Human microbiome and personalized medicine

In genomics, the eleventh annual meeting of Advances in Genome Biology and Technology (AGBT) was held February 24-27, 2010, and featured an eclectic mix of new research and bioinformatics tools. Genomic research was presented in a diversity of areas including human, animal, plant, and bacteria. Many research advances are coming from partnerships between one or more academic research teams together with commercial entities. The biggest buzz was around Pacific Biosciences, the 3rd generation sequencing darling, with their single-molecule real-time (SMRT) platform which is still on track for an estimated launch later this year. The platform could deliver a 30,000-fold improvement over current methods, and ultimately achieve sub-$100 whole human genome sequencing. Attendees were also wowed by 454 Roche’s bench top GS Junior System (initially announced in late 2009), making sequencing much quicker and easier, and priced at only $98,000 (a milestone for sequencing equipment which usually runs in the several hundreds of thousand dollars).

Sequencing data storage and transfer costs continue to increase with the computing industry still not cognizant of the whole new era of data processing and communications transfer that is necessary for Very Large Datasets. The NIH 1000 Genomes project, for example, is transferring many terabyte-sized files per day.

From a research standpoint, some of the most activity is in cancer genomics. A recent NIH study generated 100TB data sequencing a melanoma sample and a normal blood sample and has been refining the Most Probable Variant (MPV) Bayesian analysis method used to identify genetic mutations. Perhaps the most innovative new research activity is in RNA sequencing. Other specific findings of note are in the areas of the microbiome and genetic variation:

Human microbiome
The complex interactions between individual humans and their microbiomes could have a substantial impact on personalized medicine. In some cases of infectious disease in humans, the pathogenesis may be unknown 40-60% of the time (e.g.; respiratory disease, skin disease). Even rudimentary issues remain unsolved, for example, it may be undetectable from a simple blood draw showing staph infection whether the bacteria was on the skin surface or in the blood. Microbiome sequencing is allowing the identification of novel pathogens, and could also be useful at the human population level to assess the spread and mutation trajectory of pathogens.

Genetic variation: human and otherwise
The populations analyzed in human genome wide association studies are being expanded, with important findings for both ancestry reconstruction and medical genomics. Research was presented on African-American, Mexican-American, Bushmen, and Bantu genome studies. A deeper understanding of genetic variation is also being used to facilitate the selection of desirable qualities in agriculture and animal livestock. For example, a chicken sequencing project found 7 million unique SNPs, 5 million of which were novel, and several of which were useful in translational application.

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.

Massive info processing needed

Step function improvements in information processing and communications capabilities are needed now and in the future.

Massive amounts of data are becoming increasingly available and currently humanity only has narrowband access to these biomedical, genetic, astronomical, particle accelerator and other data sets.

Large and diverse data sets requiring storage, processing and upload/download will only continue to proliferate. For example, as the web goes 3-D, rapid video, audio and data download and upload are needed, as objects become IP tagged, sensor and RFID networks require instantaneous data collection and summarization.

Scientific philosophers such as Anders Sandberg correctly point to information processing capability as the main limit on any society's growth and development. To attain a new level and not just asymptote out on the current plateau, a re-envisioning of information processing is necessary.

As with energy, some alternatives are being explored at the fringes but there is no real replacement methodology on the horizon. Also as with energy, there may be a dearth of real progress until the present means is more substantially threatened, however this point is coming very soon in information processing as compared with energy.

Pace of Encephalization

Humans have so much in their brains and so little shared outside. This has to change for true intelligence and species advancement and there is a great opportunity in developing tools to facilitate this.

1) Communication and interaction are currently limited by the mindset of the individual

Human interaction is fragile and conditions have to arrive at some optimum before meaningful communication can take place. A physical presence is generally though increasingly less required. Certain mixes of other people must be there or not be there and trust which generally must be developed over time must be present.

Only the few people in close proximity circles to others [may] have some level of understanding of what is in human minds. Peers, those that share similar ideas and values, may have a deeper but still sparse knowledge.

2) Communication and interaction are currently limited by language as the dominant tool

Communication is necessarily governed by the narrowband of language. Language was certainly an amazing evolutionary advance when it arose but it is time for new communication tools. Language is essentially a few pithy comments trickling out of multi-dimensional plane of existence or thinking on a topic. Other options to language that would allow the permissioned knowing of value systems, beliefs and history would contribute to enriched communications. Mechanisms for sharing clusters of thought rather than individual ideas would also be a start.

Tools
Two types of additional tools are needed: more tools for creating and sharing content and better tools for making the content meaningful. Content has proliferated but step function increases are coming. Humans will be creating and sharing more and more personal content (ideas, creative endeavors, personal life details, how-tos, resources, etc.) on the Internet via blogs, video blogs, tumblelogs, lifeblogging, interactive lifecasting, twittering, FaceBook, LinkedIn and other new methods. Aggregation, summarization and abstraction tools (like meta tag clouds and jaiku-style diverse feed aggregation) will be increasingly important to mark content relevancy and make it findable and interactable.

Just like businesses are wikinomically learning that they should not have boundaries at the edge of their properties, employees and ideas, individuals will hopefully start to realize the great benefits of extending their personal content boundaries.

Land Grab on Free Local Voice

Who is not stampeding to AOL to take advantage of free personal local phone numbers with always-on voicemail as part of the firm's roll out of new free services? AOL tops already land-breaking voice services from Skype (free Internet-based call-in and call-out, free conferencing of up to five parties), Google Talk (free Internet-based call-in and call-out) and Yahoo Messenger ($0.02 per minute call out to non-Internet numbers).

Desirable area code phone numbers can be had for a matter of clicks. Phone numbers could proliferate as have email accounts and mobile devices. Bye-bye Ma Bell. Now we are just waiting for ubiquitous wireless broadband networks, oh, and the physical implantation of miniaturized communication devices.

The New Service Providers

The eventual squeeze-out of telcos and cable companies is starting to become clear, or at least the radically new model which threatens them. Since wireless bandwidth and storage are becoming so cheap in such massive scale, all kinds of new service providers can supplant telcos/cable, from individuals to municipalities. Many countries and municipalities have universal broadband coverage initiatives underway, California has, for example, the GBOB, gigabit or bust initiative. Old-world service providers are already scrambling as we see with the mighty AT&T succumbing to SBC's merger advances and Qwest attempting to snap up MCI. Home media centers are starting to supplant cable. There will start to be much more of teleco's display of litigation, their true core competency, and the direction set by the new FCC chairman will be important and hopefully pro-progress and pro-US competitiveness, anti-entrenchment.

With broadband a utility and perceived birthright, other individuals and companies will have the freedom to create a whole variety of applications and services, continuing the trend to personalized media from mass media.

Can widespread acceptance of ectogenesis be far behind?

The Internet is Getting Bigger Faster

In the future, we will have multiple networks with much greater profundity than we do today. Some refer to the 2005 Internet as the baby of what is to come and this may be understating it.

Some key things are starting to coalesce into hastening the bigger better Internet. First is the already-accomplished full text-indexing of the known online world by search engines. They do a good job of finding, organizing and serving up whatever is out there on demand. That is baseline.
Right now the second factor driving the improvement and the next architectural redefining of the communications networks is the exponential explosion of available information. Everyone is getting online and writing blogs, posting photos, sharing music and videos, creating podcasts, putting their collections of books/videos/media/etc. online (á la Delicious Monster and soon to be others with expanded functionality) and soon we will be putting all of our household and business objects online. Per Adam Bosworth, the information explosion scales all right at the web server and application server layers but forces a rethink of the database underlying everything into a different format with distributed information routers or information servers or other new ideas.

The third important phenomenon that is happening now is that more is possible because there is a critical mass of users on the Internet in more and more countries. Traders would say the market has become liquid in describing the feeling of presence one gets online for maybe the first time in late 2004. The sheer presence of others online is felt in such ways as selling items on Amazon almost immediately, finding online game players immediately from a variety of countries, and seeing that 1000 people update their blogs at blogger.com each 10 minutes at almost any time. In fact the depth and breadth of those out there is even bigger and more powerful than the biggest march on Tiananmen or Red Square. The Internet liquidity allows the development and test of myriad new applications benefiting large and small affinity groups.

Fourth, new Internet R&D projects can be mentioned. There are a lot of smart people trying to figure out what the communications networks of the future need to be like.

In summary, being in the continuum of search/universe management capability explosion, data explosion and participant explosion is driving the advent of a new tier of communications networks from the currently known Internet.

How to contribute to tech world

The science world is changing faster than ever now and will continue to speed up. One action for an individual to do is to try to keep up by learning about the technologies, innovation, changes, trends, current solutions and future problems in key areas like semiconductors, biotech, nanotech, physics and cosmology. Given the possible constraints of a non-science educational background, a generalist/macro not micro skillset and purview (e.g.; non-technical background, competence and interest) what are the obvious, useful and meaningful ways for an individual to participate in the massively evolving technology future?

Any role with a macro (e.g.; multi-topic) purview required is an interesting possibility. One category of roles is the popularizers, educators, explainers and evangelists/cheerleaders. Writers, synthesizers, presenters and thought-leaders with agendas are another category of roles, somehow a little more active, adding their views/vision to the explication role. Both of these categories involve other people as the consumer/observer of the content.

What are higher level categories that are more creative and content/info-generating, thereby potentially more worthwhile to certain value systems? Other forms of writing/creation: considering the implications of the technologies (though still may be heavily people/society-related), making a list of detailed predictions, adjusting life in expectation of the arrival of the technologies, drawing or other graphical abstraction of the technology or the implications of the technology. Inventing a new use or a new technology, like text-to-speech files for the iPod, is actively creating and participating. These days its easy to make or get a new technology idea made. Think about what you'd like to fix in your life and what are potential solutions. Keep a list of daily invention ideas.

Higher-level active writing, invention, ....more to come....