Going to San Francisco and the Valley, SciFoo preparations

SciFoo is coming, so I take my flight tomorrow from humid and subtropical New Orleans (running experiment terminated this afternoon, things in liquid nitrogen for downstream processing) to the cold San Francisco. Besides the Googleplex I am visiting Berkeley, Stanford, UCSF and as many of the central places of high tech culture (you know, the cooperating IT and BT interests) as possible. I become a sci-tech tourist for one week. Preparation for SciFoo equals to extending the Google Maps list, inforich contact list and PDFs on the iPhone. It is a constant joy to scan the list of the 200 or so campers (read science foo camp(fire) and meditating on the session suggestions.

See you there. Wednesday, around 4 PM, at the corner of Haight and Ashbury?

Making notes in a seminar with an iPhone: in progress (SciPhone Test)

In our lab there are seminars almost every day, and I started to use my iPhone’s Notes function to record some information and thoughts I found interesting during the seminars. I am really not experienced in typing the iPhone keyboard yet so here are my first 2 trials first as screenshots and then the texts themselves. Problem: in order to use the Notes texts in a normal text editor you have to send it to yourself as an email attachment.

First trial:

and the second trial, followed by the comparison of the 2 texts.

Physics geeks, get a retro car!

Online political marketing with embryonic stem cells

I’ve just realized that Mr. Governator’s official website is the most visible outbound link on the website of The California Institute for Regenerative Medicine. That is actually a 3 billion dollar link.

google.stanford.edu circa 1997: a little slide

This slide comes from the presentation of Google Fellow Jeff Dean on Seattle Conference on Scalability, entitled Abstractions for Handling Large Datasets. (The title Google Fellow seems to me as something similar in rank to a full professorship at Stanford.)

Here is the presentation itself embedded:

Some fresh facts about Tulane University Medical School

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.)

3 rules to protect your iPhone from a serious Safari security problem

Charlie Miller, Jake Honoroff, and Joshua Mason, members of the software security team at Independent Security Evaluators had discovered a vulnerability within two weeks of part time work and “developed a toolchain for working with the iPhone’s architecture (which also includes some tools from the #iphone-dev community), and created a proof-of-concept exploit capable of delivering files from the user’s iPhone to a remote attacker. The exploit is delivered via a malicious web page opened in the Safari browser on the iPhone.” Delivery vectors of the attack could be: an attacker controlled wireless access point, a misconfigured forum website, a link delivered via e-mail or SMS.

The professionals suggest 3 practices to diminish the iPhone’s vulnerability:

• Only visit sites you trust.
• Only use WiFi networks you trust.
• Don’t open web links from emails.

A preliminary technical paper called Security Evaluation of Apple iPhone is available.

Audobon Zoo, New Orleans: Trolls, Gators, Swamp Monsters

Pictures made with iPhone by Anna.

 

Fast networking with Apple gadgets at a Harry Potter party

On Friday we went to a Harry Potter Midnight Magic party at the Uptown Tulane Campus. There I met Noah from Michigan, who was videoskyping on his MacBook Pro with his brother in Los Angeles. Our 3 minutes talk was an excellent exemplar of what I call “fast networking”: Facebook confirmation, iPhone presentation, blog introduction, useful information exchange. When leaving I took a shot of Noah scanning Pimm’s Architecture of the scientific web post (see second picture). Without the gadgets we might not have started to talk.

How to read PDF files on iPhone via Safari instead of lame email attachments

The 2 main drawbacks to reading PDFs on the iPhone are the must-send-it in email in order to store and open “solution” and the user-unfriendly, landscapeless left-right scrolling reading mode. Not anymore. Both problems can easily be overcome with the help of a Safari browser hack using the almost forgotten data: URI schemes. From now on you can store and open your PDF files (and many others) in the iPhone’s Safari browser even in the Wi-Fi- and EDGE-less airplane mode and you can read PDFs in a landscape mode with only 1 one pich (that fits a column) and significantly less left-right scrolling in a much more satisfying, although not yet perfectly manner.

Here I show you in 4 steps how to do so.

1. Convert your source PDF file (by encoding an uploaded file from your folders or from URL) to a valid data: URI format with the help of a converter. I used the online The data: URI kitchen encoder but others are available too, you can even use a Perl script (and run it with Terminal under Mac OS X, thanks Mike). This will generate a very long and ugly URI line. (Sample PDF: Proposition 71 of the California Institute of Regenerative Medicine)

2. Copy/paste the long and ugly URI code into Safari and add it to your Bookmark Bar.

3. Sync your iPhone’s bookmarks with your Mac’s Safari bookmarks via iTunes, with that you can create a direct link for the PDF on your iPhone’s Safari bookmarks.

4. You’re ready, open the PDF file from the bookmarks and read it with a 1 pich landscape mode.

The same algorithm with screenshots:

Organ donation after death: a generous gift or an obligation?

What do you think?

Everyone ‘should donate organs’ post mortem, UK chief medical fellow says

This suggestion sounds like a proper body recycling to me: Everyone should be seen as a potential organ donor on their death unless they expressly request not to be, England’s chief medical officer says. Sir Liam Donaldson calls for a system of “presumed consent” to be introduced to tackle chronic shortages of organs.

Only 20% of the population – or 13 million – are on the register, despite the fact that surveys showed that as many as 70% of people wanted to donate their organs after death.

Donating Frozen Embryos for Stem Cell Research: a survey in Science

EMBRYONIC STEM CELLS: Willingness to Donate Frozen Embryos for Stem Cell Research by Anne Drapkin Lyerly and Ruth R. Faden, Science 6 July 2007: Vol. 317. no. 5834, pp. 46 – 47 DOI: 10.1126/science.1145067

We conducted a survey of 2210 infertility patients receiving treatment at one of nine major, geographically diverse infertility centers and asked these patients about their intentions for the embryos they currently stored. Participating centers were located in California, Colorado, the District of Columbia, Maryland, Missouri, New Jersey, North Carolina, Oregon, Pennsylvania, and Virginia. The respondents were asked to answer a set of questions with one of the following: very likely, somewhat likely, somewhat unlikely, very unlikely, or unsure/don’t know.

/Figure legend. Disposition option for some or all of cryopreserved embryos currently stored. SCNT, somatic cell nuclear transfer. Key: Somewhat likely (lavender), very likely (gray).
CREDIT: MIODRAG STOJKOVIC/SCIENCE PHOTO LIBRARY /

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 domesticated biotech future according to Freeman Dyson

Freeman Dyson, old school physics hero conceptualized his rather philosophical thoughts on future biotechnology in a visionary essay in The New York Review of Books, Volume 54, Number 12 · July 19, 2007.

What is surprising to me that according to Dyson “our biotech future” is centered around genetic engineering only, and there is not even a hint to stem cell biology and regenerative medicine, which is a bit strange concept for me concerning state of the art biology.

Anyhow, I ask the readers to form an autonomic opinion about it. Here are some cites: Biology is now bigger than physics, as measured by the size of budgets, by the size of the workforce, or by the output of major discoveries; and biology is likely to remain the biggest part of science through the twenty-first century. Biology is also more important than physics, as measured by its economic consequences, by its ethical implications, or by its effects on human welfare….

I see a bright future for the biotechnology industry when it follows the path of the computer industry, the path that von Neumann failed to foresee, becoming small and domesticated rather than big and centralized. For biotechnology to become domesticated, the next step is to become user-friendly.

Subscribed STEM audio and video podcasts on my iPhone

Just the mainstream actors of my niche STEM (science, technology, engineering and mathematics) fields. I am not too experimental when it is about new podcasts without any recommendations based on simply trial and error, although it is not the best attitude. I hope this attitude will change due to heavy iPhone usage as the time distributed to podcasts is increasing.

Say hello to Pimm, Joker, respiratory chain and science on my iPhone

As in the case of my old iPod, I’d like to use myPhone to access the scientific world and web from everywhere, not just as a tool of coolness. (Warning: Macbook shots, bad quality pictures on a good quality experience).

First post from iPhone

Dear readers, it is not so easy to write an interesting post with a one day old iPhone. Let me give you just one link manually this time: http://www3.interscience.wiley.com/cgi-bin/abstract/114290609/ABSTRACT?CRETRY=1&SRETRY=0

Reconfigure the NIH!

Although I have no time now to meditate on NIH policies (I must take care of my cells), but I spread this package from Tom further, as the timing seems good, especially what concerns stem cell research. 4 rules (1 abandoned by me), and 1 copy/paste.

1. Include in your post the links to the NIH RFI and the comments page.

2. Include the list of six topics the NIH wants information about.

Challenges of NIH System of Research Support
Please describe any specific challenges presented by NIH’s support of biomedical and behavioral research such as the current array of grant mechanisms, number of grants awarded per investigator, and the duration of grants.

Challenges of NIH Peer Review Process
Please describe any specific challenges presented by the current peer review process at NIH.

Solutions to Challenges
Please concisely describe specific approaches or concepts that would address any of the above challenges, even if it involves a radical change to the current approach.

Core Values of NIH Peer Review Process
Please describe the core values of NIH peer review that must be maintained or enhanced.

Peer Review Criteria and Scoring
Are the appropriate criteria and scoring procedures being used by NIH to evaluate applications during peer review? If not, are there changes in either that you would recommend?

Career Pathways
Is the current peer review process for investigators at specific stages in their career appropriate? If not, what changes would you recommend?

3. Comment on one or more of these issues. Reconsider the stem cell grant system completely.

4. Decide who the next seven vectors will be for this meme. Sorry, I don’t.

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.

Prospective anti-research fears around Stem Cell Labs on the Globe

Stem Cell Labs on the Globe is a public map initiative of important, worldwide stem cell locations made by Google My Maps for the sake of stem cell researchers. The original idea is to easily find all the interesting academic stem cell places that you need to know in order to proceed further professionally.

The first reaction came from Monya Baker, editor of Nature Stem Cell Reports and blogger of the Niche, who has worries about the map.

“This is cool. My one worry is whether some anti-research freaks will use this to a bad end. Like those people in the UK who actually threatened scientists’ children as an ill-guided protest against animal research. I haven’t heard of that around stem cell research yet, but I don’t want to be their tool for mischief, or worse.”

Followed by my first answer: “I think your worry is a bit too advanced, all these data are public, searchable, so your argument goes that if we collect them into one public map for the sake of real stem cell people, that could be edited only by trusted persons (the gmail account and password is needed for editing and we would give the password personally by mail) that situation will produce more danger to the academic stem cell world as it makes easier to see the targets within one map and click for anti-freaks…..well, think again.”

If somebody wants to find stem cell labs, companies, persons or institutions to attack all he/she must do is to run some Google searches and if he/she is serious he/she will pick some targets with exact geodata within maximum 10 clicks. So with the same “fear” argument it could be advisable for instance not to make the list of stem cell labs awarded by CIRM grants public and restrict Google crawlers concerning regenerative medicine information. But I think it would be crazy to prohibit Google searches, or the entire Internet just because of the fears like that. Thanks to the Internet (and especially the Web 2.0 toolkit) we are living in the world of radical transparency and open science and that produces a tremendous opportunity for useful science applications.

Nature’s Superb Many Worlds Retro Cartoon Cover, quantum physics and SF

The current issue of Nature looks like something especially targeted for geeks with a high end content. Consider again the role of comics in science popularization. Is this Nature, not Wired?
From the Editor’s Summary: “Yes, this is Nature. The cover art, by David Parkins, salutes a big year for quantum physics: 50 years ago, Hugh Everett III proposed what came to be known as the ‘many worlds’ hypothesis. He took quantum physics at face value, and imagined what it really meant. He aimed to resolve the paradoxes of quantum theory by allowing every possible outcome to every event to exist in its own world. In a News Feature, Mark Buchanan reports on modern reactions to the ‘many worlds’ idea…. Life sciences also have their place in this fiction-inspired issue and the whole is brought together in an Editorial.”

I first heard about the Many-World interpretation of quantum mechanics (proposed by Hugh Everett III) as a philosophy undergrad writing a bigger essay on the modal realism of my favourite analytic philosopher David Lewis. This philosophical-logical theory argues that possible worlds are as real and irreducible as the actual world.