The Decision Tree: Thomas Goetz’s upcoming book on predictive/personalized medicine

In the past months Thomas Goetz begun writing a book on the radical changes already ongoing but mostly upcoming in healthcare due to affordable new technologies and quantitative approaches in personalized genomics and medicine.

The book is to be called The Decision Tree (explanation below) accompanied by a new website. Thomas is the perfect man for this job, he is the deputy editor of Wired magazine (=he is well informed and connected), a good journalist who took his job (writing on science, health and medicine) so seriously that he went back to school to get a degree in Public Health. Back in the days his very early coverage on 23andMe (actually published before the official launch of the service) was actually the only serious insight on 23andMe.

With this book Thomas will have a chance to become the Chris Anderson or Malcolm Gladwell of personalized medicine and public health.

“The premise is that we are at a new phase of health and medical care, where more decisions are being made by individuals on their own behalf, rather than by physicians, and that, furthermore, these decisions are being informed by new tools based on statistics, data, and predictions. This is a good thing – it will let us, the general public, live better, happier, and even longer lives. But it will require us to be stewards of our health in ways we may not be prepared for. We will act on the basis of risk factors and predictive scores, rather than on conventional wisdom and doctors recommendations. We will act in collaboration with others, drawing on collective experience with health and disease, rather than in the isolation and ignorance that can come with “privacy” concerns. And we will act early, well before symptoms appear, opting to tap the science of genomics and proteomics in order to mitigate our risks down the road.

Together, these tools will create a new opportunity and a new responsibility for people to act – to make health decisions well before they become patients. This can be characterized as a decision tree, a series of informed choices we will make to minimize uncertainty and optimize our outcomes. Indeed, we will use decision trees to navigate most of our health decisions, sometimes in overt ways – new decision support tools will both inform us and guide us, and they’ll be steeped in statistics, prediction, and the power of collective experience.”

“blogs.nature.com v1 is live” and beyond

A new, completely rewritten, integrated nature.com website blogs.nature.com has been launched by the Natureplex people – informed his Twitter pals Euan Adie:

Also, blogs.nature.com v1 is live! Tequila and donuts all round. Early n’ often release v2 coming on the 18th so get any bug reports in now.

Suggest good science blogs that are not listed on the Nature Blogroll yet.

Sergey Brin, Gly2019Ser & a real chance against Parkinson disease/aging!

It was already known that amongst the Google top people Sergey Brin is the one who is most interested in pushing biotechnology and the biomedical sciences: in his Stanford years he was interested in biology courses according to The Google Story, he married Anne Wojcicki (who graduted from biology at Yale), Google invested $4.4 million into 23andMe the pioneering personal genomics company co-founded by Anne, then Google invested into 23andMe competitor Navigenics too.

Now Sergey Brin added another, serious and personal reason to think that he is really, personally committed to the quick progress in the biomedical sciences: in his new blog – already a bit of an Internet history – called Too he disclosed that using the 23andMe personal genetics service he figured out something worrying about his and his family’s risk of Parkinson disease (his mother and her aunt are being already diagnosed with PD):

“I learned something very important to me — I carry the G2019S mutation and when my mother checked her account, she saw she carries it too.
The exact implications of this are not entirely clear. Early studies tend to have small samples with various selection biases. Nonetheless it is clear that I have a markedly higher chance of developing Parkinson’s in my lifetime than the average person. In fact, it is somewhere between 20% to 80% depending on the study and how you measure.

The G2019S mutation is actually the rs34637584 SNP and lies in the gene LRRK2 encoding leucine-rich repeat kinase on chromosome 12. The mutation affects the first codon of the gene and is a guanine (G)-to- adenine (A) substitution resulting known as a missense and  leads to a glycine – serine (hence the name) amino acid conversion in the protein product. Here is how the SNP position looks in the 23andMe browser using the sample family, the Mendels.

23andMe’s amazingly good corporate blog The Spittoon cited a recent article about the chances:

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

Friendfeedization of my blog (and a puzzle)

It’s not about the TechCrunch post with the similar name here, but about my and the Life Scientists‘ FriendFeed life:

Hourglass, a blog carnival devoted to the biology of aging

Finally Chris over at Ouroboros came up with the idea and the quick implementation of Hourglass, a blog carnival devoted to the biology of aging/biogerontology.  For some reason I am not an explicit supporter of blog carnivals – many of my posts were chosen by carnival editors but I never hosted one -, but Hourglass will be the big exception in which I participate, submit posts and host it later. The reason: first it presents aging/biogerontology related posts, which fits my profile and second it was instigated by Chris Patil, whose work is a guarantee for keeping all this in the good direction. So if you want to read on the evolution of longevity and aging, calorie restricition, stem cells/tissue engineering/regenerative medicine, or on the association of long life and intelligence at once, Hourglass is for you.

Help Craig Newmark find a new hobby on Twitter!

Internet celebrities are not celebrities in a sense that you can easily communicate with them on services like Twitter (assuming the services are not down). There’s no such thing as an internet bodyguard except some firewalls in Windows. So this day I found Craig Newmark, Craigslist founder tweeting this:

I suggested him a forward looking hobby:

To my surprise I got an the following answer back:

80 is the new 50 so Carl Icahn has a blog without content.

Billionaire investor Carl Icahn (72) recently made the bloglines with his energetic position on the Microsoft – Yahoo deal. He has a blog too or at least it is coming soon since 01/31. /Having a blog for more than 3 months without any content is kinda equivalent with planning to sign up for Twitter but actually not doing it./

Daniel Gross, Newsweek: Eighty Is the New Fifty

“Carl Icahn has a blog (though it doesn’t contain any content)”….

“In time, it’s likely that prejudices toward older workers will be eroded less by the exploits of eternally youthful financiers, and more from a longstanding demographic trend. As they’ve moved through life, the baby boomers have altered societal attitudes on everything from smoking marijuana to Botox. As boomers coast into their golden years, it’s likely the acceptance of older workers at every rung of the corporate ladder will grow. In the 1960s, the boomers’ mantra was: don’t trust anyone over 30. In the 2010s, it’ll probably be: don’t trust anyone under 70.”

Social or semantic connections? Tell me, infofriend!

Clive Thompson – undoubtedly a good journalist – has a piece, entitled Information Overlord in May Wired issue (not online yet, but already problematic) on his experience with semantic Web app Twine. Clive also formulates a provocative though about the value of information modulated social connections.

“But the truth is, sometimes social connections are less useful than semantic ones.
I’ve experienced this myself. My Facebook page attracts my friends, with whom I share social bonds. Meanwhile, my science blog attracts complete strangers, with whom I share a common interest in a topic – like a scientific study I’ve blogged about. It’s a semantic relationship, based on shared meaning. So those strangers tend to tell me things – and point me to links – that are more useful than the social stuff on my Facebook page. Information trumps friendship”

I am not sure whether the distinction behind: emotional, social friends vs rational, information only semantic cooperators

The Tweet Cloud of a biotech geek blogger

With TweetClouds (scripting: John Krutsch design: Jared Stein) people can generate the Tweet Cloud of a Twitter user. In case of bloggers/Twitters it is an interesting question whether there are any strong differences between the category cloud/Tweet Cloud of the same person suggesting patterns in web behavior. I’ve just generated mine. One obvious difference is that with TweetClouds including replies to other Twitters (there is an option to suppress @replies, but why would you?) there is also a social/networking component (check the names after @) instantly visible on the generated cloud.

New WordPress Dashboard design – do you like it?

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:

The MitoWheel blog keeps you updated!

MitoWheel is a cool graphical interface of the circular human mitochondrial genome, which helps the user to get familiar with the mito DNA by searching, clicking and tailoring it. I introduced you MitoWheel a week or so ago, but now you can follow the updates on the MitoWheel Blog.

On the blog you get first-hand information as the posts are written by Gábor Zsurka, main developer himself and occasionally, by me. In his post Cut and Paste the Human Mitochondrial DNA Gábor introduces 2 essential techniques you can easily accomplish with MW:

a., how to search for different mutations and find their functional results on a pop-up window

Will JoVE’s new science blog service reinvent the genre?

The pioneer biological video publishing site JoVE (covered here many times) will soon launch a blogging platform and a community site. Nikita Bernstein, the main nerd behind JoVE is building the code and the platform – as Anne Kushnir informed me – should hopefully go live in the next couple of weeks. At least that is what can be known publicly.
The expectations are high and the JoVE guys (co-founders Moshe Pritsker and Nikita) themselves raised the bar with the quality and concept of video-protocols. As JoVE is a startup, not an established company with big inertia, they could be experimental but within the limits of their investors’ patience and money.

The real question for me whether JoVE’s blogging service can renew the genre of science blogging or at least bring a previously non-existing color into it? Points:

- Who will become JoVE’s first generation bloggers? Fresh blood? If yes what will be the source? Senior scientists, high school students, postdocs in the U.S.A., discovering the web?

- Existing bloggers who’d like to syndicate their content? Bloggers from Scienceblogs, Nature Network or from the DNA Network? Independent bloggers from outside theses established circles? Journalists? What will be the bait? For existing bloggers, who are tempted to commercialize their activity somehow the crucial question is whether they can generate any revenue out of this new platform? Will they be paid by traffic, and if yes how competitive are the tariffs? Is it possible to install paid ads, banners on the blogs and the bloggers could be paid based on pay per click methods just like Google AdSense?

– What about content rights? Exclusive, non-exclusive, et cetera? Would there be any topic restrictions? How can quality science blogging and credit is maintained in the long term?

The Spittoon: the eminent corporate blog of 23andMe and Consumer Enabled Research

The personal genomics service 23andMe just launched publicly a corporate blog called The Spittoon that has been internally up for a few weeks. It is a new chapter in biotech corporate blogging. Just like the web page of 23andMe, The Spittoon’s WordPress blog platform, the concept and design is excellent: amongst others you can find scientific blog posts written by Matt Crenson science writer and posts written by founders Linda Avey and Anne Wojcicki in the name of radical transparency. As Wired fellow Clive Thompson wrote:

Radical forms of transparency are now the norm at startups – and even some Fortune 500 companies. It is a strange and abrupt reversal of corporate values. Not long ago, the only public statements a company ever made were professionally written press releases and the rare, stage-managed speech by the CEO. Now firms spill information in torrents, posting internal memos and strategy goals, letting everyone from the top dog to shop-floor workers blog publicly about what their firm is doing right – and wrong. Jonathan Schwartz, the CEO of Sun Microsystems, dishes company dirt and apologizes to startups he’s accidentally screwed. Venture capitalists now demand that CEOs be fluent in blogspeak.

Radical transparency could be standard in the case of Silicon Valley tech startups but in the Biotech Industry the standards are light years away from that. For instance the 23andMe research team communicates publicly on the biparental inheritance of mitochondrial DNA which is a sensitive issue concerning their genealogy service. The reason why Spittoon is so web-friendly and uptodate and is in fact a paradigm corporate blog for every other biotech company in the future is its web-based business model and Google-like corporate culture thanks to its networking background.

For instance, Anne Wojcicki co-founder introduces the concept of Consumer Enabled Research in her introductory blog post The Power of We:

Our goal at 23andMe is to enable individuals to form communities around shared interests and to empower those communities to be actively involved with research. We call it Consumer Enabled Research. We don’t just want communities to have a voice, we want to provide a platform for them to collectively aggregate their genetic information. One of the significant bottlenecks in research is the lack of data. Researchers and physicians rarely have enough of it to really understand a disease or how to treat it. Our goal is to change that.

After registration readers can make comments and I strongly hope that the comment system will not be shut down (just like in the past at BoingBoing), but for that commenters should be on-topic and moderate. I’ve just commented Wojcicki’s post, but I’d like to share it with you here too:

Gabe Rivera of Techmeme: A Self-Meme Man

This would better fit to be a Twitter update, but I cannot resist to cite this sentence from Gabe Rivera Techmeme inventor in an older Wired conversation:

Science.tv launched a blog

I haven’t done any strict fact checking but as far as I know science.tv‘s new blog, called simply Science.tv Blog is the first web log launched by a science video sharing site in order to communicate and explore. (Usually I am accustomed to the other way in the world of online video: blog first, vlog or tv second, think about BoingBoing or Make.)

Matt Thurling, science.tv founder has some valuable considerations on how to catch (video) school kids conducting genuine experiments attempting to answer their very own hypotheses be it on Nintendo or ants.

My transatlantic air reading: Bubble City, a blog novel by Aaron Swartz

At least I know what I will read on the plane over at the Atlantic tomorrow back to old Europe: Bubble City by Aaron Swartz. What by who? Bubble city is a blog tech novel with chapters as posts. The story takes place in San Francisco and the Silicon Valley around a startup called Newsflip going deep into current web techniques, startup happenings, Google trends & types and tokens of people with the tools of fiction. It is well written, it is witty, I’ve just started but quickly became excited about it due to its experimental character and the insider angle of the writer behind. Bubble City is the brainchild of Aaron Swartz Reddit cofounder, who is an extremely talented 20 year old American programmer, hacker (think of George Hotz or young Saul Kripke tinkering with modal logics), although in his blog Raw Thought (long time blogroll guest of Pimm) he usually writes like an old central European, highbrow human intellectual with the necessary cultural references. And that makes him a very interesting phenomenon, one that is almost missing in the American tech-web scene: an intellectual with a broad spectrum of interests and arguments. I met Aaron at the last seconds of the SciFoo Camp at the Googleplex (he writes a lot about the Number One Plex) and really liked his celebrity focused gossip liveblogging account on the event with people like Tim O’ Reilly and Henry Gee explaining themselves in the comment section.

Hopefully Aaron will be able to finish Bubble City by excluding or neutralizing or properly incorporating outworld reflexion (like this and that of Blogoscoped) into it. Finishing a novel and completing a code are not the same though and epic talent has the bad habit not to let young writers reach perfection in their early trials.

Here are 2 sections from Bubble city and the links to the 11 chapters so far (it is not aggregated as far as I know and you always have to change the numbers at the end of the URL):

Chapter 1

He popped open the recording software, making sure he got his nose squarely in its frame, his face so close that spittle would land on the lens. In a world where every teenage kid could stream a live feed of himself having sex to millions, only the most aggressive vlogcasters survived. Wayne was no dummy. He didn’t get to be the number seven blog in the TechnoScene rankings by sitting back and offering his opinions. No. This was war and every show a battle.

Today’s enemy? Newsflip, one of the crummy little online news aggregator sites, which was threatening to write him out of the history books by dumping the technology he’d single-handedly invented, news notation analysis (NNA), and going with some upstart competitor that didn’t even bother to have an acronym for a name. Sure, Newsflip was a tiny site in the scheme of things, but if it switched it would set a dangerous precedent.

Chapter 2

Downtown San Francisco is a world of carefully-gridded streets and looming skyscrapers, but hidden behind a gas station on Third is a place that almost looks like another world. The sun shines brightly upon a park with green grass and tall shady trees and vibrant swings with children. The park is an oval and the perimeter is lined with small, pastel-colored buildings. Here and there are a smattering of small cafes and restaurants. And the other buildings are filled with startups. Twitter here. Adaptive Path there. Even Yahoo, when it wanted to encourage its employees to be more startup-y, opened up an office in the neighborhood. Sit on the grass and chances are you’ll sit near a friend from another company or bump into them in line at a cafe. The place crawls with companies and back on the street, surveying the scene with a distant but watchful eye, lie the journalists, whose publications cover with awe the rumblings of those below. It was here that Newsflip made its home.

Dan 1 minute of Fake Jobs Lyons wants to donate an XO laptop to get one

The web is small and the Linux freak, Forbes-driven Fake Steve Jobs would like to participate in the “Give One Get One” program in which people can donate an XO laptop to a child in the developing world and receive one. I guess that’s the reason why he published our XO unwrapping video on his nice Blogger blog. Another reason is his dream to finally test the kernel of the Red Hat’s Fedora Core 6 version of the Linux operating system behind the XO.

Google’s knollers and the bloggers: cooperation or competition?

Everybody is comparing Google’s Knol project to Wikipedia intended to be a “repository of knowledge from experts on various topics” (NYT) or “a free, ad-supported publishing system” (Wired), currently a “private, invitation-only knowledge sharing service” (Blogoscoped). But for a biotech blogger like me the first association is to compare Knol to the blogosphere. Just think about blogs and bloggers when reading these lines from the Official Google Blog by author Udi Manber:

The key idea behind the knol project is to highlight authors. Books have authors’ names right on the cover, news articles have bylines, scientific articles always have authors — but somehow the web evolved without a strong standard to keep authors names highlighted. We believe that knowing who wrote what will significantly help users make better use of web content. At the heart, a knol is just a web page; we use the word “knol” as the name of the project and as an instance of an article interchangeably. It is well-organized, nicely presented, and has a distinct look and feel, but it is still just a web page. Google will provide easy-to-use tools for writing, editing, and so on, and it will provide free hosting of the content. Writers only need to write; we’ll do the rest.

So far I could have read the message and mission of WordPress and Typepad (forget Blogger) being not just blog engines but hosts of blogs too, the only real difference is called ads and revenue:

At the discretion of the author, a knol may include ads. If an author chooses to include ads, Google will provide the author with substantial revenue share from the proceeds of those ads.

The question is how can Knol benefit from the quality blog content on particular topics written by expert bloggers and how can bloggers benefit from contributing to Knol? Would Google be inclined to pay for pivotal blog posts on a particular topic to use them as knols? In many cases the content – the one that Google would like to facilitate with Knol – is already there so it is natural to convert quality blog posts to knols. But why would I, blogger turn to a knoller?

Looks like the G guys are reinventing the blog wheel:

Biogeekipedia: collecting raw materials

Wired’s Geekipedia is marketed as “People, places, ideas and trends you need to know now“. As such you can find biology and biotech related terms in it (part of the current hip and tech-savvy culture) like ‘stem cells‘, ‘RNAi‘ or ‘brain implants‘, explained. But you won’t find the terms ‘Natureplex’, ‘executable cell biology’, ‘Open Notebook Science’, ‘SciFoo Camp’, ’23andMe’ or ‘Pharyngula’ in it. The idea of building a Geekipedia (call it Biogeekipedia) specialized to the life sciences (biology, biotech, biomedical sciences, bioengineering, biobloggers…) seems pretty straightforward. (Or you can expand it to all natural sciences, but that is not my concern here.) So here I’d like to ask my readers to suggest entries for this Biogeekipedia, exotic, rare, but cool niche terms, buzzwords, good phrases, sentences, ideas and people within the biotech realm (web included) we all need to know. Use your imagination instead of your tag cloud. I start with my own embyronic list right now on the top of my head without links and explanations (Intensive work hours are inversely correlated to the number of quality blog posts). Needless to say it is more of a joke than a serious adventure. (List updated with the suggestions of Mr. Gunn, Jon Rowley and Matthew Oki O’ Connor.)

23andMe

Adie, Euan

aging

ATP/ADP

biobase

biogerontology

biomaterials

biotech DIY (DIY biology, bioDIY, home biology , garage biology, Homebrew Molecular Biology Club)

cancer immunoediting

cell fusion

Chemical Blogspace

CIRM

Connotea

convergent medical technologies

Craig Venter

deCODE

Easton, Alf

embryome

executable cell biology

FACS

Geekipedia

Genentech

genetic reprogramming

Google First Ladies

Google Palimpsest Project

The Regeneration Station – a biotech blog by Aastrom’s Jon Rowley

Jon Rowley is a senior manager at Aastrom Biosciences with a long experience in the not too old Regenerative Medicine field. I am pleased to introduce here his new blog The Regeneration Station as one of the first biotech – regmed blog written by an industrial expert who will share with us his insights on stem cells therapies, biomaterial-based devices, tissue engineered products and … biotech stock options i.e. all the things that are shaping the face of a young industry. According to Jon: Early adopter companies form and often fail, but they do succeed in removing some risk from the technology. As risk decreases, large companies try to figure out how to play in the new technology sandbox that is littered with small companies. Today, even Baxter is running a cell therapy clinical trial for cardiac regeneration, PerkinElmer is buying up cord blood banks, Celgene is dabbling in placenta-derived cells, and Teva Pharmaceuticals has an autologous MSC long bone trail underway.

There is another thing why more academic science bloggers should read Regeneration Station. Jon will definitely show us the “time and money” gap between science and the translation of it: “I do not want to undermine the importance of the great work that was done in generating pluripotent stem cells from adult skin cells, but the only thing I think about when hearing this news is TIME and MONEY. I know I will be fielding questions from my friends and relatives over Thanksgiving weekend on whether or not Aastrom (my employer) is doing this type of work or if we have to change our business model. I will have to explain that this type of research is at such an early stage, that it will not be impacting what is going on in Biotech for 20 years, if not more. It is challenging enough to manufacture and distribute an autologous cell product

What is your (science) blogging writing style, Chris Patil?

I have to interrupt my 23andMe streaming cause there are more interesting things are goin’ on. Chris Patil of Ouroboros has already been a blogterviewee (Part 1, 2, 3) on Pimm. He then shared his detailed views on aging and life extension technologies, but I always wanted to ask Chris about his approach on blogging as it was obvious from the launch of Ouroboros that he has a style and angle on the aging literature that goes far beyond the usual and sometimes dead boring “this journal published this and that journal published that” science blogging subgenre. We all need to find new and experimental ways in science blogging to make it more than just simply echoing the peer review literature and a sharp focus, good arguments and neat English definitely helps, so below you can read the secrets of Chris in blue. I also encourage you to try to mimic him to the amount of one blog post as a blogging homework. (The picture was made by Bora of the Clock fame at Berkeley, California this August when there was a science blogger party one day before the SciFoo Camp. Chris is on the left. The other guy is an unidentified science blogger.)

It’s a challenging question. Like speech mannerisms or your own personal walk, style is something that emerges from a lot of little decisions that happen below the level of explicit consciousness. As I’m writing this, I’m wondering, ‘Is this in my style?’ It’s like listening to my own voice on tape. Nonetheless, I shall try:

My own history in science writing goes back to college, when I wrote a weekly Q&A column for the Stanford Daily (‘The Science Bug’; I had inherited it from an earlier staffer and passed it along to someone else when I left; years later, my younger brother took up the job). The audience was mostly other students, i.e. bright and educated but not necessarily scientists, so the main challenge was providing necessary factual and conceptual background without sounding like a lecturer — the readers were getting enough lectures in their coursework, and I knew that an overly didactic style would turn them off.

Unlike a reporter, I had a great deal of freedom to explore different styles, and eventually I found one that really felt like me which is not to say I didn’t have influences. I worshipped Cecil Adams (of the famous syndicated Q&A column The Straight Dope) at times perhaps veering across the line into outright imitation. From him I learned that questions don’t really want “answers”; they want “stories“, with a beginning, middle and end. You have to take the reader somewhere, from familiar ground to unfamiliar ground (and, sometimes, safely back again).

Puzzle: Which institute belongs to the following job titles?

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

What is your (science) blogging writing style, Deepak Singh?

Actually the idea of asking science bloggers about their style came to my mind reading one email remark of Deepak on the writing style. Deepak is the guy behind business/byte/genes/molecules and he was a Sci Foo camper this year. He is one amongst the few bloggers who are standing at the intersection of science and technology and being the founder of Bioscreencast he is actively experiencing the life of a bioweb entrepreneur.

My style is a heady mix of spontaneity, continuous partial attention, a total lack of time, the random connection of ideas formed at different times, semi-formal essay-style writing, attempts at humor, deep thought, tempered enthusiasm, and unbridled passion.

Today’s top story on Blogrunner Science from 2 days ago

Why? Oh, it’s the TierneyLab.

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?

What is your (science) blogging writing style?

Yesterday I’ve sent the following (slightly edited) email to a bunch of science bloggers I know and respect for very different reasons. I plan to blog the answers (if they come) one by one:

Dear Fellow Science Blogger,

Every blogger has his/her blogging writing style and in many cases we do know the components our style is made of and recognize the different sources we use and mimic. Would you be kind enough to answer this question shortly in your style for me in order to show the variety of the genre called ‘science blogging‘?

Thanks in advance,
–
Attila Csordas

P.S. For instance I am fully aware that my style is made out of the following components amongst others: spontaneity (to the extreme of originality sometimes), experimentalism, idiosyncratic non-native speaker errors, lack of time, partial attention, insider science heavy lingo that is “terminological arias” (by default), (brackets), question and exclamation marks, science essay writing style educated on British and American analytic philosophers, movie, literature and comics experiences, Wired type tech hype journalism and first of all…enthusiasm about science and technology.

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.

Feed reading trends: I am a Valleywag addict, help me!

Show me your feed reading habits and I’ll tell you who you are! I hope this statement is not true as according the item reading trends on Google Reader I have been a serious Valleywag addict in the last 30 days and more, I suspect. Although extensively reading a funny, well-informed but malicious tech gossip site like Valleywag of the Gawker Empire admits no excuse my explanation is this: after 10-12 hours of experimental lab work I do need something light and ridiculous for mental regeneration at home before switching to more serious content. I want to laugh and for some reason Valleywag is tuned to the frequency I need for entertainment (and also gives me the option to instantaneously present the posts to my wife disturbing her web time). If my click path is a body with different physiological functions, then Valleywag is my

Greg Block’s Oracy and science as an exercise in humanitarianism

Did you now what oracy means? Never mind. From late September, Oracy is the blog of Tulane grad student and colleague Gregory Block, whom you can catch now just in the middle of finding his blog voice. Topics are focused on rants about science (specially stem cells), Greg’s melancholy music and stories from New Orleans. His intro post says: My old supervisor, David, taught me that science is an exercise in humanitarianism, and that if balanced properly can be an enriching experience and a gratifying lifestyle. So, if you want to complain about your western blots not working or chat about whether your formamide has gone off, this probably isn’t the best place to be.
For advanced scientists I suggest Greg’s favorite thoughts on the The Mortality of Immortal DNA.

How to get the number of feed subscribers via Google Reader?

Problogger reveals that Google Reader Reveal Subscriber Numbers to Feeds which is a good way to monitor blog popularity. The problem is that Problogger’s howto is not a good one and hard to follow: “The subscriber numbers can be seen simply by doing a search for a blog’s name after clicking the ‘Add Subscription’ link once you’ve logged into your Google Reader account.” You don’t even need to subscribe to a site to know its subscribers. (I tried to follow Probloggers cloudy words and then Anna solved the problem at once.)

Here is how to get those numbers for a particular blog feed in 3 steps:

1. Click Browse:

Where are the quality stem cell blogs?

Honestly, there are not too many good, stem cell related blogs out there. By “good stem cell blogs” I mean blogs that are regularly updated in a niche stem cell related field full with quality science information followed by original opinions and ideas and not just human or algorithmic link blogs.

Here are 3 solid and trustworthy stem cell related blogs I regularly (but not every day) follow:

The Niche: The blog of Nature Reports Stem Cells by Monya Baker.

The California Stem Cell Report: Former political reporter and business journalist David Jensen reports every public movement around the California Institute of Regenerative Medicine.

The Stem Cell Blog: Although it is definitely not THE Stem Cell Blog, written by Christopher Thomas Scott, Director, Stanford University Program on Stem Cells in Society (PSCS), but worth checking.

Let me know what are the SC blogs you like!

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.

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.”

My gmail spam box looks like this, what about yours?

Even economists have ideas on the hows of life extension…

Uncensored gmail chat between 2 science bloggers on adult issues

me: Hi Bora, can you send me the Nature piece on the Blogging Anthology?
I am not in the Institute and do not have subscription
http://www.nature.com/nature/journal/v447/n7146/full/447779b.html
Sent at 8:58 PM on Wednesday
me: cheers
Bora: No problem. Thanks.
me: wait that is some old stuff.
Published online: 22 January 2007; | doi:10.1038/news070122-I’ve read that
I have in mind the current one: Bloggers unite p779
Paul Stevenson reviews The Open Laboratory: The Best Writing on Science Blogs 2006
doi:10.1038/447779b
Full Text | PDF (207K)
See also: Editor’s summary
Bora: Wow! That is news to me!
me: ok, who posts first?
do you have access to it right now?
Bora: No. I should have it in minutes/hour as soon as one of the sciblings check the forums and sees my query.
me: ok
I am curious how positive, or critical it is
Sent at 9:04 PM on Wednesday
Bora: http://neurophilosophy.wordpress.com/2007/06/13/open-laboratory-reviewed-in-nature/
me: good
Sent at 9:07 PM on Wednesday
me: I think, the science blogosphere now reached its adult stage

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