The Tree of Life

ADVANCE Blog Notes: Interesting article by Mary Ann Mason at Slate.Com "In the Ivory Tower, Men Only"

2013-06-18T06:58:00.001-07:00

There is a really interesting article at Slate.Com from Mary Ann Mason, the author of "Do Babies Matter" which I have written about here before. The post is titled "In the Ivory Tower, Men Only". The post tells some of the background behind the book and discusses issues about graduate school, post doctoral positions, applying for faculty jobs and more. The article also has some very good guidance for universities that would like to level the playing field:

We all know what structural changes would help to level the playing field in all of these careers and they are quite similar: paid family leave for both mothers and fathers, especially for childbirth, a flexible workplace, a flexible career track, a re-entry policy, pay equity reviews, child care assistance, dual career assistance. Those universities and corporations who have actively created these policies have found an advantage in recruitment and retention. For instance, at Berkeley, after enacting several new policies to benefit parents, including paid teaching leaves for fathers, job satisfaction scored much higher among parents, and more babies are being born to assistant professors.

Some good guidance for some of the activities at UC Davis as part of the ADVANCE program in which I am involved. And she ends by recommending

It is time for women to “lean in” and demand family policies that will at least give them a fighting chance to have both a successful career and babies.

I agree. But it is also time for men to do the same. The more that men also support and demand such policies the quicker things will change.

ADVANCE Reading of the Day: Sylvia Earle, Women in Japan and the Gulf, Spaceflight

2013-06-16T18:14:00.001-07:00

Quick post here ... Some news stories and posts I am checking out today in relation to the UC Davis ADVANCE project in which I am involved.

National Geographic: In Her Words: Sylvia Earle on Women in Science – News Watch
NY Times Japan's 'Science Women' Seek an Identity
NBC News:The Whole World Celebrates 50 Years of Women in Spaceflight
Gulf Today: Arab women in science get fellowship boost
NY Times: The Unspoken Stigma of Workplace Flexibility

How Open Are You? Part 1: Metrics to Measure Openness and Free Availability of Publications

2013-06-16T11:56:00.001-07:00

For many many years I have been raising a key questions in relation to open access publishing - how can we measure how open someone's publications are. Ideally we would have a way of measuring this in some sort of index. A few years ago I looked around and asked around and did not find anything out there of obvious direct relevance to what I wanted so I started mapping out ways to do this.

When Aaron Swartz died I started drafting some ideas on this topic. Here is what I wrote (in January 2013) but never posted:

With the death of Aaron Swartz on Friday there has been much talk of people posting their articles online (a short term solution) and moving more towards openaccess publishing (a long term solution). One key component of the move to more openaccess publishing will be assessing people on just how good a job they are doing of sharing their academic work.

I have looked around the interwebs to see if there is some existing metric for this and I could not find one. So I have decided to develop one - which I call the Swartz Openness Index (SOI).

Let A = # of objects being assessed (could be publications, data sets, software, or all of these together).

Let B = # of objects that are released to the commons with a broad, open license.

A simple (and simplistic) metric could be simply

OI = B / A

This is a decent start but misses out on the degree of openness of different objects. So a more useful metric might be the one below.

A and B as above.

Let C = # of objects available free of charge but not openly

OI = ( B + (C/D) ) / A

where D is the "penalty" for making material in C not openly available

This still seems not detailed enough. A more detailed approach might be to weight diverse aspects of the openness of the objects. Consider for example the "Open Access Spectrum." This has divided objects (publications in this case) into six categories in terms of potential openness: reader rights, reuse rights, copyrights, author posting rights, automatic posting, and machine readability. And each of these is given different categories that assess the level of openness. Seems like a useful parsing in ways. Alas, since bizarrely the OAS is released under a somewhat restrictive CC BY-NC-ND license I cannot technically make derivatives of it. So I will not. Mostly because I am pissed at PLoS and SPARC for releasing something in this way. Inane.

But I can make my own openness spectrum.

And then I stopped writing because I was so pissed off at PLOS and SPARC for making something like this and then restricting it's use. I had a heated discussion with people from PLOS and SPARC about this but not sure if they updated their policy. Regardless, the concept of an Openness Index of some kind fell out of my head after this buzzkill. And it only just now came back to me. (Though I note - I did not find the Draft post I made until AFTER I wrote the rest of this post below ... ).

To get some measure of openness in publications maybe a simple metric would be useful. Something like the following

P = # of publications
A = # of fully open access papers
OI = Openness index

A simple OI would be

OI = 100 * A/P

However, one might want to account for relative levels of openness in this metric. For example

AR = # of papers with a open but somewhat restricted license
F = # of papers that are freely available but not with an open license
C = some measure of how cheap the non freely available papers are

And so on.

Given that I am not into library science myself and not really familiar with playing around with this type of data I thought a much simpler metric would be to just go to Pubmed (which of course works only for publications in the arenas covered by Pubmed).

From Pubmed one can pull out some simple data.

# of publications (for a person or Institution)
# of those publications in PubMed Central (a measure of free availability)

Thus one could easily measure the "Pubmed Central" index as

PMCI = 100 * (# publications in PMC / # of publications in Pubmed)

Some examples of the PMCI for various authors including some bigger names in my field, and some people I have worked with.

Name	#s	PMCI
Eisen JA	224/269	83.2
Eisen MB	76/104	73.1
Collins FS	192/521	36.8
Lander ES	160/377	42.4
Lipman DJ	58/73	79.4
Nussinov R	170/462	36.7
Mardis E	127/187	67.9
Colwell RR	237/435	54.5
Varmus H	165/408	40.4
Brown PO	164/234	70.1
Darling AE	20/27	74.0
Coop G	23/39	59.0
Salzberg SL	107/162	61.7
Venter JC	53/237	22.4
Ward NL	24/58	41.4
Fraser CM	78/262	29.8
Quackenbush J	95/225	42.2
Ghedin E	47/82	57.3
Langille MG	10/14	71.4

And so on. Obviously this is of limited value / accuracy in many ways. Many papers are freely available but not in Pubmed Central. Many papers are not covered by Pubmed or Pubmed Central. Times change, so some measure of recent publications might be better than measuring all publications. Author identification is challenging (until systems like ORCID get more use). And so on.

Another thing one can do with Pubmed is to identify papers with free full text available somewhere (not just in PMC). This can be useful for cases where material is not put into PMC for some reason. And then with a similar search one can narrow this to just the last five years. As openaccess has become more common maybe some people have shifted to it more and more over time (I have -- so this search should give me a better index).

Lets call the % of publications with free full text somewhere the "Free Index" or FI. Here are the values for the same authors.

Name	PMC % Pudmed	PMCI	Free % Pubmed 5 years	FI - 5	Free % Pubmed All	FI-ALL
Eisen JA	224/269	83.2	178/180	98.9	237	88.1
Eisen MB	76/104	73.1	32/34	94.1	83	79.8
Collins FS	192/521	36.8	104/128	81.3	263	50.5
Lander ES	160/377	42.4	78/104	75.0	200	53.1
Lipman DJ	58/73	79.4	20/22	90.9	59	80.8
Mardis E	127/187	67.9	90/115	78.3	135	72.2
Colwell RR	237/435	54.5	31/63	49.2	258	59.3
Varmus H	165/408	40.4	21/28	75.0	206	50.5
Brown PO	164/234	70.1	20/21	95.2	185	79.0
Darling AE	20/27	74.0	18/21	85.7	21	77.8
Coop G	23/39	59.0	16/20	80.0	28	71.8
Salzberg SL	107/162	61.7	54/58	93.1	128	79.0
Venter JC	53/237	22.4	20/33	60.6	85	35.9
Ward NL	24/58	41.4	18/27	66.6	30	51.7
Fraser CM	78/262	29.8	9/13	69.2	109	41.6
Quackenbush J	95/225	42.2	54/75	72.0	131	58.2
Ghedin E	47/82	57.3	30/36	83.3	56	68.3
Langille MG	10/14	71.4	11/13	84.6	11	78.6

Very happy to see that I score very well for the last five years. 180 papers in Pubmed. 178 of them with free full text somewhere that Pubmed recognizes. The large number of publications comes mostly from genome reports in the open access journals Standards in Genomic Sciences and Genome Announcements. But most of my non genome report papers are also freely available.

I think in general it would be very useful to have measures of the degree of openness. And such metrics should take into account sharing of other material like data, methods, etc. In a way this could be a form of the altmetric calculations going on.

But before going any further I decided to look again into what has been done in this area. When I first thought of doing this a few years ago I searched and asked around and did not see much of anything. (Although I do remember someone out there - maybe Carl Bergstrom - saying there were some metrics that might be relevant - but can't figure out who / what this information in the back of my head is).

So I decided to do some searching anew. And lo and behold there was something directly relevant. There is a paper in the Journal of Librarianship and Scholarly Communication called: The Accessibility Quotient: A New Measure of Open Access. By Mathew A. Willmott, Katharine H. Dunn, and Ellen Finnie Duranceau from MIT.

Full Citation: Willmott, MA, Dunn, KH, Duranceau, EF. (2012). The Accessibility Quotient: A New Measure of Open Access. Journal of Librarianship and Scholarly Communication 1(1):eP1025. http://dx.doi.org/10.7710/2162-3309.1025

Here is the abstract:

Abstract
INTRODUCTION The Accessibility Quotient (AQ), a new measure for assisting authors and librarians in assessing and characterizing the degree of accessibility for a group of papers, is proposed and described. The AQ offers a concise measure that assesses the accessibility of peer-reviewed research produced by an individual or group, by incorporating data on open availability to readers worldwide, the degree of financial barrier to access, and journal quality. The paper reports on the context for developing this measure, how the AQ is calculated, how it can be used in faculty outreach, and why it is a useful lens to use in assessing progress towards more open access to research.
METHODS Journal articles published in 2009 and 2010 by faculty members from one department in each of MIT’s five schools were examined. The AQ was calculated using economist Ted Bergstrom’s Relative Price Index to assess affordability and quality, and data from SHERPA/RoMEO to assess the right to share the peer-reviewed version of an article.
RESULTS The results show that 2009 and 2010 publications by the Media Lab and Physics have the potential to be more open than those of Sloan (Management), Mechanical Engineering, and Linguistics & Philosophy.
DISCUSSION Appropriate interpretation and applications of the AQ are discussed and some limitations of the measure are examined, with suggestions for future studies which may improve the accuracy and relevance of the AQ.
CONCLUSION The AQ offers a concise assessment of accessibility for authors, departments, disciplines, or universities who wish to characterize or understand the degree of access to their research output, capturing additional dimensions of accessibility that matter to faculty.

The full PDF is available here.

I completely love it. After all. it is directly related to what I have been thinking about and, well, they actually did some systematic analysis of their metrics. I hope more things like this come out and are readily available for anyone to calculate. Just how open someone is could be yet another metric used to evaluate them ...

And then I did a little more searching and found the following which also seem directly relevant

So - it is good to see various people working on such metrics. And I hope there are more and more.

Anyway - I know this is a bit incomplete but I simply do not have time right now to turn this into a full study or paper and I wanted to get these ideas out there. I hope someone finds them useful ...

Another week - another microbial art project

2013-06-14T01:40:00.001-07:00

The use of microbes in art projects continues to spread. Here is another example: Bioluminescent art: Beautiful bacteria glow in the dark | MNN - Mother Nature Network. The article discusses the Bioglyphs project which involved "some microbiology training, imagination, and a lot of petri dishes." Definitely worth checking out ...

ADVANCE Journal Club: Developing Graduate Students of Color for the Professoriate in STEM

2013-06-13T13:16:00.001-07:00

As I have posted about before - I am involved in the UC Davis ADVANCE project funded by NSF. From the project website:

UC Davis ADVANCE is a newly funded Institutional Transformation grant that began in September of 2012. Our program is supported by the National Science Foundation’s ADVANCE Program which aims to increase the participation and advancement of women in academic science and engineering careers.

My role in this project is as a member (and now Co-Chair) of one of the "Policies and Practices Review Initiative" Committee. As part of my work on this committee I am trying to read various papers on related topics. And I figured I would simultaneously post about these papers as much as I can because it would be great to get a broader discussion going on these topics.

So today I am reading the following:CSHE - Developing Graduate Students of Color for the Professoriate in Science, Technology, Engineering, and Mathematics (STEM) which I was pointed to in our Committee meeting yesterday. It is quite interesting. It is by Anne MacLachlan from the Center for Studies in Higher Education at UC Berkeley.

The abstract:

This paper presents part of the results of a completed study entitled A Longitudinal Study of Minority Ph.D.s from 1980-1990: Progress and Outcomes in Science and Engineering at the University of California during Graduate School and Professional Life. It focuses particularly on the graduate school experience and degree of preparation for the professoriate of African American doctoral students in the sciences and engineering, and presents the results of a survey of 33 African American STEM Ph.D.s from the University of California earned between 1980-1990. Relationships with thesis advisors and principal investigators are evaluated by the study participants in fifteen specific areas from highly-ranked intellectual development to low-ranked training in grant writing. Deficits in training and socialization are discussed along with the tension between being both an African American and a graduate student. Career choices and outcomes are presented. These findings, in conjunction with current analyses of graduate education in STEM, suggest ways in which graduate training for all could be improved.

Lots of interesting information in there. Perhaps most important for my current goals is what she describes at the end in terms of a Proposed Development Program. She starts this section by commenting on the general situation in terms of training scientists in the US today. She then identifies what she refers to a "discontinuities" in federal and local policy which can hinder "developing faculty of color." These include "compartmentalized, externally mandated sets of programs" and the "nature of Ph.D. training". Of the 33 Ph.D.s surveyed in the study, nearly all of them recommended diversity training for faculty. They also recommend better laying out of expectations and requirements for students and more involvement of current faculty in recruiting. They also made many recommendations for improving the life of current students of color.

Anyway - a lot of this material and the concepts involved are bit new to me so I am still digesting the article. But I thought I would share it with others in the hope that this will help catalyze more open discussion of issues involved women and underrepresented minorities in STEM fields.

Weird things coming up from automated Google Scholar searches pointing to hea1thandfitness.com

2013-06-12T18:07:00.002-07:00

I noticed some really weird stuff coming up in automated Google Scholar searches. Example - see this one below:

Scholar Alert: [ metagenomics phylogeny ]

[HTML] Asthma and the Diversity of Fungal Spores in Air

A Pringle - PLoS Pathogens, 2013

... cause and effect between spores and asthma may remain a challenge, metagenomictechnologies
will ... Metagenomics data are likely to provide a very different understanding of the potential diversity ...
(2006) Reconstructing the early evolution of fungi using a six-gene phylogeny. ...

[HTML] Insights inside often the progression amongst Archaea additionally eukaryotic required protein modifier metabolism exposed simply because amongst often the …

T Nunoura, Y Takaki, J Kakuta, S Nishi, J Sugahara… - Life Sciences

... ' ', gives become proposed centred on SSU rRNA gene phylogeny (10 ), unfortunately a ...type II
SSU rRNA gene set identified on the metagenomic library; AB566230. ... Archaea: sides ranging
from microbial ecology and regarding consequence metagenomics GarrettRA KlenkH-P ...

The second paper listed there takes one to a very strange site. It appears to be a pseudo-mirror of the journal site all embedded within the domain "Hea1thandFitness.Com". Note - this domain name has the number "1" replacing the letter "l" in the domain name - I assume as a trick of sorts. Clicking on the link takes you to a site for which I have done a screen shot below

The whole thing is weird - with the number instead of the letter and the weird formatting of the site. Just a tiny glitch? Well, I don't think so since in some of my other Google Scholar alerts other links to this same domain came up. See examples below:

Scholar Alert: New articles in Phil Hugenholtz's profile

[HTML] Contrasting Life Strategies involving Viruses that's Infect Photo-certainly to positively not mention Heterotrophic Bacteria, considering that's Revealed by simply Viral …

L Deng, A Gregory, S Yilmaz, BT Poulos, P Hugenholtz…

Ocean infections are usually all-pervasive and also numerous and also play the game main
jobs relating to be the inside overseas biogeochemical menstrual cycles thru their mortality,
horizontally gene transfer, and also mind games about put in relationship metabolism. ...

and

Scholar Alert: [ PhylogenoMics ]

[HTML] PIECE: a collection to help your entire family take also gene rules comparing and then progression

Y Wang, FM You, GR Lazo, MC Luo, R Thilmony… - Life Sciences

... structural repair for retrogenes appearing in the organization for the Populus genome 2009 151
1943 1951 AbstractFREE Full Text Garcia-Espana Mares SunTT Desalle Intron evolution: checking
hypotheses for intron development by consuming phylogenomics for tetraspanins ...

[HTML] Integration of sequence-similarity and therefore practical union information definitely likely surmounted inbuilt factors found in orthology mapping through bacterial …

G Li, Q Ma, X Mao, Y Yin, X Zhu, Y Xu - Life Sciences

... Chen MackeyAJ VermuntJK RoosDS Assessing entire performance of orthology discovery
strategies put to practice found on eukaryotic genomes 2007 e383 CrossRef Medline ZmasekCM
EddySR RIO: analyzing proteomes by automated phylogenomics wearing resampled ...

and

Scholar Alert: [ microbial forensics ]

Effect of modified montmorillonites on the biodegradation and adsorption of biomarkers such as hopanes, steranes and diasteranes

UC Ugochukwu, IM Head, DAC Manning - 2013

... Several studies have demonstrated that some solid sur- faces such as clay minerals are able
to stimulate microbial ... Indigenous microbial cells of Whitley Bay sediments were iso- lated and
proliferated via several subcultures prior to use for laboratory biodegradation studies. ...

[HTML] Deconstruction created by Lignocellulose interested in Soluble Sugars by the Native and even Designer Cellulosomes

S Moraïs, E Morag, Y Barak, D Goldman, Y Hadar…

... be in charge created by for the focusing on sense made out created by the comprehensive
forensics education a ... Previous SectionNext Section Designer cellulosome technology also has
also been recommended to your indigenous microbial enzymatic destruction created by ...

[HTML] Molecular multiplying associated with polymerases for resistor to environmental inhibitors

C Baar, M d'Abbadie, A Vaisman, ME Arana… - Life Sciences

... associated with plans in medicine and biology running ranging from analysis and diagnostics,
prognostics, forensics to molecular ... using the QiaAmp DNA miniature apparatus (Qiagen) being
for each and every manufacturer's instructions, upcoming microbial standard protocol C ...

So incredibly weird. Is there some site out there that figured out how to scam Google Scholar into linking to them? Anyone seen anything like this before?

Yes, microbes are likely important everywhere, but evidence would be nice (re Atlantic piece on Soil)

2013-06-12T09:53:00.003-07:00

Just read this article in the Atlantic: Healthy Soil Bacteria, Healthy People - Mike Amaranthus & Bruce Allyn - The Atlantic. It is interesting in a few ways. But what got me a bit up in arms about it is the number of statements and claims that are not backed up by any reference to evidence. Consider the following:

"Just as we have unwittingly destroyed vital microbes in the human gut through overuse of antibiotics and highly processed foods, we have recklessly devastated soil microbiota essential to plant health through overuse of certain chemical fertilizers, fungicides, herbicides, pesticides, failure to add sufficient organic matter (upon which they feed), and heavy tillage."

OK - sounds serious. But is it really true? Have pesticides really devastated soil microbiota? What about tillage? Seems possible, but also seems possible that this would not be true. Would be nice to see the evidence behind this claim.

How about this one:

"Reintroducing the right bacteria and fungi to facilitate the dark fermentation process in depleted and sterile soils is analogous to eating yogurt (or taking those targeted probiotic "drugs of the future") to restore the right microbiota deep in your digestive tract."

Sounds good too. But way too overly simplistic. I mean - probiotics for people are a bit of a complicated mess right now. Some work. Most probably don't. Most of the claims are overblown. So to say we know how to do this well in "soil" definitely seems to be an overstatement. Again, specific evidence for this would be nice.

And then this:

"Due to new genetic sequencing and production technologies, we have now come to a point where we can effectively and at low cost identify and grow key bacteria and the right species of fungi and apply them in large-scale agriculture."

Soil is a very very complicated place in terms of microbes. I personally think we are really far away from this utopian view of growing the key species to apply them to large scale ag. Evidence that this is true? I don't know of much. Yes we can sequence things. We can sequence a lot of things. But "identify and grow key bacteria and the right species of fungi" - I think we are far from being able to do this robustly.

Another claim in the article has some ring of truth:

We can sow the "seeds" of microorganisms with our crop seeds and, as hundreds of independent studies confirm, increase our crop yields and reduce the need for irrigation and chemical fertilizers.

Yes, this has a ring of truth. Certainly there are studies - many of them - involving adding microbes to seeds and how that impacts yield and nutrient and water requirements. And without a doubt in many cases such inoculation can help in many ways. But the "hundreds of independent studies" claim is a bit misleading as there are also many cases where inoculation does not help. So we should be cautious before adding microbes to seeds becomes the equivalent of probiotics for people. Not all probiotics that are claimed to help people actually do anything. And not all microbes added to seeds will do much of anything useful either.

How about the claim:

Thus the microbial community in the soil, like in the human biome, provides "invasion resistance" services to its symbiotic partner. We disturb this association at our peril

Sounds good. And has a ring of truth too. And in general I agree with the sentiment that we should not screw with ecosystems without recognizing that the microbes in those systems may play important and useful roles. However, just because SOME microbes play important and useful roles in systems does not of course mean that ALL are ones we want to keep. There will be some in the soil that damage plants and hurt yield and pathogen resistance just as there will be some that are "good" from our point of view.

And then there is this

We are now at a point where microbes that thrive in healthy soil have been largely rendered inactive or eliminated in most commercial agricultural lands; they are unable to do what they have done for hundreds of millions of years, to access, conserve, and cycle nutrients and water for plants and regulate the climate.

And also

The mass destruction of soil microorganisms began with technological advances in the early twentieth century.

Sounds nice. But I don't really know of much evidence that the microbes have been rendered inactive or eliminated in commercial agricultural lands.

I suppose this is all building up to the following

Fortunately, there is now a strong business case for the reintroduction of soil microorganisms in both small farms and large-scale agribusiness. Scientific advances have now allowed us to take soil organisms from an eco-farming niche to mainstream agribusiness. We can replenish the soil and save billions of dollars.

and

For all these reasons, bio fertility products are now a $500 million industry and growing fast. The major agricultural chemical companies, like Bayer, BASF, Novozymes, Pioneer, and Syngenta are now actively selling, acquiring or developing these products.

So --- this is in a way an article promoting the financial benefit of adding microbes to soil. I think this is reasonable although not completely convincing. Alas, after reading the article I discovered this about one of the authors

Mike Amaranthus is the chief scientist at Mycorrhizal Applications, Inc., a company working on innovations in soil biology.

This is not to say that someone with a financial role in convincing the world to add microbes to soil cannot be trusted to provide a good guide about microbes in the soil. But it would have been nice for this to be mentioned more prominently in the article. Many of the claims in this article do not pass the smell test to me. And all of them seem to be pointing towards a solution involving a company that one of the authors is involved in. If this were about human medical treatments many many people might get bent out of shape by this. Again, not to say people with financial interests cannot write good articles. But the potential for conflicts in such cases, as in the case here, is great. And thus we should view with a tint of extra skepticism some of the claims made by such individuals. And in this case here I already felt uncomfortable with many of the claims. I think the Atlantic could do better and could certainly require the author to make more clear in the article itself what the author's personal interest in the claims are.

Important read for those interested in gender, family & academia: Do Babies Matter

2013-06-07T07:30:00.001-07:00

Just got pointed to this by Julie Huber on Facebook: New book on gender, family and academe shows how kids affect careers in higher education | Inside Higher Ed. The book is "Do Babies Matter? Gender and Family in the Ivory Tower." This looks like a very important book and is especially relevant to me in my role in the UC Davis ADVANCE project where we are working on related issues. It is from Mary Ann Mason at Berkeley Law School, Nicholas Wolfinger from Utah, and Marc Goulden from the UC Berkeley Office for Faculty Equity and Welfare. It is definitely worth checking out.

I am ordering it right now ...

Better late than never - video interview of me from #AAAS2012 - Evolvability, the Built Environment and Open Science

2013-06-06T11:29:00.000-07:00

Well, better late than never. An interview of me by Stan Malloy at the AAAS Meeting from February 2012 has been posted at MWV Episode 72 - Jonathan Eisen - Evolvability, the Built Environment and Open Science. From their site

On this episode, Jonathan talks about "evolvability," the probability that organisms can invent new functions. To do this, he has been using genome data in conjunction with experimental information to try and understand the mechanisms by which new functions have originated.

Another area of interest for Eisen is the "built environment." We live and work in buildings or structures which are non-natural environments, new to microbes. These "new" environments represent a controlled system in which to study the rules by which microbial communities form.

Jonathan is interested in these environments as basic science vehicle and he shares the importance of studying the built environment for science and human health.
Finally Jonathan explains his interest in "open science," the ways in which science is shared. At it's core, Eisen wants to leverage cheaper technologies to accelerate the progress of science in a positive way.

This episode was recorded at the American Association for the Advancement of Science Meeting in Vancouver, British Columbia on February 18, 2012.

See the interview via Youtube below:

Tweets from Nancy Moran's talk at #UCDavis on "Two sides of symbiosis" storified

2013-06-06T07:34:00.001-07:00

I went to a talk yesterday by Nancy Moran at UC Davis. Nancy is one of my science heroes. I have worked on a few projects with her and am just a big fan of her body of work on symbioses. I have written about her work her on this blog many times before including

Anyway - I live tweeted her talk and then tried to "Storify" those tweets but Storify was not working well. Thankfully Surya Saha made a storify which I then edited (with his permission).

@phylogenomics's tweets re Nancy Moran's talk at #UCDavis storified bit.ly/111dHgj #symbiosis CC @symbionticism
— Surya Saha (@SahaSurya) June 6, 2013

The storify is embedded below:

Some new preprints of interest and comments on "The case for preprints in biology"

2013-06-06T06:46:00.001-07:00

Getting more and more into preprints (see for example these posts Guest post from Jake Scott: Building trust: a sine qua non for successful acceptance of preprints in the biological sciences and More bio preprint discussion sites ...). So am starting to browse preprint servers a bit more and I have found some recently posted preprints of interest:
http://arxiv.org/abs/1306.1206

From arVix:

From PeerJ preprints

Supertrees based on the subtree prune-and-regraft distance from Whidden et al.
Microenvironmental variables need to effect intrinsic phenotypic parameters of cancer stem cells to affect tumourigenicity from Jake Scott et al.
GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework from Rob Beiko et al.

I wondered - where else might one find Biology themed preprints. And a little google searching let me to this new PLOS Biology paper which somehow I had missed a few weeks ago: The Case for Open Preprints in Biology

(Full citation: Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, et al. (2013) The Case for Open Preprints in Biology. PLoS Biol 11(5): e1001563. doi:10.1371/journal.pbio.1001563)

Wow - how perfect. In their paper they not only lay out the case for why preprints would be a good thing in biology but discuss some of the options. And in addition to PeerJ and arXiv they point to Figshare, Github, and ResearchGate.

Below is Figure 1 from their paper:


Figure 1. It can take several months before a submitted paper is officially published and citable.. Meanwhile, few people are aware of the research that has been done since, typically, only close colleagues are given access to the preprints. With public preprint servers, the science is immediately available and can be openly discussed, analyzed, and integrated into current research. doi:10.1371/journal.pbio.1001563.g001

They also show that in arXiv submissions in the qBio section are going up but not nearly as much as submissions in other fields

Figure 2. Submissions to the quantitative biology section lag behind physics, mathematics, and computer science. Data from [19]. doi:10.1371/journal.pbio.1001563.g002. The reference to 19 is to Warner S (2012) Data for arXiv submissions by subject and year. Available: http://dx.doi.org/10.6084/m9.figshare.96966. Accessed 14 April 2013.

I think this paper is worth a look for anyone interest in scientific publishing. I like their last line and will end my post with it:

Preprints are simply bypassing this model for what we believe is the progress of science: they speed up the dissemination of scientific discoveries and put on readers' shoulders the responsibility to judge originality and pertinence.

I am highly skeptical of the CHORUS system proposed by scientific publishers as an end run around PubMed Central

2013-06-04T13:13:00.001-07:00

Just read this news story ... Scientific Publishers Offer Solution to White House's Public Access Mandate - ScienceInsider

It reports on an effort by various scientific publishers to create something they call "CHORUS" which stands for "Clearinghouse for the Open Research of the United States." They claim this will be used to meet the guidelines issued by the White House OSTP for making papers for which the work was supported by federal grants available for free within 12 months of being published.

This appears to be an attempt to kill databases like Pubmed Central which is where such freely available publications now are archived. I am very skeptical of the claims made by publishers that papers that are supposed to be freely available will in fact be made freely available on their own websites. Why you may ask am I skeptical of this? I suggest you read my prior posts on how Nature Publishing Group continuously failed to fulfill their promises to make genome papers freely available on their website.

See for example:

We need to make sure such papers are freely available permanently and the only way to do this is via making them available outside of the publishers own sites. Pubmed Central seems to be a good solution for this. I would be happy to hear other possible solutions - but leaving "free" papers under the control of the publishers is a bad idea.

Guest post from Jake Scott: Building trust: a sine qua non for successful acceptance of preprints in the biological sciences

2013-06-03T09:13:00.001-07:00

Today I am happy to have a guest post from my friend and colleague Jake Scott. The topic of the day is preprints in biology and medicine.

Hi - I'm Jake Scott. I met Jonathan last year when he and I spoke at TEDMED 2012. Both Jonathan and I have posted recently about the need for, and (slowly) growing movement in the biological sciences to post #preprints of manuscripts in openly accessible fora to circumvent some problems associated with standard academic publishing. Most worrisome are the issues surrounding #openaccess and the length of time it takes to get information from one's brain to the literature - drastically slowing down the pace of science.

This has worked GREAT in the physics community, where this trend really began quite some time ago when the high energy physicists started the arXiv. Now, the precedent is set, and no one in physics bats an eye about sticking their paper on the arXiv, and cite other works presented there as standard publications.

The climate in biology, sadly, is much different. Whether this is because of a more competitive climate for funding, or just a field diluted by more talented scientists, I don't know. But there is a pervasive attitude of fear and mistrust around the idea of preprints.

Before you read on (and become biased by my opinions) take a few second (really, probably 1.5 minutes) and take this quick survey:

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When I preach to my biological colleagues about the virtue of pre-print servers, I most often, I hear:

Why should I post my papers on a pre-print server where anyone can see it before it is published!? They could scoop me!

I honestly don't understand this argument, but I hear it all the time. By nature of pre-print servers, like the arXiv, the idea is yours! Time and date stamped. And, better yet, it is completely #openaccess, free of charge, and helps move science along at a better pace. Only a very few journals have problems with posting of pre-prints before they get their (greedy) hands on the results of all your hard work, but most are totally OK with it.

The arXiv isn't really interested in shopping its (free) service out to the biological sciences, not because they don't think it would be of value, but because it just doesn't have the infrastructure to support it. This is a problem that is being with newly created repositories like Nature Precedings, PeerJ and soon, the bioRxiv. So, the only thing holding us up is, IMHO, trust.

How can we rectify this?

I think the way forward is to create something that we are all missing now, except when we are at our home conference, among friends or if we got into a time machine and went back 100 years - community.

Science is such a juggernaut now that putting your work onto a pre-print server where anyone in the world can see your as of yet unvetted work can be daunting. Worse, the idea of commenting on it is a tough sell when the world is a witness. I think we need to (re)create micro-communities of our specialist peers where these initial discussions can be held. Two examples of this are Haldane's Sieve and more recently created, an initiative I'm involved with, Warburg's Lens. These two sites are micro-communities where population and evolutionary biologists, and mathematical oncologists (respectively) congregate to discuss pre-prints culled from any repository but necessarily of interest to the micro-community.

This does two things: it allows a common place for easy browsing in topics of interest to a specialist (like reading your favorite journal), and increases the chances that the readers and commenters are your (at large) peers.

So, those are my two cents. #Openaccess for all is coming, and preprints are a part of the wave. The sooner we all adopt an open science attitude, the sooner we'll come to the conclusions and make the discoveries that make doing science AWESOME. There is no better job than science, and sharing and communication are central to it

So START SHARING your science. Commit to this - when you are ready to submit your next paper, put that version on a pre-print server as you start the submission process. Then tweet about it, G+ about it, blog about it, do whatever, but let your peers know!

Anyone else interested in starting a micro-community discussion forum, or to just discuss this issue further, please contact me.

If you are against it - please leave some comments about why, I'd love to try to convince you otherwise! If you are a biologist (or know one) who DOES post pre-prints, weigh in and share your good experiences!

About me: I am a radiation oncologist and I approach the understanding of cancer like my original training in physics taught me - from the ground up, using the descriptive language of mathematics. Using established mathematics in new ways, guided by the principles of evolution, I hope to better understand (and maybe treat!) cancer. I am a proud member of the Integrated Mathematical Oncology group at the Moffitt Cancer Center and the Centre for Mathematical Biology at Oxford University. You can follow me on twitter @CancerConnector or read my blog Connecting the Dots.

More bio preprint discussion sites ...

2013-05-30T14:31:00.001-07:00

Another Bio-related preprint discussion site has popped up: Connecting the Dots: Warburg's Lens: A pre-print discussion forum for the mathematical oncology community. From my friend and colleague Jacob Scott. A good addition to Haldane's Sieve. Seems to me preprints are the next wave in open access in biology ...

Re-reading this on "Why women leave academia and why universities should be worried"

2013-05-29T17:09:00.001-07:00

Been reading some somewhat old material out there on women in academia. I am getting more and more interested in this issue especially as I have become more involved in the UC Davis ADVANCE Program. The ADVANCE program from the National Science Foundation "aims to increase the participation and advancement of women in academic science and engineering careers."

I was pointed to this Guardian article from 2012 today based on "The chemistry PhD: the impact on women's retention": Why women leave academia and why universities should be worried | Higher Education Network | Guardian Professional. This Guardian article has a lot of detail and links to other information. Definitely worth checking out if you had not seen it or forgotten it.

The human microbiome never looked so good

2013-05-28T08:41:00.000-07:00

Another week, another microbial art project --- this one is from Erno-Erik Raitanen who is creating self portrait "bacteriograms" using his own microbiome. See stories at Petapixel: Photographer Erno-Erik Raitanen Creates 'Self-Portraits' Using His Own Bacteria and CoCreate: INSTAGERMS: SEE A PHOTOGRAPHER’S STRANGELY BEAUTIFUL PORTRAITS OF HIS OWN BACTERIA.

From CoCreate

“The process itself is pretty much a replication of the processes used in microbiology to cultivate bacteria on agar in petri dishes,” Raitenan says. “Instead of agar, I just used the film gelatin as my growth medium. As the bacteria grows, it consumes the gelatin layers that together make all the colors in a color photograph, and creates all these random patterns and colors.”

The human microbiome never looked so good ...

Is the New York Times microbial diversity centric?

2013-05-27T19:35:00.003-07:00

The answer to the question in the title - I think - is yes. Here are some recent stories in the Times on topics of relevance to microbial diversity.

Getting to Know Our Microbial Roommates 5/27/13 Peter Andrey Smith
Microbes Hitch a Ride on the Subway 5/27/13 by Peter Andrey Smith
Behind the Cover Story: Michael Pollan on Why Bacteria Aren't the Enemy ... 5/20/13 by Rachel Nolan
Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome 5/15/13 by Michael Pollen
The Hidden World of Soil Under Our Feet 5/111/13 by Jim Robbins
Sucking Your Child's Pacifier Clean May Have Benefits - NYTimes ...- 5/6/13 by Anahad O' Connor
Eggs, Too, May Provoke Bacteria to Raise Heart Risk - 4/24/13 by Gina Kolata
Prognosis: Circumcision and AIDS - 4/18/13 by Nicholas Bakalar
The Boy With a Thorn in His Joints 2/1/13 - by Susannah Meadows
Malnourished Gain Lifesaver in Antibiotics 1/30/13 by Denise Grady
Antibiotics Are a Gift to Be Handled With Care - 11/12/12 by Perri Klass
Fermentation Guru Seeks Out New (and Old) Flavors - 9/17/12 by Jeff Gordinier
WELL - Vital Signs - Risks - Weight Implications for Infant Antibiotics ... 8/28/12 by Nicholas Bakalar

Plus - of course - there is a continuous stream of information on microbes from Carl Zimmer who writes frequently for the NY Times. Perhaps the best example of this is his coverage of the Human Microbiome Project papers: Studies of Human Microbiome Yield New Insights June 18, 2012. But there have been and I am sure will be others.

Sure - the NY Times is not the only place with a bunch of stories about microbial diversity and microbiomes. But they do seem tto have a good ratio of "diversity" themed coverage vs. germoophobia themed topics which are common in many other places.

Twisted Tree of Life Award #16: Nature & Authors doing taxonomic alchemy converting an archaeon to a bacterium

2013-05-27T13:07:00.001-07:00

Well, this is one of the bigger screw ups in terms of evolution I have seen at a major journal in a while. See the following paper in Nature: The catalytic mechanism for aerobic formation of methane by bacteria : Nature. The paper discusses some functions of "the ocean-dwelling bacterium Nitrosopumilus maritimus." Some of what is reported in the paper is perhaps interesting (alas I do not have access). But painfully, there is one big big big big mistake - you see Nitrosopumilus maritimus is not a bacterium. It is an archaeon (see for example this paper on its genome).

I got pointed to this by Uri Gophna (in an email and in a comment on my blog)(all see this on Twitter) Sure - some people debate the structure of the tree of life. But I am pretty certain the authors here (Siddhesh S. Kamat, Howard J. Williams, Lawrence J. Dangott, Mrinmoy Chakrabarti & Frank M. Raushel) are not trying to make a statement about monophyly of bacteria or just what archaea are. They just made what seems to be a colossal screw up. And Nature not only let them, but added to it with things like their "Editors Summary":

Novel bacterial biosynthesis of methane
Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S-adenosyl-L-methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate.

And for this taxonomic alchemy (converting an archaeon to a bacterium) I am awarding them and Nature my coveted "Twisted Tree of Life Award #16".

UPDATE 5/28 7AM

I love the ad that came up while I was writing this post and searching for some information. I think Nature could use the services from this ad:

I so want a few 1000 of these: Mobile Robotic Laboratory from MBARI

2013-05-27T11:21:00.001-07:00

Thanks to Michael Ferrari for pointing me to this:: Mobile Robotic Laboratory Will Track Ocean Toxins - Popular Mechanics. The article discusses some developments at MBARI for mobile sensor / sampler devices that could be used for various marine microbiology studies. A few years ago I got a tour of MBARI from Alex Worden (see pics below) and got to see some of their toys but many of the developments in this article are new to me. I can't wait until it is possible to deploy a few hundred thousand of these and get massive amounts of data ...

ASM2013 - One of the best parts - meeting the "Young Ambassadors"

2013-05-26T17:53:00.001-07:00

I attended the American Society for Microbiology (ASM) meeting in Denver last week. It was a bit overwhelming as usual, with the 1000s of people there. One surprise for me was an invitation to a after dinner party hosted by Nathan Wolfe and others from Metabiota. I am not really a big fan of parties (as many who know me know) but this was small and even better it was mostly populated by the recipients of the ASM International Young Ambassador Award winners. Wolfe was one of the keynote speakers at the ASM Meeting and I think he was hosting this party in part as a reception for the Young Ambassador's.

For more on the winners see

Anyway - it was very interesting to talk to many of them. And I even got a picture with one of them - Yu Xia from Hong Kong (we were trying to form some sort of Tree of Life with our fingers).

All societies have their good and bad parts. Sponsoring Young Ambassadors from other countries is definitely one of the very good things ASM does.

Worth a look: PhyloFacts FAT-CAT web server: ortholog identification & function prediction

2013-05-23T08:59:00.001-07:00

Quick post. This seems like a potentially useful resource and tool: The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

Abstract:
The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.

Story behind the paper: from Jeremy Barr on "Bacteriophage and mucus. Two unlikely entities, or an exceptional symbiosis? "

2013-05-22T10:30:00.000-07:00

I am pleased to have a guest post in my "Story behind the paper" series. This one is from Jeremy Barr in Forest Rohwer's lab about a new PNAS paper.

Bacteriophage and mucus. Two unlikely entities, or an exceptional symbiosis?

By Jeremy J. Barr

Our recent research at The Rohwer Lab at San Diego State University investigates a new symbiosis formed between bacteriophage, viruses that only infect and kill bacteria, and mucus, that slimy stuff coating your mouth, nose, lungs and gut.

Bacteriophage, or phage for short are ubiquitous throughout nature. They are found everywhere. So it shouldn’t surprise you to learn that these phage are also found within mucus. In fact, if you actually sat down and thought about the best place you would look for phage, you might have picked mucus as a great starting point. Mucus is loaded with bacteria, and like phage, is found everywhere. Almost every animal uses mucus, or a mucus-like substance, to protect its environmentally exposed epithelium from the surrounding environment. Phage in mucus is nothing novel.

But what if there were more phage in mucus? What if the phage, immotile though they may be, were actually sticking within it?

It turns out that there are more phage in mucus, over four times more phage, and this appears true across extremely divergent animal mucosa. But this apparent increase in phage could very simply be explained by increased replication due to access to increased bacterial hosts residing within mucus layers. But this assumption alone doesn’t hold up. Applying phage T4 to sterile tissue culture cells resulted in significantly more phage sticking to the cell lines that produced a mucus layer, compared to those that did not. There were no bacterial hosts for phage replication in these experiments. Yet still, more phage accumulated in mucus.

Surely the law of mass-action could explain this apparent accumulation. The more phage we apply to an aqueous external environment, the more phage will diffuse into and enter the mucus layer, being slowed in the process due to the gel-like properties, and eventually resulting in an apparent accumulation of phage in mucus. But when we removed mass-action from the equation, and simply coated mucus-macromolecules onto a surface, still more phage stuck. Our assumptions were too simple.
Phage are ingenious. They have evolved, traded, and disseminated biological solutions to almost every biological problem, whether we are aware of it or not. So in order to solve the phage-mucus quandary, we needed to look to one of the most ubiquitous and populous families of proteins found in nature: the immunoglobulin superfamily. This protein fold is so ubiquitous that it appears in almost every form of life. Within our own bodies, it is the protein that affords us immunological protection. Bacteria utilize the protein fold to adhere to each other, to surfaces, and as a form of communication. And as it would turn out, phage make an innovative use of the same protein fold to stick to mucus.

Immunoglobulin, phage and mucus, are all pervasive throughout environments. The interaction between these three entities forms a new symbiosis between phage and their animal hosts. This symbiosis contributes a previously unrecognized immune system that reduces bacterial numbers in mucus, and protects the animal host from attack. We call this symbiosis/immunity, Bacteriophage Adherence to Mucus, or BAM for short.

Our work is open access and available through PNAS .

If you would like to read further about BAM and its implications see these two commentaries by Carl Zimmer at National Geographic and by Ed Yong at Nature News

Cool bacterial art makes gizmodo #MicrobialArt

2013-05-20T19:45:00.001-07:00

Quick post - cool bacterial art project has made Gizmodo. See Bacteria Never Looked So Beautiful. From an Art of Science competition at Princeton. I wonder what Artologica - my favorite microbial art artist - thinks of this.

For some other posts about microbial art see:

Thoughts on Citizen Microbiology and upcoming session at #ASM2013

2013-05-19T11:24:00.003-07:00

I am sitting on a Southwest Airlines flight heading to Denver for the American Society for Microbiology 2013 meeting. At 3 PM today I am scheduled to co-chair (with David Coil from my lab) a session on “Citizen Microbiology” (well the full title is Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public). The schedule of the session is at the bottom of this post but it promises to be very interesting and exciting (no bias here at all).

As far as I know, this is the first session ever on “Citizen Microbiology” at a large meeting of any kind. We held a small workshop at UC Davis in January of 2012 on Citizen Microbiology but that was quite small. I note - I use a very broad definition for Citizen Microbiology including basically any project that engages the public in some way to participate in a research project relating to microbes. This is the perfect time to have such a session at a large meeting and the ASM General Meeting is an ideal setting. There are a series of converging forces that makes this timing ideal including:

There is a growing appreciation of microbes and the role they play on the planet. Some of this appreciation is broad - covering all microbes - all the time - everywhere. But much of it is due to a growing interest in the microbes closer to us - those that live in and on us (the human microbiome) - those that live in and on plants and animals and other organisms we care about - and those that live in the places where we spend much of our time (the microbes of the built environment). I mean - come on - everyone is talking about fecal transplants now in public - in cover stories of the NY Times Magazine and in Ted talks.

Technological and scientific advances have made it possible to better sample the microbes found in any particular location. Clearly, DNA sequencing technology and associated analytical tools are a central component of these advances, but other factors are important too.
The world is becoming more and more digital which makes the sharing of information (which is key to Citizen Science) easier and better. And social media has made it easier to communicate and discuss actions like Citizen Microbiology.
Citizen Science is growing by leaps and bounds in other areas (e.g., check out http://www.scistarter.com).
Crowdsourcing (not the same thing as Citizen Science - more on this another time perhaps) is also growing in leaps and bounds.
Crowdfunding is providing new ways to fund scientific activities.
Sensors of all kinds are getting cheaper and easier to use and are being deployed widely.
Many people are becoming more and more interesting in recording information about themselves and sharing it with others.
The “open science” movement is making the literature, software, methods and data and more available to everyone with no or few restrictions thus allowing for more people in diverse environments to become engaged in research.
Microbiology education and outreach is spreading with some great journalists and diverse other sources of information including hundreds of microbiology blogs and many other forms of social media being used.

These are but a few of the reasons why I believe the time is right for Citizen Microbiology. But there are also what I would call somewhat negative reasons why the time is right too. These include

Germophobia is rampant and fueled by media hype and marketing forces.
We have done, and continue to do, serious harm to our microbial world. Antibiotics are overused. Antimicrobials are in everything. More and more children and missing out on vaginal birth. And so on
Although our understanding of the importance of microbes is everywhere, there are also many who are overselling what we know - claiming that probiotics will cure all ailments for example.
Some information about microbes that is out there on the web is, well, less that ideal
The ethics of engaging the public in studies of microbes are not fully appreciated by some and not completely understood by most.

So this is both an exciting and a critical time for microbes and microbiology. And I hope that this session will not only help launch the field of Citizen Microbiology, but will help get everyone to think about the bigger issues and how to move the field forward in the right directions. For there is so much we need to do and think about including

Ethics
Funding
Openness and sharing
Visualization
Analysis tools
Communication
Outreach

And of course - the people at the session are not the only ones engaged in Citizen Microbiology or related activities (see a list we made a while back here). If you are doing a project please post something about it here. And if you are not doing a Citizen Microbiology project - well - why not? Get your act together.

Anyway - got to put away the computer as we land in Denver soon and I will rush off to the conference center, hopefully on time, to chair this exciting session. And I hope to see you there or have you follow online (check out the Twitter hash tag #ASM2013). And keep your eyes open for more excitement in this area.

-------------------------
Today’s session at ASM 2013:

(Division W Lecture) Authentic Research for Novice Scientists: Phage Discovery and Genomics by Undergraduate Students
Graham Hatfull;
Univ. of Pittsburgh, Pittsburgh, PA.

Understanding Human Influence on Microbial Distribution Patterns in the United States: A Citizen Science Approach
G. Barguil Colares1, J. Marcell1, D. Smith1,2, J. A. Eisen3, J. Gilbert1,2;
1Argonne Natl. Lab., Lemont, IL, 2Univ. of Chicago, IL, 3UC Davis, Davis, CA.

The Home MIcrobiome Project: Learning the Lessons of Citizen Science and Communication
J. A. Gilbert, D. Smith;
Argonne Natl. Lab., Lemont, IL.

The New National Lab: How Citizen Science is Transforming American Research
Darlene Cavalier;
Sci. Starter, Sci. Cheerleader, Philadelphia, PA.

Sequencing the Human Microbiome with Citizen Science
Z. Apte1, J. Richman2, W. Ludington3;
1uBiome, Inc, San Francisco, CA, 2Oxford Univ., Oxford, UNITED KINGDOM, 3Univ. of California, Berkeley, Berkeley, CA.

The American Gut Project: Challenges and opportunities for crowdsourcingmicrobial ecology
Antonio Gonzalez Peña;
Univ Colorado at Boulder, Boulder, CO.

Public Science in Private Places: A Study of the Microbial Ecology of One Thousand Houses in Fifty States and Five Countries
Rob Dunn;
NC State Univ., Raleigh, NC.

UPDATE: Notes from the Session Added 5/23

Here are some notes from the meeting:
Meeting Report: ASM 2013 in Denver, Day 1
ASM 2013, Day 1: From Oceans to Guts
Citizens doing Science, or Science on Citizens? (ASM 2013: Post 1)
Symbionticism: ASM 2013 LINKS
Storify by SPONCH

My storify embedded below

Excellent piece in the NY Times Magazine by @michaelpollan "Some of my best friends are germs" #ASM2013

2013-05-19T06:41:00.001-07:00

Quick post here. There is a really nice piece on in the New York Times Sunday Magazine by Michael Pollan on the human microbiome: Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome. In it he discusses how he had his microbiome typed by the American Gut Project and he discusses browsing through the output. He also discusses a diversity of issues in the microbiome and work of various folks. People featured include Justin Sonnenburg, Rob Knight, Burce German, Catherine Lozupone, Stanley Falkow, Jeffrey Gordon, Michael Fischback, Maria Gloria Dominguez-Bello, Martin Blaser, Ruth Ley, Andrew Gewirtz, Patrice Cani, Erica Sonnenburg, and Stephen O'Keefe. The article does a really good job of highlighting why the microbiome is important yet does not oversell what we know at this point.

I note - Pollan came to UC Davis as part of his research for the article a little while back. Below are some pics of him getting a tour of the UC Davis LEED Platinum brewing facility. Anyway the article is definitely worth a look. And just in time for the ASM 2013 Meeting which I am about to head to this AM.