"bio" entries

Four short links: 11 November 2013

Four short links: 11 November 2013

Squid in the Dark, Beautiful Automation, Fan Criticism, and Petabyte Queries

  1. Living Light — 3D printed cephalopods filled with bioluminescent bacteria. PAGING CORY DOCTOROW, YOUR ORGASMATRON HAS ARRIVED. (via Sci Blogs)
  2. Repacking Lego Batteries with a CNC Mill — check out the video. Patrick programmed a CNC machine to drill out the rivets holding the Mindstorms battery pack together. Coding away a repetitive task like this is gorgeous to see at every scale. We don’t have to teach our kids a particular programming language, but they should know how to automate cruft.
  3. My Thoughts on Google+ (YouTube) — when your fans make hatey videos like this one protesting Google putting the pig of Google Plus onto the lipstick that was YouTube, you are Doin’ It Wrong.
  4. Presto: Interacting with Petabytes of Data at Facebooka distributed SQL query engine optimized for ad-hoc analysis at interactive speed. It supports standard ANSI SQL, including complex queries, aggregations, joins, and window functions. For details, see the Facebook post about its launch.
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Four short links: 23 August 2013

Four short links: 23 August 2013

The Internet of Americas, Pharma Pricey, Who's Watching, and Data Mining Course

  1. Bradley Manning and the Two Americas (Quinn Norton) — The first America built the Internet, but the second America moved onto it. And they both think they own the place now. The best explanation you’ll find for wtf is going on.
  2. Staggering Cost of Inventing New Drugs (Forbes) — $5BB to develop a new drug; and subject to an inverse-Moore’s law: A 2012 article in Nature Reviews Drug Discovery says the number of drugs invented per billion dollars of R&D invested has been cut in half every nine years for half a century.
  3. Who’s Watching You — (Tim Bray) threat modelling. Everyone should know this.
  4. Data Mining with Weka — learn data mining with the popular open source Weka platform.
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Four short links: 30 July 2013

Four short links: 30 July 2013

Transit and Peering, Quick Web Interfaces, Open Source Licensing, and RC Roach

  1. Why YouTube Buffers (ArsTechnica) — When asked if ISPs are degrading Netflix and YouTube traffic to steer users toward their own video services, Crawford told Ars that “the very powerful eyeball networks in the US (and particularly Comcast and Time Warner Cable) have ample incentive and ability to protect the IP services in which they have economic interests. Their real goal, however, is simpler and richer. They have enormous incentives to build a moat around their high-speed data networks and charge for entry because data is a very high-margin (north of 95 percent for the cable companies), addictive, utility product over which they have local monopoly control. They have told Wall Street they will do this. Yes, charging for entry serves the same purposes as discrimination in favor of their own VOD [video-on-demand], but it is a richer and blunter proposition for them.”
  2. Ink — MIT-licensed interface kit for quick development of web interfaces, simple to use and expand on.
  3. Licensing in a Post-Copyright WorldThis article is opening up a bit of the history of Open Source software licensing, how it seems to change and what we could do to improve it. Caught my eye: Oracle that relicensed Berkeley DB from BSD to APGLv3 [… effectively changing] the effective license for 106 other packages to AGPLv3 as well.
  4. RC Cockroaches (Vine) — video from Dale Dougherty of Backyard Brains Bluetooth RoboRoach. (via Dale Dougherty)
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Four short links: 26 June 2013

Four short links: 26 June 2013

Neural Memory Allocation, DoD Synthbio, Sierra Leone Makers, and Complex Humanities Networks

  1. Memory Allocation in Brains (PDF) — The results reviewed here suggest that there are competitive mechanisms that affect memory allocation. For example, new dentate gyrus neurons, amygdala cells with higher excitability, and synapses near previously potentiated synapses seem to have the competitive edge over other cells and synapses and thus affect memory allocation with time scales of weeks, hours, and minutes. Are all memory allocation mechanisms competitive, or are there mechanisms of memory allocation that do not involve competition? Even though it is difficult to resolve this question at the current time, it is important to note that most mechanisms of memory allocation in computers do not involve competition. Does the dissector use a slab allocator? Tip your waiter, try the veal.
  2. Living Foundries (DARPA) — one motivating, widespread and currently intractable problem is that of corrosion/materials degradation. The DoD must operate in all environments, including some of the most corrosively aggressive on Earth, and do so with increasingly complex heterogeneous materials systems. This multifaceted and ubiquitous problem costs the DoD approximately $23 Billion per year. The ability to truly program and engineer biology, would enable the capability to design and engineer systems to rapidly and dynamically prevent, seek out, identify and repair corrosion/materials degradation. (via Motley Fool)
  3. Innovate Salone — finalists from a Sierra Leone maker/innovation contest. Part of David Sengeh‘s excellent work.
  4. Arts, Humanities, and Complex Networks — ebook series, conferences, talks, on network analysis in the humanities. Everything from Protestant letter networks in the reign of Mary, to the repertory of 16th century polyphony, to a data-driven update to Alfred Barr’s diagram of cubism and abstract art (original here).
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Four short links: 24 June 2013

Four short links: 24 June 2013

Location Data, Online Science, Mythbusting for Education, and Cheap Music For All

  1. Reading Runes in Animal Movement (YouTube) — accessible TEDxRiverTawe 2013 talk by Professor Rory Wilson, on his work tracking movements of animals in time and space. The value comes from high-resolution time series data: many samples/second, very granular.
  2. Best Science Writing Online 2012 (Amazon) — edited collection of the best blog posts on science from 2012. Some very good science writing happening online.
  3. Designing Effective Multimedia for Physics Education (PDF) — Derek Muller’s PhD thesis, summarised as “mythbusting beats lectures, hands down”. See also his TED@Sydney talk.
  4. Melomics — royalty-free computer-generated music, all genres, for sale (genius business model). Academic spinoff from Dr. Francisco J. Vico’s work at UMA in Spain.
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Four short links: 21 May 2013

Four short links: 21 May 2013

Videogame Hyperinflation, Thumbdrive Computing, Distributed Consensus, and Organism Simulation

  1. Hyperinflation in Diablo 3 — interesting discussion about how video games regulate currency availability, and how Diablo 3 appears to have messed up. several weeks after the game’s debut a source claimed that there were at least 1,000 bots active 24/7 in the Diablo 3 game world, allegedly “harvesting” (producing) 4 million virtual gold per hour. Most of the gold generated by the ruthlessly productive, rapidly adapting bots found its way to third party vendors in a black market which undercut the prices in the sanctioned, in-game auction houses.
  2. Dell Project Ophelia (PC World) — $100 USB-stick-sized Android computer.
  3. Call Me Maybe (Kyle Kingsbury) — a series on network partitions. We’re going to learn about distributed consensus, discuss the CAP theorem’s implications, and demonstrate how different databases behave under partition.
  4. OpenWorm (The Atlantic) — simulating the c. elegans nematode worm in software. OpenWorm isn’t like these other initiatives; it’s a scrappy, open-source project that began with a tweet and that’s coordinated on Google Hangouts by scientists spread from San Diego to Russia. If it succeeds, it will have created a first in executable biology: a simulated animal using the principles of life to exist on a computer.
Comments: 2

Glowing Plants

I just invested in BioCurious’ Glowing Plants project on Kickstarter. I don’t watch Kickstarter closely, but this is about as fast as I’ve ever seen a project get funded. It went live on Wednesday; in the afternoon, I was backer #170 (more or less), but could see the number of backers ticking upwards constantly as I watched. It was fully funded for $65,000 Thursday; and now sits at 1340 backers (more by the time you read this), with about $84,000 in funding. And there’s a new “stretch” goal: if they make $400,000, they will work on bigger plants, and attempt to create a glowing rose.

Glowing plants are a curiosity; I don’t take seriously the idea that trees will be an alternative to streetlights any time in the near future. But that’s not the point. What’s exciting is that an important and serious biology project can take place in a biohacking lab, rather than in a university or an industrial facility. It’s exciting that this project could potentially become a business; I’m sure there’s a boutique market for glowing roses and living nightlights, if not for biological street lighting. And it’s exciting that we can make new things out of biological parts.

In a conversation last year, Drew Endy said that he wanted synthetic biology to “stay weird,” and that if in ten years, all we had accomplished was create bacteria that made oil from cellulose, we will have failed. Glowing plants are weird. And beautiful. Take a look at their project, fund it, and be the first on your block to have a self-illuminating garden.

Comments: 4
Four short links: 11 April 2013

Four short links: 11 April 2013

Automating NES Games, Code Review Tool, SaaS KPIs, and No Free Lunch

  1. A General Technique for Automating NES Gamessoftware that learns how to play NES games and plays them automatically, using an aesthetically pleasing technique. With video, research paper, and code.
  2. rietveld — open source tool like Mondrian, Google’s code review tool. Developed by Guido van Rossum, who developed Mondrian. Still being actively developed. (via Nelson Minar)
  3. KPI Dashboard for Early-Stage SaaS Startups — as Google Docs sheet. Nice.
  4. Life Without Sleep — interesting critique of Provigil as performance-enhancing drug for information workers. It is very difficult to design a stimulant that offers focus without tunnelling – that is, without losing the ability to relate well to one’s wider environment and therefore make socially nuanced decisions. Irritability and impatience grate on team dynamics and social skills, but such nuances are usually missed in drug studies, where they are usually treated as unreliable self-reported data. These problems were largely ignored in the early enthusiasm for drug-based ways to reduce sleep. […] Volunteers on the stimulant modafinil omitted these feedback requests, instead providing brusque, non-question instructions, such as: ‘Exit West at the roundabout, then turn left at the park.’ Their dialogues were shorter and they produced less accurate maps than control volunteers. What is more, modafinil causes an overestimation of one’s own performance: those individuals on modafinil not only performed worse, but were less likely to notice that they did. (via Dave Pell)
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Four short links: 24 January 2013

Four short links: 24 January 2013

Google's Autonomous Cars, DIY BioPrinter, Forms Validation, and Machine Learning Workflow

  1. Google’s Driverless Car is Worth Trillions (Forbes) — Much of the reporting about Google’s driverless car has mistakenly focused on its science-fiction feel. […] In fact, the driverless car has broad implications for society, for the economy and for individual businesses. Just in the U.S., the car puts up for grab some $2 trillion a year in revenue and even more market cap. It creates business opportunities that dwarf Google’s current search-based business and unleashes existential challenges to market leaders across numerous industries, including car makers, auto insurers, energy companies and others that share in car-related revenue.
  2. DIY BioPrinter (Instructables) — Think of it as 3D printing, but with squishier ingredients! How to piggyback on inkjet printer technology to print with your own biomaterials. It’s an exciting time for biohackery: FOO Ewan Birney is kicking ass and taking names, he was just involved in a project storing and retrieving data from DNA.
  3. Parsley — open-sourced forms validation library in Javascript.
  4. ADAMS — open sourced workflow tool for machine learning, from the excellent people at Waikato who brought you WEKA. ADAMS = Advanced Data mining And Machine learning System.
Comment: 1
Four short links: 6 September 2012

Four short links: 6 September 2012

Human Genome Doxed, Programmed by Movies, CritterDrones, and Responsive Websites

  1. ENCODE Project — International project (headed by Ewan Birney of BioPerl fame) doxes the human genome, bigtime. See the Nature piece, and Ed Yong’s explanation of the awesome for more. Not only did they release the data, but also the software, including a custom VM.
  2. 5 Ways You Don’t Realize Movies Are Controlling Your Brain — this! is! awesome!
  3. RC Grasshoppers — not a band name, an Israeli research project funded by the US Army, to remotely-control insects in flight. Instead of building a tiny plane whose dimensions would be measured in centimeters, the researchers are taking advantage of 300 million years of evolution.
  4. enquire.js — small Javascript library for building responsive websites. (via Darren Wood)
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