Category Archives: Science2.0/Health2.0

Hashtags of the Week (HOTW): National Women’s Health Week and Prophylactic Mastectomies (Week of May 13, 2013)

Posted on May 17, 2013 by | Leave a comment

Originally posted at THL Blog hashtags-of-the-week-hotw-national-womens-health-week-week-of-may-13-2013 by Chris Bulin, @Arduanne.

While I was preparing last week’s post, I saw some tweets about National Women’s Health Week this week. I thought that was quite appropriate considering the week started with Mother’s Day. Mother’s Day itself was full of trials and triumphs as noted in these tweets:

From there, I looked to #NationalWomensHealthWeek and #NWHW to find the most interesting tweets about Women’s Health.

I don’t know if Angelina Jolie decided to hold her press conference because it was National Women’s Health Week, or because she just felt is was the right time, but the revelation of her prophylactic double mastectomy certainly had people talking about women’s health issues. It started with an outpouring of support and well wishes for Jolie and evolved to include conversations surrounding Supreme Court cases, economic and healthcare realities, and patent law. You can follow these conversations on #brca and #breastcancer.

Finally, I came across a reference to #WD2013 which is the annual Women Deliver conference. This global conference is being held in Kuala Lumpur May 28-30, 2013. While you may not be able to attend in person, they will have online streaming content. The conference focuses on the “health and empowerment of girls and women” through political and economic engagement, particularly as it relates to maternal and newborn health and wellness.

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At the Movies: Think Local (TEDxUofM mini, Part One)

Posted on April 7, 2013 by | 3 Comments

The TEDxUofM event last Friday was fabulous. I don’t know how long it will be before they have the videos up, so I thought I’d try to find some other videos by the same people, just to whet your appetite.

OLIVER UBERTI


TEDxNASA – Oliver Uberti – Smash The Design Button http://www.youtube.com/watch?v=cE4D7OsIzuk

“The design process begins and ends with research — so he shares an office with a human skeleton. Oliver Uberti is a visual journalist and designer who dabbles in maps, infographics and words. He is a Design Editor at National Geographic magazine. On a given day at Geographic, Uberti says he may be found painting with crude oil, charting man’s migration from Africa, drawing Stonehenge, counting jelly beans or directing a photo shoot of highway litter. He’s drawn to images that make him feel something — joy, sorrow, surprise or wonder. Uberti writes a blog titled The Process, the stories behind National Geographic’s award-winning art, maps and designs. Here he answers the oft-asked question, “How did they do that?”"

Friday he had an incredible data visualization he’d created focusing on peak points of creativity throughout the human lifespan. I can’t seem to stop telling people about it. I want a copy!

DAN MORSE


The Beet Box: http://www.youtube.com/watch?v=wO-9PTdG1-Q

“Inspired by an internship in Gabon, Africa, in 2011, Dan Morse and Kay Feker collaborated in the hopes of focusing on food and youth empowerment to create The Beet Box. Joined by fellow University of Michigan students, Alex Pearlman and Kendra Hall, the group raised funds to create The Beet Box in the hopes of starting a health food revolution. They had a vision; now they needed the product.” Beet Box: Food for the Future: http://liveinthelead.com/features/02/beet-box-food-for-the-future/

Dan gave a wonderful talk about meeting unexpected trials and not giving up. Me, I loved the slides, the beautiful pictures of beets.

STERLING SPEIRN


Sterling K. Speirn, W.K. Kellogg Foundation President and CE http://www.youtube.com/watch?v=9TTxDVprvo4

“Ultimately, we want to make a positive difference by improving opportunities for children, families and communities and still meet our financial investment goals,” says Sterling Speirn, president and chief executive officer of the Foundation. “Mission driven investing is another tool that we can use to leverage our resources. Among other things, it allows us to preserve and grow our financial resources, while realizing greater social change by being able leverage our endowment to help vulnerable children.” Mission Driven Investing: Overview http://mdi.wkkf.org/our-mission/overview.aspx

Sterling inspired and provoked with alternative views of what philanthropy can be, could be, and should be; a view of philanthropy as an active and purposeful somewhat heroic activity.

SHARON POMERANTZ


Novelist Sharon Pomerantz discusses her inspiration for RICH BOY http://www.youtube.com/watch?v=f0ijuWoJNLk

“[W]riter Sharon Pomerantz (author of RICH BOY, published by Hachette/Twelve) describes her experience supporting herself as a shoe shine girl– revealing what a man’s shoes say about him, and describing how her labors influenced her future as a writer.”

MIKE BARWIS


Barwis Methods Training — Brock Mealer Walks Without Canes! http://www.youtube.com/watch?v=oie8ou_ViMg

“Constrained to a wheelchair for two years, in October 2009, Brock visited his brother at the University of Michigan where he was playing football. After an impromptu meeting with the coaching staff, strength and conditioning coach Mike Barwis invited Brock to train with them. According to the Associated Press, although Barwis had no previous experience training paraplegics, Brock took up the offer to attempt rehabilitation in the athletic training center…. Brock and Barwis set a goal. Not only was Brock going to walk again, unsupported, but he would lead the Michigan football team onto the stadium in their season opener against Connecticut.” Brock Mealer, Ohio Car Crash Victim, Defies Doctors To Walk Again (VIDEO) http://www.huffingtonpost.com/2012/10/02/brock-mealer-_n_1934050.html

You should have heard the roar from the crowd, the thunderous applause, the entire audience leaping to their feet en masse when Mike finished talking and Brock walked out on stage.

GINA ATHENA ULYSSE


Gina Athena Ulysse: http://www.youtube.com/watch?v=nL5xSjsT_uY

“Gina Athena Ulysse, In spoken-word performance of: Because When God is Too Busy: Haiti, me and the World, 2007″

Gina was one of my very favorite performers and speakers of the event. She brought such vision and passion to her performance, such clarity to both her voice and her story.

NOTES

TEDxUofM Untapped_ Voices: http://news.tedxuofm.com/post/45988920365/tedxuofm-untapped-voices

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Hashtags of the Week (HOTW): World Autism Day (Week of April 1, 2013)

Posted on April 6, 2013 by | Leave a comment

Originally posted at THL Blog http://thlibrary.wordpress.com/2013/04/05/hashtags-of-the-week-hotw-week-of-april-1-2013/ by Chris Bulin, @Arduanne.

This has been a whirlwind of a week. We started with April Fools Day, which seemed to involve a lot of cats and alternative search methods this year. April is Autism Awareness Acceptance Month and Tuesday was World Autism Day. Tuesday was also the groundbreaking announcement of the BRAIN Initiative that was outlined yesterday on the THL Blog.

I decided to focus on the autism portion of the week, although, as you’ll see from the tweets, the other two are related. I started with the most obvious hashtag #autism. I focused on research and personal stories about autism. As you can see, Twitter delivered.

I clicked through into the #neuroscience and #psychology streams to see what scientists and researchers were talking about this week as well.

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Hashtags of the Week (HOTW): Naming and Shaming (Week of March 25, 2013)

Posted on March 31, 2013 by | Leave a comment

First posted at the THL Blog by Chris Bulin (@Arduane): http://thlibrary.wordpress.com/2013/03/29/hashtags-of-the-week-hotw-naming-and-shaming-week-of-march-25-2013/

I was amazed (and a little horrified) by the number of stories having to do with ethics in science over the last week. As a student at the School of Information, we heard quite a bit about the incident of public shaming and resulting fallout from PyCon (a conference about the Python programming language). There was a lot of scuttlebutt and some serious discussion about the role of sexism in STEM. On the heels of this came the “revelation” that the I F*cking Love Science (IFLS) blog was run by *gasp* a woman! Twitter was absolutely flooded with posts about #science, #ethics and #sexism.

Around the same time these issues were being discussed, the European Molecular Biology Laboratory at Heidelberg published a paper which released the full genomic sequencing of a strain of commonly used HeLa cells, as noted by Forbes. This brought up questions about personal genomics and privacy. You can follow this conversation on the following hashtags #HeLa, #privacy, #bioethics, #genomics.

And, to add a strange twist to our ethics discussions this week, Australian scientists have been able to resurrect an extinct frog as part of the Lazarus Project, while researchers in the US attempt to bring back the carrier pigeon. Both of these #deextinction initiatives have gotten Twitter talking about woolly mammoths and Jurassic Park.

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Stack O’ Books — Sources on Transparency and Privacy. Part Eight

Posted on March 29, 2013 by | 1 Comment

Stack O' Books

Back in the 1950s, Kochen (a mathematician) and Pool (a political scientist) were the first to think about it but couldn’t find a solution without computers. Milgram (a psychologist), aided by White (a physicist-sociologist) and followed by Bernard (an anthropologist) and Killworth (an oceanographer), then attacked the problem empirically but couldn’t explain how it actually worked. Thirty years later, Steve and I (mathematicians) turned the problem into one about networks generally but failed to see its algorithmic component, leaving that door for Jon (a computer scientist) to open. Jon, in turn, left the door open for Mark (a physicist), Peter (a mathematician), and me (now a sociologist of sorts) to walk through and pick up the solution that now seems to have been lying there all along. It’s been a long trail, almost fifty years, and now we think we finally understand the problem, it seems like someone ought to have figured it out long ago. But it had to happen this way. (pp. 160-161)

Six Degrees, by Dunan J. Watts.

Comment: I admit, part of the reason I selected this quote was because it mentioned Fred, and I wanted to show that I’m not the only person who thinks he did some important work. More importantly, however, is the way in which this wonderful story illustrates the essential importance of boundary-spanning and collaboration in knowledge discovery. I spend a fair amount of time on this in the chapter, and while this particular quote didn’t fit into the story I was trying to craft, it supports it nicely, and I wish I could have included it.


Duncan Watts and Dalton Conley discuss Six Degrees of Separation http://www.youtube.com/watch?v=pFK1bpQwHF4

This new “immune system” may be imperfect … but at least we started noticing some dangers, like ozone depletion and species extinction, long before the trends grew too severe. Passionate advocates and antagonists swarm around each problem, hollering so loud we can’t ignore the peril, even when we squeeze our eyes shut and hope it goes away. This trend is especially important given society’s growing complexity and the rapid pace of change. Science and technology must progress swiftly, in order to offer any hope of solving the world’s problems. Still, with every advance, new questions and dilemmas burst forth to confound even a culture filled with large numbers of college graduates. As the recent furor over human cloning showed, it takes time for people to listen, argue among themselves, overreact, learn some more, and finally start making the sort of practical, as we go decisions that may (with luck) take us into the twenty-first century in fairly decent shape. (pp. 142-143)

The irony here is that our relative immunity against fallacy is in large part carried out via the adversarial tug and push of countless indignant, righteous, and often narrow-minded individuals, many of whome would be anything but tolerant or democratically inclined if by some magic or intrigue they ever achieved coercive power. The service they provide for the rest of us — the calm, relatively contented majority — cannot be overstated. (p. 143)

The Transparent Society, by David Brin.

Comment: For me, choosing quotes from this book is almost impossible. My first copy is studded with little shreds of torn paper marking places where David said something especially important. I agonized over the quotes to include in the book chapter, because I had limited space and many voices to include. I was trying so hard to give equal space to both sides of the debate, when what I wanted to do was just hand people copies of David’s book and make them read it. It was so hard for me to think of anything unique that I could bring to the conversation. I tried anyway.

The first time I met David was when he was on tour for this important book, having fought with his reluctant publishers to get it out in print. He spoke on campus in a rather unusual and elegant room in the UM Law School, a room which reminded me of a church in some ways. We chatted afterwards, and have stayed in touch over the years through various social media.

This was the most important book for me while I was working on my chapter. I bought extra copies of it, so that I would have access to it in many places without needing to depend on carrying it around with me. Then I carried it around anyway. David is quoted in my chapter several times, but not as many as I wanted.

This book is beyond being a must-read on the topic. After the book had been out for a few years, reviewers started to denigrate it based on its age, saying things like, “Surprisingly relevant, given how dated it is.” I always want to blow raspberries when I hear things like that. This book has at no point since publication been anything less than the most important work available on the topic of the dynamics of transparency and privacy in our evolving society. READ THIS! There are others that go into specific aspects in more depth, but I know of no other single work that does such a brilliant job of tersely describing the issues, trends, risks and benefits of various scenarios. (Not to mention that David studs the book with little gems of quotations from other writers, giving you clues about who else to read to extend your reading in this area.) David himself does take this to the next level with his new fiction masterpiece, Existence, which places many of these core concepts in story form for easy digestion. Read both!


The Transparent Society: Secrecy vs. Privacy, Part 1 http://www.youtube.com/watch?v=r0AX79lT4_c


The Transparent Society: Secrecy vs. Privacy, Part 2 http://www.youtube.com/watch?v=8oz2CZgrm8k

Playlist: http://www.youtube.com/watch?v=8oz2CZgrm8k&playnext=1&list=PL454460A507A72911&feature=results_main

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Posted in At the Movies, Health, Healthcare, Support, Science, Librarianship, Reading, Research, Science2.0/Health2.0, Thoughts, Trends

Stack O’ Books — Sources on Transparency and Privacy. Part Seven

Posted on March 28, 2013 by | 1 Comment

Stack O' Books

The trouble seems to be that it is no man’s business to understand the general patterns and reactions of science as the economist understands the business world. Given some knowledge of economics, a national business policy can be formulated, decrees can be promulgated, recessions have some chance of being controlled, the electorate can be educated. I do not know, indeed, whether one might in fact understand the crises of modern science so well as to have the power to do anything about them. I must, however, suggest that the petty illnesses of science — its superabundance of literature, its manpower shortages, its increasing specialization, its tendency to deteriorate in quality — all these things are but symptoms of a general disease. That disease is partly understood by the historian, and might be understood better if it were any man’s professional province to do so. Even if we could not control the crisis that is almost upon us, there would at least be some satisfaction in understanding what is hitting us. (p. 193)

Science Since Babylon (1961), by Derek John DeSolla Price

Comment: Another important work from the classics I read in graduate school. I find it ironic that the challenges for the practice of science explicitly articulated here — “its superabundance of literature, its manpower shortages, its increasing specialization, its tendency to deteriorate in quality” — are even more prominent now, fifty years later, than they were in 1961 when Price described them as a disease.

You see, I have the advantage of having found out how hard it is to really get to know something, how careful you have to be about checking the experiments, how easy it is to make mistakes and fool yourself. I know what it means to know something, and therefore I see how they get their information and I can’t believe that they know it, they haven’t done the work necessary, haven’t done the checks necessary, haven’t done the care necessary. (p. 22)

The Pleasure of Finding Things Out, by Richard Feynman.

Comment: It is always entertaining to read Feynman, and his insights into the practice of science, its dynamics, strengths and weaknesses, are valuable to consider even when you disagree with him. If you disagree with him, can you refute him, and if so, based on what evidence? The issues he raises here, about making mistakes and fooling yourself, are especially critical for each innovator to consider in this time of rapid change when innovations arise, crest, and vanish before we have time to evaluate their unknown risks and hidden costs.


The Pleasure of Finding Things Out, Richard Feynman Interview (1981) http://www.youtube.com/watch?v=FXiOg5-l3fk

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Stack O’ Books — Sources on Transparency and Privacy. Part Six

Posted on March 27, 2013 by | 1 Comment

Stack O' Books

There is some evidence that the diffusion of a scientific innovation is a fashion-like process in which influence is transmitted through steadily expanding networks of scientists. Thus it is plausible to view science as an enormous cluster of innovations, of which the most successful are diffused by means of a contagion process that produces a logistic curve in all facets of scientific activity. Behind the seemingly impersonal structure of scientific knowledge, there is a vast interpersonal network that screens new ideas in terms of a central theme or paradigm, permitting some a wide audience and consigning many to oblivion. (p. 76)

Invisible Colleges (1972), by Diana Crane.

Comment: Some debate the scholarship and design of the research on which this work is based, but say what you will, this was at that time one of the works that most influenced thought on how social relationships shape knowledge and our understanding of scientific discovery. Much of our current work on the influence of social networks on scholarship and policy development is based at root on the thoughts expressed in this book by Diana Crane. The influence of this book extends far past academia to the design and development of such now-everyday tools as Facebook and Twitter, and even to popular culture, with this anecdotal example:
IF “Invisible = Unseen”
AND “College = University”
THEN “Invisible College” = “Unseen University”.

It makes sense that having two cerebral hemispheres that process information in uniquely different ways would increase our brain’s capacity to experience the world around us and increase our chances for survival as a species. Because our two hemispheres are so adept at weaving together a single seamless perception of the world, it is virtually impossible for us to consciously distinguish between what is going on in our left hemisphere versus our right hemisphere. (p. 28)

My Stroke of Insight (2006), by Dr. Jill Bolte Taylor.

Comment: There were two specific ways in which this book caught my interest. One was this concept shown in the quote above that apparent opposites need not necessarily actually function in opposition to each other, but may instead be complementary and necessary aspects of forming a functional whole. The other aspect is the idea that we cannot easily perceive that which is part of our body or part of our existence when it functions normally, but only when it does not. Like Dr. Jill, I also suffered a kind of brain damage, most notably when I suffered severe chronic long term carbon monoxide poisoning a dozen years ago. We are often told that we cannot feel things inside our brain, but as part of the damage and healing process, I had powerful visceral sensations associated with trying to think about memories or skills located in the damaged area, as well as the sensations of the neurons sending out new or extended axons, probing around the damage, trying to find a new path to the old information. Similarly, we don’t tend to notice our feet unless they hurt, our lungs unless we are struggling to breathe, etcetera. Both of these are important lessons not just for how we as individuals listen and learn, but also how professions discover creativity, nations change economic and policy strategies, and possibly even for us as a species.


How it feels to have a stroke. http://www.youtube.com/watch?v=UyyjU8fzEYU

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Posted in At the Movies, Health, Healthcare, Support, Science, Librarianship, Reading, Science2.0/Health2.0, Thoughts, Trends

Stack O’ Books — Sources on Transparency and Privacy. Part Five

Posted on March 25, 2013 by | 1 Comment

Stack O' Books

Assuming it to be possible, should organized knowledge, codified understanding, and wisdom play a greater role in the political processes than has so far been the case? Have we perhaps reached limits on how much wisdom can be systematized for use in policy making? Is there such a thing as “wisdom in the wrong hearts”? Evil rulers, cruel tyrants, self-seeking potentates may act wisely on their own behalf but to the detriment of others. If they have at their command a concentrated, organized source of knowledge, understanding, wisdom, then their hold is even harder to break. When is it preferable to use incomplete, imperfect knowledge, understanding, wisdom rather than waiting until such knowledge and its organization is more perfect, though by then the issues may be even more complex? (p. 16)

Information for Action (1975), by Manfred Kochen.

Comment: One of the aspects of Fred’s work that I most admired was his fervor for illustrating and documenting the potential role of information for good, for positive change, for advocacy, for social welfare, for action. Fred was such a sweet man, so generous and kind to others. This book was published before his most interesting articles in this area, but as a book, it still ended up in my pile of books. I was lucky to get a copy he had inscribed to one of his friends, so you can see some of that sweetness in the inscription.

After Fred’s passing, I watched how the Internet / Web evolved, took shape, formed itself. Over the years, I’ve gone in circles regarding his thoughts in this area. Fred believed that if the general public was given access to the same types of information used by policy makers, decision leaders, and our government, that regular people would indeed select the best information from what was available, and make high quality and well informed decisions on matters of both personal and national importance.

At first, I watched and waited for this to happen. But what happened instead was that all the high quality information was mixed up with biased and inaccurate information, some of which was designed to intentionally mislead. I became disheartened, and thought Fred had been naïve. Little by little, especially watching health information online, I came back around to something closer to Fred’s original optimistic view, which I see as aligning closely with the thoughts of David Brin on the need for diverse views, diverse information sources, and engaged conversations in order to get at truths that may not be popular or credible at the moment they are first proposed. I also see this as respecting the rights of the individual to select their own information sources, make their own choices, and then live with the results of those choice.

Inscription from Fred

The threat to privacy is perhaps the gravest danger of a centralized, coordinated network. Centralization also threatens free competition and the informed choices available to clients, thus weakening quality and competition. It also widens the distance between the server and the client, making servers less responsive to clients and more to one another. Insofar as the service system proposed by Long is aimed at helping the disadvantaged — i.e., those most in need of such help — it is plagued by the basic problem of distrust. … Coordination does not remedy this: those that want business either give poor care, are too expensive, or both. The rare good ones have more cases than they can handle. (p. 5)

Merely to desire to inform is to judge that information is valuable and ought to be more freely available. In fact, that is perhaps in itself the most significant judgment, especially at a time when governments, industry, and social organizations appear increasingly able and willing to impose severe limits on the rights of the citizen to be informed. The desire to provide unbiased information should not be construed as an indifference to values; rather it should be seen as a commitment to the recipient’s right to all pertinent data, as well as the right to make his own judgment. (p. 17)

Information for the Community, by Manfred Kochen.

Comment: Here you see it again. Another book by Fred relating to the same types of concepts, those that led to the birth of the Internet, and shaping our understanding of information access and use as a force for good. Fred really was a formidable thinker in these areas. He is still highly regarded by those who knew him, but is under appreciated by many currently working in spaces that Fred first shaped.

Manfred Kochen 1987

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Human Microbiome 101

Posted on March 21, 2013 by | 3 Comments

I’ve been tracking the Human Microbiome Project for a few years now. I was going to blog about it, and then the New York Times published articles about it, and I assumed that meant I didn’t need to say anything. Last week I was talking with a few friends about the human microbiome, and absolutely blasted their minds into outer space. Not only had they not heard about it, the very idea was hard for them to wrap their minds around. So, here is a very brief intro, grabbing wonderful pieces from other folk. Brief take-aways.

1. Most of our body, say roughly 99% (by cell count), is comprised of critters that don’t have any human DNA. Surprise!
2. The groups of critters, a.k.a. microbes, that make up most of our bodies are surprisingly different from person to person.
3. The whole idea of antibiotics might turn out to be one of those really really bad social experiments, in that while killing the “bad” microbes, the antibiotics are also killing our good ones, the ones that we need to live and be healthy.
4. The research into what microbes make up part of different people, and how this impacts on physical and mental health, is provocative, potentially quite valuable, and extremely complicated.
5. This area of research brings up yet more challenges to the ideas of personal privacy and transparency in healthcare.

Brief video explanation (about 3 minutes).


Human Microbiome Project: Analyzing microbes that play a role in health and disease http://www.youtube.com/watch?v=axB_8O4WHYg

Excellent longer video introduction (about ten minutes).

Human Microbiome Research: An Introduction http://www.youtube.com/watch?v=DNZ2e8O7svs

Slides to go into a little more depth and context.


Jonathan Eisen: Human Microbiome 101, Future of Genomic Medicine Meeting #FOGM13, http://www.slideshare.net/phylogenomics/jonathan-eisen-talk-at-fogm13

HUMAN MICROBIOME PROJECT (HMP)

Broad Institute: http://www.broadinstitute.org/scientific-community/science/projects/microbiome-projects/hmp/human-microbiome-project

J. Craig Venter Institute: http://hmp.jcvi.org/

NIH Common Fund Human Microbiome Project (HMP) http://commonfund.nih.gov/hmp/

NIH Human Microbiome Project: http://www.hmpdacc.org/

RESEARCH BASICS

Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight, Jeffrey I. Gordon. The Human Microbiome Project. Nature 449:18 October 2007
http://obs.rc.fas.harvard.edu/turnbaugh/Papers/Turnbaugh_HMP.pdf

“Before the Human Genome Project was completed, some researchers predicted that ~100,000 genes would be found. So, many were surprised and perhaps humbled by the announcement that the human genome contains only ~20,000 protein-coding genes, not much different from the fruitfly genome. However, if the view of what constitutes a human is extended, then it is clear that 100,000 genes is probably an underestimate. The microorganisms that live inside and on humans (known as the microbiota) are estimated to outnumber human somatic and germ cells by a factor of ten. Together, the genomes of these microbial symbionts (collectively defined as the microbiome) provide traits that humans did not need to evolve on their own. If humans are thought of as a composite of microbial and human cells, the human genetic landscape as an aggregate of the genes in the human genome and the microbiome, and human metabolic features as a blend of human and microbial traits, then the picture that emerges is one of a human ‘supraorganism’.”

Elizabeth K. Costello, Christian L. Lauber, Micah Hamady, Noah Fierer, Jeffrey I. Gordon, Rob Knight. Bacterial Community Variation in Human Body Habitats Across Space and Time. Science (18 December 2009) 326(5960):1694-1697. http://www.sciencemag.org/content/326/5960/1694.abstract

“Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. … Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.”

Chris S. Smillie, Mark B. Smith, Jonathan Friedman, Otto X. Cordero, Lawrence A. David, Eric J. Alm. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241–244 (08 December 2011).
http://www.nature.com/nature/journal/v480/n7376/full/nature10571.html

“Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution1, 2. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence3, antibiotic resistance4 and xenobiotic metabolism5 to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events4, 5. … We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.”

Kjersti Aagaard, Joseph Petrosino, Wendy Keitel, Mark Watson, James Katancik, Nathalia Garcia, Shital Patel, Mary Cutting, Tessa Madden, Holli Hamilton, Emily Harris, Dirk Gevers, Gina Simone, Pamela McInnes, James Versalovic. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB Journal March 2013 27(3):1012-1022.
http://www.fasebj.org/content/27/3/1012.abstract

“In the future, human microbiomes will be defined at many body sites and during different periods in the human life span. A metagenomic survey alone can describe the microbial communities present, but clinical data are required to understand the factors that affect community composition. Studies must consider the role of sex, diet, race/ethnicity, age, residence location, use of medications, dietary supplements, and hygiene products, and many other factors that shape and cause fluctuations in individual microbiomes. Current NIH-funded demonstration projects are exploring differences in microbial communities and whole metagenomes in disease states.”

PLoS Collections: Table of Contents: The Human Microbiome Project Collection: http://www.ploscollections.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcol.v01.i13

ABOUT THE HMP

Becker, Kate. Less Than One Percent Human. Inside NOVA (PBS) February 18, 2011 1:53 PM. http://www.pbs.org/wgbh/nova/insidenova/2011/02/less-than-one-percent-human.html

Gonzalez, Robert T. 10 Ways the Human Microbiome Project Could Change the Future of Science and Medicine. io9. 6/25/12 10:28am.
http://io9.com/5920874/10-ways-the-human-microbiome-project-could-change-the-future-of-science-and-medicine

Kolata, Gina. In Good Health? Thank Your 100 Trillion Bacteria. New York Times June 13, 2012. http://www.nytimes.com/2012/06/14/health/human-microbiome-project-decodes-our-100-trillion-good-bacteria.html?pagewanted=all

Yong, Ed. The bacterial zoo living on your skin. Discover Magazine May 28, 2009. http://scienceblogs.com/notrocketscience/2009/05/28/the-bacterial-zoo-living-on-your-skin/

Yong, Ed. I, Microbes – my Radio 4 talk on the hordes of microbes inside us. Discover Magazine October 19, 2011 4:35 pm. http://blogs.discovermagazine.com/notrocketscience/2011/10/19/i-microbes-my-radio-4-talk-on-the-hordes-of-microbes-inside-us/

Yong, Ed. Microbial Menagerie: A massive study catalogues the microbes in the healthy human body, uncovering an unexpected level of individual variation in microbial makeup, among other surprises.
The Scientist June 13, 2012. http://www.the-scientist.com/?articles.view/articleNo/32215/title/Microbial-Menagerie-/

Yong, Ed. Our bodies are a global marketplace where bacteria trade genes. Discover Magazine October 31, 2011 9:00 am. http://blogs.discovermagazine.com/notrocketscience/2011/10/31/our-bodies-are-a-global-marketplace-where-bacteria-trade-genes/

Zimmer, Carl. How Microbes Defend and Define Us. New York Times July 12, 2010. http://www.nytimes.com/2010/07/13/science/13micro.html

Zimmer, Carl. Our Microbiomes, Ourselves. New York Times December 3, 2011. http://www.nytimes.com/2011/12/04/opinion/sunday/our-microbiomes-ourselves.html

Zimmer, Carl. Tending the Body’s Microbial Garden. New York Times June 18, 2012
http://www.nytimes.com/2012/06/19/science/studies-of-human-microbiome-yield-new-insights.html

DIY “MICROBIOMICS” – CITIZEN SCIENCE

American Gut: http://www.indiegogo.com/projects/american-gut

uBiome: http://www.indiegogo.com/projects/ubiome-sequencing-your-microbiome?website_name=ubiome

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Stack O’ Books — Sources on Transparency and Privacy. Part Four

Posted on March 20, 2013 by | 1 Comment

Stack O' Books

As Larry Lessig says, “A political response is possible only when regulation is transparent.” And there’s more than a little irony in the fact that companies whose public ideologies revolve around openness and transparency are so opaque themselves. (p. 229)

The Filter Bubble (2011), by Eli Pariser.

Comment: The Filter Bubble is deservedly famous. Like several other books in this post, choosing one quote was a real challenge, there is so much of value in the work as a whole.


Eli Pariser: Beware online “filter bubbles” http://www.youtube.com/watch?v=B8ofWFx525s

The issue is whether or not research and development should continue to proceed solely in the direction of information-dispensing systems. By this we mean the providing of efficient procedures for dispensing pertinent and only pertinent information in immediate response to queries by researchers at the frontiers of their specialty. The stand taken here is to suggest an alternative goal for information-retrieval systems which deserves greater priority than the dispensing of information. This alternative is to assimilate and weld newly generated knowledge into a coherent overall image at sufficient speed, so as to counteract the tendency of knowledge to scatter centrifugally into isolated fragments; to impart understanding rather than dispense information; and to aim to serve primarily the interested nonspecialist and only secondarily the skilled specialist. Whereas the keyword of most enterprises and projects in information retrieval is access, the keywords proposed here as an alternative as evaluation and synthesis. (pp. xi-xii)

Growth of Knowledge (1967), edited by Manfred Kochen.

Comment: If you only get one book by Fred Kochen, make it this one. Look at this! 1967! And this was when he first collected thoughts that shaped his vision of what became the World Wide Web. In the 1980s, when I took a class with him, he still was requiring portions of this as readings, and it was still mind-blowing. We talked about this collection and the related concepts fairly often, since this is where both of us shared so much intellectual passion and excitement. I was able to share with him one additional piece that he wanted to add to this collection if he ever reworked it, which never happened, due to his unexpected death not long after. The piece I shared was a section of Gordon Dickson’s The Final Encyclopedia, around page 100 and for several pages following, where Dickson first describes the shape and function of the ultimate encyclopedia.

Manfred Kochen 1987

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