Guest post from Joshua Weitz: Talking about the PI Sabbatical Beforehand: A Brief Guide for Faculty, Postdocs, and PhD Students in the Sciences

Guest Post by Joshua Weitz, Associate Professor, School of Biology and School of Physics, Georgia Institute of Technology

Introduction

I direct a theoretical ecology and quantitative biology group based in the School of Biology at Georgia Tech.  I am going on a 9 month “leave” (Georgia Tech does not call them sabbaticals) to the Department of Ecology and Evolutionary Biology at the U of Arizona in Tucson, AZ from August 2013-May 2014 where I will be based in Matthew Sullivan’s Tucson Marine Phage Laboratory.  In preparation for this leave, our group held an interactive discussion on challenges and opportunities arising from the PI sabbatical for faculty, postdocs and PhD students in the sciences.  The discussion took place in four parts in a one-hour period.  Below I describe the setup of the discussion followed by specific recommendations for faculty, postdocs and PhD students prior to the PI sabbatical. 

How to Talk about the PI Sabbatical

Part 1 – the setup: I asked for a show of hands of group members who had thought about how my sabbatical would change the group and its dynamics?  Nearly all members raised their hands.  When asked, the group members also noted that they were most concerned about how the sabbatical would affect them.  Hence, in an effort to try and understand the effect of the sabbatical on all members, we split into three small discussion groups which were asked to identify challenges and opportunities for (i) the PI; (ii) postdocs; (iii) PhD students. 

Part 2 – small group discussion: The individual groups talked about how the sabbatical would affect different group members.  There are currently 9 members in the group (not including the PI), so we divided into three groups of three (I did not actively participate in the small group discussions, but did check in on all three groups).  The PI group was comprised of one postdoc, 1 graduate and 1 undergraduate.  The postdoc group had 1 postdoc and 2 graduate students.  The grad student group had 3 graduate students.  Hence, the first item of discussion was an effort to identify issues at stake at each career stage.  Then, the groups began to discuss how the sabbatical might change business as usual.  The groups spoke for ~15 minutes.

Part 3 - reporting: Challenges and opportunities were identified for each of the three categories.  A number of salient themes emerged that serve as general recommendations.   The consensus was that a number of common themes would emerge prior to a sabbatical although each science research group may differ in its own interactions.  Our presumption is that the PI was going alone and this shaped the nature of our recommendations.  First, as suggested by one of the students, there was a sense that the PI sabbatical would lead the students into a “Spiderman situation” in the sense that “with great power comes great responsibility”.  The PI sabbatical would lead to greater independence for group members and that this independence involves greater need for self-motivation, taking a holistic (long-term) view of one’s research, and increased pre-planning given the changes to the PI’s availability.  Second, clear communication is essential. For example, if a PI plans to be incommunicado for long stretches of time, this may be manageable (even if non-ideal from a student perspective), so long as provisions have been made to handle both the administrative and research duties that the PI normally would handle.  As a rule of thumb, the greater the change in PI availability, the greater the need for pre-planning to ensure that students and postdocs remain on track for research, career and personal development goals.

Part 4 – the view of the PI:  I provided additional feedback, tailored to the group and specifically addressed an issue that could create the most anxiety: my availability for one-on-one interactions.  I also distributed an initial recommendation list, modified here in light of group discussion. 

Storify-based notes on #SMBE13 session on evolution of microbes and their genomes

Just finally getting notes up from the SMBE 2013 meeting session on "Diversity and evolution of microbes and their genomes" that I chaired.  After some issues with Storify I managed to record a "storification" with Twitter posts from the session. It is embedded below.

The talks were as follows:
Invited Talks

• Holly Bik, UC Davis, Microbial Metazoa and the Taxonomic Abyss 
• Lauras Katz, Smith College, Genome Dynamics across the Eukaryotic Tree of Life 
• Jennifer Gardy, Of Snow and Short Reads: How Microbial Genomics Is Changing Public Health, British Columbia Center for Disease Control 
• Tanja Woyke, Insights into the Phylogeny and Coding Potential of Microbial Dark Matter DOE Joint Genome Institute 

Talks selected from submitted abstracts

• Pedro H. Oliveira: A Comparative Genomics Approach Provides New Insights into the Distribution and Evolutionary History of Restriction Modification Systems in Bacteria, Institut Pasteur 
• Daniel J. Wilson, Genomic Insights into Within-Host Evolution and Pathogenesis in Staphylococcus aureus, University of Oxford 
• John P. McCutcheon, Extensive Horizontal Gene Transfer Complements Missing Symbiont Genes in Mealybugs, U. Montana, 
• Florent Lassalle, Biased Gene Conversion Shapes the Bacterial Genome Landscape, University of Lyon

New paper from the Eisen lab: Sporulation phylogenetic profiling

Quick post here. This paper came out a few months ago but it was not freely available so I did not write about it until now as it just showed up in Pubmed Central. It was published in the Journal of Bacteriology but they do not release material for free onto their website or Pubmed Central for a few months. Alas, as I was kind of a peripheral player in the main work in the paper (I helped them with the phylogenetic profiling part) I did not end up pushing as hard as I should have for paying the open access fee to make it available earlier / openly.

Here is a link to the paper: Gene Conservation among Endospore-Forming Bacteria Reveals Additional Sporulation Genes in Bacillus subtilis.

It is from Richard Losick's lab at Harvard and it is one I am very very pleased with. Basically, Losick's lab has been studying sporulation in Bacillus subtilis like forever. And in 2005 we wrote a paper on the genome of another member of the same phylum that also sporulates (Carboxydothermus hydrogenoformans): Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901.

And in that paper we did a phylogenetic profile based analysis of sporulation genes and found a set of genes that were (on average) in all the sporulating species and not in non sporulating species.  Among this set of genes were quite a few that nobody had ever shown to be involved in sporulation.  We predicted that they were likely involved in sporulation. 

And then I waited, since I did not really work on sporulation.  And in a series of discussions with Losick and people in his lab found out that they had evidence that many of these genes in B. subtilis were involved in sporulation.  And the latest paper is in essence a follow up on some of those discussions (well, really it is a lot of work from Losick's lab with a little input from those conversations to guide some of the experimental tests). 

New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

(Cross post from my lab blog)

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my choice – lead author did not choose that option and I was not really in the loop when that choice was made).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. [Proc Natl Acad Sci U S A. 2013] – PubMed – NCBI.

Anyway – it is now in Pubmed Central and at least freely available so I felt OK posting about it now.  It is in a way a follow up to the “A phylogeny driven genomic encyclopedia of bacteria and archaea” paper (AKA GEBA) from 2009 with this paper a zooming in on the cyanobacteria.

Dangerous overcrowdng at the Aquarium by the Bay in San Francisco

Bad bad bad experience at the Aquarium by the Bay on 7/7/13.

We went into the tunnel area (where you are in essence inside the big tank). And they announced they were having a shark feeding. We (11 of us including four kids) waited in the tunnel where they told us to.

The tunnel has a moving walkway in it on one side of the floor that slowly moves people through the area. On the other side of the floor there is solid ground. At the end of the walkway is a waiting area for the elevator. As the show started they turned on the walkway and people started moving past us.  The walkway was wall to wall people.

As they turned on the walkway, the elevator could not keep up with the crowd pouring in off the walkway and it started to get very crowded there. We decided to try and get out because it felt unsafe in the tunnel. We squeezed onto the moving walkway (my wife first, with my two kids and then me).

Lies, damn lies, and press releases - trouble with recent PR about autism and microbiomes

Uggh.  Just saw a bunch of stories about autism and the microbiome.   Many of the comments in the news stories I read seemed, well, not so good.  So I decided to sniff around.  Seems that many of the comments and stories are based on a new PLOS One paper and the comments and press release from the group behind the paper.

Here is the press release I found: Clues about autism may come from the gut.  From Arizona State University.   So I read it.  But I had a hard time getting past paragraph 2:

In new research appearing in the journal PLOS ONE, a team led by Rosa Krajmalnik-Brown, a researcher at Arizona State University's Biodesign Institute, present the first comprehensive bacterial analysis focusing on commensal or beneficial bacteria in children with autism spectrum disorder (ASD).

This did not sound true and sounded a bit overblown as I could have sworn I had seen other "comprehensive" studies of the microbiome in children with ASD. So first I decided to look at the paper.  And - thanks a lot - there was no link in the PR or the stories I had seen.  So I had to go to PLOS One and do a little searching and I found it:

Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children

Kang D-W, Park JG, Ilhan ZE, Wallstrom G, LaBaer J, et al. (2013) Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children. PLoS ONE 8(7): e68322. doi:10.1371/journal.pone.0068322

So - first I asked - did they make the same claim in the paper or was this just in the PR?  Usually such things are just in the PR but amazingly they have this claim in the paper too, with lines like:

"previous studies describing the relationship between autism and gut microbes have either mostly focused on the emergence of harmful bacteria or mainly paid attention to already-known beneficial bacteria"

So I decided to then look at Pubmed and Google Scholar for other papers on autism and the microbiome. Here are some that I found:

• Pyrosequencing study of fecal microflora of autistic and control children from 2010.
• The Gut Microbiome: A New Frontier in Autism Research
• Molecular Characterisation of Gastrointestinal Microbiota of Children With Autism (With and Without Gastrointestinal Dysfunction) and Their Neurotypical Siblings
• Gastrointestinal microbiology in autistic spectrum disorder: a review
• Faecal microbiota of individuals with autism spectrum disorder
• Gastrointestinal flora and gastrointestinal status in children with autism--comparisons to typical children and correlation with autism severity
• Analysis of Small Intestinal Microbiome in Children with Autism
• A microbial association with autism
• Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances.

Not all of these are what one would call comprehensive.  But some of them are at least approaching the scale of what was done here.  And surprisingly, not all of them are cited in the new study.  In particular, the papers by Gondalia et al including one on "Molecular Characterisation of Gastrointestinal Microbiota of Children With Autism (With and Without Gastrointestinal Dysfunction) and Their Neurotypical Siblings" is not references despite it doing some similar things.  I guess, if you don't cite other comparable studies, and pretend they don't exist, then that makes one's work seem a but more novel right?  Weird not to cite that work though - not sure why that happened.  And certainly some of the other studies, even though they are cited, seem like they could be referred to as comprehensive.  I mean - Ian Lipkin's study did metagenomics not just PCR based sequencing.  Isn't metagenomics sort of more comprehensive than PCR?  

Anyway - let's just say this is not the first "comprehensive" study of autism and the microbome.

Moving on in the press release I encountered another painful statement.

The work also offers hope for new prevention and treatment methods for ASD itself, which has been on a mysterious and rapid ascent around the world.

Just what exactly does this new study say about prevention or treatment?  Actually, as far as I can tell - nothing.  So this is a bonus overselling statement just for the PR

Oh but then the PR just get's worse:

Their new study is the first to approach autism from a different angle, by examining the possible role of so-called commensal or beneficial bacteria.

Seriously?  We have gone from trying to claim this is the first comprehensive study of the microbiome and autism to now saying it is the first?  Fu#*(@@# ridiculous.

Other lines that are troubling are encountered further on including

• "The authors stress that bacterial richness and diversity are essential for maintaining a robust and adaptable bacterial community capable of fighting off environmental challenges.".  Hmm.  What is the difference between richness and diversity? And what is the evidence that they are essential for such functions?
• "The species is a common component in normal children exhibiting more diverse and robust microbial communities."  Again - what makes that robust?
• Michael Polan's recent New York Times Magazine story on the microbiome points to the fact that he is proud that his gut microbiome is rich in Prevotella regarding it as a possible sign of a healthy non-Western diet.  Really?  They brought Michael Pollan (with a mis-spelling that might be on purpose so that Pollan does not see this) into their PR?  Uggh

Anyway - I kind of wanted to give them an overselling the microbiome award for some of their statements.  But in the end I would rather give them an "Overselling ourselves" award.  It is a shame too.  I think continuing to explore possible connections between autism and the microbiome will be important.  Making misleading statements about what you have done and not citing / properly referencing other work will not help.

From io9: Even more microbial art "Bacterial communities swarm into gorgeous works of art"

Another quick post.  There is an article in io9 about art from Eshel Ben-Jacob and his beloved Paenibacillus: Bacterial communities swarm into gorgeous works of art.  Some pretty cool images there of these organisms grown on plates and then artistically enhanced.

Definitely worth a look.

Must read of the week: For Better Science Meetings, Invite an Artist The Finch and Pea

Art by @artologica in my living room

This is just such a good idea: For Better Science Meetings, Invite an Artist | The Finch and Pea.  Michelle Banks, also known as artologica, writing at The Finch and the Pea, goes through a detailed argument, with examples, of why one should invite artists to science meetings.

I have been inspired by Michele at many meetings.  And I have been inspired by her art with a science theme (see for example the posts listed below).

• My new microbe art corner w/ three works by @artologica 
• Microbial & Evolution art by @artologica has whole new meaning now that I met her at @scio12 
• Oh frabjous day! Callooh! Callay!' I chortled in my joy - I have received my Tree of Life art from @artologica 
• So psyched. Got my new artwork from @artologica .... Even better than I imagined from web pics).

I have written a bit here and there about the mixing of science and art.  See for example

• The human microbiome never looked so good
• Cool bacterial art makes gizmodo #MicrobialArt
• Microbial art for the holidays from the J. Craig Venter Institute
• Headline says it all "Opera singer grows algae on her face by feeding it w/ her breath & then the audience eats it"
• This is both crazy and completely brilliant: The Microbial Academy Of Sciences
• Art Meets Science at the Keck Center in DC
• Yes I like mixing science and art - but "DNA2Art" seems a bit, well, non artsy #visualiztion≠art
• More pics of hand painted poster from #synbio5
• More art & science - hand painted poster at Synthetic Biology #synbio5 - by Karmella Haynes
• Absolutely spectacular - glass microbes
• Nice Darwin Art at #UCDavis Evolution/Ecology Dept.
• More Airport Dinosaurs - Denver This Time
• Tree of Life Art
• Art-Science Fusion and Darwin's Face at Davis
• Germophobia: wanna get people in the mood for "Contagion" movie about killer virus - grow harmless microbes in public #microbialart
• Another week - another microbial art project
• Fun science art example: Jennifer Welsh on Zachary Copfer glowing microbe drawings
• Preparation Y: Michelle Ellsworth - Performance art mixing dance, genomics, evolution, humor, sex #brilliant
• Microbes, art, science all rolled into one - yum

But if you read one thing about science and art - read Michele's new post.  Or, even better, start inviting artists to any science conference you have any role in.

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

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

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

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

• Open Academic Practice – How open are you?
• OpenAccess Index

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

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

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

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)

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

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

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

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

• Holy lateral transfer batman; amazing story on fungal to aphid transfer from Nancy Moran
• Sharpshooters, dual symbioses and new ways to sequence a genome
• Why endosymbionts rule - see #PLoS Genetics paper on origin of an alternative genetic code
• Aphid-bacterial symbiosis in more detail, and in the New York Times
• You could call it symbiomics (but please do not)... but whatever name you use, this is $^@#&* so cool.
• World's Smallest Genome of a Cellular Organism?
• Glassy winged sharpshooter symbionts

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"

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:

• [1305.7256] tRNA signatures reveal polyphyletic origins of streamlined SAR11 genomes among the alphaproteobacteria
• Coalescence, genetic diversity and adaptation in sexual populations from Neher et al. 
• Reducing assembly complexity of microbial genomes with single-molecule sequencing from Koren et al. 
• Antibiotic resistance landscapes: a quantification of theory-data incompatibility for fitness landscapes from Crona et al. 

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.96​966. 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

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:

• Calling on Nature Publishing Group to return all money received for genome papers and article corrections
• A Solution to Nature Publishing Group's Inability to Keep Free Papers Free: Deposit them in Pubmed Central
• Please help keep the pressure on Nature Publishing Group to restore free access to genome papers #opengate
• Today is a day to be annoyed with Nature (Publishing Group that is) #NatureFail
• The Tree of Life: Nature's publishing machine really wants you to pay for stuff even if it is supposed to be free.

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.

UPDATE 6/27/2013

Saw this Tweet

We just published the story yesterday about the 700.000 year old horse that we sequenced. Check it out ! http://t.co/jAym3HLAC0

— Bent Petersen (@bentpetersen) June 27, 2013

Seemed potentially really interesting. Read the story and got pointed to a new Nature paper on the ancient horse genome. I guess not so surprisingly, despite the fact that they report a new genome sequence, it is not openly available. We really cannot trust Nature on this can we? They could say "Well, this is a draft genome, and we did not mean to apply our policy to draft genomes." Well, that would be weird since, well, they have applied this to draft genomes before. And then I decided to search for other examples ... and in about ten minutes I found a few. See

And this paper too? http://t.co/rCC1A4AKj0 - promises from Nature Publishing Group http://t.co/vlDAd7KFOR not being met #CHORUS

— Jonathan Eisen (@phylogenomics) June 28, 2013

Correction: Here is another non open genome paper http://t.co/X6TgWBKR9u promises from Nature http://t.co/vlDAd7KFOR not being met #CHORUS

— Jonathan Eisen (@phylogenomics) June 28, 2013

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

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: