Red Mars before sleep &after JavaScript:dropping windmills=>spin=>heat in coils=>release to atmosphere, winds slowing down=>dust storms down 17 hours ago
Hard to believe, learn in what sense? See/trial & error? RT @GreatDismal I learn more watching people use new tech than using it myself 19 hours ago
nephews (11,13) just learned how to run, modify & debug the 'Hello World' JavaScript on the iPhone w/ Notes, variables & functions next ;) 1 day ago
Family party this afternoon: preparing w/little JavaScript snippets on the iPhone for my nephews so they can run scripts on their iPod touch 1 day ago
Safari is losing http requests to Chrome/Firefox on my laptop due to the lack of an omnibox capability 1 day ago
When I first wrote about Aaron Swartz’s unfinished nervous nerd novel, Bubble City, I had just been through chapter 1 and 2. But at the Dallas International Airport, waiting for the London connection on December 22 I had no choice but quickly finish the other 9 chapters posted so far under the pressure of the compelling narrative. Bubble City turned out to be my biggest literature experience of this year and the emphasis is on “literature” here.
The plot in one sentence based on the 11 chapters so far: Jason Barsto (an alternative Swartz) coder of a San Francisco news aggregator startup, called Newsflip (an alternative Reddit) gets hunted down by Google (an alternative Google) because he explores a backdoor in the tricky S-boxes behind the Notated News Analysis (NNA) system of the aggregator code at Newsflip (developed formerly at an alternative Yahoo), by which alternative Google or alternative others can manipulate and dangerously homogenize news recommendations for users.
It is a paranoid parody, a contemporary classic hacker fiction: it is crime and anti-crime, it is love and anti-love, it is real and anti-real but most importantly it is about Google or rather it is the best artistic expression of the emerging Hassliebe to Google so far, that every well informed and networked, responsible alpha geek (like Swartz) feels today. I suspect that even Google employees can feel the same way toward their own company.
Everybody in the tech world has plans with Google and Google has plans with almost everybody. Read the rest of this entry »
What’s the best thing to do if Google wants track you down and you are“a geek, the kind of person who searched Google every time a thought passed through his head”. Well, Aaron Swartz’s nervous nerd novel, Bubble City (I summarize my thoughts on it in the next post) has a geeky algorithm to play with in Chapter 9:
Thus, to be sure Google can’t track you, you need to do at least three things: never long in, never accept tracking cookies, and use some kind of anonymization of your IP address (like Scroogle or Tor). And that’s just for the Web.
Another comment turns to blog post to make it more visible: Following my post on science.TV, Matt Thurling, founder explained the concept of it in a lengthy comment, that sheds light on the ins and outs of science.TV (emphasis added by me):
Although science.tv has been some three years in the making, we’re still in the very early stages. The site is live, but it should probably be labelled ‘alpha version’ because, in terms of functionality, it’s only about 10% of what’s to come. And in terms of content, it’s even less developed.
The content that’s on the site at the moment is admittedly something of a mixed bag. It actually represents one small part of science.tv – fun resources for teachers to use in classes to demonstrate phenomena. The few films that have been uploaded or linked have come from the focus group of teachers involved in the project.
We did some interesting research a while back on what ’science’ means to different kinds of people. For scientists and academics, it’s about pursuit of the truth via the scientific method; for pretty much everyone else, it’s actually more about the products of science. What’s also interesting is the meaning of ‘experiment’, and what seems to be taught to school students is not experimentation at all, but the ‘correct’ performance of rituals with set outcomes.Read the rest of this entry »
science.TV is one amongst the newest actors of the online video sharing marketplace, based in Bristol, UK.
As Matt Thurling, founder says:
“My vision for science.tv is simply to provide the best possible set of tools to enable interaction via video between the science community. My definition of the science community is probably broader than the other sites in that it includes hobbyists and school students as well as research scientists. The idea is that, given the right tools, everybody will find their level and their role in science.tv, be it creator, distributor, educator or consumer of niche content.”
With a domain name like this, I expected a lot more science content, but the emphasis at this early point is on entertaining Make-like tech and DIY videos (think of Instructables), many of them coming from YouTube. While I am in favor of merging science with tech and had a little role in popularizing tech sites like Make and O’Reilly Radar in the science blogosphere I do not think that science.TV is a good name choice for such type of combined content. However, in the long run, not the name that matters but the content. If science.TV can aggregate, share or produce quality content at the science-tech interface than it will be a colorful and appreciated member of the family of science video sites ranging from the research focused JoVE and SciVee to the less academic DNATube or Lab Action.
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 SaulKripke 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):
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.
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. Read the rest of this entry »
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. Read the rest of this entry »
I am not watching to many videocasts, but the last 5 epizodes of the Make Weekend Projects with Bre Pettis are always on my iPhone and viewed every time. Now Anna over at Videovooreports on the coming Make:TV featuring half-hour episodes that will be presented in High-Def TV and streamed on the web in as early as 2008. Anna made a detailed email Q&A with Philip Torrone, senior editor and alpha nerd on the emerging video and TV side of Make:
The first Make video was uploaded on YouTube in March 22, 2006 (if I’m not mistaken), while Make TV show started to run on Blip.TV in July 2006. As for Blip.TV, Phillip Torrone senior Make editor says “we like the player, the high quality playback and the team at blip”. However, YouTube still brings more eyeballs than Blip.TV – maybe more revenue too? Since December 2007 Make magazine has been in the YouTube Partner program, so they will get some revenue from the most popular video social networking site too. In 2008 they are also getting on air more ‘officially,’ harvesting more exposure on more screens, which is a nice example of an online success story spreading out on a national TV channel well-known for educational science programs. What can we expect in 2008? Read the rest of this entry »
I hope that scientists and IT and financial managers of scientists worldwide will be able to utilize the collective lab website culture and wisdom accumulated by the first ever Laboratory Web Site Awards by The Scientist!
And I personally would like to say thank you for the following editors of The Scientist (The Scientists) for so quickly and professionally getting this thing done: Ivan Oransky, Richard Gallagher, Andrea Gawrylewski and last, but not least Simon Frantz, who is now at the Nobel Foundation.
We have now the winners announced, but practically all the 60 nominated labs are winners and all those labs who can follow their way.
We know from Larry Page, (ex Stanford grad student) that “Science has a really serious marketing problem and nobody pays attention to that since none of the marketers work for science”.
The Lab Site Awards was a good science marketing opportunity for the labs involved and here are the announced winners, congratulations:
Here is what I wrote on the Redfield Lab as a judge: “Researchers have blogs on the day-to-day experiments. Funds, grants are public and listed. The Redfield lab is the most web friendly and gives us clues on how the lab sites of the future should look like.” The confirmation of this opinion comes from BoingBoing itself (it is not a frequent event when one of the oldest and biggest blog posts on lab websites): Lab requires EVERYONE to keep a science blog
Our new Boo XO laptop is not just smart, but has nothing to be shamed about when compared to, say Apple laptops in design. It is an excellent source of funny pictures too. Picture composition: Anna.
In November we participated 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. Yesterday we got ours, named Boo and Anna recorded the first moments of Boo at our home and published it on her blog Videovoo with detailed account. Unfortunately we don’t have information on where our “Give one” laptop has been landed and who (and how old) is the happy owner of it from now on.
When I had worked on my MSc thesis in biology on the relation of human mitochondrial mutations and aging the paper I used most frequently was Sequence and organization of the human mitochondrial genome by Anderson et al. published in Nature, 1981. The reason was simple: it is more of a database than a hypothesis driven article with the published 16.569 base pair sequence of the circular human mitochondrial genome (L-strand) containing 37 genes and a bigger non-coding, regulatory region. Throughout my work I had to use it as a basic reference. The sequence is a reconstruction of a single European individual’s mtDNA and contains several rare alleles. Nice figure isn’t it?
I’ve just realized with the help of genomics pioneer and warrior Craig Venter’s recent molecular autobiography Life decoded, that the brilliant two time Nobel laureate, sequencing urfather Frederick Sanger is also a coauthor of the paper. Here comes Venter: Read the rest of this entry »
New Orleans, Louisiana is a home of many weird people full with bizarre stories. One of them was Sandor Szalmas a Katrina survivor, jack-of all trades DIY Hungarian, who lived in the town since 1981. When I first heard the story of his fatal Dec. 5. motorcycle accident last week, he was in a coma with not much chance to survive. On Tuesday, he died of head and spinal injuries suffered in the accident. What makes his death really weird is the rattlesnake on his motorcycle. According to Walt Philbin of the Times Picayune (photo by George Berke):
“Police think Szalmas failed to negotiate a curve on Almonaster Avenue and struck a curb because he was distracted by a rattlesnake he was transporting on the back of the motorcycle….In the week before he died, Szalmas came upon a rattlesnake in the woods and shot it dead. When he brought it back, possibly to show his grandson, a Vietnamese woman who runs a manicure shop near his house saw it and had it cooked for him. Some of his friends speculate the reason he was taking another snake back with him at the time of the accident was that he wanted to eat this one, too.
Long before his unusual death, Szalmas was considered by those who knew him to be a larger-than-life character.
Carl Mack said his friend was “the kind of guy who would be talking with you and catching a fly out of the air at the same time or playing with geckos or eating termites he plucked off a board as he worked on a house.”
Since the fatal accident, friends recalled the time Szalmas rode his bicycle around the country, the time he chopped an alligator’s head off in a swamp when it attacked his inflatable boat, and the time he kept a rattlesnake in his living room as a pet for at least a year, using a covered-over billiards table as a makeshift cage. When he let the snake out for exercise, he would shut the living room doors and post signs saying, “Snake out,” Connelly said. Read the rest of this entry »
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?
I guess I will submit this question to the Ask the Experts section of Scientific American. It was a witty remark by a senior scientist at a presentation on neural stem cells and aging last week, here at Tulane. I laughed so much that I had to blow my nose disproving that good jokes keep us smart. Here we are:
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.)
In my former blog post inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa? I meditated on 23andMe’s capability of detecting paternal mitochondrial DNA in their customers’ saliva with their Illumina microarray chips scanning around 2000 mitochondrial single nucleotide variants. Published here the initial answer of the 23andMe Editorial Team to this fairly technical, but nevertheless crucial question with permission granted. Besides, I am happy to report that I am working on a blogterview with one of the key member of 23andMe’s Research Team. Hopefully I’ll be able to get back to you with some first-hand information on the science and technology behind the personal genome service of 23andMe and on how 23andMe can facilitate academic research.
Dear Attila Csordas,
Thank you for your interest in 23andMe’s research mission. The question of paternal inheritance of mtDNA is a fascinating one, and the debate in the literature has continued over the past couple of decades. Currently, there is little evidence for paternal inheritance of mtDNA, outside of isolated individuals. However, the array platform lets us resolve multiple SNP states independently. 23andMe’s technology and throughput may indeed provide a novel way to address the question. We will include the question in our consideration of research projects. In the meantime, here are a couple of articles discussing the subject:
The question is crucial for a personalized genetics company like 23andMe providing Maternal Ancestry Tree service for the customers based on the exclusively maternal inheritance of mitochondrial DNA. As one of my correspondent partner wrote: Read the rest of this entry »
In the 15 November Nature issue Judy Illes neurology professor turned neuroethics expert reviewsEnhancing Evolution: The Ethical Case for Making Better People by John Harris and Ending Aging: The Rejuvenation Breakthroughs That Could Reverse Human Aging in Our Lifetime by Aubrey de Grey & Michael Rae.
From the review:
“Ending Aging is a more “new wave” treatment of enhancement, longevity and immortality…. The authors rather unnecessarily brand ageing as repugnant and curse, and use their book to preach on fund-raising opportunities.
The freedom to pursue ways to enhance human mental and physical capacities and to eliminate negative aspects of the human condition, such as suffering and death, is a fundamental tenet of the trans-humanist movement. Although seemingly worthy, there are problems ahead for the futurists, including for Harris, de Grey and Rae….
…Let’s not throw away today for tomorrow. Ending Aging is likely to appeal to those already converted to the author’s views, and perhaps will find some traction among those who are more curious than interested in deeper scientific engagement.”
Unfortunately Illes completely mixes transhumanism with the belief that robust life extension is possible and desirable due to handling the 2 books together and I think this is not a fair angle on life extension. Consequently she can say on the whole that those beliefs are “going well beyond what might be imaginable, or ethical today.”
But most life extension supporters are simply not transhumanists at all and it is a simple logical fault to think that ‘if A then B’ is true (every transhumanist is a life extension supporter), than it follows that ‘if B then A’. For instance, most life extension supporters that I’ve met, say in the SENS3 conference, are not transhumanists, but simply young life scientists for whom life extension is just the technological frame (the highest aim) of their translational science. Think systems biology: human organismal aging is a complex dynamics of a complex system and if you want to modify it you should think on the systemic level. Read the rest of this entry »
According to the newest Request For Applications (RFA) of the California Institute for Regenerative Medicine (CIRM), the New Cell Line Awards will support two categories of research:
Category 1: Derivation of new hESC lines using excess or rejected early stage human
embryos generated by in vitro fertilization.
Category 2: Derivation of pluripotent human stem cell lines from other sources using
alternative methods such as (but not limited to) SCNT or reprogramming of neonatal or
adult cells (iPS cells).
The real news is encoded in category 2: from now on even adult stem cell research can be backed by California Embryonic Stem Cell Dollars. The same idea in another form in the text:
• disease-specific or otherwise genetically diverse, pluripotent stem cell lines to support
studying the effects of genetic variation on disease mechanism and response to
treatment, and the discovery and evaluation of new drug candidates
• the discovery and implementation of alternative methods for generating pluripotent
human stem cells, including technology leading to the generation of patient-matched or
disease-specific cell lines
What research trend is behind? The generation of induced pluripotent stem (iPS) cells. The successful reprogramming of differentiated human somatic cells into a pluripotent, embryonic stem (ES) cell-like state that would allow creation of patient- and disease-specific stem cells instead of using controversial embryonic stem cells was recently reported by 2 groups of researchers: the Yamanaka and the Thomson lab.
Under this RFA, CIRM intends to commit up to $25 million to support up to 16 awards,
eight (8) in each of the two categories of research. CIRM proposes to fund each award
for up to three (3) years for direct project costs of up to $300,000 per year.
I’ve found the following fine paragraph in the Autumn edition of Nurture, the magazine for past and present Nature journal authors. Linda Cooper writes on “How to make research accessible”:
Take the overuse of the passive voice. Scientists tend to think that the passive voice creates an objective tone. But when they rely too heavily on passive constructions, researchers rarely captures the enthusiasm they have for their work. Although such writing may be fine for bureaucrats, removing the scientist from an article, drains life from the paper.
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):
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.
When I first wrote about Aaron Swartz’s unfinished nervous nerd novel, Bubble City, I had just been through chapter 1 and 2. But at the Dallas International Airport, waiting for the London connection on December 22 I had no choice but quickly finish the other 9 chapters posted so far under the pressure of the compelling narrative. Bubble City turned out to be my biggest literature experience of this year and the emphasis is on “literature” here. 
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 
The web is small and the 
When I had worked on my MSc thesis in biology on the relation of human mitochondrial mutations and aging the paper I used most frequently was 
Everybody is comparing Google’s Knol project to Wikipedia intended to be a “repository of knowledge from experts on various topics” (
