Sunday, August 30, 2009

Real-time unified search

It is surprising that a unified search application across different types of web content does not yet exist.

According to OneRiot, 40% of web searches at present are for real-time content such as that from Twitter, FaceBook, PeopleBrowsr, digg, bookmarking sites, blogging and microblogging sites (friendfeed, etc.).

One vision of a unified search 'megafeed' app would be a customizable html page with search across many types of web content, automatically updated and delivered together or organized into categories such as events, articles, comments, people, etc. The types of web content to search would be:

  • Traditional web search: Google, Bing, etc., which could be more richly granularized with content-tagging per a variety of parameters such as information type (news, blog, video, book, event, etc.), time (time added to web, time of occurrence), original vs. subsequent post and other distinctions.
  • Real-time web search: The emerging real-time content search engines should be extended and unified into one digital social interaction feed for Twitter, FaceBook, LinkedIn, bookmarking, email, blogging, microblogging and possibly IM/SMS notification AND response. User-permissioned credentials can be browser-stored for such a unified action platform. In addition to usability, the fast-growing real-time web search companies are also focused on monetization, reinventing generating AdSense-like models.
  • Local search: New restaurant and retail notifications, events, craigslist and other commercial postings of interest, friends traveling to the area (links to feeds from GeckoGo, Dopplr and other travel social networking and public calendaring websites).
  • Academic search: notification of new papers, articles or news. Federated PubMed, ArXiv-like journal portals are needed for all academic fields, including economics and liberal arts.
  • Multimedia search: notification of non-text postings of photo, music, podcast and video content.

Content demand mechanisms: ambience to supersede keywords
Content could be searched by the usual user-entered keywords or a deeper variety of content demand-interaction mechanisms could be developed, for example, permissioning-in by users such that ambient profiles from hard-drive content and previous web interactions automatically form and evolve (a precursor to pre-AI web interactions).

Sunday, August 23, 2009

Automatic Markets

At Singularity University, one of the most pervasive memes was the “routing packets” metaphor; that many current activities are just like routing packets on the Internet. This includes areas such as people in driverless cars, electrons in electric vehicle charging and power entry, load-balancing, routing and delivery on smartgrid electricity networks.

Fungible resources and quantized packet-routing
The packet-routing concept could be extended to neurons (routed in humans or AIs), clean water, clean air, food, disease management, health care system access and navigation, and in the farther future, information (neurally-summoned) and emotional support (automatically-summoned per human dopamine levels from nearby people or robots). It is all routing…directing quantized fungible resources to where they are needed and requested.

Automatic Markets
Since these various resources are not uniformly demanded, the idea of markets as a resource allocation mechanism is immediately obvious.

Further that automated, or automatic markets with pre-specified user preferences, analogous to limit orders, could be optimum. Markets could meet in equilibrium and transact, buying, selling, and adjusting automatically per evolving conditions and pre-programmed user profiles, permissions, and bidding functions.

Truly smart grids would have automatic bidding functions (as a precursor to more intelligence-like utility functions) that would indicate preferences and bid and equalize resource allocation, the truly invisible digital hand.

The key parameters of a working market, liquidity, price discovery and ease of exchange would seem to be present in these cases with large numbers of participants and market monitoring and bidding via web or SMS interfaces. The next layer, secondary markets and futures and options could also evolve as an improvement to market efficiency, if designed with appropriate incentives.

Automatic markets are not without flaw, they exist now in traditional financial markets, causing occasional but volatile disruptions in the form of quantitative program-trading (blamed for exacerbating the 1987 Black Monday stock market crash) and flash-trading. Speculative aspects are not trivial and would be a critical area for market designers to watch, particularly managing for high liquidity and equal access (e.g.; faster Internet connections do not matter).

Markets to grow as a digitized resource allocation tool
At present, markets are not pervasive in life. The most notable examples are traditional financial markets, eBay, peer-to-peer finance websites and prediction markets. Being in a global digital era with the ability to use resources in a more fungible and transferable way could further promulgate the use of markets as a resource allocation tool.

A focus on preference rather than monetary value, and other currencies such as attention, authority, trust, etc. could vastly extend the range of implementation of market principles.

Sunday, August 16, 2009

iPhone Biodefense App

Right now it would be nice for people to be able to perform a detailed inspection of whatever environment they are in, and of themselves internally. As the future evolves, it could become an exigency. Portable personal biosensing devices for biothreat defense and medical self-diagnosis could become de rigueur, most logically as an extension of current mobile device platforms.

Hardware Requirements:

  • Integrated Lab-on-a-chip module with flow cytometer, real-time PCR, microarray and sequencing unit (genome, proteome, metabolome, lipidome, etc.)
  • Disposable finger-prick lancets
Software Requirements:
  • Data is collected and perhaps digitized locally, then transmitted for processing and interpretation via web services
What is the current status of the iPhone Biodefense App?
  • A. Order online
  • B. DIY with components from Fry’s
  • C. Have a roadmap, getting supplies and building tools
  • D. Homesteads and landgrab available to pioneers
  • E. “Ahead of the science,” aka it’s always 20 years out!
Answer: C. Have a roadmap, getting supplies and building tools
Single-cell identification, extraction and genotyping is starting to be possible from a research perspective (ex: Love Lab, MIT). Lab-on-a-chip functionality has been miniaturized (e.g.; small flow cytometers, small PCR machines). Now the trick is to integrate and add features to these systems, extend the functionality, shrink them further and reduce constraints. Microarrays and sequencing also have several innovation cycles ahead.

Key constraint: time
In addition to moving down the cost curve (most relevant for sequencing), performance time is the key constraint. Substances, expressed genes, blood biomarkers, etc. can be detected but it is taking hours and days when it needs to be immediate.

Declassify custom biodefense microarrays
Lawrence Livermore National Laboratory has one of the most advanced biodefense labs in the country. Custom microarrays have been developed for government agencies that the lab would now like to transfer into the public health domain. This could revolutionize and hasten commercial biosensing applications much like the declassification of adaptive optics revolutionized astronomy. At least three custom microarrays have been developed:
  • Microbial Detection Array: identify what a substance is
  • Virulence Array: identify how much damage a substance could do
  • Microbial Defense Genotyping Array: identify SNPs, indels

Sunday, August 09, 2009

Open Global Courseware

The U.K., long an adopter of surveillance technology, announced recently that high-definition CCTV cameras from Classwatch have been installed in 94 schools. The result has been improved classroom management and there are plans to install hundreds more cameras nationwide in primary and secondary schools.

Free global education resource
With minimal effort, this internal surveillance initiative could be expanded into a worldwide sousveillance victory. A global education resource could be generated by broadcasting and archiving the live feeds to the web for access by teachers and students worldwide in their own classrooms and via cell phones. This is essentially an extension of MIT’s open courseware concept.

Language imperialism and the return of the British Empire?
The U.K. might briefly enjoy the notion of re-establishing the British Empire by exporting English-language education, but

language is becoming more fungible over time
The issue of language imperialism could be avoided with the use of audio translation tools (Google Translate – audio version?) and by opting in CCTV broadcasts from schools in other countries. The pilot project phases could be U.K. transmissions targeted at India and Beijing, etc. transmissions targets at rural Chinese schools.

PenPal 2.0 flattens the world
Classroom broadcasts could quickly become interactive with commenting and messaging on the streams. Students worldwide could get to know each other and work on team projects together in virtual world classrooms like Second Life’s Teen Grid; a multi-dimensional PenPal 2.0. Students in India could come up with ideas to work on problems in the U.K. by interviewing British students and vice versa. Teacher and student exchange programs could arise. Students could vote on the curriculum.
The real way to raise test scores would be to have live head-to-head competitions between different schools in a district, country or around the world (“The class in Chennai did 5% better….”).

Local community engagement tool
Internet broadcast could also enable the local community. Parents could tune in to their children’s classrooms (“Mom, did you see what I did around 10:30?”…”What happened at school today?” “Mom, just watch the feed archive…”). The social networking dimension could deepen student, teacher and parent interaction as many are already managing homework assignments colaboratively on the web.

American Idol Teacher: injecting abundance
Classroom broadcast could bring more abundance to teaching by providing acknowledgement (whuffie) for good teachers. Innovative and engaging teachers could reach a global audience and become YouTube celebrities. There could be competitions for the Best Teacher of the Pythagorean theorem, Best Teacher in Swindon, etc. as nominated through video clips. Videos could be linked to teacher ranking websites. From a policy perspective, education could become easier to evaluate and standardize. Countrywide best practices could be culled to train new teachers.

Conclusion: inevitablility of full-life recording
It seems inevitable that video surveillance/sousveillance will increasingly penetrate public and private areas for a variety of reasons ranging from safety and crime control to life-logging. One classic opposition argument is that recording inhibits ‘natural’ behavior, however most people quickly forget and adjust and it could be likely that the ongoing recording of society will advance without much opposition as long as there is a balance between surveillance and sousveillance (e.g.; there is popular access to the technologies and streams).

Sunday, August 02, 2009

Bio-design automation and synbio tools

The ability to write DNA could have an even greater impact than the ability to read it. Synthetic biologists are developing standardized methodologies and tools to engineer biology into new and improved forms, and presented their progress at the first-of-its-kind Bio-Design Automation workshop (agenda, proceedings) in San Francisco, CA on July 27, 2009, co-located with the computing industry’s annual Design Automation Conference. As with many areas of technological advancement, the requisite focus is on tools, tools, tools! (A PDF of this article is available here.)

Experimental evidence has helped to solidify the mindset that biology is an engineering substrate like any other and the work is now centered on creating standardized tools that are useful and reliable in an experimental setting. The metaphor is very much that of computing: just as most contemporary software developers work at high levels of abstraction and need not concern themselves with the 1s and 0s of machine language, in the future, synthetic biology programmers would not need to work directly with the Ac, Cs, Gs and Ts of DNA or understand the architecture of promoters, terminators, open reading frames and such. However, with synthetic biology being in its early stages, the groundwork to define and assemble these abstraction layers is currently at task.

Status of DNA synthesis
At present, the DNA synthesis process is relatively unautomated, unstandardized and expensive ($0.50-$1.00 per base pair (bp)); it would cost $1.5-3 billion to synthesize a full human genome. Synthesized DNA, which can be ordered from numerous contract labs such as DNA 2.0 in Menlo Park, CA and Tech Dragon in Hong Kong, has been following Moore’s Law (actually faster than Moore’s Law Carlson Curves doubling at 2x/yr vs. 1.5x/yr), but is still slow compared to what is needed. Right now short oligos, oligonucleotide sequences up to 200 bp, can be reliably synthesized but a low-cost repeatable basis for genes and genomes extending into the millions of bp is needed. Further, design capability lags synthesis capability, being about 400-800-fold less capable and allowing only 10,000-20,000 bp systems to be fully forward-engineered at present.

So far, practitioners have organized the design and construction of DNA into four hierarchical tiers: DNA, parts, devices and systems. The status is that the first two tiers, DNA and parts (simple modules such as toggle switches and oscillators), are starting to be consistently identified, characterized and produced. This is allowing more of an upstream focus on the next two tiers, complex devices and systems, and the methodologies that are needed to assemble components together into large-scale structures, for example those containing 10 million bp of DNA.

Standardizing the manipulation of biology
A variety of applied research techniques for standardizing, simulating, predicting, modulating and controlling biology with computational chemistry, quantitative modeling, languages and software tools are under development and were presented at the workshop.

Models and algorithms
In the models and algorithms session, there were some examples of the use of biochemical reactions for computation and optimization, performing arithmetic computation essentially the same way a digital computer would. Basic mathematical models such as the CME (Chemical Master Equation) and SSA (Stochastic Simulation Algorithm) were applied and extended to model, predict and optimize pathways and describe and design networks of reactions.

Experimental biology
The experimental biology session considered some potential applications of synthetic biology, first the automated design of synthetic ribosome binding sites to make protein production faster or slower (finding that the translation rate can be predicted if the Gibbs free energy (delta G) can be predicted). Second, an in-cell disease protection mechanism was presented where synthetic genetic controllers were used to prevent the lysis normally occurring in the lysis-lysogeny switch turned on in the disease process (lysogeny is the no-harm state and lysis is the death state).

Tools and parts
In the tools and parts session, several software-based frameworks and design tools were presented, many of which are listed in the software tools section below.

Languages and standardization
The languages and standardization session had discussions of language standardization projects such as the BioStream language, PoBol (Provisional BioBrick Language) and the BioBrick Open Language (BOL).

Software tools: a SynBio CrunchUp
Several rigorous computer-aided design and validation software tools and platforms are emerging for applied synthetic biology, many of which are freely available and open-source.

  • Clotho: An interoperable design framework supporting symbol, data model and data structure standardization; a toolset designed in a platform-based paradigm to consolidate existing synthetic biology tools into one working, integrated toolbox
  • SynBioSS - Synthetic Biology Software Suite: A computer-aided synthetic biology tool for the design of synthetic gene regulatory networks; computational synthetic biology
  • RBS Calculator: A biological engineering tool that predicts the translation initiation rate of a protein in bacteria; it may be used in Reverse Engineering or Forward Engineering modes
  • SeEd - Sequence Editor (work in progress): A tool for designing coding sequence alterations, a system conceptually built around constraints instead of sequences
  • Cellucidate: A web-based workspace for investigating the causal and dynamic properties of biological systems; a framework for modeling modular DNA parts for the predictable design of synthetic systems
  • iBioSim: A design automation software for analyzing biochemical reaction network models including genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems
  • GenoCAD: An experimental tool for building and verifying complex genetic constructs derived from a library of standard genetic parts
  • TinkerCell: A computer-aided design software for synthetic biology

Future of BioCAD
One of the most encouraging aspects in the current evolution of synthetic biology is the integrations the field is forging with other disciplines, particularly electronics design and manufacture, DNA nanotechnology and bioinformatics.

Scientists are meticulously applying engineering principles to synthetic biology and realize that novel innovations are also required since there are issues specific to engineering biological systems. Some of these technical issues include device characterization, impedance, matching, rules of composition, noise, cellular context, environmental conditions, rational design vs. directed evolution, persistence, mutations, crosstalk, cell death, chemical diffusion, motility and incomplete biological models.

As it happened in computing, and is happening now in biology, the broader benefit of humanity having the ability to develop and standardize abstraction layers in any field can be envisioned.
Clearly there will be ongoing efforts to more granularly manipulate and create all manner of biology and matter. Some of the subsequent areas where standards and abstraction hierarchies could be useful, though not immediate, are the next generations of computing and communications, molecular nanotechnology (atomically precise matter construction from the bottom up), climate, weather and atmosphere management, planet terraforming and space colony construction.

(Image credits:,