Monday, November 24, 2014

A night with Matt Groening and the importance of faeces, feces and faces

So - I participated in a fundraiser for Emily Levine's "The Edge of Chaos" film a week ago. And one of the key guests was Matt Groening. Not only did I get to hang out with him and discuss fecal transplants with him (really) but I had a front row seat to Matt discussing the history of how he came up with the general outline of the Simpson's characters.

And in addition to this being just awesome to witness, one part of it struck me. See the video below and in particular the part that struck me was the beginning:

basically said that only a few simple changes in faces can be recognized by people very easily. This reminds me of Jenna Lang's talk at the Lake Arrowhead meeting this year where she discussed using facial drawings as a form of visualizing microbiome data.


So - since I discussed fecal transplants with Matt and since he gave a good description of facial characteristics being easy to identify, I think we should definitely (1) try and get him to include microbiomes on the Simpsons and (2) for our work we should use Simpsons characters as model faces for different microbiomes ...

Oh and I also showed Groening some of the pics of my kids reading his "Hell" books:

So - basically it was a night of feces, faeces and faces.  Seems ideal.

Sunday, November 23, 2014

Whole issues of Genome Biology/Genome Medicine on "Genomics of Infectious Disease"

Wow this has really got some nice papers: BioMed Central | Article collections | Genomics of infectious diseases special issue.  I note - this goes well as a follow up to the series I co-coordinated in PLOS a few years back: Genomics of Emerging Infectious Disease - PLOS Collections

From their site:
Infectious diseases are major contributors to global morbidity and mortality, and have a devastating impact on public health. The World Health Organization estimates that 1 in 3 deaths worldwide are due to an infectious disease, with a disproportionate number occurring in developing regions. 
While the completion of the first genome sequence of a pathogen, Haemophilus influenzae, in 1995 took decades of work, in recent years, high-throughput technologies have revolutionized the study of pathogens. Whole-genome sequences are now achievable within days and available for multiple pathogens, including those that cause neglected tropical diseases, which has advanced our understanding of the biology and evolution of pathogens. Crucially, such research has enabled important advances in the clinical management of infectious diseases, and continues to guide public health interventions worldwide. 
In this cross-journal special issue, guest edited by George Weinstock (The Jackson Laboratory for Genomic Medicine, USA) and Sharon Peacock (University of Cambridge, UK), Genome Biology and Genome Medicine take stock of where we are now, with a collection of primary research and commissioned articles that discuss different aspects of the genomics of infectious diseases in human populations, including the progress made towards their eradication, and the remaining challenges in terms of both fundamental science and clinical management.
I have copied the list from their site (I am pretty sure this is OK since these are #OpenAccess journals but not 100% sure):

Saturday, November 22, 2014

Strangest microbial headline of month: Bacteria on Russian ‘sex satellite’ survive reentry

There is really not much to say other than to point everyone to this article: Bacteria on Russian ‘sex satellite’ survive reentry | Science | The Guardian

It defininely wins the strangest microbial headline of the month.  The article restates some of the silly claims about how what they are finding supports panspermia .. but ignore the article and just enjoy the headline.

Moore Foundation: Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

Got this from the Gordon and Betty Moore Foundation and they said I could post it here.

Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

Marine Microbiology Initiative Gordon and Betty Moore Foundation November 21, 2014

The Marine Microbiology Initiative (MMI) at the Gordon and Betty Moore Foundation aims to enable scientists to uncover the principles that govern the interactions among microbes and that influence nutrient flow in the marine environment. MMI is targeting closing gaps in and supporting the advancement of experimental model systems in microbial oceanography to enable new ways to uncover fundamental biological mechanisms.

We are soliciting expressions of interest (EOIs) for early-stage research projects to develop methods to genetically manipulate marine microeukaryotes as a first step in breaking current bottlenecks in the advancement of experimental model systems. MMI has two primary foci for this expression of interest:
  1. Development of genetic tools for diatoms. Diatoms are key players in the world’s oceans, generating ~20% of the world’s organic carbon, and a strong community of researchers is in place suggesting broad use of successfully developed methods. We are specifically interested in projects to develop reverse and/or forward genetics.
  2. Screening laboratory-scale culture collections for transformable marine microeukaryotes.
MMI will also consider projects to develop genetic tools and methods with other microeukaryotes that show promise for expanding the way the field can test hypotheses. If your idea does not fit category 1 or 2 above, please contact us prior to submitting your EOI.

MMI encourages EOIs from “inter-organismal” teams of researchers – i.e., complementary groups that have experience in a well-established model system and with a microeukaryote that is not currently genetically tractable – whose collaborative effort will bring innovative approaches to the field.

MMI invites you to send an expression of interest via email that briefly outlines a research project (one paragraph or less), using the following template:

  1. The lead researcher’s name, institution, and expertise.
  2. Indication of focus on genetic tools for diatoms (category 1 above) or laboratory culture screening for transformability (category 2 above).
  3. For category 1, the name of the organism(s); or, for category 2, the taxonomic group(s) to be screened. 
  4. A methodological or technical challenge that is hindering the development of a genetically manipulable marine microeukaryotic system that is ripe for solving and how you would address this challenge (3-5 sentences).
  5. The research team that would tackle this challenge, and why each team member’s expertise is relevant (one sentence per team member; please include institutional affiliations).

The opportunities that best align with MMI’s strategies and goals will be invited to submit proposals. MMI has allocated $7–10M to support this effort and anticipates making multiple, 2–3 year awards beginning in mid- 2015.

Please submit your EOI by Tuesday January 6, 2015 to Samantha Forde at

Post-doc w/ me, Jessica Green, Jay Stachowicz, and Jenna Lang on seagrass microbiomes

Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon Green ( is currently seeking a postdoctoral researcher to explore fundamental questions in microbial ecology and evolution. Applicants should have a PhD in a biological, computational, mathematical, or statistical field with extensive training using theory and/or modeling to understand the ecology and evolution of complex biological communities, and strong writing skills. Experience developing and applying quantitative phylogenetic ecological methods is highly desirable, but not explicitly required for candidates who have otherwise demonstrated strong quantitative skills.
The successful candidate will play a key role in the Seagrass Microbiome Project ( in collaboration among Jonathan Eisen, Jay Stachowicz, and Jenna Lang ( at the University of California, Davis. The Seagrass Microbiome Project aims to integrate the long interest in seagrass ecology and ecosystem science with more recent work on microbiomes to produce a deeper, more mechanistic understanding of the ecology and evolution of seagrasses and the ecosystems on which they depend. Our studies of the community of microorganisms that live in and on seagrasses – the seagrass “microbiome” – will contribute to a broader understanding of host-microbe systems biology, and will benefit from ongoing University of Oregon research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology ( and the Biology and Built Environment Center (
The position is available for 1 year with the possibility for renewal depending on performance. The start date is flexible. Please email questions regarding the position to Jessica Green (jlgreen).
To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references
Submit materials to ie2jobs. Subject: Posting 14431
To ensure consideration, please submit applications by November 1, 2014, but the position will remain open until filled.
Women and minorities encouraged to apply. We invite applications from qualified candidates who share our commitment to diversity.
The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

Friday, November 21, 2014

Repeated, extremely biased ratio of M:F at meetings from SFB 680 "Evolutionary Innovations" group #YAMMM

Well, this is disappointing, to say the least - there is a conference coming up in July 2015 on "Forecasting Evolution":  SFB 680 | Molecular Basis of Evolutionary Innovations at the Gulbenkian Foundation in Lisbon.

Here is the listed lineup of invited speakers:
  1. Andersson (Uppsala University), (NOTE I AM ASSUMING THIS IS DAN ANDERSSON)
  2. Trevor Bedford (Hutchinson Cancer Research Center), 
  3. Jesse Bloom (Fred Hutchinson Cancer Research Center), 
  4. Arup Chakraborty (MIT)
  5. Michael Desai (Harvard University), 
  6. Michael Doebeli (University of British Columbia), 
  7. Marco Gerlinger (Institute of Cancer Research, London, 
  8. Michael Hochberg (CRNS, Montpellier), 
  9. Christopher Illingworth (Cambridge University), 
  10. Roy Kishoni (Harvard University), 
  11. Richard Lenski (Michigan State University), 
  12. Stanislas Leibler (Rockefeller University), 
  13. Marta Luksza (IAS Princeton), 
  14. Luke Mahler (University of California, Davis), 
  15. Leonid Mirny (MIT), 
  16. Richard Neher (MPI Tuebingen), 
  17. Julian Parkhill (Sanger Institute), 
  18. Colin Russell (University of Cambridge), 
  19. Sohrab Shah (University of British Columbia), 
  20. Boris Shraiman (UCSB), 
  21. Olivier Tenaillon (Inserm Paris).
For a whopping 20:1 ratio of men to women or 4.8% women. And this in a field that is just overflowing with excellent female researchers.

So I dug around a little bit.  Here is another meeting from the same group at the University of Cologne - a group known as SFB 680. SFB 680: Molecular Ecology and Evolution: Cologne Spring Meeting 2012.

Sunday, November 16, 2014

Really cool: 3D printed microbes for the visually impaired

Image from Nanowerk story.
This is one of the most interesting things I have seen relating to microbiology recently:  3D printed giant germs help visually impaired see the world of microorganisms reported by Nanowork News on October 31.  This work has done by researchers from the BBSRC (the Biotechnology and Biological Sciences Research Council in the UK) who hosted an event called "Giant Germs" for the blind and visually impaired.  In discussing various microbes (alas, the story implies that all they discussed were pathogens), they had accompanying tactile sessions to feel the structures of the microbes.  Just a really brilliant, important idea.

Tuesday, November 11, 2014

Job Announcement: Moore Foundation Program Associate

This seems like a potentially interesting job.  I note - I love the Moore Foundation - and just about everything they are doing in science.  Below is the email I recieved from the Project Lead Jon Kaye:

We have opened a search for a Program Associate. Details at the link below and attached. Please share with Bachelor’s and Master’s level individuals who may be interested. We will also be opening a search for a PhD-level Program Officer position soonstay tuned for details.

Full text of the announcement is below:

Sunday, November 02, 2014

Crosspost from #microBEnet: More scary than Halloween: this month in germophobia microbophobia

Crossposting this from the microBEnet blog where I originally posted it 10/31/14:

It seems that any time a holiday comes around in the US, the press starts to ramp up the writing of stories about evil microbes that are lurking all around us. And Halloween appears to be no exception. I am now planning on referring to this attitude as "microbophobia" rather than "germophobia" because to some "germ" implies pathogen and many of these stories fan the flames of fear about any kind of microbe not just pathogens. I note - the term microbophobia comes from some searches I did recently of Google books.

I was thinking of writing up yet another post trying to counter this excessive microbophobia but decided instead to just provide a collection of links to stories over the last month that have a distinctive microbophobia flavor.  Mind you - there are real reasons to be afraid of some of the microbes circulating around these days.  But the links below seem to me to be serious overkill.
These are but a few of the many examples of microbophobia being pushed by the press. Again, there are certainly things to worry about in terms of pathogens in our immediate environment.  Flu season is coming.  Enterovirus might be on the upswing.  Antibiotic resistance is a massive and troubling problem.  And so on.  But please let us not go completely over the top because the more we promote the idea that we should be killing all microbes, the more trouble we are likely to cause, rather than prevent.