"biology" entries

Four short links: 12 May 2009

Four short links: 12 May 2009

Storage Superfluity, Data-Driven Design, Twit-Mapping, and DIY Biohacking

  1. Lacie 10TB Storage — for what used to be the price of a good computer, you can now buy 10TB of storage. Storage on sale goes for less than $100 a terabyte. This obviously promotes collecting, hoarding, packratting, and the search technology necessary to find what you’ve stashed away. Analogies to be drawn between McMansions full of Chinese-made crap and terabyte drive full of downloaded crap. Do we need to keep it? Are there psychological consequences to clutter? (via gizmodo)
  2. In Defense of Data-Driven Design — a thoughtful response to the “Google hates design!” hashmob formed around designer Douglas Bowman’s departure from Google. When you’ve got the enormous traffic necessary to work out if miniscule changes have some minor, statistically significant effect, then sure, if you can do it quickly, why wouldn’t you? But that’s optimization that should happen at the very end of the design cycle. The cart goes after the horse. Put it the other way ‘round and you have a broken setup. It doesn’t mean horses suck. It doesn’t mean carts suck. Carts are not the enemy of horses. Optimization is not the enemy of design. Get them in the right order and you have something really useful. Get them the wrong way around and you have something broken.
  3. Just Landed: Processing + Twitter + Metacarta + Hidden Data — Jer searched Twitter for “just landed in”, used Metacarta to extract the locations mentioned, and then used Processing to build visualizations.
  4. Do It Yourself Genetic Sleuthing — MIT is starting a hotbed of DIY biologists. The 23-year-old MIT graduate uses tools that fit neatly next to her shoe rack. There is a vintage thermal cycler she uses to alternately heat and cool snippets of DNA, a high-voltage power supply scored on eBay, and chemicals stored in the freezer in a box that had once held vegan “bacon” strips. Aull is on a quirky journey of self-discovery for the genetics age, seeking the footprint of a disease that can be fatal but is easily treated if identified. But her quest also raises a broader question: If hobbyists working on computers in their garages can create companies such as Apple, could genetics follow suit? It’s unclear what those DIY-started “genetics” companies would look like–the potential is there, but it’s yet to met the right problem. (via Andy Oram)

Just Landed – 36 Hours from blprnt on Vimeo.

Comment: 1
Four short links: 5 May 2009

Four short links: 5 May 2009

Spies, Community, International Success, and DNA Origami

  1. Supermap — The CIA’s venture capital arm, In-Q-Tel, is paying an undisclosed sum to California-based Geosemble Technologies to develop an intelligence version of the “geospatial data integration and layering technology” that the company developed for use by urban planners, real estate investors and market analysts. The technology combines overhead imagery, maps and heavy-duty data mining to create a map-based intelligence capability reminiscent of the Pentagon’s former Total Information Awareness program. When the project is done – and In-Q-Tel won’t say how soon that might be – CIA agents will be able to merge aerial images and electronic maps on a computer screen. Then they will be able to click on the building or other item of interest and all manner of information will pop up: who the tenants are, phone numbers, company records, links to company and organization Web sites, news reports related to the tenants or incidents at the address, property records, tax data and more. I love that Cheap Suit Susan, your local real estate agent, had the technology before the CIA. It’s like learning that Lionel Hutz has a missile defense system to stop his house being TPed.
  2. 7 Harsh Truths About Running CommunitiesAs the leader of your community, your personality sets the tone. As a result if the community behaves in ways you do not want, then you only have yourself to blame. I have seen many bloggers write about the negative comments they get on their posts. In most cases this is due to the tone they themselves strike in their writing. Although there are exceptions I believe that users will respond in the same voice you yourself set. If you are irreverent, then so will your users be. If you are rude, expect rude responses. “Social software” is an anachronism-software that doesn’t let users interact has become antisocial software. Every web creator needs to know what successful communities have in common. (via Julie Starr)
  3. Lingopal is Big in Japan (Lance Wiggs) — Turns out we are biggest in Japan. We have done no marketing there – it is all organic growth as our google ad writing and PR ability is not so good in Japanese. More anecdata for my belief that, while chance favours the prepared mind (as Louis Pasteur said), we routinely use post-hoc rationalisation to explain why it was inevitable that this or that lucky SOB hit it big.
  4. DNA Origami Seeds: Bottom-Up Methods for Molecular Self-Assembly (US News) — Winfree’s coworker at Caltech, Paul W. K. Rothemund, pioneered the seed-DNA technology that allows tiny “DNA origami” structures to self-assemble into nearly arbitrary shapes (such as a smiley face and a map of the Western Hemisphere). The researchers designed several different versions of a DNA origami rectangle, 95 by 75 nanometers, which served as the seeds for the growth of different types of ribbon-like DNA crystals. The seeds were combined in a test tube with other bits of DNA, called “tiles,” heated, and then cooled slowly. At the lower temperature, the tiles start to stick to each other and to the origami. In this way, the DNA ribbons self-assemble, but only into forms such as ribbons with particular widths and ribbons with stripe patterns prescribed by the original seed.
Comments Off
Four short links: 4 May 2009

Four short links: 4 May 2009

Maps, Africa, Protein, and Rockets

  1. Old Japanese Maps on Google Earth Unveil Secrets — Google criticised for putting up map layers showing the towns where a discriminated-against class came from, because that class is still discriminated against and Google didn’t put any “cultural context” around it. Google and their maps didn’t make the underclass, Japanese society did. Because they’re sensitive about having the problem, they redirect their embarrassment into anger at Google. You could make a long and profitable career in IT consulting simply by charging to say “it’s not a technical problem” and you’d be right more times than wrong.
  2. See Africa Differently — using the Internet to reframe a continent. Videos, essays, and more, all designed to get you seeing the majority of Africa, which isn’t defined by conflict and famine. (via NY Times book review)
  3. Fold.it – Solve Puzzles for Science — science harnesses our “cognitive surplus” by inviting us to help solve the problem of protein folding, one of the hardest in biology. (via auckland_museum on Twitter)
  4. Arduino Telemetry Payload in Class C Rocket (Jon Oxer) — Because class-C rockets are so small and light they can’t lift much of a payload and I had to keep the mass of the electronics as small as possible. You can get a sense of scale from this photo which shows a small white bundle in the bottom of the nosecone. Inside that bundle is an Arduino Pro Mini 5V/16Mhz, a 433Mhz transmitter module, and a Lilypad 3-axis accelerometer. PCBs … in … Spaaaaace!

Arduino rocket picture showing circuitry inside a foot-long rocket

Comments: 3
Four short links: 23 Apr 2009

Four short links: 23 Apr 2009

Multitouch, visualizations, body hacks, and ubicomp:

  1. Dell Demos Multitouch on the Studio One 19 (Engadget) — the multitouch software on this baby is Fingertapps from the New Zealand company Unlimited Realities, whose founder was at Kiwi Foo Camp this year. Multitouch hits consumer PCs in a very mainstream way.
  2. Circos — open source Perl library to produce beautiful circular data displays. (via flowing data)
  3. Brain Gain: The Underground World of “Neuroenhancing” Drugs (New Yorker) — more on the body hacks theme of radical and literal self-improvement, as originally documented by Quinn Norton. What I found interesting was that when BoingBoing linked to it, they quoted the “Provigil might make us smarter” bit, and when MInd Hacks linked to it, they quoted the negative effects of amphetamine-based drugs.
  4. Towards the Web of Things: Web Mashups for Embedded Devices — slides and notes for a presentation given at MEM 2009. Basically saying that the Internet of Things should be built on JSON and REST, with demo. (via Freaklabs)

Comments: 3
Four short links: 8 Apr 2009

Four short links: 8 Apr 2009

Bias, RFCs, virus batteries, and a glimpse at life beyond record labels (the last item features profanity, beware):

  1. Bias We Can Believe In (Mind Hacks) — Vaughn asks the tricky question about the current enthusiasm for Behavioural Economics in government: where are the sceptical voices? As he points out, It’s perhaps no accident that almost all the articles cite a 2001 study that found that simply making the US’s 401(k) retirement savings scheme opt-out instead of opt-in vastly increased participation simply because it’s a hassle to change and employees perceive the ‘default’ as investment advice.
    But it’s probably true to say that this example has been so widely repeated but it’s one of the minority of behavioural economics studies that have looked at the relation between the existence of a cognitive bias and real-world economic data from the population.
    And it’s notable that behavioural economists who specialise in making this link, a field they call behavioural macroeconomics, seem absent from the Obama inner circle.
  2. How The Internet Got Its Rules (NYTimes) — about the first RFCs, which became IETF. The early R.F.C.’s ranged from grand visions to mundane details, although the latter quickly became the most common. Less important than the content of those first documents was that they were available free of charge and anyone could write one. Instead of authority-based decision-making, we relied on a process we called “rough consensus and running code.” Everyone was welcome to propose ideas, and if enough people liked it and used it, the design became a standard. (via Glynn Moody)
  3. Viruses Could Power Devices (Science News) — Ions and electrons can move through smaller particles more quickly. But fabricating nano-sized particles of iron phosphate is a difficult and expensive process, the researchers say. So Belcher’s team let the virus do the work. By manipulating a gene of the M13 virus to make the viruses coat themselves in iron phosphate, the researchers created very small iron phosphate particles. (via BoingBoing)
  4. Amanda Palmer’s Label-Dropping Game — interesting email from Amanda Palmer to her fans about trying to get dropped from her label. i had to EXPLAIN to the so-called “head of digital media” of roadrunner australia WHAT TWITTER WAS. and his brush-off that “it hasn’t caught on here yet” was ABSURD because the next day i twittered that i was doing an impromptu gathering in a public park and 12 hours later, 150 underage fans – who couldn’t attend the show – showed up to get their records signed. no manager knew! i didn’t even warn or tell her! no agents! no security! no venue! we were in a fucking public park!
    life is becoming awesome.
    and then the times they are a-changing fucking dramatically, when pong-twittering with trent reznor means way more to your fan-base/business than whether or not the record is in fucking stores (and in my case, it ain’t in fucking stores).
Comments: 2
ETech Preview: Creating Biological Legos

ETech Preview: Creating Biological Legos

If you've gotten tired of hacking firewalls or cloud computing, maybe it's time to try your hand with DNA. That's what Reshma Shetty is doing with her Doctorate in Biological Engineering from MIT. Apart from her crowning achievement of getting bacteria to smell like mint and bananas, she's also active in the developing field of synthetic biology and has recently helped found a company called Gingko BioWorks which is developing enabling technologies to allow for rapid prototyping of biological systems. She will be giving a talk entitled, "Real Hackers Program DNA" at O'Reilly's Emerging Technologies Conference in March.

Comments: 23
Four short links: 9 Jan 2009

Four short links: 9 Jan 2009

Four questions, one per link: what next, can it solve a big problem, what’s the final boss for Python programming, and why on earth would anyone want yogurt that glows in the dark?

  1. End Times – gloomy piece on the future of journalism, to be added to the large pile of other gloomy pieces on the future of journalism (e.g., Bad News, Good News). The critical problem is still how to pay for journalism if the new media revenues are significant lower than old, and if the new media economics decree that journalism is dead then who fills the social good role that journalism’s death will leave?
  2. Ward Cunningham’s Visible Workings – an intriguing glimpse, from March last year, into the way Ward lays out web interactions. Nice system for laying out these interactions, but it’s also fascinating for how it makes transparent what will happen as a result of the data you submit. How scalable is this? Could it tackle privacy?
  3. Project Euler – fun programming exercises that require more than math to finish. We learn by doing, not by reading, so interesting exercises are part and parcel of training. It’s interesting to see educators are moving from being authors to being game designers, providing a series of staged challenges that make us stronger by defeating them. I’m presently dieing in as many ways as I can while learning iterators and generators in Python, as a way of ensuring I have Python’s “game physics” sussed.
  4. Rise of the Garage Genome Hackers – more on hobbyist molecular biology. It mentions DIYBio, the Cambridge biohacker collective that I first heard about at BioBarCamp. (via Glynn Moody)
Comments Off

Richard Jefferson Interviewed in Com Ciência

I enjoyed this interview with Richard Jefferson (caution: PDF) from Com Ciência No. 102, October 05, 2008. Richard runs CAMBIA, a group that fights for open innovation in biological sciences. He's particularly cautionary about the potential for patents to greatly restrict the development of Synthetic Biology (SB): But don't doubt there will be some very interesting biological understanding that emerges…

Comments Off

Auckland University Bioengineering Institute

I am an industry advisor to the Auckland University Bioengineering Institute and got a tour on Tuesday. It was inspirational! They sprawl over several floors of a tall concrete building in Auckland, expanding from their cramped one-floor presence. Everywhere you look there are people with soldering irons, laptops, and batteries working on devices that sit between hardware and biology. I've…

Comment: 1

Improving High School Science Education

As I read this fascinating NYTimes piece on a Florida teacher covering evolution, I was reminded of an interesting email exchange I had recently with Kevin Padian, a UC Berkeley professor in the Dept of Integrative Biology, and curator of the UC Museum of Paleontology. He was at Science Foo Camp, and afterward wrote in email: My area is evolution,…

Comments: 3