Bitcoin and Science: DNA is the Original Decentralized System

What is the role (if any) of Bitcoin and blockchain technology with regard to the natural world and traditional science? One obvious link is using the blockchain as a means of improving distributed community computing projects with tracking and remuneration. BOINC, whose software runs SETI@home, has introduced Gridcoin, and [Protein]Folding@home has introduced Foldingcoin. In addition, these distributed community computing models could be extended using blockchain technology as a way to coordinate and offer supercomputing time to DIYscientists; opening up access to a scarce resource which was previously only available to professional researchers (Zennet). Other projects are investigating a way to harness otherwise wasted crypto-mining cycles (where the computing problem (computing a nonce) must be deliberately intensive, wasteful, and one-way), like Primecoin’s system (http://primecoin.io/, of requiring miners to find long chains of prime numbers instead of otherwise unusable hashes.

Sense-making Models: Religion, Science, Political-Economy, Information
There is a more fundamental link between the blockchain and science in the grand scope of our human models for making sense of the world: religion, science, political-economy, and now information. Information is an interesting paradigm by which we are starting to see the structure of the world and make sense of it, both in physical and digital reality. The blockchain is an information technology, and the Internet and the blockchain provide a heightened information climate; a means of improving and modulating the resolution of information through faster more-expedient transfer, discovery, deployment, and use.

Information as a Sense-making Paradigm Reconfigures Science
The reach of information as a sense-making paradigm can be seen in how this idea is reconfiguring approaches to science. One way is in the growth and pervasiveness of big data and data-intensive science. Nearly every field of traditional study now has a computational complement (computational biology, computational astronomy, computational philosophy, computational law, etc.). The scientific method is transformed from a narrow hypothesis-experimentation loop to dynamic hypothesis formation per large-data results, vastly scaling the degree of experimental activity.

DNA: The Original Decentralized System
Even more profoundly, information is changing how we think about problems in science. For example, the old thinking was that chemistry and molecular biology are the conditions for life, and this is true in the sense that they are the substrate, the hardware for life. But now life is being seen as an information problem. Biology is a software system that runs on the substrate of chemistry and molecular biology. Wetware biology is the language of information, a software system to signal, transcribe, transmit information, encode and decode information, and send secure messages; a lot like a blockchain system. Biology is perhaps the original decentralized system; every cell has the full instruction set, the organism’s entire DNA, like Bitcoind nodes have the full ledger of every transaction.

Venter's Deep Linkage: Microbiome, Synbio, Genomics, and Computing

As usual, Craig Venter’s remarks on April 16, 2013 at UC Berkeley did not disappoint - they were inspirational, informative, and demonstrative of progress. Of note is the multidisciplinarity amongst different branches of his labs’ work, for example using synthetic DNA to perform genomic error correction in stem cell operations, genome transplantation between yeast and bacterial species, and linking microbiome activities to pathology and synthetic biology/biofuel synthesis. Some key points were:

• Microbiome – YASP (yet another sequencing problem) – While the human genome is currently thought to contain about 42,000 genes, the microbiome has 10 million genes across diverse phyla, taxa, and species 
• Biofuel – to obtain engineered algae with the desired phenotype that would be a viable alternative to oil, 300 parameters must be engineered 
• Gene function – even in the minimal genome for Mycoplasma genitalium, there are 50 genes whose function is unknown 
• New gene discovery – so far in general scientific discovery, 80 million genes have been found, 95% from ocean water sampling; again in these ‘design components for the future,’ function is unknown 
• ‘Digital phenotype’ is needed for health advance and big health data stream integration – an extended EMR with standardized transmittable digital data for all manner of phenotypic data, both phenotype 1.0 (e.g.; health history, prescriptions, lab results, etc.) and phenotype 2.0 (e.g.; digital omics profiles like proteomics and metabolomics).

Personal genome: data analysis challenge

Five themes emerged from the material presented at the 3rd annual personal genomes meeting at Cold Spring Harbor Laboratory held September 10-12, 2010.

First was the trend of family sequencing becoming more of a norm; looking at genetic disease as it is represented in trios, quartets or other family groups.

Second was the trend of increasingly common multi-level analysis, investigating traditional genotype data together with structural variation, expression data, pathways, and cell lines.

Third was the trend of greater breadth and sophistication in cancer genome analysis; the fledgling field of a few years ago now including dozens of sequenced cancer tumor genomes, the first cancer methylome, and cancer transcriptome analysis.

Fourth was the trend of the oft-heard challenge of scaling personal genome interpretation, making it automated, affordable, and actionable.

The fifth theme was the continued improvement in genome sequencing technology through new approaches such as quantum dot nanocrystal sequencing and strobe sequencing.

Unified health data climate

The future of health management and biosecurity is having always-on access to the health data climate of individuals, families, communities, and countries. A whole new era of health awareness and self-management could be possible. Ideally, health data streams would be automatically captured and parsed into a comprehensive tableau of status monitoring and action-taking.

Key health data streams (Figure 1):

1. Genome - whole human genome sequence, abnormal tissue sequences (cancer, etc.)
2. Phenotype - current status of a wide range of biophysical markers including blood-based organ-secreted proteins prognosticating disease, cholesterol levels, blood pressure, and emotional state
3. Diseasome - catalog of cumulative immune system exposures and predicted response to toxins
4. Microbiome - microflora bacteria profile (gut, genital, skin, oral, etc.)
5. Environmentome - external environment measures including air and water quality, pollen/allergens count

Figure 1: Key health data streams.

DNA - the real Identity 2.0

Right now is an exciting time with at least eleven advancing technologies that could have an even bigger impact than the Internet in the next fifty years. More than any other area, biotechnology is showing potential for revolutionary change with interesting recent developments in personal genome services, synthetic biology and online health portals.

Personal genome services
Genetically, humans are 99.9% the same. The variations can be referred to as SNPs, single nucleotide polymorphisms. Medical tests have existed to look for specific SNPs and there are now recently launched general tests, $1,000 personal DNA services from 23andme and deCODEme, to scan for up to 1 million known possible SNPs on an individual’s genome checking for 18 diseases such as cancer, diabetes and Parkinson's. Dr. Hsien-Hsien Lei writes an excellent blog tracking advances in DNA.

As with any new technology, reactions are myriad and stratified by age. Middle-aged and older people are far more reticent than younger people to try it. There are many open questions such as are we ready for the information? Will the information be substantive? What use is the information if it is not readily actionable? Given the high similarity of DNA amongst family members, is it most ethically appropriate to discuss the situation with relatives ahead of time? In any case, this is the first time the consumer can be in the driver's seat with their medical information in a powerful new way and

the appetite for personal genetic data may prove insatiable.

Of course it is always prudent and fun to consider the darker uses for new technology and one can imagine Identity Theft 2.0, when someone's DNA is stolen and a newly synthesized mix injected as a replacement, waking up and really not feeling like yourself...or worse, being injected with genes that cause all of your cells to de-differentiate back into stem cells!

Synthetic biology
Until last week, synthetic biologists had only been able to create small DNA segments from scratch using computer synthesizers but then genomic pioneer Craig Venter announced that his lab had synthesized the full genome of the smallest known bacterium. It contains 485 genes and has 582,970 base pairs making it roughly 2% the size of the human genome. So far, it has been difficult to synthesize full genomes because long strands of manufactured DNA have tended to break but this new method utilizes the DNA repair mechanism of yeast to stitch the full genome together. It also includes a watermark to tag the bacteria and a gene so that it won’t infect humans or animals.

There is considerable controversy about the future implications of the technology, somewhat similar to those at the advent of genetically-modified food. The desired endgame of Venter's synthetic biology and this advance is to create synthetic biofuels and organisms that could combat global warming by absorbing carbon emissions and other related high impact solutions to open challenges.

The potential applications could be wide-ranging as biological machines automatically persevere once set to task; clean water, nuclear and hazardous waste cleanup and food generation may also be within their purview, not to mention building repair and cleansing, human and animal grooming and nutrient and drug delivery, potentially rivaling the as yet not arrived nanotech mites in a multiplicity of tasks...

Online health portal
Microsoft launched its online health portal, HealthVault in October 2007, allowing people to centralize and store personal medical records and prescription history, manage records, upload data from medical devices such as blood pressure monitors, and analyze and manage the data. A similar offering from Google is expected sometime in 2008 and Adam Bosworth, formerly leading the Google health effort now how his own startup in the personal health services space, Keas.

These Web 2.0 information portals help people to aggregate and proactively manage their health information and will probably continue to add valuable services, especially mobile-device based; at a glance: news, stock tickers, blood pressure and caloric expenditure...