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February 25 2014

August 30 2013

Podcast: emerging technology and the coming disruption in design

On a recent trip to our company offices in Cambridge, MA, I was fortunate enough to sit down with Jonathan Follett, a principal at Involution Studios and an O’Reilly author, and Mary Treseler, editorial strategist at O’Reilly. Follett currently is working with experts around the country to produce a book on designing for emerging technology. In this podcast, Follett, Treseler, and I discuss the magnitude of the coming disruption in the design space. Some tidbits covered in our discussion include:

And speaking of that lab burger, here’s Sergey Brin explaining why he bankrolled it:

Subscribe to the O’Reilly Radar Podcast through iTunesSoundCloud, or directly through our podcast’s RSS feed.

July 12 2013

Podcast: George Church on genomics

A few weeks ago some of my colleagues and I recorded a conversation with George Church, a Harvard University geneticist and one of the founders of modern genomics. In the resulting podcast, you’ll hear Church offer his thoughts on the coming transformation of medicine, whether genes should be patentable, and whether the public is prepared to deal with genetic data.

Here’s how Church characterizes the state of genomics:

It’s kind of like ’93 on the Web. In fact, in a certain sense, it’s more sophisticated than electronics because we have inherited three billion years of amazing technology that was just like a spaceship that was parked in our back yard and we’re just reverse-engineering and probably not fully utilizing even the stuff that we’ve discovered so far.

A few other helpful links:

  • CRISPR technology, which might find applications in a handful of sub-fields of bioengineering
  • The Supreme Court’s 9-0 decision in Association for Molecular Pathology vs. Myriad Genetics, Inc. held that “A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated, but cDNA is patent eligible because it is not naturally occurring.”
  • Church founded PersonalGenomes.org to make genomic and health-record data freely available

On this podcast from O’Reilly Media: Tim O’Reilly, Roger Magoulas, Jim Stogdill, Mike Loukides, and Jon Bruner. Subscribe to the O’Reilly Radar podcast through iTunes or SoundCloud, or directly through our podcast’s RSS feed.

September 06 2012

Four short links: 6 September 2012

  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)

August 20 2012

DNA: The perfect backup medium

It wasn’t enough for Dr. George Church to help Gilbert “discover” DNA sequencing 30 years ago, create the foundations for genomics, create the Personal Genome Project, drive down the cost of sequencing,  and start humanity down the road of synthetic biology. No, that wasn’t enough.

He and his team decided to publish an easily understood scientific paper (““Next-generation Information Storage in DNA“) that promises to change the way we store and archive information. While this technology may take years to perfect, it provides a roadmap toward an energy efficient, archival storage medium with a host of built-in advantages.

The paper demonstrates the feasibility of using DNA as a storage medium with a theoretical capacity of 455 exabytes per gram. (An exabyte is 1 million terabytes.) Now before you throw away your massive RAID 5 cluster and purchase a series of sequencing machines, know that DNA storage appears to be very high latency. Also know that Church, Yuan Gao, and Sriram Kosuri are not yet writing 455 exabytes of data, they’ve started with a more modest goal of writing Church’s recent book on genomics to a 5.29 MB “bitstream,” here’s an excerpt from the paper:

We converted an html-coded draft of a book that included 53,426 words, 11 JPG images and 1 JavaScript program into a 5.27 megabit bitstream. We then encoded these bits onto 54,898 159nt oligonucleotides (oligos) each encoding a 96-bit data block (96nt), a 19-bit address specifying the location of the data block in the bit stream (19nt), and flanking 22nt common sequences for amplification and sequencing. The oligo library was synthesized by ink-jet printed, high-fidelity DNA microchips. To read the encoded book, we amplified the library by limited-cycle PCR and then sequenced on a single lane of an Illumina HiSeq.

If you know anything about filesystems, this is an amazing paragraph. They’ve essentially defined a new standard for filesystem inodes on DNA. Each 96-bit block has a 19-bit descriptor. They then read this DNA bitstream by using something called Polymerase Chain Reaction (PCR). This is important because it means that reading this information involves generating millions of copies of the data in a format that has been proven to be durable. This biological “backup system” has replication capabilities “built-in.” Not just that, but this replication process has had billions of years of reliability data available.

While this technology may only be practical for long-term storage and high-latency archival purposes, you can already see that this paper makes a strong case for the viability of this approach. Of all biological storage media, this work has demonstrated the longest bit stream and is built atop a set of technologies (DNA sequencing) that have been focused on repeatability and error correction for decades.

In addition to these advantages, DNA storage has other advantages over tape or hard drive — it has a steady-state storage cost of zero, a lifetime that far exceeds that of magnetic storage, and very small space requirements.

If you have a huge amount of data that needs to be archived, the advantages of DNA as a storage medium (once the technology matures) could quickly translate to significant cost savings. Think about the energy requirements of a data center that needs to store and archive an exabyte of data. Compare that to the cost of maintaining a sequencing lab and a few Petri dishes.

For most of us, this reality is still science fiction, but Church’s work makes it less so every day. Google is uniquely positioned to realize this technology. It has already been established that Google’s founders pay close attention to genomics. They invested an unspecified amount in Church’s Personal Genome Project (PGP) in 2008, and they have invested a company much closer to home: 23andme. Google also has a large research arm focused on energy savings and efficiency with scientists like Urs Hozle looking for new ways to get more out of the energy that Google spends to run data centers.

If this technology points the way to the future of very high latency, archival storage, I predict that Google will lead the way in implementation. It is the perfect convergence of massive data and genomics, and just the kind of dent that company is trying to make in the universe.

July 23 2012

Four short links: 23 July 2012

  1. Unmanned Systems North America 2012 — huge tradeshow for drones. (via Directions Magazine)
  2. On Thneeds and the Death of Display Ads (John Battelle) — the video interstitial. Once anathema to nearly every publisher on the planet, this full page unit is now standard on the New York Times, Wired, Forbes, and countless other publishing sites. And while audiences may balk at seeing a full-page video ad after clicking from a search engine or other referring agent, the fact is, skipping the ad is about as hard as turning the page in a magazine. And in magazines, full page ads work for marketers. If you’d raised a kid on AdBlocker, and then at age 15 she saw the ad-filled Internet for the first time, she’d think her browser had been taken over by malware. (via Tim Bray)
  3. The Most Important Social Network: GitHubI suspect that GitHub’s servers now contain the world’s largest corpus of commentary around intellectual production.
  4. Crowdfunded Genomics — a girl with a never-before-seen developmental disorder had her exome (the useful bits of DNA) sequenced, and a never-before-seen DNA mutation found. The money for it was raised by crowdfunding. (via Ed Yong)

June 07 2012

Four short links: 7 June 2012

  1. Electric Imp -- yet another group working on the necessary middleware for ubiquitous networked devices.
  2. How Big Data Transformed the Dairy Industry (The Atlantic) -- cutting-edge genomics company Illumina has precisely one applied market: animal science. They make a chip that measures 50,000 markers on the cow genome for attributes that control the economically important functions of those animals.
  3. The Curious Case of Internet Privacy (Cory Doctorow) -- I'm with Cory on the perniciousness of privacy-digesting deals between free sites and users, but I'm increasingly becoming convinced that privacy is built into business models and not technology.
  4. Chronoline (Github) -- Javascript to make a horizontal timeline out of a list of events.

July 28 2011

Four short links: 28 July 2011

  1. 23andMe Disproves Its Own Business Model -- a hostile article talking about how there's little predictive power in genetics for diabetes and Parkinson's so what's the point of buying a 23andMe subscription? The wider issue is that, as we've known for a while, mapping out your genome only helps with a few clearcut conditions. For most medical things that we care about, environment is critical too--but that doesn't mean that personalized genomics won't help us better target therapies.
  2. jsftp -- lightweight implementation of FTP client protocol for NodeJS. (via Sergi Mansilla)
  3. Really Bad Workshops -- PDF eBook with rock-solid advice for everyone who runs a workshop.
  4. PigEditor (GitHub) -- Eclipse plugin for those working with Pig and Hadoop. (via Josh Patterson)

June 28 2010

Four short links: 28 June 2010

  1. They Don’t Complain and They Die Quietly (Derek Powazek) -- In this hyper-modern age of real-time always-on location-based info-overload, perhaps a moment of true peace and quiet is the greatest gift one can receive.
  2. The Slow Media Manifesto -- Slow Media inspire, continuously affect the users’ thoughts and actions and are still perceptible years later. Steven Levy ran a Slow Media session at Foo. (via Bruce Sterling)
  3. The Dragon's DNA (The Economist) -- Beijing Genomics Institute putting more DNA-sequencing capacity into the top floor of a refurbished printing works than is available in the whole USA.
  4. Scribd Coding Blog -- very interesting blog about the technology behind and inside Scribd. They process over 150M polygons a day, building web fonts from the fonts in PDF files, and tell you why it's not straightforward. I wish there were more of these genuinely interesting technology blogs from companies that do interesting things.

June 25 2010

Four short links: 25 June 2010

  1. Membase -- an open-source (Apache 2.0 license) distributed, key-value database management system optimized for storing data behind interactive web applications. These applications must service many concurrent users; creating, storing, retrieving, aggregating, manipulating and presenting data in real-time. Supporting these requirements, membase processes data operations with quasi-deterministic low latency and high sustained throughput. (via Hacker News)
  2. Sergey's Search (Wired) -- Sergey Brin, one of the Google founders, learned he had a gene allele that gave him much higher odds of getting Parkinson's. His response has been to help medical research, both with money and through 23andme. Langston decided to see whether the 23andMe Research Initiative might be able to shed some insight on the correlation, so he rang up 23andMe’s Eriksson, and asked him to run a search. In a few minutes, Eriksson was able to identify 350 people who had the mutation responsible for Gaucher’s. A few clicks more and he was able to calculate that they were five times more likely to have Parkinson’s disease, a result practically identical to the NEJM study. All told, it took about 20 minutes. “It would’ve taken years to learn that in traditional epidemiology,” Langston says. “Even though we’re in the Wright brothers early days with this stuff, to get a result so strongly and so quickly is remarkable.”
  3. Startup.gov (YouTube) -- Anil Dash talk at Personal Democracy Forum on applying insights from startups to government. I hope the more people say this, the greater the odds it'll be acted on.
  4. Open Core Software -- Marten Mickos (ex-MySQL) talks up "open core" (open source base, proprietary extensions) as a way to resolve the conflict of "change the world with open source" and "make money". Brian Aker disagrees: There has been no successful launch of an open core company that has reached any significant size, especially of the size that Marten hints at in the article. My take: there are three reasons for open source (freedoms, price, and development scale) and if you close the source to part of your product then the whole product loses those benefits. If you open source enough that the open source bit has massive momentum, then you probably don't have enough left proprietary to gain huge financial benefit.

May 14 2010

March 29 2010

Four short links: 29 March 2010

  1. Salmon Protocol -- protocol to unite comments and annotations with original web pages. A distributed solution to the problem that Disqus tackles in a centralised fashion. Important because we'll all be historians of our earlier lives and dissipated prolific micro-content is a historian's nightmare.
  2. Gephi -- open source (GPLv3) interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. I believe tools for data exploration, versus static infographics, are the only way to develop a new sense for data. (via mattb on Delicious)
  3. Skinput -- a bio-acoustic sensor lets you use your skin to write, tap, drag, etc. See also BBC article. (via Mike Loukides)
  4. First Synthetic Genome Secret Messages Decoded (Wired) -- the first synthetic genome contained advertisements ("VENTNERINSTITVTE", "CRAIGVENTNER"). I can't figure out whether it's a cheeky easter egg in the finest geek tradition, or whether it's as if the Apollo 11 had "BUY COKE" on the side or Magellan's yachts had sails emblazoned with "VENETIAN GLASS: BEST IN THE WORLD!". (via christianbok on Twitter)

November 20 2009

November 10 2009

Four short links: 10 November 2009

  1. A children’s toy inspires a cheap, easy production method for high-tech diagnostic chips -- microfluidic chips (with tiny liquid-filled channels) can cost $100k and more. Michelle Khine used the Shrinky Dinks childrens' toy to make her own. "I thought if I could print out the [designs] at a certain resolution and then make them shrink, I could make channels the right size for micro­fluidics," she says. (via BoingBoing)
  2. Complete Genomics publishes in Science on low-cost sequencing of 3 human genomes (press release) -- The consumables cost for these three genomes sequenced on the proof-of-principle genomic DNA nanoarrays ranged from $8,005 for 87x coverage to $1,726 for 45x coverage for the samples described in this report. Drive that cost down! There's a gold rush in biological discovery at the moment as we pick the low-hanging fruit of gross correlations between genome and physiome, but the science to reveal the workings of cause and effect is still in its infancy. We're in the position of the 18th century natural philosophers who were playing with static electricity, oxygen, anaesthetics, and so on but who lacked today's deeper insights into physical and chemical structure that explain the effects they were able to obtain. More data at this stage means more low-hanging fruit can be plucked, but the real power comes when we understand "how" and not just "what". (via BoingBoing)
  3. Far From a Lab? Turn a Cellphone into a Microscope (NY Times) -- for some tests, you can use a camphone instead of a microscope. In one prototype, a slide holding a finger prick of blood can be inserted over the phone’s camera sensor. The sensor detects the slide’s contents and sends the information wirelessly to a hospital or regional health center. For instance, the phones can detect the asymmetric shape of diseased blood cells or other abnormal cells, or note an increase of white blood cells, a sign of infection, he said.
  4. Augmented reality helps Marine mechanics carry out repair work (MIT TR) -- A user wears a head-worn display, and the AR system provides assistance by showing 3-D arrows that point to a relevant component, text instructions, floating labels and warnings, and animated, 3-D models of the appropriate tools. An Android-powered G1 smart phone attached to the mechanic's wrist provides touchscreen controls for cueing up the next sequence of instructions. [...] The mechanics using the AR system located and started repair tasks 56 percent faster, on average, than when wearing the untracked headset, and 47 percent faster than when using just a stationary computer screen.

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