Friday, December 13, 2013

Fun to see how Resistance the Film is coming along ... teaser released

Did an interview a while back with Michael Graziano for a film he was working on -- "Resistance the Film" which is coming out soon. They released a trailer for the movie, and it has part of the interview with me as the narration ..


RESISTANCE TEASER I from uji films on Vimeo.

Thursday, December 12, 2013

Some new posts by, well, me, of possible interest

So - I am trying to get some new project specific blogs up and running and have been writing some posts at those sites.  And I thought I would just post a summary here of other posts I have written of possible interest.

Wednesday, December 11, 2013

Nice microbe-art-education example from Cornell

Cool story from the Cornell News: Bacteria research inspires students' creative artwork | Cornell Chronicle.  It discusses a course taught by Prof. Greg Page "Introduction to Print Media".  As part of the course the students got a guest lecture from none other than Ruth Ley - who is a faculty member at Cornell and who does some of the most interesting microbiome work around.

Anyway - this guest lecture inspired some of the students in the course to make some microbial themed art works.  And the ones shown on the Cornell News site are wonderful.  Consider this one:
Image obtained from Cornell News.
"Tribal Warfare," lithography and screen print.by Rebecca Potash.
I also love the lines from Ruth Ley on why she got involved in this and what she plans to do in the future.  Consider this:
“As part of my teaching at Cornell, I plan on training science students in the interpretation of concepts in visual arts and eventually even have them learn some basic skills for producing images or video,” Ley said. “I also want to bring science to fine arts students, and my collaboration with Professor Page was my first attempt at this.”
Nice.  Got to try and do more things like this myself ... 

Tuesday, December 10, 2013

Things I don't understand episode 2000: Why in comparing humans & other animals the null hypothesis people always use (and thus try to disprove) is that humans ≠ animals

Well, this is something I just do not understand.  I am sure others out there have thought about this more than I have.  Just read this article: Considering the Humanity of Nonhumans - NYTimes.com discussing humans vs. non human animals.  And there is this extensive discussion in there about whether animals have self awareness, and whether they deserve legal rights, and such.  All very interesting I think.

But one part I do not understand.  It is very clear that humans and other animals have many homologous features.  It is very clear that humans are more closely related to some animals (e.g., primates) than to others.  For many comparative studies of animals, if one wants to claim that some animal has a feature that is different from it's close relatives, it is frequently up to the person proposing such a difference to disprove the null hypothesis that the close relatives are the same.  This is the case when studying molecular processes, cell structures, physiology, genome structure, and so on.

Yet, there are a few biological features regarding humans for which it seems the null hypothesis everyone is forced to work with is the reverse.  In these cases the null hypothesis is that we (i.e., humans) are unique and those who wish to claim that humans and other animals are similar / the same have to disprove the null hypothesis.  This seems, well, awkward, at best.  Basically, for some features - especially those that relate to intelligence and behavior  -  if one wants to claim that they are not unique one has to disprove the null.  And yet, for all other features, the null hypothesis is that humans are not unique and those wanting to show uniqueness are forced to disprove this.  On the one hand, I get this.  There are many reasons why one might want to treat "humans are unique" in regards to intelligence and behavior - as the null hypothesis.  But on the other hand - this seems exceptionally anthropocentric and has almost certainly prevented us from discovering and understanding certain behaviors and intelligence-related issues in non human animals.  How do we as a community decided which null hypothesis to use for each phenotype?

Anyway - there it is.  Something I do not understand.

Sunday, December 08, 2013

CVS marketing probiotics for everyone - even kids - & the disclaimers are barely visible

Just got back from the CVS drug store in Davis, CA and thought I would share some of the probiotic promotion they are doing.  Not only are the probiotics now right next to the pharmacy counter (moving up in the world I suppose) but the probiotics are being marketed to all sorts of targeted groups.  Alas, the science behind the claims here are dubious.  And - sadly - CVS makes the disclaimer barely visible in many of the signs.





Wednesday, December 04, 2013

Transitions in the CAMERA metagenomics database ---

Just got this email announcement that I thought would be of interest:

Thank you for being a CAMERA user during its first phases of operation as a
resource for environmental genomics. During the past few years, CAMERA has
been able to offer a number of important community resources, including an
exceptionally well curated environmental genomic database, the ability for
researchers to deposit molecular sequence datasets with associated
environmental parameters (metadata), open access to computational resources
to enable metagenomic comparisons, educational resources and helpdesk
services. These efforts have been funded through the Gordon and Betty Moore
Foundation (GBMF) Marine Microbiology Initiative and the National Science
Foundation to serve the needs of the marine microbiology community and
other users.

As we announced earlier this year, CAMERA is undergoing a transition,
shifting from the Testing and Development phase of CAMERA 2.0 into multiple
entities that are supported by federal and foundation-funded projects for
developing and managing databases. Toward this end, we are re-prioritizing
access to the advanced data analysis capabilities of the system (see below)
while maintaining free and open access to CAMERA’s rich collection of
curated data and metadata. This will involve CAMERA being restructured into
a publicly accessible Data Distribution Center consisting of a simplified
website to enable streamlined access for downloading of sequence datasets
and associated metadata. This new interface will serve as an intuitively
accessible central repository, facilitating direct access to genomic,
metagenomic, transcriptomic, and metatransciptomic projects. Further, the
CAMERA 3.0 database will continue to grow and be maintained with the
inclusion of additional marine microbial datasets, such as the ~700 new
marine microbial eukaryote transcriptome datasets as part of the Marine
Microbial Eukaryote Transcriptome Sequencing Project
(marinemicroeukaryotes.org).

In the past, the CAMERA 2.0 compute resources, which include large-scale
BLAST capabilities and other workflow-enabled analysis capabilities, were
generously supported by the GBMF, the San Diego Supercomputer Center, the
NSF XSEDE program, and commercial Cloud computing resource providers,
Amazon and CODONiS. Due to increasing computational costs and the need for
scalability to larger, more complex datasets, it is now necessary for
CAMERA 3.0 to adopt a resource access model wherein projects will need to
identify sources of funding to cover their use of these advanced
capabilities. Starting January 1, 2014, CAMERA 3.0 will no longer offer the
use of computational resources to projects that cannot identify a source of
support for this component of CAMERA 3.0 services. As we shift to this new
usage model, we urge current users to download and save customized data
cart holdings and workflow analysis results before January 1, 2014.

While we are shifting to a restricted resource compute model, we will
continue to improve the capabilities of the system to expand the scientific
breadth of the data managed by CAMERA 3.0. For example, CAMERA 3.0 includes
fully functioning workflows for Illumina datasets, which can be made
available to those users who can identify a source of support for the
associated computational costs. In addition, CAMERA is actively seeking
resources to continue to take community data submissions. If you are now
collecting or have plans to collect data which you wish to deposit in
CAMERA, we urge you to contact us to help you to determine how to obtain
the resources required for these data to be archived and made available
through CAMERA.

Tuesday, December 03, 2013

Hope from sadness: Loreto Godoy Memorial Fellowship (needs $5K more to become permanently endowed)

I received tonight an email from Dr. Holly Ernest, a colleague of mine who is a Professor at UC Davis and I am posting it below. The email relates to a fundraiser for a Memorial Fellowship in honor of Loreto Godoy who was a PhD student here at UC Davis in the Graduate Group in Ecology.  She tragically died this summer in a car crash that also took the life of her husband's parents.  The email relates to a fund that was established in her honor - which needs only an additional $5000 to become a permanently endowed fund at UC Davis.  Holly Ernest was her PhD Advisor and I encourage everyone to read the email below and consider donating to the fund.  Life is so incredibly tragic sometimes.  Loreto was not just a brilliant scientist, but also a wonderful person and a mother of two young girls.  But hopefully through this fellowship some good things can happen for others and her memory can live on.


Dear Ecology community,

Our dreams for a permanently endowed Loreto Godoy Memorial Fellowship are nearly realized.

This fellowship is intended to be awarded regularly to UC Davis graduate students who exemplify Loreto's ideals. Loreto was a PhD candidate in the Ecology Graduate group, brilliant scientist, a loving mother of two little girls, Chilean, veterinarian, and all-around wonderful sunny person.

In order to help us reach our goal of endowing the fellowship and having a lasting legacy of Loreto's wonderful and generous life, my husband Bruce and I are making another gift of $1000 to help inspire others to donate (any size donation is very welcome).

With this donation and that of a new anonymous donor, the fund is now at $20,000. It needs to reach $25,000 to be permanently endowed by UC Davis for a lasting legacy to Loreto's memory.

Please consider joining us to reach this goal!

Also - please feel free to share this email so that others can get involved.

Please send checks to the following address, and write, "for Loreto Godoy Fellowship Fund" in subject line of check:

University of California, Davis
Janet Berry—University Development
UC Davis Conference Center, 2nd floor
One Shields Ave.
Davis, CA 95616-5270

Questions can be directed to Janet by email jsberry@ucdavis.edu or phone (530) 902-1624. If you prefer to pay by credit card, you may also call Janet at this number in order to provide this information.

Thank you,

Sincerely Holly Ernest
Loreto's graduate school adviser
530-754-8245
hbernest@ucdavis.edu

https://www.facebook.com/Loreto.Godoy.Scholarship

(Note by Jonathan Eisen - donations can also be made via the online site http://www.gofundme.com/loreto-godoy-scholarship). 

Wednesday, November 27, 2013

Possibly interesting new microbiome study but can't get past misleading quote

Just got done reading: Restoring helpful bacteria of the gut and intestines may treat patients with RCDI, find scientists.  A lot in the story is interesting.  And it discusses work by friends / colleagues of mine.  But I just don't feel like writing about the work because the end of the article rubs me the wrong way.  Here is the whole paragraph that bothers me:
"This study helps underscore the importance of the microbiome in maintaining health and demonstrates that good bacteria play an integral role in immune defenses against disease," says E. Albert Reece, M.D., Ph.D., M.B.A., Vice President for Medical Affairs at the University of Maryland and the John Z. and Akiko K. Bowers Distinguished Professor and Dean of the University of Maryland School of Medicine. "These findings also provide a potential therapeutic model for other diseases that have been linked to changes in the human intestinal microbiota, such as obesity and diabetes."
What is wrong with this?  Well, #1 - the 1st sentence implies a bit too much to me that this study is novel in demonstrating that "good" bacteria play a role in immune defense.   When of course this has been shown for many many years.  But let's let that slide.  Not a big deal.

It is the last line that irks me:  "These findings also provide a potential therapeutic model for other diseases that have been linked to changes in the human intestinal microbiota, such as obesity and diabetes."

Hmm.  Obesity and diabetes in humans have not been shown to be caused by changes in the microbiome.  And therefore it is inaccurate to imply that one could take the fecal transplant for C. difficile model (which is what this current work is about) and extended it to obesity and diabetes.  You could say he is careful with words here by saying "linked to" not "caused by" but I think the clear implication here is that he is promoting fecal transplants as a therapy for obesity and diabetes.  And he should be more careful (especially as Dean of the University of Maryland School of Medicine).  I beg of people out there.  Please please please.  Microbiome studies have enormous potential.  In so many areas.  But we risk turning microbiome work into the next medical snake oil if we are not careful with our words.

Sunday, November 24, 2013

Mini journal club: staged phage attack of a humanizes microbiome of mouse

Doing another mini journal club here.  Just got notified of this paper through some automated Google Scholar searches: Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut

Full citation: Reyes, A., Wu, M., McNulty, N. P., Rohwer, F. L., & Gordon, J. I. (2013). Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut. Proceedings of the National Academy of Sciences, 201319470.

The paper seems pretty fascinating at first glance. Basically they built on the Jeff Gordon germ free mouse model and introduced a defined set of cultured microbes that came from humans.  And then they stages a phage attack on the system and monitored the response of the community to the phage attack.

Figure 1 from Reyes et al.

They (of course) also did a control - in this case with heat killed phage.  And they compared what happened to the live phage.  I love this concept as they are able to control the microbial community and then test dynamics of how specific phage affect that community inside a living host.  Very cool.

Thursday, November 21, 2013

Journal club light: skeptical of "Phylo SI: a new genome-wide approach for prokaryotic phylogeny"

Just reading this paper and thought I would start a new "section" here on my blog.  Journal club light.  Just some notes and quick comments.

Today I am selecting this paper: Phylo SI: a new genome-wide approach for prokaryotic phylogeny.  It caught my eye because, well, I am interested in genome-wide phylogeny.

So I glanced at the paper's abstract:
The evolutionary history of all life forms is usually represented as a vertical tree-like process. In prokaryotes, however, the vertical signal is partly obscured by the massive influence of horizontal gene transfer (HGT). The HGT creates widespread discordance between evolutionary histories of different genes as genomes become mosaics of gene histories. Thus, the Tree of Life (TOL) has been questioned as an appropriate representation of the evolution of prokaryotes. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, and a routine effort is made to place new isolates in their appropriate location in the TOL. Moreover, it appears desirable to exploit non–tree-like evolutionary processes for the task of microbial classification. In this work, we present a novel technique that builds on the straightforward observation that gene order conservation (‘synteny’) decreases in time as a result of gene mobility. This is particularly true in prokaryotes, mainly due to HGT. Using a ‘synteny index’ (SI) that measures the average synteny between a pair of genomes, we developed the phylogenetic reconstruction tool ‘Phylo SI’. Phylo SI offers several attractive properties such as easy bootstrapping, high sensitivity in cases where phylogenetic signal is weak and computational efficiency. Phylo SI was tested both on simulated data and on two bacterial data sets and compared with two well-established phylogenetic methods. Phylo SI is particularly efficient on short evolutionary distances where synteny footprints remain detectable, whereas the nucleotide substitution signal is too weak for reliable sequence-based phylogenetic reconstruction. The method is publicly available at http://research.haifa.ac.il/ssagi/software/PhyloSI.zip.
And something continued to catch my eye there.  It was the use of "gene order conservation" as the data for the phylogenetic analysis.  Hmm.  I am generally skeptical of most uses of gene order for inferring phylogeny that I have seen.  Why?  Well, because it seems to me that gene order is less likely to be a useful character than sequences in alignments (which is the standard for inferring phylogeny).  Why do I feel this way?  Well, for two main reasons:

1) Sequence alignments are robust.  They have been used and used and used and shown to be quite powerful and useful (even though they are not perfect).  The rich literature on alignments has shown where and when and how they are useful.  And where and when and how they are not.  And we have powerful, tested methods to use such alignments.

2) Gene order seems less likely to be robust.  I am not saying it is not useful.  But the literature I have seen suggests to me that gene order is more prone to convergent evolution than sequence.  And gene order is more prone to enormous variation in rates and patterns of evolution.  And gene order does not actually have a lot of characters to use compared to whole genome alignment based phylogenetics.

Strange email of the week: "Publication Integrity and Ethics"

Just got this email that I have pasted below. This seems very very strange. Something is amiss here I think but not sure what. Anyone out there know anything about this?


Dear
You are invited to join the Publication Integrity and Ethics (herein referred to as PIE) as one of its founding members. PIE, a not-for profit organisation, offers free membershipto all interested individuals. Please join us and become part of this exciting new movement in the world of publishing ethics:http://www.integrity-ethics.com/register/member/ (for standard membership)http://www.integrity-ethics.com/register/editor-in-chief/ (for editor-in-chiefmembership)
As a founding member you will play a central role in shaping the organisation; you will benefit from the many and varied facilities the PIE organisation provides in the world of publishing and ethics. This includes its own guidelines and code of conduct for all membership categories, regular updates in the field, newsletters, e-learning with online exercises and access to our sub-committee’s database. The complaint’s section allows members and adherents to raise issues, regarding any possible breach in the code of ethics and integrity in the publishing sector. PIE provides advice and represents members and adherents freely; it aims to deal with complaints in an ethical manner and resolve them promptly.
As part of the commitment to being a member-led, UK-wide and world-wide organisation, PIE intends to identify regional leads to promote the society and ensure that it remains diffuse, responsive and reflects the publication integrity and ethics priorities across the UK and with a global outreach. Members are invited to take part in a shaping PIE by directly communicating with the PIE’s council and other members with regards to the many issues related to this field; they may issue specific guidelines which can be communicated with other national and international organisations.
PIE is able to recommend short online courses, online diplomas and advanced diplomas to its members; these are specifically related to the integrity and ethics in publication and research, law and medical ethics, research governance, strong ethical practice and management. The course title, description and link to the course registration are usually posted on the PIE’s website as a service to our members.
Our online member’s and adherent’s directory is a valuable asset and will allow communications and collaborations between authors, editors, publishers, scientists and a variety of academics in shaping and advancing  the world of publishing ethics in the service of humanity.
We welcome you to being part of the PIE family. Tim ReevesThe Publication Integrity & Ethics CouncilLondon, United Kingdom

Update 10 AM 11/26: Ivan Oransky at Retraction Watch has a post with information about PIE

Update 8 AM 11/27: Neuroskeptic has posted a detailed investigation of PIE.


How to make a funny video commenting on gender issues in science and engineering

Not much to say other than, well, watch it

Saturday, November 16, 2013

PBS Digital Studios Offensive Thanksgiving Special includes Einstein sexually assaulting Marie Curie

Wow.  I just do not know even what to say here really.  My Facebook feed is filling up with discussion about this video "A Very Special Thanksgiving Special | It's Okay to be Smart" from PBS Digital Studios and I thought it would be important to share this with a wider audience.

The video includes scenes like the following:

Marie Curie is the only female scientist represented who says "It was very nice to be included".















Later there is a scene of Einstein harassing Marie Curie.















Sunday, November 03, 2013

Short post- a bad taste in my mouth for overselling the microbiome

Well, this just leaves a bad taste in my mouth: Oral Bacteria Create a ‘Fingerprint’ in Your Mouth.  Basically, the researchers compared microbial diversity in the oral microbiome of people and they looked at how correlated the microbiome was with ethnicity.  And they published a PLOS One paper and wrote a press release about it.  And there are many lines in the PR and some in the paper I take issue with.  These include:

  • PR: "The most important point of this paper is discovering that ethnicity-specific oral microbial communities may predispose individuals to future disease”.
    • Uggh.  I cannot find anything anywhere that indicates anything about predisposition to disease
  • PR: “Nature appears to win over nurture in shaping these communities,” Kumar noted, because African Americans and whites had distinct microbial signatures despite sharing environmental exposures to nutrition and lifestyle over several generations.
    • Double uggh.  So - different ethnic groups have different microbes.  And since some of the ethnic groups have similar environmental exposures to each other (actually, they do not even test this - they simply assume this) yet do not have similar micro biomes, therefore the cause of the differences in the microbiomes must be genetic differences between the ethnic groups.
  • Paper: "Our data demonstrates that ethnicity exerts a selection pressure on the oral microbiome, and that this selection pressure is genetic rather than environmental, since the two ethnicities that shared a common food, nutritional and lifestyle heritage (Caucasians and African Americans) demonstrated significant microbial divergence." 
    • Triple uggh.  This should not have been allowed in the paper.  Their work in no way demonstrates any genetic component to the differences in the microbiome.  

This is certainly a case of overselling the microbiome.  But it is also a case of just bad science in relation to the "nature vs. nurture" issues.

Draft Outline of Workshop "Publish or perish? The future of academic publishing and careers" #UCDavis 2/13-2/14

Thanks to EVERYONE on Twitter and elsewhere who gave useful feedback on my request for ideas about a workshop we are planning to have at UC Davis.  For background see:
Over the last few days I have discussed the meeting with many many people and we have come up with a more detailed / revised draft of the whole meeting.  I thought I would share that here -- a formal announcement will be coming soon with details on registering and submitting abstracts for short talks and such.


Publish or Perish? The Future of Academic Publishing and Careers (tentative title ...)

February 13-14, 2013
University of California, Davis

Hosted by the UC Davis IFHA Innovating Communication in Scholarship (ICIS) Project

Day 1: Innovations in Scholarly Publishing
  • The Changing Nature of the Journal 
  • Beyond Journals and New Forms of Digital Publishing
  • Peer Review: Assessment and Evolution
  • Keynote talk by Yochai Benkler (which will also be part of the UC Davis Provost's Forum)
Day 2: Assessment 
  • Tracking and Measuring Impact
  • Assessment by Institutions: Current Practices 
  • Assessment by Institutions: How to Change 

Saturday, November 02, 2013

Twitter chatter / links of interest: October 2013

Well, I post to Twitter a lot of links to stories of possible interest to readers of this blog.  If you want to keep up with all of this chatter and discussion from me and others, you should probably hang out on Twitter a bit.  But I know that is not for all.  So I am going to try to start posting some of the more relevant links here.

Wednesday, October 30, 2013

Crosspost: I never meta data I didn't like - especially re: standards for the built environment #IndoorMicro

New paper out from the microbiology of the built environment community: MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. The joint first authors are Elizabeth Glass and Yekaterina Dribinsky. And the senior author is Lynn Schriml.

The paper is simple but I think very important – it describes the development of what is a “suggested list of parameters to record and report for each sequenced sample and to compare data across studies”. Or, in other words, it is a recommended list of metadata to collect and record about samples from the built environment that are being sequenced. If you are interested in microbial diversity and/or the indoor/built environment, this is worth a look.

Oh, and, full disclosure, I am an author too.

Thursday, October 24, 2013

RIP Monica Riley of MBL, one of the true greats of E. coli biology, genetics & genomics


Just got this from Guy Plunkett III
 The E. coli annotation community lost a founding member when Monica Riley died from heart failure on October 11, 2013 in Richmond, CA. She was 87 years old. Monica will be missed by very many of us. There has not been any announcement that I can find, but I have some information from Gretta Serres at the Marine Biological Laboratory in Woods Hole, who is preparing an obituary for Microbe (the ASM newsletter). In lieu of flowers donations can be made to the Alumnae Association of Smith College. Nothing specific has been set up yet, but donations can be made in memory of Monica Riley, class of 1947, at <https://www.smith.edu/future/giving/giftform.php>.
Very sad.  Monica was an incredible woman.  I interacted with her on and off for the last twenty or so years and she played prominent roles much of my earlier work.  Among her many achievements she was central to the annotation of the E. coli genome and in keeping track of all the studies that had been done on various E. coli genes.  See for example http://nar.oxfordjournals.org/content/34/1/1.short.  Perhaps most important, she was just a wonderful wonderful person.  I will miss her.

Tuesday, October 22, 2013

Interview of me and my brother (@mbeisen) regarding history of #PLOSBiology ...

Interview of me and my brother regarding the history of PLOS Biology ...

Ideas wanted for workshop on the "Future of Academic Publishing and Careers"

UPDATE - the Workshop will be February 13-14 at UC Davis.  More information coming soon.

So - I am involved in this really cool new project at UC Davis on the "Innovation in Scholarly Communication" which is a collaboration between myself, Mario Biagioli from the UC Davis Law School and Mackenzie Smith, the Head Librarian at CU Davis  Anyway - much much more on the whole project later.  Right now I am writing to, well, be open.  And to ask for input.  You see, as part of our project we are going to be hosting a workshop at UC Davis in February 2014 on the Future of Scholarly Publishing where we hope to discuss two major issues - how scholarly publishing is changing (Day 1) and then how researchers are evaluated (given jobs, tenure, promotions, etc) in the context of the changing landscape of publishing.  More will be coming shortly on the details of the workshop (i.e., days, registration, etc).

Yesterday I posted a request on Twitter for ideas about Day 1 of the meeting.  I created a Storify post with the responses, which were diverse and very interesting and very helpful.  The Storify is embedded at the bottom. .

Among the major categories of ideas suggested:
  • Differences ...
    • Between fields of science
    • Between science vs. humanities
    • Between types of professions (e.g., tenure track vs. AltAc)
  • New forms of papers
    • The living paper
    • Executable papers
    • Git pull
    • Web read views of content
    • Beyond JATS
    • Hypertextual book
    • Enhanced visuals, interactives, animations, 
    • Micropublication / accumulation of micro pubs
    • Nanopublications
    • Breaking the journal vs. monograph dichotomy
    • Interactive visualizations
    • Blurring of lines between blogs and papers
  • Beyond manuscripts
    • Data publishing
      • data curation and archiving
      • data papers
    • Code: 
      • publishing
      • openness
      • reproducibility
      • review
    • Full integration with research / scholarly workflow and notebooks
  • Mechanism of publishing
    • Uniform standards and styles (e.g., citation)
    • Semantic citations
    • Better authoring tools
    • Versioning
    • Better tools to connect small publishers
  • Peer review changes
    • Open, non anonymous peer review
    • Post publication review
    • Technical merit review
    • Adoption of the reviewers oath
    • Preprint deposition
    • Journal independent review
  • Changing face of the journal and where material is published
    • Role of societies in publishing
    • Journals s collections of preprints
    • Spread of open access spam
    • Preprints and repositories
  • Distribution
    • Getting scholarly research to the reader
    • Getting research to the public
    • Mobile computing
  • Privacy issues esp. in clinical data
  • Assessment and credit
    • Alt metrics
    • Giving and getting credit
    • Finding and sharing best practices for assessment
  • Using published material
    • Text mining
    • Figure/Image mining
  • Social media
    • New forms of papers
    • Assessment and alt metrics
  • Reproducibility
    • Publishing all methods, data, code, 
    • Making everything open

UCDavis ADVANCE Reading of the Day: How not to run a women in science campaign

Interesting article in The Guardian the other day that is worth taking a look at: How not to run a women in science campaign | Science | theguardian.com.  It is by Alice Bell and discusses, among many things, the European Commission video from last year on "Science: It's a Girl Thing" (shown below) that sparked a lot of controversy.  The article also discusses many issues of relevance of improving the representation of women and minorities in the sciences including: the leaky pipe, the whiteness of science, and social mobility.  It is definitely worth a read for anyone interested in issues relating to women in science and minorities in science.


Friday, October 18, 2013

Some great post doc opportunities at UC Davis

See these posts for more detail:

Another great post doc opportunity at #UCDavis
Great opportunity: Postdoc Fellowship at #UCDavis in Population Biology

And if you want to apply and want more information contact the people in the ads or me or comment here.  And furthermore if you are thinking of applying and want to work with me ... well ... definitely let me know.

Tuesday, October 15, 2013

Spammy journal invite of the day: Journal of Immunology & Clinical Research!


I like sharing these SPAMMY journal invites on my blog so that when people google the name of the journal they might end up here.  Here is the latest invite I have gotten:

Dear Dr. Jonathan Eisen,Greetings from Journal of Immunology & Clinical Research!It is our privilege to invite you, in view of your scientific reputation and trustworthiness in your field, we would like to invite you to submit your valuable Research/Review/ Short communication/Perspective on your research area for publication in our upcoming issue.We have gone your latest quality research with work “ ”Journal of Immunology & Clinical Research is ardent to promote erudite, pragmatic, and contemporaneous research in the fields of Immunology & Clinical Research through open Access platform. This open access journal facilitates rapid publication with unlimited dissemination of knowledge to readers.As you are an eminent researcher we request you to support us.If you are interested, kindly let us know your possible date of submission.Anticipating your kind positive response, please revert promptly.Sincerely,
Thanks & Regards

Saturday, October 12, 2013

All figures from all my papers

Made a collection of all the figures from all the papers on which I am an author (well all of the papers that are not genome report papers (e.g., papers in the SIGS journal - going to take some time to add those since I am an author on 150+ ..). Thought it would be fun to share this slideshow - in temporal order ...

Friday, October 11, 2013

Giving thanks ... Acknowledgements cannot be said / posted enough ...

Got reminded on Twitter today about the Acknowledgements in my PhD thesis.








I think Acknowledgements are a very undervalued part of science and I always have tried to spend serious effort remembering and thanking people who contributed to my work.  Science is not done in isolation and so many people play a role in each piece of work - and they deserve to be recognized and thanked if they helped in any way.

Thursday, October 10, 2013

Victoria Schlesinger in Al Jazeera America on Open Data Pros and Cons

Got interviewed last week by Victoria Schlesinger about open science and open data issues and she has now posted her article: Scientists threatened by demands to share data | Al Jazeera America.  The article includes a discussion primarily about the push for more open release of data (and also a bit about papers) and some of the challenges associated with this push.  There are some good quotes in the article both from Schlesinger's text and from some key players in the field of data access including:

  • Christopher Lortie:  “There will be fantastic discoveries, and that’s all that really matters,” says Lortie.
  • From Schlesigner (a quote I do not agree with all of but some may like the metaphor): Sharing the results of scientific research is a bit like unveiling a newly built house, and scientists generally want it widely viewed, so the growth in open access publishing is a boon for most. Sharing data, on the other hand, is comparable to handing over the architectural plans and building materials used to construct the house. Others can scrutinize the quality of work and reuse the basic components to build their own house. That raises fears about discovery of errors and theft of future research ideas.
  • Heather Piwowar: “I think the public thinks that we’re all learning from everyone else’s work. That’s not true, and furthermore, it’s not true in ways that are even worse than you might think,” says Piwowar=
  • Me: “People are busy,” says Jonathan Eisen, a genetics professor at the University of California, Davis. “Everyone is overwhelmed with life and email and, in academia, trying to get funding and write papers. Whether something is open or not open is not highest on the priority list. There’s still need for making people aware of open science issues and making it easy for them to participate if they want to.”
  • Titus Brown: “My general attitude about open science is that I’d much rather be relevant. In science, that’s harder than anything else,” says Titus Brown, an assistant professor at Michigan State University who runs a genomics, evolution and development lab and practices open science. “If I make my work available, I have a higher chance of being relevant.” 
  • It has transformed the way we do science across biological scales, from the molecular all the way up to studying whole ecosystems,” says Carl Boettiger, a postdoctoral student at UC Santa Cruz. “The value is in enabling science to progress faster.”
The article is worth a look ...

Rob Desalle Talk at UC Davis - Storification of Twitter Notes

Wednesday, October 09, 2013

Sunday, October 06, 2013

It may have been a flawed #OpenAccess "Sting" but WE ROCKED IT so submit to our journal ...

I suppose I knew this was coming ... but did not expect it so soon ... see the email I received below.  Focus in particular on the part highlighted in yellow .... 

Dear Colleague, 
British Biotechnology Journal (BBJ) is an OPEN peer-reviewed, OPEN access, INTERNATIONAL journal, inspired from the great OPEN Access Movement. We offer both Online publication as well as Reprints (Hard copy) options. Article Processing Charge is only 50 US$ as per present offer. This journal is at present publishing Volume 4 (i.e. Fourth year of operation). 
2. Transparent and High standard Peer review:
In order to maintain highest level of transparency and high standard of review, this journal presently follows highly respected and toughest Advanced OPEN peer-review system(Example Link1, Link2, Link3, Link4, Link5, Link6, Link7, Link8, Link9, Link10,Link11, etc). We hope that you will appreciate this Advanced OPEN peer-review system, which is expected to give doubtless scholarly benefit and impact to the authors in long run. Additionally we strongly encourage and promote “Post-publication Peer review” by ourcomment section. 
As per a recent report (Link) of Science journal (present Impact factor 31), one of our journal passed a stringent test of quality of Peer review by rejecting a fake article (Link1,Link2, Link3). We applaud the dedication and hard-work of our peer reviewers and editors to maintain the high standard of our journals. It was reported that only few journals (20), out of total 304 journals tested, rejected the fake article after substantial peer review. We are happy that our journal was among these few successful journals along with industry leaders like PLoS One, Hindawi, etc. We believe that the result of this experiment also proved the efficacy of our Advanced OPEN peer review and ‘post publication’ peer review system. Though the report is debated, as it did not include subscription journals, we normally support any effort to improve the quality and transparency of peer review. 
3. Proposed Time Schedule:
Submission to first editorial decision with review comments: 3 weeks
Submission to publication: 6 weeks
State-of-the-art ‘running issue’ concept gives authors the benefit of 'Zero Waiting Time' for the officially accepted manuscripts to be published.
4. Abstracting/indexing:
Many respected abstracting/indexing services covered our journals.

Saturday, October 05, 2013

Love these QTL experiment where microbe relative abundance is the quantitative trait being studied

Just got pointed to this very interesting paper by one of the authors: Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering : Nature Communications : Nature Publishing Group.  I really really love this new approach of doing QTL experiments where the quantitative trait being measured is the relative abundance of various microbes.  The first paper of this kind I know of that did such a QTL analysis was Benson et al. 2010 in PNAS in mouse.  There have been a few others using this approach (e.g., Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits) and I am sure we will see many many more.  Basically this approach allows one to identify genes / polymorphisms / regions of the genome in a host that influence the relative abundance of specific microbes.  And such information will be critical in understanding the interactions of microbial communities with hosts.

Friday, October 04, 2013

Who are the microbes in your neighborhood? Quite a few are from Melainabacteria - a new phylum sister to Cyanobacteria

I just love this paper ... The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria | eLife from the labs of Ruth Ley and Jill Banfield (1st author is the co-first authors are Sara C. Di Rienzi and Itai Sharon).  It represents a landmark study in something that has intrigued many microbial diversity / human microbiome researchers for many years.  Early in the history of sequencing rRNA genes from human microbiome samples, researchers discovered something a bit weird - quite a few sequences were coming from what appeared to be close relatives of Cyanobacteria.  This was weird because all known Cyanobacteria were thought to be photosynthetic and - well - there is not too much light in the human gut.

Now - one possible explanation for this was that these sequences were coming from photosynthetic bacteria but these bacteria were not residents of the human gut but came via consumable items (i.e., food and drink).  Perhaps they were actually from chloroplasts of something in the diet (after all - chloroplasts are derived versions of cyanobacteria). This idea was discussed at many meetings I attended.  But there was no evidence for this.  Another possibility was that there was in fact some light in the human gut - leaking through from the outside or being produced from the inside. And perhaps this was enough to do a little photosynthesis.  Sound crazy?  Well, not so crazy after reports of photosynthesis in the deep sea.  A third possibility was that these sequences were coming from residents of the human gut that were related to (or even within) cyanobacteria but were not photosynthetic.  More detail on possible explanations are in this new paper and in some of the material cited therein.

Anyway - Ruth Ley has been discussing these unusual sequences for years and now in this paper her group and the group of Jill Banfield at Berkeley (along with some others) has used metagenomics and detailed assembly and phylogenetic analysis to reveal many new insights into these sequences.  I could write much more about this.  But, I think the paper really speaks for itself.  And it is open access so anyone and everyone can check it out.  And you should.  It is wonderful.
Fig 2 from Di Rienzi et al.

UPDATED 10/9/2013 to correct that there were co-first authors

Monday, September 30, 2013

Time for a Nobel Prize for the human microbiome? I think so ... what do you think?

Well, previously I have written about how I thought that there should have been a Nobel Prize awarded  to Carl Woese and Norm Pace for pioneering work on microbial diversity.  See for example "Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize".  Alas Carl Woese passed away recently and is no longer eligible.  However, in a way this opens up things to a perhaps more medical driven Nobel prize in Medicine for the microbiome.  I believe that the human microbiome has been shown to be important enough in medicine to be deserving of a Nobel Prize in medicine.

And if that is true, then we can ask "Are there any people who would deserve a prize in this area?"  And the answer is pretty clearly yes.  I would suggest that there are two people who deserve such a recognition: Norm Pace and Jeff Gordon.  Norm Pace for his pioneering work on characterizing microbes indirectly via sequencing their RNA and DNA, especially their ribosomal RNA genes.  And Jeffrey Gordon for his pioneering work on animal and the human micro biome and in showing that the microbiome plays fundamental roles in animals and human health and phenotypes.

I will write more about this later but just wanted to get this thought out there ... and see what people think.

UPDATE September 2015 I note. I have been and continue to be concerned with the spread of "microbiomania" which is the term I use to refer to "Overselling the Microbiome". Even though this still is a problem, I also believe the microbiome has now been clearly shown to be critically important to human health in diverse ways and I do think it is appropriate to award a Nobel Prize in this area.

Also note Reuters is reporting that Jeffrey Gordon is on their candidate list this year (based on ISI predictions).

Wednesday, September 25, 2013

Fecal transplants as treatment for anxiety? Not so fast (but worth pondering)

 Just read this: Gut Bacteria Transplant: A New Treatment For Anxiety? | Psychology Today: calm vs. anxious.  On the one hand, I agree that the microbiome very well may have interesting effects on human behavior.  Well, actually, we know the microbiome does impact human emotion and behavior.  For example, I get pretty anxious when I have gut problems, and we certainly know that the microbiome has a major impact on gut health.  And of course, we know lots of examples of microbes affecting behavior of animals.  The latest on this that I am aware of comes from studies by Wendy Ingram in my brother's lab at UC Berkeley - who has been looking at Toxoplasma and it's effect on mouse behavior (e.g., see Toxoplasma infection permanently shifts balance in cat-and-mouse ... and Cats, Mice and Toxoplasma Gondii Parasite Weird Love Triangle and Mice Aren't Scaredy-Cats When Infected By Toxoplasma).

On the other hand, despite the apparent connections between microbes and emotion and behavior in some cases, this does not mean either that (1) microbes have a role in causing anxiety in people or (2) even if microbes CAUSE anxiety that microbiome transplants could treat the anxiety.  Anyway - I certainly think this is an interesting area of research but I urge caution before we go overboard in marketing fecal transplants for everyone with any issues connected to behavior or emotions ...

Best evidence yet that we should do away with the "Candidatus" terminology used for uncultured microbes

Just got this email:
Dear Jonathan , I am relatively new to phylogenetics and have developed a keen interest in bacterial phylogenies. I read one the papers which you have published in Nature on the same topic. I needed some help. Thing is, I have constructed a bacterial phylogeny based on 16s rRNA and have found that Candidatus species differ by a really great extent from one another, and appear to be in completely different clades. I need some way to verify this and was wondering if you could send me the phylogeny you have created in order for me to verify. Thank you
I have been arguing for years that the use of the term "Candidatus" to describe microbes is a bad idea.  This email is exactly the kind of thing I worry about.  Candidatus is a term used "for well characterized but as yet uncultured organisms." (A nice description of the history of the term is here).  The problem with Candidatus are many - including the confusion such as evidenced by this email - in that people who are not used to dealing with the term have no clue what it means.  But in addition, the constraint that one is not "allowed" to name things unless they have been cultured is silly, outdated, and damaging to the field.  But I can write about that some other time.  For now, this email will suffice ...

Some examples of Candidatus names from http://www.bacterio.net/candidatus.html


Monday, September 23, 2013

Lovely - Entangled Bank conference not only only includes men, but has obnoxious FAQ about doing that

Just got pointed to this: These men would like you to kindly shut up about gendered conferences | Feminist Philosophers.  It discusses a painful example of Gender Bias associated with Science conferences.  In this example a charity "or, a supposed charity" is organizing a meeting featuring only male speakers.  And they included a FAQ on the meeting website to explain why there were only men:

Wow.  That is just horrendous.

More about this is available now on Jezebel.

Note - the same group organized another meeting also with only male speakers. http://www.entangled-bank.co.uk/dawkins-in-bristol.html

Guest post by Josh Weitz: IP vs. PI-s: On Intellectual Property and Intellectual Exchange in the Sciences and Engineering as Practiced in Academia


Today I am pleased to publish this guest post from my friend and colleague Joshua Weitz. He does some fantastically interesting research but that is not what he is writing about here. Instead he is focusing on intellectual property and sabbaticals ...

Joshua S. Weitz
School of Biology and School of Physics
Georgia Institute of Technology


Preface:

This blog entry is inspired by a recent personal experience. However, I believe it serves to illustrate a larger issue that requires open discussion amongst and between faculty, administrators, and the tech transfer offices of research universities.

Context:

I am temporarily based at the U of Arizona (hereafter UA) working in Matthew Sullivan’s group where I am on a 9 month leave from my home institution, Georgia Tech (hereafter GT), spanning the term: August 15, 2013 to May 15, 2014. I arrived on campus and began the process of signing various electronic forms to allow me to use the campus network, get keys, etc.

The gateway to this process was a request to sign a “Designated Campus Colleague (DCC)” agreement: http://www.hr.arizona.edu/dcc. The DCC agreement is the official way the UA establishes an “association” with long-term visitors who do not receive any form of payment from UA (as applies in my case). I would be an Associate of the Department of Ecology and Evolutionary Biology, where the Sullivan group is based. The privileges of the DCC include receiving a UA email, keys to an office, a “CatCard” (Cat = short for Wildcats, the UA mascot) which enables me to access the building after hours, as well as other discounts. The DCC makes it quite clear that I am not an employee and that I will receive no form of payment whatsoever from UA. Indeed, all of this is rather immaterial to my real reason for spending 9 months here – to work in closer collaboration with the Sullivan group on problems of mutual interest. The obligations I must affirm are largely boilerplate (i.e., do no harm) but do include the following identified in Clause 11 of the DCC:
“11. INTELLECTUAL PROPERTY – Associate hereby assigns to the ABOR all his or her right, title and interest to intellectual property created or invented by Associate in which the ABOR claims an ownership interest under its Intellectual Property Policy (the "ABOR IP Policy"). Associate agrees to promptly disclose such intellectual property as required by the ABOR IP Policy, and to sign all documents and do all things necessary and proper to effect this assignment of rights. Associate has not agreed (and will not agree) in consulting or other agreements to grant intellectual property rights to any other person or entity that would conflict with this assignment or with the ABORs' ownership interests under the ABOR IP Policy”
This clause is worth reading twice. I did. I then refused to sign the agreement. This clause, my refusal to sign the agreement, and what happened next are the basis for this blog entry.

Note that the template upon which my particular agreement is based can be found on the UA website. For those unfamiliar with intellectual property (IP) clauses that universities routinely request visitors to sign, here is a small (random) sample:
  1. U of Texas
  2. U of Maryland Baltimore
  3. Emory University
  4. Washington University @ St. Louis
  5. Northwestern University
It would be possible to collect many more such agreements that apply to both employees and to visitors of research universities.

The issues
The central issue at stake is one of ownership of future intellectual property. Presumably a visitor has decided to visit U of X because U of X is the best in the world and that new, monetizable discoveries will emerge as a direct result of the “resources” at U of X. This may be true. Or, it may not be. However, rather than try and chase IP after it has been created (a tenuous legal position), universities would rather have all visitors assign future IP immediately upon arrival and sort it out later (if and when IP is generated).

This language of “hereby assigns” (as quoted above) is not chance legal-ese. To the contrary, it is clear that the legal staff and upper administration at universities are concerned with respect to the repercussions of Stanford vs. Roche. If you haven’t read up on this case, I encourage you to do so. The key take-away message is that the Supreme Court has ruled that inventions remain the property of the inventor to assign as they see fit unless the inventor assigns inventions to a specific entity (e.g., an employer). As the U of California memo to faculty makes clear, the way that many universities want to deal with this problem moving forward is to reword their employment contracts so that employees immediately assign their IP to their university, rather than “agree to assign” their IP. “Agree to assign” (a clause meant to describe a potential future action) was the language found in Stanford’s prior IP agreement and represented one key component of Stanford losing their Supreme Court case to Roche, to the disappointment of Stanford, other major research universities and the federal government.

Figure 1 - Supreme Court decision on Stanford vs. Roche, remainder available here: http://www.supremecourt.gov/opinions/10pdf/09-1159.pdf
However, scientific visits to other institutions create a complex contradiction whereby institutions ask their visitors to sign agreements that they would never want their own employees to sign while visiting other institutions!

Sunday, September 22, 2013

Jerusalem Post on Allergy and Fecal transplants

Some interesting tidbits in this Jerusalem Post article: Health Scan: Ungluing the complexity of allergy | JPost | Israel News (a bit overenthusiastic too but just thought I would point some of these lines /quotes out):

  • "Studies in adults show that more than 90 percent of patients are cured following such therapy and, experts say, they have every reason to believe the numbers would be equally impressive in children." - not sure this is true (i.e., the 90% cured level).
  • In less than a decade, we’ll have lab-cooked poop that we can administer to restore balance in the guts of people with a wide array of conditions caused by the imbalance between good and bad germs.” OK - a bit overenthusiastic 
  • But this is my favorite: "The concept is hardly new. The method originated with ancient Chinese healers who gave their diarrhea-ravaged patients “yellow soup,” a concoction of fecal matter and water. Thousands of years later, the delivery approach has evolved" - So - I have been writing and talking about fecal transplants for a while now (e.g., see this) and have linked them to coprophagy and poo tea and such but never heard of the yellow soup thing.

Friday, September 20, 2013

The Saga of Howard Zochlinski, ex-#UCDavis PhD Student

I met with Howard Zochlinski last week at UC Davis.  His story is like none I have ever heard.  Howard does not have ready web access.  He has little money.  He needs to go to the library to check his email.  And he met with me to ask me to share his story.  And I readily agreed to.  I do not know ANY of the history personally.  I do not even know whether all of what he says is true or not.  But the story is worth putting out there in my opinion for people to make their own judgements.

To begin to get to know the details behind the saga of Howard Zochlinski you might want to start with the petition he just posted on Change.Org: Petitioning To The Honorable John G. Roberts, Chief Justice, and the Honorable Justices of the Supreme Court of the United States.

Other sources of information about Howard's story are linked below:
The DavisWiki page summarizes some of the details on the saga and I have copied the current text from there below:
Howard Zochlinski has been the center of academic and judicial controversy within California and the UC System, including at UC Davis. 
When Howard was an undergraduate at UC Santa Barbara in the early 1970s he was arrested; none of the charges stuck. 20 years later he was a Genetics doctoral candidate at UC Davis and was arrested by the same policeman who had arrested him back in Santa Barbara. 
The arrests in Santa Barbara resulted in either dropped charges or were thrown out of court. All three of these arrests were made by the same two officers, John Jones and John MacPherson. Howard believes that these arrests were the result of his being a Vietnam War protestor. During his detainment he claims that he was sexually assaulted while in police custody and believes that officer Jones was instrumental in arranging it.
He transferred to UC Berkeley where four years later he graduated with a Bachelors degree. He then earned two Masters over the next six years from University of Hawaii and John Hopkins University. During this time officer Jones transferred from UC Santa Barbara to the UC Davis Police Department. 
In 1984 Howard was admitted to UC Davis as a PhD candidate. In 1992 officer Jones again arrested Howard, this time for stalking. Jones claims that there was nothing personal or targeted about the arrest; Howard claims that the arrest was the result of Jones holding a vendetta and being an anti-semite. This charge as well was dropped when the victim did not appear in court. Howard also maintains that Jones arrest report does not meet the legal definition for the charges that were filled against him. 
In 1993 he was arrested again, but acquitted in court. His defense attorney claimed that the police were not conscientious in the manner in which they handled the case. It does not appear that officer Jones was involved in this case. 
Shortly prior to the time of this last arrest after having been a PhD candidate for 9 years Howard was dismissed for not filling an acceptable thesis by the deadline his committee had assigned. 
Howard believes that the stalking arrest had prejudiced his department against him. Part of his feelings of persecution stem from having had a conduct hold placed on his academic record; one with an end date in the year 2099. Student Judicial Affairs says that this was a clerical error. Howard thinks that this contributed to his difficulty in landing a job.
Howard filed a lawsuit with the University in regards to his dismissal as a student. As of 2006, the details and status of this lawsuit are unknown. In 2005, the Academic Senate of UC Davis overwhelmingly ruled to re-admit Zochlinski as a student. Such a ruling by the Academic Senate is fairly unheard of, prompting University officials to question what would happen next. However Jeff Gibeling, Dean of Graduate Studies, ruled against readmitting Zochlinski on the basis that his predecessor had made the same ruling. As such, this case is still ongoing.
I am still trying to wrap my brain around the whole saga.  But if even a tiny fraction of it is true, which certainly seems to be these case, he has been pretty badly treated.  Again, I do not know all the details or what is the "truth" but I can say for certain that Howard continues to struggle and I cannot for the life of me see any reason not to allow him to be readmitted as a student.