-there approach of JoVE. Video players mentioned on the pop side: LabAction and PloS backed SciVee. The real question of this niche market is: In order to penetrate the mainstream science audience what is the proper mix of anti-Web 2.0 professional science rules and Web 2.0 techniques science video site builders should apply. Profit is not on the agenda yet.

“Highlighting little tricks in a video that might not be apparent in a paper can save an enormous amount of time,” said Dr. Arnold Kriegstein, whose University of California-San Francisco lab has posted a video about “cortical neurogenesis,” or the growth of neurons in the cerebral cortex. “There’s an old adage in medicine about learning: See one, do one, teach one. It carries over to the research lab, too.”

Sharing those little tricks with scientists everywhere is the idea behind the Journal of Visualized Experiments, an all-video scientific journal that launched its microfluidics-focused eighth issue in early October.

Dry, jargon-laden scientific papers can leave out what scientist and blogger Attila Csordas calls “the tacit dimension” on his blog.”

Mr. Madrigal has chosen a good post of mine to refer as that early post, Science: video protocols can help to share the tacit dimension was the starting point in 2 respects: a., in the comment section Moshe Pritsker introduced JoVE one month later to the blogosphere, so I could spend the same day to cover it instead of hanging around in Cambridge with my girlfriend b., at the same time the idea of LabAction was born.

I finish the post later, just let me get the breakfast and go to the lab first…. ok, I am here again.

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:

Freeing dark, negative research data is the next in open access science?

Positive, published scientific data form the tip of the iceberg of any scientific data produced in labs. As at least 90% (my guess) of all experiments are failed or lead to negative results, those data sets become “dark data“. But those dark data are as important for making science happen as positive data and this information must be free – argues Thomas Goetz Wired’s deputy editor (and another SciFoo camper) in an opinionated piece in the October issue of Wired (available only offline at this moment, update: it is now online), called Mind the gaps. The idea is to push open access science to its limits.

“Liberating dark data makes many scientists deeply uncomfortable, because it calls for them to reveal their “failures”. But in this data-intense age, those apparent dead ends could be more important than the breakthroughs….Your dead end may be another scientist’s missing link. Freeing up dark data could represent one of the biggest boons to research in decades, fueling advances in genetics, neuroscience, and biotech.”

“Advocating the release of dark data is one thing, but it’s quite another to actually collect it, juggling different formats and standards. There’s the issue of storage….Google, among others, is lending a hand with its Palimpsest project, offering to store and share monster-size data sets (making the data searchable isn’t part of the effort.)”

Stop for a minute! The Palimpsest project was entertainingly presented at SciFoo by Jon Trowbridge (my iPhone shot of one his slide published here with Jon’s permission) and my guess is that this presentation is the source of Thomas Goetz’s sentence. I tried to make a hint of this project in my SciFoo Camp, 2007: data (Google) publishing (Nature) geeks (O’Reilly) post:

“scientific data”

One of the most frequently used key term was “scientific data”. And the question is: how to collect, upload, organize and index them. With the exponentially increasing data sets, that are produced by scientists worldwide, it is obvious that we need really powerful tools to benefit them. After a couple of beta years it is highly probable that Google (according to its mission statement) will offer new ways to manage the enormous amount of valuable scientific data. Without that, the efficiency of the science industry will dramatically decline.

But it was Deepak, who later shared his experience on the presentation in details:
Scifoo: Google and large scientific datasets

Here is my favorite part out Goetz’s article about the science culture problem of freeing dark data:
“If their research is successful, many academics guard their data like Gollum, wringing all the publication opportunities they can out of it over years. If the research doesn’t pan out, there’s strong incentive to move on ASAP, and a disincentive to linger in eddies that may not advance one’s job prospects.”

Wait for a sec! During the summer I did 2 experiments that failed (=negative data), but then I explored in the literature why I exactly failed and now this knowledge and insight presumably will lead me to successful experiments.

Blogs invade The Scientist: vote for your favorite life science blog!

At The Scientist, the editors are awaiting your suggestions on your favorite life science blogs to gather the list of blogs that are especially hot for life science researchers. They asked 7 science bloggers, 5 from ScienceBlogs by SEED (Abel Pharmboy, Bora Zivkovic, Carl Zimmer, Newamul Khan, PZ Myers) and 2 independent bloggers (Ed Silverman and me) to nominate some of their favorite blogs for a start. Below you can find my answer:

Instead of picking three individual blogs, I’d like to mention three topic-related branches of blogs or blog aggregators, referring this way to many individual bloggers and a larger amount of information and information filters. This approach follows from my blog reading habit as my starting point for blogs and all web related science and technology things, are the web sites that could be reached through RSS feeds using a feed reader, which is Google Reader, in my case.
The groups are: a) science blogs written by scientists, b) science related blogs written by journalists and editors, and c) technology and web related blogs written by “alpha geeks and early adopters.”

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.

Pimm’s Pubmed filter post in Nurture’s “Science 2.0″ issue

The edited version of Pimm’s January 30th, 2007 post How to filter and read PubMed articles through RSS feeds? was published in The Summer 2007 issue of Nurture, the magazine for past and present Nature journal authors. According to Maxine Clarke, Nurture editor: The Summer 2007 Issue of Nurture celebrates our blossoming “science 2.0″ activities, which invite authors and reviewers to participate with Nature Publishing Group in an interactive, global scientific community. Indeed, there are quick intros to Nature Precedings, Nature Network London, Nature Report Stem Cells, Scintilla, but besides that my favourite reading are the personal editor and author profiles. (On the cover of Nurture you can find one of my confocal microscopy pictures out of the Nature Precedings poster.)

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.

SciFoo Camp, 2007: data (Google) publishing (Nature) geeks (O’Reilly)

SciFoo is over, and I’ve just arrived back to New Orleans from SF. First of all: a big thanks for the organizers (Chris DiBona, Timo Hannay, Tim O’Reilly, Google, Nature, O’Reilly) and campers, it was really the highest end. Here is a quick SciFoo key terms summary (photos, detailed accounts later):

“scientific data”

One of the most frequently used key term was “scientific data”. And the question is: how to collect, upload, organize and index them. With the exponentially increasing data sets, that are produced by scientists worldwide, it is obvious that we need really powerful tools to benefit them. After a couple of beta years it is highly probable that Google (according to its mission statement) will offer new ways to manage the enormous amount of valuable scientific data. Without that, the efficiency of the science industry will dramatically decline.

“science publishing”

Yes, the old question ranging from open access science to different pre- and post publishing opportunities, addressing peer-review tools. A new and clear vocabulary is needed. Nature people were honest about the problems, asking for the optimal solutions.

“the geek factor”

Mainstream scientists are rather conservative folks, they can easily have revolutionary thoughts in their niche research fields, but are not too open minded and experimental when it is about new web and technology tools. The alpha geeks from the O’Reilly Media reminded the science population of the SciFoo (not the typical technology neutral mainstream scientists) that there are many innovative things that could be done in and out of science too. (You don’t necessarily need the newest Mac gadgets for that, just try out some mind performance hacks)

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.

Science on the iPhone, is it a good SciPhone? Aspects for a test series

I like Google and Apple products, but my expectations are focusing on how these products can help and facilitate me as a scientist, especially as a biomedical research scientist. With the Science on the iPhone test series I’d like to examine in details how proper and user friendly is the iPhone as an ultimate portable, mobile, convergent handheld gadget (or at least the first version of that line) for scientific purposes based on real experience. Briefly: can we use it as a SciPhone?

Amongst others I’ll concentrate on the following: the passive, science consuming opportunities like text reading, photo, presentation and science video watching and the active, science-making issues like writing texts, making photos and giving presentations.

Also I’d like to take a look on how the iPhone fits into the frame of the present scientific web, and how good is for scientific communication. (Photo: my bench this afternoon.)

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.