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
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 BiagioliMacKenzie SmithJonathan 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:

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. 

Five Specific pre-Sabbatical Recommendations for Faculty, Postdocs and PhD Students

PI
1.     Develop a plan for your year ahead: what are the key goals for the sabbatical?
2.     Identify what is going to be different and what is going to remain the same: e.g., a new project(s), less/no teaching; less/no administrative duties, a new interaction schedule with the group, etc.
3.     Communicate your plans for the sabbatical and your expectations of group members to the group (ideally, after a group discussion of the kind outlined here).
4.     Talk to your Chair about expectations for your year and new expectations (if any) upon your return (and talk to your departmental admin team to make sure they are aware of your plans).
5.     Establish new interactions with your local host and host community.
Postdocs
1.     Establish a regular schedule of interactions with your adviser.
2.     Keep focused on your research & career goals (i.e., do not become a proxy adviser in the absence of the PI, i.e., see 3 & 4 below)
3.     Determine your supervisory responsibilities – what is your (limited) role to advise the students, technicians in the group?
4.     Determine your lab management responsibilities – what is your (limited) role in ordering and other admin duties?
5.     Travel to collaborators and mentors – do not just stay put while your adviser is away.
PhD students
1.     Identify the major research and career development expectations during your adviser’s time away – how will the adviser’s absence affect your thesis (if at all)?
2.     Establish a regular schedule of interactions with your adviser and senior members of the group.
3.     Contact your adviser, even off-schedule if you really need advice.
4.     Remember: your PI’s sabbatical is an opportunity for independence, increased self-motivated work and development as a scholar, not a “holiday”.
5.     Identify a local faculty member who can serve as an occasional resource to provide input and thoughts on your thesis work (this should be coordinated in advance, with your PI).
Final thoughts:
A PI sabbatical can be a very positive opportunity for all group members to become more independent, to set off on new directions, and to bring greater creativity and productivity to a group.  However, two notes of caution.  First, if you are not yet in a group, think carefully before joining with an absent PI, as the initial period in a group (regardless of your status) often sets the frame for the long-term interaction.  Second, the PI remains the PI, so be wary of a sabbatical plan that involves anyone other than the PI becoming the acting group leader.   Although certain senior members may take over duties, the sabbatical plan should (ideally) involve availability of the PI to make key decisions critical to the group, including thesis advancement, hiring/firing and mediation of major conflicts.

And, I suppose I’ll have to revisit this guide next year to report back on what worked and what we should have thought of in advance!

Participants:

  •  Dr. Joshua Weitz
  •  Dr. Alexander Bucksch
  •  Dr. Michael Cortez
  •  Abhiram Das, PhD candidate
  •  Cesar Flores, PhD candidate
  •  Luis Jover, PhD candidate
  •  Gabriel Mitchell, PhD candidate
  •  Bradford Taylor, PhD candidate
  •  Charles Wigington, PhD candidate
  •  Victoria Chou, NSF REU student
Further reading
Many blogs are available detailing sabbatical “adventures” and “diaries”.

A letter from Chair of the Board of Regents Bruce Varner

Forwarding this

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).