Gene Encyclopedia of all Life

A tremendous resource would be an open gene database of all of the genes present in eukaryotic, archaeal and bacterial life. There are several open genomic databases now but the information is organized around genomes and organisms rather than specific genes and gene function.

A gene database of all life is in the same vein as E.O. Wilson’s Encyclopedia of Life, but at the next level of detail. The Encyclopedia of Life hopes to provide a webpage with scientific information for every known species on Earth. The gene database would provide a webpage and scientific details for each gene present in life and include other information such as a cross reference to all of the different species in which the gene is expressed.

Merge the Entrez Genome Project and the PartsRegistry
The foundations and perhaps the vision and obviousness of a gene database of all life exist but not its targeted pursuit as a funded research priority. Existing genomics databases such as the U.S. NCBI’s Entrez Genome Project database could be extended and merged into one database that is more explicitly searchable by gene function, possibly joining forces with the PartsRegistry from synthetic biology which provides a homepage, datasheet and genomic sequence by gene or biological function.

NCBI’s Entrez Genome Project database genomic catalog of all life

Unifying the work of E.O. Wilson, Craig Venter, Penny Boston and Drew Endy
An interesting project would be the unification of the Encyclopedia of Life, genomics-by-organism databases and parts registry-by-gene databases together with the aggressive pursuit of cataloguing and sequencing newly discovered organisms and genes. A gene encyclopedia could rapidly extend human knowledge and facilitate the era of personalized medicine as these novel genes could have extensive application in human therapies and pharmaceuticals, energy, climate management, agriculture and other areas.

Tremendous novelty and diversity remains unstudied with species (E.O. Wilson), with organisms in the sea (Craig Venter), and with extremophile life in caves (Penny Boston); 70-90% novel organisms, most of which have not had any gene identification and sequencing, functional assessment and cataloging.

A data resource like a gene encyclopedia could also uplevel the research focus to analytics. It will be interesting to see if an era of fully fungible genes across life arises, how easy it is to transplant function and how function expresses differently in different life forms.

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...