Misleading microbial headline of the month: Bacteria in Brains Suggest Alzheimer’s-Gum Disease Link

Wow.  Check out this story from Bloomberg: Bacteria in Brains Suggest Alzheimer’s-Gum Disease Link - Bloomberg.  The title suggests that there is some connection between Alzheimer's and Gum Disease.  And so does the story.  Plus check out these other stories:

• Bad dental hygiene linked to Alzheimer's
• Study links poor oral hygiene with a greater risk of developing Alzheimer's
• Could gum disease and poor dental health be an early sign of Alzheimer's disease? 

All based on the same work.  Sounds like a real connection was made in this new work showing a link between bad dental hygiene and Alzheimer's, and also between the bacterium Porphyromonas gingivalis and Alzheimer's.  These would both be a big big deal.  After all - tooth decay is something you can do something about.  And if tooth decay causes Alzheimer's - then - well - we could probably prevent Alzheimer's.

Sounds awesome.  Was going to go invest in companies that are working on this topic.  Then I made a dreadful mistake.  I decided to look at the paper that all of this is based on: Determining the Presence of Periodontopathic Virulence Factors in Short-Term Postmortem Alzheimer's Disease Brain Tissue.

Hmm .. that is weird.  The paper does not seem to have anything in it really closely tied to all the claims in the news stories. Here is the Abstract:

The aim of this study was to establish a link between periodontal disease and Alzheimer's disease (AD) with a view to identifying the major periodontal disease bacteria (Treponema denticola, Tannerella forsythia, and Porphyromonas gingivalis) and/or bacterial components in brain tissue from 12 h postmortem delay. Our request matched 10 AD cases for tissue from Brains for Dementia Research alongside 10 non-AD age-related controls with similar or greater postmortem interval. We exposed SVGp12, an astrocyte cell line, to culture supernatant containing lipopolysaccharide (LPS) from the putative periodontal bacteria P. gingivalis. The challenged SVGp12 cells and cryosections from AD and control brains were immunolabeled and immunoblotted using a battery of antibodies including the anti-P. gingivalis-specific monoclonal antibody. Immunofluorescence labeling demonstrated the SVGp12 cell line was able to adsorb LPS from culture supernatant on its surface membrane; similar labeling was observed in four out of 10 AD cases. Immunoblotting demonstrated bands corresponding to LPS from P. gingivalis in the SVGp12 cell lysate and in the same four AD brain specimens which were positive when screened by immunofluorescence. All controls remained negative throughout while the same four cases were consistently positive for P. gingivalis LPS (p = 0.029). This study confirms that LPS from periodontal bacteria can access the AD brain during life as labeling in the corresponding controls, with equivalent/longer postmortem interval, was absent. Demonstration of a known chronic oral-pathogen-related virulence factor reaching the human brains suggests an inflammatory role in the existing AD pathology.

Alas, even via UC Davis Libraries I do not have access to the full article.  So my inferences will have to be based on the abstract (note to authors, if you want people to judge your full papers not just your abstracts, well, it would be good to have your paper be available).  From what I can tell - what they showed in this paper is that antibodies that are known to find to lipopolysaccharide (LPS) from P. gingivalis showed positive binding to brain material from a few patients who had Alzheimer's and did not show binding to brain material from controls.  So let's ask and try to answer a few questions about this:

• Does LPS from a specific organism in the brain mean that the organism was in the brain: I don't think so - LPS could move around?
• Does binding by the antibody they used mean that there is LPS from P. gingivalis there?  Definitely no - there could be cross reactivity with other LPSs or even other molecules?
• Did they do any more specific tests (e.g., DNA)? Doesn't seem like it.

But let us just assume that they really did detect P. gingivalis in the brains of Alzheimer's patients.  Would this mean PG causes Alzheimer's? Obviously it does not mean that. Let us even assume (ridiculously) that PG causes Alzheimer's.  Would this mean the periodontal disease leads to Alzheimer's? No - PG could come into brains in other ways.

I could go on and on.  There are so so so so so so so many jumps that are needed to go from the limited results presented in this paper to getting anywhere near supporting a hypothesis that periodontal disease causes Alzheimer's that it makes we want to scream.  The news reporting here is awful.  The scientists involved seem to be overhyping their work to extremes with risky, dangerous possible consequences (e.g., - oh - so you have Alzheimer's - it's your fault for not taking care of your teeth ... we need more money for dental care to prevent Alzheimer's; everyone should take prophylactic antibiotics to prevent Alzheimer's and so on).

Another genomics meeting featuring men men men and men: International Forum on "Genomics, Innovation and economic growth"

Well this is just peachy.  Saw this tweet

The International Forum on Genomics, Innovation & Economic Growth will be held on 25 - 27 Nov 2013 in Mexico City. http://t.co/0M54BLg1IU.
— Human Genome Org (@humangenomeorg) July 29, 2013

And my first thought was - please - please - please let this meeting have a decent gender ratio. I am so so sick of genome meetings that have gender ratio issues. Alas, then I went to their site: International Forum "Genomics, Innovation and economic growth"

11 plenary speakers. All of them men.  See here.
Forum president: 1 man
Advisory Board: 5 men

Crap crap crap. What is WRONG WITH PEOPLE?

Nothing else to say really.  But I will not be going I guess I can say that.

Cool open science project: rOpenSci just got 180K funding boost

Just a quick post here.  Just found out from Carl Boettiger that this cool project "rOpenSci" in which he is involved just got a boost in funding with a grant from the Alfred P. Sloan Foundation - see rOpenSci - What we hope to accomplish with the new funding.  The goals of the project are summarized on their site

"At rOpenSci we are creating packages that allow access to data repositories through the R statistical programming environment that is already a familiar part of the workflow of many scientists. We hope that our tools will not only facilitate drawing data into an environment where it can readily be manipulated, but also one in which those analyses and methods can be easily shared, replicated, and extended by other researchers. While all the pieces for connecting researchers with these data sources exist as disparate entities, our efforts will provide a unified framework that will be quickly connect researchers to open data."

Worst science by press release of the year: nitrogen fixation in crops

Well, this is one heck of a science - by - press release case.

Was pointed to this press release: World-Changing Technology Enables Crops to Take Nitrogen from the Air which comes to us from the University of Nottingham.  It makes some really bold claims like

A major new technology has been developed by The University of Nottingham, which enables all of the world's crops to take nitrogen from the air rather than expensive and environmentally damaging fertilisers

And

This ground-breaking development potentially provides every cell in the plant with the ability to fix atmospheric nitrogen. The implications for agriculture are enormous as this new technology can provide much of the plant's nitrogen needs.

And

Applied to the cells of plants (intra-cellular) via the seed, it provides every cell in the plant with the ability to fix nitrogen. Plant seeds are coated with these bacteria in order to create a symbiotic, mutually beneficial relationship and naturally produce nitrogen.

And

N-Fix is a natural nitrogen seed coating that provides a sustainable solution to fertiliser overuse and Nitrogen pollution. It is environmentally friendly and can be applied to all crops. Over the last 10 years, The University of Nottingham has conducted a series of extensive research programmes which have established proof of principal of the technology in the laboratory, growth rooms and glasshouses.

And

There is a substantial global market for the N-Fix technology, as it can be applied globally to all crops. N-Fix has the power to transform agriculture, while at the same time offering a significant cost benefit to the grower through the savings that they will make in the reduced costs of fertilisers. It is a great example of how University research can have a world-changing impact.

And

The proof of concept has already been demonstrated. The uptake and fixation of nitrogen in a range of crop species has been proven to work in the laboratory and Azotic is now working on field trials in order to produce robust efficacy data. This will be followed by seeking regulatory approval for N-Fix initially in the UK, Europe, USA, Canada and Brazil, with more countries to follow.

Sounds f$*@#$# awesome.  So awesome that it was picked up by multiple news sources including

• Better Crops: Building In Automatic Nitrogen Fixation - RedOrbit
• Technology could enable all crops to take nitrogen from the air - R & D magazine
• Burrowing bacteria may end need to fertilise plants - Telegraph
• Bacteria discovery could revolutionize crop science - Examiner

The only problem is - they don't present any evidence.  None.  No data.  No paper.  No poster.  Nothing.  It is simply a press release with a bunch of words. Ridiculous.  I think I am going to announce I have a way to not only get all crops to fix nitrogen, but that it will work by telepathy.  This is one of the worst science-by-press-release cases I have ever ever seen.

UPDATE 7/27/13

Richard Conniff, who was the one who pointed me to the PR has a post about this too: http://strangebehaviors.wordpress.com/2013/07/27/best-news-ever-in-agriculture-or-utter-bullshit/

Postdoc position in innovating scholarly communication at #UCDavis w/ me, Mario Biagioli & Mackenzie Smith

7/26/13

Postdoc Position in Innovating Scholarly Communication

A new UC Davis initiative on "Innovating the Communication of Scholarship" is hiring a 3-year postdoctoral fellow, starting September 1, 2013. This is a cross-disciplinary project to study the future of academic publishing, involving faculty from the Center for Science and Innovation Studies, the Library, the Genome Center, and the School of Law (with additional collaborators in Computer Science, English, Philosophy, and the Graduate School of Management). Research topics include open access models, peer review, new forms of quality metrics, data publication, use of social media, and new forms of misconduct.

The successful candidate will conduct research, collaborate on or lead organization of conferences, workshops, pedagogical activities, and grant writing. A Ph.D. is required in a relevant field such as Science and Technology Studies, Library and Information Sciences, Communication, Law, Science, or English. Other disciplines will be considered depending on the specific focus of the candidate?s research and other experience. Qualified applicants will have experience working successfully in teams and managing multi-year projects. He or she will possess excellent written and oral communication and administrative skills.

Salary is based on experience and qualifications according to UC Davis guidelines.

To apply: E-mail a PDF file containing your CV, short description of your research experience relevant to this position, and contact details for three references to Mario Biagioli, MacKenzie Smith, Jonathan Eisen.

Another quick post - condoms and probiotics

Another quick post.  Just read this article in LiveScience about a new PLOS One paper: Condoms May Boost Beneficial Vaginal Bacteria | LiveScience.  Am wondering - when will condoms start coming with probiotics in them?  Anyone out there know if this has been done yet?  I mean, I do not want to oversell the microbiome but hey it seems like there could be something to do here ...

Quick post - very interesting interview of Peter Suber by Richard Poynder

For those interested in Academic Publishing and OpenAccess issues this is really worth a read: Open and Shut?: Peter Suber on the state of Open Access: Where are we, what still needs to be done?.  It is an interview of Peter Suber by Richard Poynder.

UPDATE 10 minutes later - not saying I endorse or support everything Suber says (I am much more enthusiastic about gold open access than green OA which I find limited in use).  But the interview is worth a read.

Do small organisms form species? New paper suggests not ...

Quick post here about a press release about a new paper: New mathematical theory says small organisms may not form species.  Seems that this new theoretical paper might be of interest to people out there. The paper is available openly here: http://rspb.royalsocietypublishing.org/content/280/1767/20131248.abstract.  Not sure quite what to make of this but thought it would be of interest.  The abstract is below:

The rapid advance in genetic sequencing technologies has provided an unprecedented amount of data on the biodiversity of meiofauna. It was hoped that these data would allow the identification and counting of species, distinguished as tight clusters of similar genomes. Surprisingly, this appears not to be the case. Here, we begin a theoretical discussion of this phenomenon, drawing on an individual-based ecological model to inform our arguments. The determining factor in the emergence (or not) of distinguishable genetic clusters in the model is the product of population size with mutation rate—a measure of the adaptability of the population as a whole. This result suggests that indeed one should not expect to observe clearly distinguishable species groupings in data gathered from ultrasequencing of meiofauna.

Expansion of Academic Freedom at the University of California

Just got pointed to this revision of the UC Faculty Code of Conduct which was recently approved by the UC Regents: http://regents.universityofcalifornia.edu/aar/jule.pdf

I was pointed to it by Greg Pasternack from UC Davis who has been a major force in trying to guarantee academic freedoms at UC Davis.

Colleagues, 

  Four years and one month after the UCD Committee on Academic Freedom and Responsibility first raise the alarm about the danger of unjust discipline faculty in the UC system may face (and certainty have faced) for speech and actions regarding institutional matters, I am very happy to report to you all that on July 18 the UC Regents approved our proposed amendment to APM-015 that guarantees faculty academic freedom to speak out about institutional matters.  Given the number of judges that have ruled that faculty speech on institutional matters is *not* protected by the First Amendment, even in public universities, getting this freedom inscribed into APM-015 provides a policy-based guarantee no longer reliant on external interpretation. 

  See attached, notably the underlines in attachment 2.  You can also download it from http://regents.universityofcalifornia.edu/aar/aar.html under "committee on educational policy" 

  This is the greatest expansion in academic freedom in the history of the UC system, because all previous notions of academic freedom limited the application of the idea to just one's area of scholarship.  Prior to this, the biggest change was to no longer require "dispassionate" scholarship.  However, academic freedom is no longer shackled to scholarship.  We are free to speak on all institutional matters, whether they are within our sphere of scholarship or not.  We may do so using any forum or medium. 

  Now go out and use your freedom to stir up brilliant controversies ;) 

Best wishes, 

-Prof. Greg Pasternack

The section he called particular attention to is in line 4 in the part on "Professional Rights of Faculty" which reads "freedom to address any matter of institutional policy or action when acting as a member of the faculty whether or not as a member of an agency of institutional governance." This clearly relates to some real and perceived challenges to academic freedom at various UCs and it is good to have a formal policy that says such a freedom is a right of the faculty.

You go Greg ...

Related posts:

• Report on "Egregious Academic Freedom Violation" at #UCDavis
• The Tree of Life: Updates on the #UCDavis Academic Freedom ...
• The Tree of Life: #UCDavis Provost Ralph Hexter very strong ...

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?