Saturday, July 17, 2010

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:

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!


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:  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: 
Idea Generation and Solving:

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



    Wednesday, July 14, 2010

    Sit less, Move more

    I am typing this standing in front of my computer. My tall chair is aside. 

    About a year ago, I realized that I felt better when I stood while working. It turned out I was not alone in this discovery; more and more people are opting for a vertical approach to work, and the benefits are becoming increasingly evident.

    We're all familiar with the age-old advice to "eat less and exercise". But this may not be enough. As shown in a recent study, exercise does not counteract the ill effects of sedentary lives, we should keep moving (or at least squatting) throughout the day too.  New York Times article about the study (The men who stare at screens) immediately got up-votes from over 100 hackers - those who spend hours staring at screens to code, along with 100+ comments from those staring at screens to read and comment on the news.  Stand up while you read this, asked NYT earlier this year. Prolonged sedentarity affects not only cardiovascular and metabolic health, blood clotting, diabetes and cancer. Countless hours of sitting could cause many other ailments reducing the quality of life such as skewed microbial ecology accompanied by strong body odor, diminishing overall quality of life.

    Health promotion efforts targeting physical inactivity should emphasize both reducing sedentary activity and increasing regular physical activity for optimal health.

    The lead author of the 2010 study says: "Stand up. Pace around your office. Get off the couch and grab a mop or change a light bulb the next time you watch ‘‘Dancing With the Stars.’’ A five-minute stroll is recommended every half hour.

    Stand-up desks and treadmill desk were available years ago, a web site just stand was created for office workers who sit long hours each day, but either the desks are not very usable yet, lobbying your boss for a stand-up workstation is still tricky or most people just like sitting too much. Let's hope this will change. References

    Warren TY, Barry V, Hooker SP, Sui X, Church TS, & Blair SN (2010). Sedentary behaviors increase risk of cardiovascular disease mortality in men. Medicine and science in sports and exercise, 42 (5), 879-85 PMID: 19996993 DOI: 10.1249/MSS.0b013e3181c3aa7e

    Dunstan DW, Barr EL, Healy GN, Salmon J, Shaw JE, Balkau B, Magliano DJ, Cameron AJ, Zimmet PZ, & Owen N (2010). Television viewing time and mortality: the Australian Diabetes, Obesity and Lifestyle Study (AusDiab). Circulation, 121 (3), 384-91 PMID: 20065160 
    DOI: 10.1161/CIRCULATIONAHA.109.894824

    Katzmarzyk PT, Church TS, Craig CL, & Bouchard C (2009). Sitting time and mortality from all causes, cardiovascular disease, and cancer. Medicine and science in sports and exercise, 41 (5), 998-1005 PMID: 19346988 DOI: 10.1249/MSS.0b013e3181930355

    Healy GN, Dunstan DW, Salmon J, Shaw JE, Zimmet PZ, Owen N. (2008). Television time and continuous metabolic risk in physically active adults. Medicine and Science in Sports and Exercise 40, 639-645.(PMID: 18317383

    Khaw K-T, Wareham N, Bingham S, Welch A, Luben R, et al. (2008) Combined Impact of Health Behaviours and Mortality in Men and Women: The EPIC-Norfolk Prospective Population Study. PLoS Med 5(1): e12. doi:10.1371/journal.pmed.0050012 (PMID: 18184033)

    Beasley R, Raymond N, Hill S, Nowitz M, Hughes R. (2003) eThrombosis: the 21st century variant of venous thromboembolism associated with immobility. Eur Respir J.  21(2), 374-6. (PMID: 12608454 )

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    Additional references post-initial publication:
    Gao W, Sanna M, Chen YH, Tsai MK, Wen CP. Occupational Sitting Time, Leisure Physical Activity, and All-Cause and Cardiovascular Disease Mortality. JAMA Network Open. 2024 Jan 2;7(1):e2350680-.

    Saturday, July 3, 2010

    Microbial sequencing for food applications is gaining momentum, but challenges remain

    Blue Stilton PDO Cheese, one quarter of a half...
    Microbes bring us a wide variety of foods, transforming texture and intensifying flavors. Jake Lahne, posted a great overview of some of the good microorganisms in cheese - like Penicillium molds in Cabrales cheese shown on the right - that adds to other ingredients such as milk, salt and coagulants.

    While modern cheeses are made with preselected cultures, traditional cheeses carry dozens of types of microbes, some highly unusual and uncharacterized.

    Lactic acid bacteria, including lactococci and lactobacilli, not only convert the basic milk sugar, lactose, into lactic acid but also make the cheese inhospitable to many spoilage organisms and is the first step towards deliciousness. Streptococci are also important in cheese and yogurt-making, adding flavor to alpine (Emmental, Gruyere, etc) and Italian hard (Grana Padana, Pecorino Romano, etc) cheeses. Lactococcus lactis, Staphylococcus, Trichococcus, and Monascus are strongly associated with the 36 key aroma compounds of Monascus-fermented cheese. Lactococcus lactis was found to be the dominant bacterium while Monascus was confirmed to be the dominant fungus.

    Propionobacter shermanii, are able to digest acetic acid and convert it to sharp, sweaty-smelling propionic acid and carbon dioxide. Several species of propionibacteria also inhabit human skin, producing less wanted odors.

    Most of the molds that grow on cheese are species of Penicillium, but some cheeses, like St. Nectaire, develop others such as blue mold, P. roqueforti and P. glaucum in blue cheese. Blues include Roquefort, Stilton, Gorgonzola, and Cabrales, and goat cheese Monte Enebro.
    White molds, which are found on the outside of all types of soft-ripened cheeses, are subspecies of P. camembertii (also called P. candidum). These white molds produce enzymes that break down the milk proteins and producing garlicky or earthy, also ammonia smells.

    Room-clearing ability of Epoisses, Münster, and Limburger owe to the smear bacteria officially known as Brevibacter linens. They need salty (up to 15%), moist environments to grow,and create stinky odor compounds, producing oniony or garlicky, fishy, and sweaty aromas. The aroma of the washed-rind cheeses is often compared to smelly feet - and, yes, brevibacter grow well on human skin.

    But it is not only cheese that carries myriads of microbes. There are many other foods. And not all of the bacteria we consume with the foods is good for you.

    Genome sequencing was predicted to bring practical benefits to the field of microbial food safety, identifying and controlling emerging microbial pathogens. It is still not as readily available and inexpensive as needed for practical applications, but a few pilot projects have showed a promise.

    GenomeWeb's Andrea Anderson recently published this article about academic researchers and public health agencies exploring the use of genomics-based approaches to complement existing food safety and surveillance methods.

    Common foodborne pathogens include E. coli 0157:H7, Salmonella, Listeria, and Campylobacter, but there are many more in need of identification. Having effective ways to distinguish between dangerous and neutral microbes is crucial for food safety.

    Many identification methods exist, but whole-genome sequencing could give unprecedented wealth of information, allowing predictions about the nature of organisms, their potential sources and associated risk,

    In a paper published in the Journal of Food Protection in May, USDA's Ward and his colleagues reported on their findings from a multi-locus genotyping study of more than 500 Listeria monocytogenes isolates collected by the USDA-FSIS from a variety of ready-to-eat foods.
    "Integration of PFGE and DNA-sequence-based sub-typing provides an improved framework for prediction of relative risk associated with L. monocytogenes strains from [ready-to-eat] foods," they wrote.

    In another recent paper, Ward and collaborators from Colorado State University used genotyping to show that a virulence-decreasing inlA mutation in L. monocytogenes was more common in isolates from ready-to-eat than from isolates from actual human listeriosis cases.
    Honisch presented a poster outlining work done with collaborators from London's Health Protection Agency at the American Society for Microbiology annual meeting in San Diego this May, describing how the team used the Sequenom MassArray platform to do multi-locus sequence typing, or MLST, on hundreds of Salmonella isolates. Honisch told GWDN that the approach is promising, in part, because mass spec is high-throughput and generates very reproducible data.
    During a session at the recent ASM meeting, Eric Brown, a microbiologist with the US Food and Drug Administration, explained that the FDA has been exploring the use of Roche 454 sequencing to characterize Salmonella isolates and to find markers for tracing outbreak strains back to their source.
    And in Canada, the NML's Gilmour was lead author on a paper appearing in BMC Genomics this February in which researchers used the Roche 454 GS FLX platform to sequence the genomes of two L. monocytogenes strains isolated during a 2008 outbreak of listeriosis in Canada that killed 22 people and caused serious illness in dozens more.
    "This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events," Gilmour and his co-authors wrote, "and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole-genome sequences in the context of epidemiology."
    Even so, Gilmour said it will take time for whole-genome sequencing to become a standard traceback method — largely due to remaining bioinformatics challenges.
    "It's our job to learn how to use those [sequencing] technologies and glean the interesting information or the informative information," Gilmour said. "That's kind of the bottleneck we're at right now, is developing those bioinformatics tools to take that raw data and quickly parse through it and find relevant information."

    There is still a long way before genome-sequencing or methods developed based on sequencing results will be standardized and incorporated into practice, but the results look promising and are opening new horizons for health applications.


    Ward TJ, Evans P, Wiedmann M, Usgaard T, Roof SE, Stroika SG, & Hise K (2010). Molecular and phenotypic characterization of Listeria monocytogenes from U.S. Department of Agriculture Food Safety and Inspection Service surveillance of ready-to-eat foods and processing facilities. Journal of food protection, 73 (5), 861-9 PMID: 20501037

    Van Stelten A, Simpson JM, Ward TJ, & Nightingale KK (2010). Revelation by single-nucleotide polymorphism genotyping that mutations leading to a premature stop codon in inlA are common among Listeria monocytogenes isolates from ready-to-eat foods but not human listeriosis cases. Applied and environmental microbiology, 76 (9), 2783-90 PMID: 20208021

    St-Gelais D, Lessard J, Champagne CP, & Vuillemard JC (2009). Production of fresh Cheddar cheese curds with controlled postacidification and enhanced flavor. Journal of dairy science, 92 (5), 1856-63 PMID: 19389943

    Rossetti L, Fornasari ME, Gatti M, Lazzi C, Neviani E, Giraffa G. (2008). Grana Padano cheese whey starters: microbial composition and strain distribution. Int J Food Microbiol. 2008 Sep 30;127(1-2):168-71. Epub 2008 Jun 12.PMID: 18620769

    Flórez AB, Mayo B. (2006) Microbial diversity and succession during the manufacture and ripening of traditional, Spanish, blue-veined Cabrales cheese, as determined by PCR-DGGE. Int J Food Microbiol. 2006 Jul 15;110(2):165-71. Epub 2006 Jun 27.PMID: 16806553

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