You are the Chosen One, at least by your bacteria

Host genomics is not the main decision-making factor for bacteria immigrating into human body, but  it is an important factor. Two papers recently published in the Proceedings of the National Academy of Sciences help to understand why you are chosen and how the choosers make their decisions.

Benson et al studied microbes of mice C57BL/6J, HR and their offspring. BL6 is a common inbred line prone to diet-induced obesity, type 2 diabetes, and atherosclerosis. They also develop age-related hearing loss, if are not following recommended dietary allowance. High runner (HR) mice is lean and fit and loves to exercise - it's in the genes.

Noninvasive 16S RNA sequencing (Roche 454) showed that the abundance of microbes in "core measurable microbiota" depended on 530 host SNPs, mostly those located in 13 quantitative trait loci and was influenced by 5 more QTLs.

Some of the genetic regions appear to determine what kind of bacteria immigrate and strive in the host, other regions influence the immigration rate, attracting a wide variety pf or specific nationalities. Supplementary material elaborates on  sources of variation and genotype frequencies at given SNP locations. 

How are bacteria making their decisions to colonize or not to colonize?

In another PNAS article, Ben-Jacob and Schultz explain why microbes could be smarter than humans. We may think that our decisions are well thought and sophisticated, but we are, indeed, influenced by other people and our over-interpretations of other people's reactions. Bacteria can assess the noisy and stressful environment around them more objectively and rationally. They anticipate possible drastic changes in the environment and find the best decisions by providing every bacterium with the freedom to choose its own fate. This may look like throwing dice, but the colony manages the odds and effectively programs the effect of the noise on the gene circuit performance.

Our genes may be shaping microbial communities that could, in their turn, control our physical and mental health. Yet our lifestyle choices could break the patterns and let us decide what types of bacteria we want to live with.

And for those whose fight against unwanted microbes is too hard, there may be light in the end of the tunnel: Personal Genomes project has just announced a new collaboration with Rob Knight and Noah Fierer that will enable to explore the microbial diversity of various habitats of the human body and correlate it to the genotype.

References

• Andrew K. Benson,, Scott A. Kelly,, Ryan Legge,, Fangrui Ma,, Soo Jen Low,, Jaehyoung Kim,, Min Zhang,, Phaik Lyn Oh,, Derrick Nehrenberg,, Kunjie Hu,, Stephen D. Kachman,, Etsuko N. Moriyama,, Jens Walter,, Daniel A. Peterson,, & Daniel Pomp10.1073/pnas.1007028107 (2010). Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors Proceedings of the National Academy of Sciences of the United States of America, Published online before print October 11, 2010
• Ben-Jacob E, &; Schultz D (2010). Bacteria determine fate by playing dice with controlled odds. Proceedings of the National Academy of Sciences of the United States of America, 107 (30), 13197-8 PMID: 20660309

Predicting catastrophic health events - noninvasively and short term

"I've just picked up a fault in the AE35 unit. It's going to go 100% failure in 72 hours". These were famous words of the almighty computer HAL in "2001: A Space Odyssey". Few of us believe too much in software forecasts - be it weather, earthquakes or computer hard disk failures. Yet, we all know that sometimes it works. And such systems are very valuable, assuming they continuously improve.

Word cloud generated from QS #15 intros

Wellness is always a common theme of the many presentations and experiments of Quantified Self enthusiasts - citizen scientists quantifying everyday life in order to improve it.  "Health" was the most frequent word among the two-word introductions of QS #15 attendees, followed by variations of sleep and happiness, and ways to measure and understand it.
Are health failures predictable?  Nobody argues they are, although most available services  - such as genomic testing - provide only long term predictions.  Biomarkers that scientists are interested in are obtained through invasive or costly interventions - like blood proteins or intracranial electroencephalograms. Technologies such as Mobile Cardiac Outpatient Telemetry™ (MCOT™) developed by CardioNet  are based on real time EKG focused on heart rhythm abnormalities that can't be detected in small 24 or 48 hour windows. These relatively rare events are correlated with symptoms and used for diagnostics.

Your husband just died, … here’s his black box
(from Gordon Bell's presentation)

Perhaps in the future every one of us will leave a black box holding all the truth about our health, helping next generations to better maintain, test and repair their bodies. Many lives have already contributed to the understanding of causes and effects such as the link between cholesterol levels, diet and heart attack. But what about the short term prediction horizon,  like the 72-hour window of HAL or 30 seconds to 15-to-45 minutes warning by seizure dogs?
Could computer luminary Gordon Bell predict his heart attack if he wore his heart monitor strap while bicycling?  A cardiologist would say "no way", but maybe sometimes it's better to keep quantifying and experiment despite of what medical establishment has to say?
Data from the Women’s Health Initiative study (129,135 postmenopausal women observed over a period of nearly eight years) show that a woman’s resting heart rate may be a good indicator of her risk for a heart attack. Hsia and others (2009) found that women whose resting heart rate is more than 76 beats per minute are significantly more likely to have a heart attack than women with resting heart rate less than 62 beats a minute. This risk factor is particularly strong for women between the ages of 50 and 64, less so for women over the age of 65. (Trial NCT00000611)

Of course, women have different kinds of heart attacks than men do. They are more likely to die from a spasms of heart and the blood vessels leading to the heart, and are more likely to complain of fatigue and sleep disturbances in the weeks and months leading up to a heart attack. Sleep disturbances and decreased physiological differences between day and night are increasing heart attack and stroke risks for males too, at least for shift workers. Exercise tests  - known for their false positive results - have better cardiovascular prognostic value for smokers with high cholesterol than healthy men.

Finger arterial pulsatile volume changes or finger blood flow - related to blood pressure - is another medium-to-long term predictor of pending cardiac events. A simple, noninvasive finger sensor test called EndoPAT  can predict major cardiac events such as a heart attack or stroke for people who are considered at low or moderate risk.

AngelMed Guardian System (inventor: Dr. Tim Fischell) is an early warning system - telling 24 hrs to a week before if heart attack is coming. Average time between the cardiac event and hospital arrival is 3 hrs, and about 5 hrs before the surgery starts. By that time 90% of muscles could be dead, so 5 or 10 minute warnings could save lives.  Unfortunately, Guardian is highly invasive - sized as an iPod, it is implanted directly into the patient's chest, monitoring electrogram  waveforms and other crucial heart-signal data 24-7.

Many portable oximeters and ECG are already in the market - and even though consumers are complaining about noise and difficulties in getting readings of diagnostic intervals, the technologies will continue to improve and self-quantifiers will be finding solutions for better health.

REFERENCES
Hsia, J., Larson, J., Ockene, J., Sarto, G., Allison, M., Hendrix, S., Robinson, J., LaCroix, A., Manson, J., & , . (2009). Resting heart rate as a low tech predictor of coronary events in women: prospective cohort study BMJ, 338 (feb03 2) DOI: 10.1136/bmj.b219


Mayo Clinic (2009). High resting heart rate could predict heart attack in women. Mayo Clinic women's healthsource, 13 (7) PMID: 19498326

Collaboration 2.0

Information technology is letting people around the world come together in unprecedented ways. Wikis, blogs and microblogs like twitter, 

crowdsourcing and crowd-task-solving sites continue to flatten the planet.  

Scientific innovation used to be a very private endeavor, with narrowly specialized scientists delving deeply into specific research areas.  The Internet changed some of this giving rise to Wikipedia  - now orders of magnitude larger than the Encyclopedia Britannica, and similar wiki resources for gene annotations, RNA libraries, radiology images, open-source software and other content.
 
Science funding agencies may appear to be crowdsourcing solutions too - as they employ broad calls for proposals and utilize peer reviews to evaluate the proposed ideas. Their models , however, are not very effective in triggering societal impacts. They impede collaboration in many ways as the researchers are not truly working together and the feedback is not constructive. Reviewers are experts but not direct stakeholders of  proposed projects . They add management overhead (Latour, 1996).

One may argue that science is highly competitive and will always be driven by egos and desire for personal vs collective success. Yet, as Johnston and Hauser note, these very human needs could be met by more efficiently designed open source models, extending beyond snapshots of consensus,  enabling to capture specific contributions of each participant and  permanent record of the life history of the project from conception to completion.

The ease of discovery declines every year - scientists have to search for smaller asteroids, heavier chemical elements and more complicated connections. This has to be matched with either exponential increase in the number of scientists or more innovative collaboration.

People take pleasure in synchronized activities - such as singing or marching together, folding proteins or syncing their brains in a conversation.  Could scientists have meaningful conversations on unimaginable scales, conversations including citizen scientists and people whose health needs could be solved by science?
Some researchers are already using help from crowds collecting their donations to support research - like the recently started open-source research project to develop cure for neglected tropical disease schistosomiasis.
Or the Open Source PCR project supported by the public.

Recent call for collaboration asked for a framework to exchange and disseminate information,  produce guidelines and summarize finding for Participatory health research (PHR) addressing local health issues. Government agencies are using twitter and expect crowds to supply epidemiological metrics to test health policy efficacy.

Meanwhile, many are already utilizing google docs in the quest for collaborators and exchange of ideas. See for example this Folder of Useful Google Docs including:

• Startup Ideas - Front page linking to Editable Table
• Innovators - Form to Submit Your Data to appear in this Table  (see HN Yellow Pages Thread)
• Entrepreneurs looking for Co-founders -  Front page linking to Editable Table
• Seed accelerators and their companies
• Startups Hiring - Form for Employers displaying info in this Table
• Software Contractors - Editable Table    (HN Contractors Thread about it)

Or check this call for collaborations in the microbiome and metabolome spaces, to solve neglected medical conditions.

Scientists, let's unite and start collaborating in even more creative ways!




References 

Johnston SC, & Hauser SL (2009). Crowdsourcing scientific innovation. Annals of neurology, 65 (6) PMID: 19562693 
Wright MT, Roche B, von Unger H, Block M, & Gardner B (2010). A call for an international collaboration on participatory research for health. Health promotion international, 25 (1), 115-22 PMID: 19854843

Auer S, Braun-Thurmann H. Towards bottom-up, stakeholder-driven research funding — open science and open peer review: Available at:  http://www.informatik.uni-leipzig.de/~auer/publication/OpenScience.pdf.  Accessed May 21, 2009 

Lawrence PA (2009) Real Lives and White Lies in the Funding of Scientific Research. PLoS Biol 7(9): e1000197. doi:10.1371/journal.pbio.1000197


Marsh A, Carroll D, & Foggie R (2010). Using collective intelligence to fine-tune public health policy. Studies in health technology and informatics, 156, 13-8 PMID: 20543334 

Huss JW 3rd, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, & Su AI (2010). The Gene Wiki: community intelligence applied to human gene annotation. Nucleic acids research, 38 (Database issue) PMID: 19755503 

Latour, B. 1996. Aramis, or, The love of technology Harvard University Press, Cambridge, Mass 
Butler, D. (2010). Open-source science takes on neglected disease Nature DOI: 10.1038/news.2010.50
Facebook page, Just giving fundraiser page. 

Scientific collaboration: 

• Innocentive - crowdsourcing scientific solutions to organization's problems
• Science Commons - generic license agreements
• TekScout - crowdsourcing R&D solutions
• YourEncore - crowd of retired veteran scientists and engineers
• Biocrowd - social network for bioscience professionals
• Eureka medical - medical open innovation platform

Idea Generation and Solving:

• AddictLab - creative think tank
• Brain Reactions - post questions and get ideas/feedback on them
• Fellowforce - innovation challenge board covering many disciplines
• iBridge Network - platform for university innovation
• IdeaConnection - idea marketplace and problem solving
• Idea Crossing - organize innovation quests
• IdeaMagnet - powering idea generation
• Ideawicket - open innovation portal
• Innovation Exchange - open innovation market place
• WhyNot - idea exchange
• IdeaBlob - monthly contest for entrepreneurial ideas
• Bodyshock - call for ideas to improve health in the next decade 
• Incuby - online community for inventors
• Cofundos - open-source software ideas

Crowd-Task-Solving and Freelance

• World4brains, collaboration instead of competition for best ideas, advice and solutions - innovative payment system rewards all valuable input given
• TaskRabbit,  linking over-stretched consumers with runners for errands, tasks and other to-do’s
• oDesk - global marketplace for remote work
• Elance - freelance marketplace
• Guru - freelance community
• Ki Work - sourcing online work
• Amazon Mechanical Turk - micro-task crowdsourcing
• HumanGrid - small online tasks solving

 

Crowd-Funding

• A Swarm of Angels - crowdfunding a film
• Kickstarter - fund ideas and endeavours
• Kiva – crowdfunded micro-loans
• IndieGoGo - a collaborative way to fund ideas 
• WePay - ways to collect and manage money