Sunday, February 28, 2010

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.

Sunday, February 21, 2010

Technology shapes man or man shapes technology?

An interesting philosophical question to probe is the nature of technology. One view is that technology is simply tools that humanity has created to further its will, to enable and reinforce human nature and evolutionary tendencies. Another view is that there are places of crossover, where technology can actually change humans, human nature, and biological drives, both unintentionally and by design.

In the contemporary era of exponentially growing technologies in multiple fields, it is critical to understand what sorts of impacts different technologies may have. One analysis framework is to group technologies by those which could have an immediate direct influence on human morphology, and those that would not. For example, there could be the rapid advent of significantly more dramatic technologies than have been experienced to date. While these new technologies could change some aspects of life, human biological drives could remain unchanged, and therefore the structure and dynamics of human societal organization, interaction, and goal pursuit could also remain unchanged. Some examples of these advances could include the realization of molecular nanotechnology, quantum computing, cold fusion, and immortality. Even with several of these technologies implemented, in the seemingly different world of a post-scarcity economy where material goods and energy would be essentially free, humanity could still be ordered around the same familiar biologically-driven goals.

The other group of technologies is those which could possibly have a near-term impact on the structure and form of what it means to be human. The area with the greatest possible change is improving human mental capability. There have been several significant advances in a variety of neurology-related fields in the last few years that if ultimately realized, could potentially alter human morphology. Even the resolution of all mental pathologies such as Parkinson’s disease, depression, stroke rehabilitation, and addiction would constitute morphological change at a basic level. Augmenting cognition and deliberately managing biophysical states would constitute morphological change at other levels.

Sunday, February 14, 2010

Mental enhancement through neuroimaging

In The Neuro Revolution, Zack Lynch contends that there is a coming revolution in neuroimaging technology that could be on the same order as the industrial revolution and the information revolution.

1. Neuroimaging for truth detection
Perhaps the most important application area for neuroimaging is truth detection. According to Joel Huizenga, CEO of NoLieMRI, the annual worldwide market is $36 billion for truth verification. The U.S. government does 40,000 lie detection tests per day, and the Supreme Court acceptance standard is results that have a 95% chance of accuracy. Businesses buy 400,000 tests per year, some of which only have 50% accuracy. FMRIs are much better lie detectors than current tests. Mechanically, more blood goes to other parts of the brain which are related to deception when someone is lying. Explicit lie detection is one demand area but truth verification is much broader. The notion of brain fingerprinting can be used to detect the presence or absence of information in the brain, for example testing knowledge of crime scene details.

2. Neuroimaging for mental illness assessment and rehabilitation
A second important application area for neuroimaging is mental illness identification and rehabilitation. A government-sponsored survey published in 2005 found that almost half of Americans meet the criteria for a mental illness at some point in their lives, and that 25% met the criteria for having a mental illness within the past year. The categories of mental illness assessed were anxiety disorders (panic, post-traumatic stress disorders); mood disorders (major depression, bipolar disease); impulse control disorders (attention-deficit/hyperactivity disorder); and substance abuse.

In 1990 there were 1.1 million people in U.S. prisons; sixteen years later, in 2006, the number had nearly doubled to 2.1 million. There is a high rate of drug abuse in individuals who are arrested for crime in cities. One claim is that many are self-treating a mental condition (any variety of unproductive mental states) with the primitive tools of drugs and alcohol. 30% of state offenders and 40% of federal offenders are brought on drug charges. Further, a significant percent of inmates have some sort of brain damage or suboptimal brain issue. In the long term, it might be possible to identify and automatically rehabilitate these issues in both at-risk populations and the populace as a whole to improve ongoing mental health.

For fMRI usage to become widespread and routine, there would need to be improvements in several areas including cost, user experience, science findings, and clinical use. However, over time, the wider use of neuroimaging could potentially have a significant impact on human interaction and mental health. There could be interesting cultural changes if there is progress towards a truth-based culture where deception is known and improved levels of mental wellness are sustained across the populace.

Sunday, February 07, 2010

Integrating life and technology with body-area networks

Long before brain computer interfaces (BCIs) and brain co-processors are available, acceptable, and appropriate for general enhancement use, body-area networks (BANs) could be a key means of integrating life and technology. Processing and communications could be brought on-board the person for medical, consumer electronics, entertainment, and other applications. At present, BANs consist of one or a few wearable or implanted biosensors gathering basic biological data and transmitting it wirelessly to a computer. The IEEE’s BAN communication standards protocol is 802.15.6.

Medical BANs

  • Toumaz: wireless digital plaster; externally-worn disposable medical BANs for measuring blood pH, glucose, oxygen levels, and temperature
  • CardioMEMs: implantable wireless sensing devices less than one tenth the size of a dime for monitoring heart failure, aneurysms, and hypertension
Consumer BANs
A consumer application of BANs is health activity monitors such as the FitBit, DirectL ife, and WIN Human Recorder, and to some extent smart phones. All contain accelerometers that can measure movement and activity.

The next phases of BANs could be enabled by continued electronics miniaturization and next-generation communications networks (WiMAX, 4G, and beyond). In the farther future, BANs could include larger more complex networks of intercommunicating sensors and eventually autonomous sensors with two-way broadcast.

Biocompatibility and bandwidth are important concerns for human-machine integration interfaces, particularly implanted interfaces. However, the biggest challenge is energy, providing adequate ongoing power to devices. Several interesting methods of power generation are being investigated including thermal, vibrational, radio frequency (RF), photovoltaic (PV), and bio-chemical energy. ATP could possibly provide power to implanted devices, for example using DNA nanotechnology to synthesize ATP with nanoscale rotary motors, or nanodevices to produce ATP from naturally circulating glucose.