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.).

Megafeed
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).

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.

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

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).

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: www.3dscience.com, www.biodesignautomation.org)

Ethics of brainless humans

As a thought experiment, if it were possible, would it be ethical to make humans without brains for research purposes?

The idea arises since a more accurate model of humans for drug testing would be quite helpful. Drugs may work in mice, rats and monkeys but not in humans or in some humans but not others. Human biology is more complex and the detailed pathways and mechanisms are not yet understood.

Of course by definition, a brainless human is not really a human; a human form without a brain would be more equivalent to a test culture of liver cells than a cognitive agent.

Tissue culturing, regenerative medicine and 3D organ printing
The less contentious versions of the idea of growing brainless humans is currently under initial exploration in taking tissue from a human, growing it up in culture and testing drugs or other therapies on it. A further step up is regenerative medicine, producing artificial organs from a person’s cells such as the Wake Forest bladder and Gabor Forgacs 3D organ printing work.

Brain as executive agent may be required
The next steps for testing would be creating systems of interoperating tissue and organs (e.g.; how would this person’s heart and liver respond to this heart drug?) and possibly a complete collection of human biological systems sans brain. One obvious issue is that this might not even work since the brain is obviously a critical component of a human and that a brainless human could not be built, that some sort of executive organizing system like the brain would be needed. Also medical testing would need to include the impact on the brain and the brain’s role and interaction with the other biological systems and the drug.

Ethical but impractical
Where it is quite clear that generating a full living human for research purposes would be unethical, it is hard to argue that generating a brainless human, a complex collection of human biological systems without a brain, which is not really human and does not have consciousness or personhood, would be unethical. Certainly some arguments could be made to the contrary regarding the lack of specific knowledge about consciousness and concepts of personhood, but would seem to be outweighed.

Unlikely to arise
It is extremely unlikely that the situation of manufacturing brainless humans for research purposes would ever arise, first since a lot of testing and therapy may be possible with personalized tissue cultures and regenerative medicine, and informed by genomic and proteomic sequencing. Also, in an eventual era where it might be possible to construct a brainless human or a collection of live interacting tissues and organ systems, it would probably be more expedient to model the whole biological system digitally.

The biomolecular interface and the definition of living

Definitional and classification issues often arise in any field of heightened focus and progress (e.g.; what is a planet?). For the many fields integrating organic and inorganic materials, an interesting issue comes up as to what is the definition of life. Many different gradations of living things are emerging.

Some interesting new cases of living materials are the idea of organic sensors made of biomaterial placed on buildings, self-replicating crystals and biological scaffolding for stem cell grown organs and 3D tissue printing.

De novo materials synthesis
One exciting aspect of the living/non-living classification is the new synthesis of both organic and inorganic materials. Scientists are creating de novo engineered proteins and other biological materials, non-naturally occurring inorganic materials with superior properties using molecular manufacturing techniques and hybrid organic-inorganic materials, with the best of organic and inorganic properties in one object, for example rotaxanes which could be used in quantum computing.

Definition of integration
Not just the definition of what is living arises, but also the definition of the integration of organic and inorganic materials. Alan H. Goldstein proposes that a true integration of organic and inorganic material involves communicating back and forth, not just a system which has properties or components of both organic and inorganic systems.

The future of biomolecular interfaces

The future of biomolecular interfaces is probably a further blurring of the underlying substrates as the focus is more relevantly on the properties and requirements of any challenge at hand.

Ethics of the future: self-copies

Just as the future of science and technology is rife with legal opportunities and psychological study possibilities, so is it with ethical issues. One interesting example is the case of individuals having multiple copies of themselves, either embodied or digital.

1. Can I self-copy?

The first issue is how different societies will set norms and legal standards for having copies. The least offensive first level would be having a backup copy of mindfiles for emergency and archival purposes, much like computer backups at present. People take pictures and videos of their experiences, why not of their minds? The other end of the extreme would be the most liberal societies allowing all manner of digital and embodied copies. The notion of regulating copies brings up an interesting potential precedent, that currently, the creation of children is largely unregulated on a global basis.

2. When and where can I run my self-copy(ies)?

A second issue is, given copies, under what circumstances can and should they be run. A daily backup is quite different from unleashing hundreds of embodied copies of oneself. Physically embodied copies would consume resources just as any other person in the world and there would likely be some stiff initial regulations since national population doubling, trebling or more overnight would not likely be a useful shock to society. Not to mention the difficulty in quickly obtaining and assembling the required resources for a full human copy; despite the potential advances in 3D human tissue and organ home printers by then.

Digital copies is the more obvious opportunity for running self-copies and could be much more challenging to regulate. In the early days, the size and processing requirements of uncompressed mindfiles would likely be so large that a runtime environment would not be readily available on any home machine or network but would rather require a supercomputer.

3. Am I a copy?

A third interesting problem is whether it would be moral for copies to know that they are copies, and the related legal issues regarding memory redaction as explored in Wright's "Golden Age" trilogy. Depending how interaction between originals and copies is organized, it may not matter. Psychologically for the originals and the copies, it may matter a lot. The original may 'own' the copies or the copies may have self-determination rights. In the case of an embodied copy, it is hard not to argue for their full personhood but somehow a digital instance seems to have fewer rights, although it may come to be that shutting down an instance of a digital mind, even with a recent full memory backup and integration, is just as wrong as a physical homicide.

Interesting ethical issues could arise for originals and copies alike as to what to share with the others; should horrifying experiences be edited out as Brin's Kiln People do at times? There would be both benefits and costs to experiencing the death of a self-copy, for example. It would not seem ethical to make self-copies explicitly for scientific research purposes to garner information from their deaths, but it does seem fully ethical to have multiple self-copies for with different life styles, some healthier and some less healthy to investigate a) whether a healthy life style matters and b) to selfishly share exciting experiences from less risk averse copies back with the longer-lived healthier copy.

Indeed in the new medical era of a systemic understanding of health and disease where n=1, what better control examples to have than of yourself! However, epigenetic mutations and post-translational modifications may be much harder to equalize across copies than memories and experiences.

The issue of the definition of life arises as some people may want the abridged meta-message or take-away from experiences, indeed this is one of the great potential benefits of multiple copies, while others may wish to preserve the full resolution of all experiences. The standard could accommodate both, with the summary being the routine information transfer with the detail archived for on-demand access.

4. What can I do with my self-copies?

Societies might like to attempt to establish checks and balances to prevent originals from selling copies of themselves or others into slavery to reap economic benefits, as dystopially portrayed in Ballantyne's "Capacity". Especially in a potential realm of digital minds, there are many potential future challenges with rights determination and enforcement.

The 'AI abdication' defense is the argument that societies that are sufficiently advanced to have the ability to run self-copies would also have other advancements developed and in use such as some sort of consciousness sensor identifying existing and emerging sentient beings and looking after their well-being, a beneficent policing. There are numerous issues with the AI abdication defense, including its unlikely existence from a technical standpoint, whether humans would agree to use such a tool, whether a caregiving AI could be hacked and other issues. However, technology does not advance in a vacuum and society generally matures around technologies so it is likely that some detriment-balancing counter initiatives would exist.

For example, would it be moral to create sub-sentient beings as sex slaves or personal assistants? This may be an improvement over the current situation but is not devoid of moral issues. At some point, as more about consciousness has been characterized and defined, a list of intelligence stratifications and capabilities could be a standard societal tool. Animals, humans and AIs would be included at minimum. A future world with many different levels of sentience seems quite possible.

Next-gen computing for terabase transfer

The single biggest challenge presently facing humanity is the new era of ICT (information and communication technology) required to advance the progress of science and technology. This constitutes more of a grand challenge than do disease, poverty, climate change, etc. because solutions are not immediately clear, and are likely to be more technical than political in nature. The raw capacity in information processing and transfer is required and also the software to drive these processes at higher levels of abstraction to make the information useable and meaningful. The computing and communications industries have been focused on incremental Moore’s Law extensions rather than new paradigms and do not appear to be cognizant of the current needs of science, and particularly the magnitude.

Computational era of science
One trigger for a new ICT era is the shift in the way that science is conducted. The old trial and error lab experimentation has been supplemented with informatics and computational science for characterizing, modeling, simulating, predicting and designing. Life sciences is the most prominent area of science requiring ICT advances, for a variety of purposes including biological process characterization and simulation. Genomics is possibly the field with the most ICT urgency; genomic data is growing at 10x/year vs. Moore’s Law at 1.5x/year for example, however nearly every field of science has progressed to large data sets and computational models.

Mindfile deletion

How do you know that your mindfile will not be deleted, either on purpose or by accident? What would you do if your mindfile is stored in memory and not allowed to run? How would you know that you are not being run? Is not running the equivalent of being dead? How will you know that you are getting the processing power and bandwidth in your contract when reality is simulated and hardware test results could be simulated too?

There are at least two levels of challenges to address, akin to current physical world needs, first, survival needs and second, needs and rights when interacting with others.

Establishing rights for mindfiles
There will need to be ways to assure basic ‘human’ rights in a potential era of uploading brains to digital software files. There could be many misuses of massive databanks of mindfiles: they could be deleted at will (digital genocide) or by mistake by careless ISPs/data center managers, sold, kidnapped, copied, bred, hiveminded or discriminated against via less bandwidth and processing power. If the reality experienced by mindfiles is simulated, how would anyone know that the virtual reality they experience is the one they want to experience? A code or key could be created so that individual mindfiles could not be copied without the owners permission, agreement or knowing; perhaps like the telomere-shortening system used by biological cells. Pervasive externally run audit software could maintain lists of mindfile citizens (a future role for the nation-state) and periodically query each mindfile to determine its status and whether it is running. As usual, the white hats would need to stay ahead of the black hats.

Reducing naked Darwinism
With less transparency and social pressure, it is possible that the behavioral smoothing that has arisen in contemporary society would dissolve. Codes of conduct for mindfiles could be developed, probably with a much heightened awareness and refinement of the respectful treatment of consciousnesses. If virtuality is 100% sousveilled, this should not be a problem. In addition, mechanisms such as barriers, permissioning tiers and firewalled gardens could arise to prevent stronger minds from terrorizing and controlling weaker minds or different minds. The real goal would be to rearchitect social pressure in ways that are continually empowering to all individuals. Some mindfiles may prefer heavily controlled virtual environments, others may wish to venture onto the interstitial wildnets.