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