Nice PBS Newshour Piece on Alan Alda's flame challenge and communicating science

This is worth watching ...

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.

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.

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

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.

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:

• My previous blog post: Ideas wanted for workshop on the "Future of Academic Publishing and Careers"
• The Storify I keep updating regarding my original request for comments: Request for ideas / topics on the future of scholarly publishing

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 

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.

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.

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.

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.

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.

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

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 ...

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

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

We clearly need a #MyFavoriteNaturePaper hashtag.
— Leonid Kruglyak (@leonidkruglyak) October 11, 2013

@leonidkruglyak ???? that seems like a bizarre topic
— Jonathan Eisen (@phylogenomics) October 11, 2013

.@phylogenomics @leonidkruglyak How about Cairns et al, 8 Sept 1988, on "directed" mutations? Almost hooked one young J Eisen, no? (1/2)
— Richard E. Lenski (@RELenski) October 12, 2013

@RELenski @leonidkruglyak DID hook me for 3+ years until a fateful encounter w/ Rich Lenski at a Gordon Conference knocked sense into me
— Jonathan Eisen (@phylogenomics) October 12, 2013

.@phylogenomics @leonidkruglyak Or maybe you'd have your Nobel Prize now? Life is funny, no?
— Richard E. Lenski (@RELenski) October 12, 2013

@RELenski @leonidkruglyak see page-vi of my PHD http://t.co/JNfv6dbOh0 where I thank A. Campbell & R. Lenski for leading me to new areas
— Jonathan Eisen (@phylogenomics) October 12, 2013

.@phylogenomics @leonidkruglyak Never saw that, but I do remember our chat like yesterday ... how many years ago? Not sure want to know ;>)
— Richard E. Lenski (@RELenski) October 12, 2013

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.

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

#UCDavis Phaff Yeast Collection & Kyria Boundy-Mills featured on Radio New Zealand

Cool story on Radio New Zealand featuring one of my favorite microbiologists (Kyria Boundy-Mills) and one of my favorite microbiology related things at UC Davis (the Phaff Yeast Collection).
 

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.

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.

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

The government shutdown of science - a screenshot gallery

---

See full screen slideshow via Picasa here. Individual pics below:

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).

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

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

Email: jsweitz@gatech.edu

Web: http://ecotheory.biology.gatech.edu

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!

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.

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:

• DavisWiki page: Howard Zochlinski‎ (with lots of background and links)
• Sacramento News and Review Story from 2001: Howard's End
• UC Davis student paper "The Aggie" story from 2011: Two-decade-long fight for Ph.D. continues
• Facebook Page maintained by Howard (I think): Justice for Howard Zochlinski

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.

Really? Nature put the #HeLa genome paper behind a paywall? Time for Nature Publishing Group to return ALL money obtained from genome papers

This is just fucking ridiculous.  As I have written about many many times - Nature Publishing Group many years ago promised to make papers reporting genome sequence data freely available.  They do not generally live up to this promise well.  See for example

• Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh
• Please help keep the pressure on Nature Publishing Group to restore free access to genome papers #opengate
• I am highly skeptical of the CHORUS system proposed by scientific publishers as an end run around PubMed Central
• Calling on Nature Publishing Group to return all money received for genome papers and article corrections
• A Solution to Nature Publishing Group's Inability to Keep Free Papers Free: Deposit them in Pubmed Central

Today I discovered that not only are some important genome papers not freely available but one for the ages - the paper on the HeLa genome - reported with much fanfare recently as a triumph of an agreement with the family of Henrietta Lacks - is only available if you pay.

Once again I call on Nature Publishing Group to publicly disclose all financial gains that have come from people paying for the these genome papers and for the money to be returned.

Can academics use the "copyright termination" system to recover academic works?

Heard an interesting story on copyright termination on NPR last night: Taking Back 'Funkytown': Songwriters Prepare For A Custody Battle  By Joel Rose.  This in turn led me to a New York Times article on the same general topic: A Copyright Victory, 35 Years Later - NYTimes.com.

The gist of these stories is that it turns out UC Copyright law has a "termination" provision which allows artists / writers / etc to terminate copyright agreements that they made for work they produced.  This is allowed 35 years after the copyright was assigned.  And many musicians are using this provision of copyright law to reacquire some works they made three and a half decades ago.

So - I am asking the world out there - could this same provision be applied to scientific or academic works?  Would this be a way to move a lot of material that is behind a wall back into the hands of authors and/or into the public domain?  I am looking into doing this with work published by my father as a test case (as part of my long struggle of  Freeing My Father's Publications (since termination rights apparently transfer to family members if the holder passes away as my dad did in 1987).

So - anyone out there know if this termination has been used for scientific or academic works?

UPDATE: Other reading

• U.S. Copyright Office - Copyright Law: Chapter 2
• Navigating US Copyright Termination Rights - WIPO
• United States Copyright Termination Rights: What Does the Future ...
• Copyright Termination Rights: Giving Artists Their Second Bite at the ...
• Superman Lawsuit Tests Copyright Termination Rights | Astronomy ...

Story behind the paper guest post by Corey Nislow (w/ Metka Lenassi) on "Genomics w/o Borders"

Below is another in the "Story behind the paper" series of guest posts here.  This one is from Corey Nislow w/ Metka Lenassi.  If anyone else has published an open access paper on anything relating to this blog and would like to write a guest post on the Story behind the paper, please let me know.

---

Genomics without Borders: Genome Sequence of the Extremely Halotolerant Yeast Hortaea werneckii 

by Corey Nislow (with Metka Lenassi)

In this guest post (thank you Jonathan!) I wanted to tell the story behind a paper that my colleagues and I published two weeks ago in PLoS ONE. The story also offers an opportunity to talk about what role, if any, a middle author can play in a scientific study.

The story is set in Slovenia a beautiful country which was part of the former Yugoslavia and which is home to about 2 million inhabitants, 2400+ fungal species (thanks Wikipedia) and some very interesting environments. One of these environments is the Secovlje Salterns where one can find the yeast Hortaea werneckii.

A worker harvests sea salt in the Secovlje salterns, July 17, 2010. Some 2600 tons of salt is expected to be produced during the two and a half month season at the salterns.(Xinhua/Reuters Photo)

I hadn't heard of Hortaea until I started googling around looking for a yeast extremophile that I can grow in the lab to dissect out its nucleosomes to ask questions regarding nucleosome occupancy and transcription in the face of extreme environments. Turns out it was not a crazy idea--

13 years ago a peculiar black yeast Hortaea werneckii was isolated from its natural habitat: waters containing so much salt, it would kill most living organisms instantly. Since then, two small (but enthusiastic) Slovenian groups have tried to understand its halotolerance. This demanded field trips to the beautiful Slovenian coast, but also a lot of hard work and inventiveness to optimizing protocols used for other organisms – and to do it on a low budget. The first important obstacle was actually cultural - to persuade the scientific community that such extreme yeast even exists in nature! You can see it below. We now have ample evidence as Hortaea has been isolated from many seawater-related environments, saline lakes, but also from surface layers of tropical microbial mats in salterns and even from spider webs in Atacama Desert caves. All these different Hortaea strains are now waiting in their freezer (the Ex culture collection) to be analyzed.

Hortaea werneckii growing happily on 2M salt.

Nice show on KQED on Inspiring Girls and Women to Code #Diversity #STEM

Listened to a nice show on KQED this AM on my bike ride in to work (note - I listen with one earplug in, and one ear free to hear the world around me, and I listed on relatively low volume ...).  We still need to do so much to make STEM fields and related fields more diverse ...


Inspiring Girls and Women to Code:

 

Families that share everything: Health2Fit video on brother helping sister by being a donor for a fecal transplant

I guess today is fecal transplant day. So why not a little news story from Health2Fit about families that share everything ...

 

Fecal transplants taken up by American Hospital Association in letter to HHS about Medicare/Medicaid

Interesting discussion of Fecal Transplants is this letter from the American Hospital Association to HHS about Medicaid / Medicare: Marilyn Tavenner September 6, 2013 Page 1 of 33 September 6 ...

Key text is below:

"FECAL MICROBIOTA TRANSPLANTATION
Fecal microbiota transplantation (FMT), also known as fecal bacteriotherapy, or human probiotic infusion, is a medical treatment for patients with Clostridium difficile (C. difficile) enteritis or ulcerative colitis. C. difficile infection occurs in patients who have been administered antibiotics for a long period of time. The antibiotics destroy important disease-fighting bacterial flora in the intestine. Fecal transplants are believed to restore the bacteria back to normal, and the patient can recover. The fecal transplant works by repopulating friendly flora in the infected intestines. The donated feces is screened for disease and then mixed with a saline solution to the consistency of a “milkshake.” FMT can be performed by various routes including nasogastric (NG) tube, nasojejunal tube, upper tract endoscopy (EGD), colonoscopically or by retention enema. However, based on an editorial published in the Journal of Clinical Gastroenterology (Volume 45, Number 8, September 2011), colonoscopic FMT is the preferred method for the vast majority of C. difficile infection patients, and if carried out early, may prevent development of severe infection.

Effective with the 2013 edition of the CPT manual, the American Medical Association developed the CPT code 44705 (Preparation of fecal microbiota for instillation, including assessment of donor specimen) that includes:

• development of the intestinal instillate for the recipient; and
• evaluation of the donor specimen, including the physician review of results of testing the donor’s specimen for infectious pathogens

The CPT manual instructions require that the actual instillation or fecal microbiota transplant be coded separately using CPT 44799 for either oro-nasogastric tube or enema. Additional instruction in the CPT manual identifies that all laboratory testing provided for the patient is to be reported separately. Based on this instruction and the intent of the CPT code 44705, this is an add-on or “list separately in addition to the primary procedure,” which would be the instillation procedure, e.g., the oro-nasogastric tube or enema.

Fecal transplant recruiting on Craigslist

See this Craigslist post for the Boston area: Are you a healthy adult, 18-50 years old? - copied below.  It seems that fecal transplants really are everywhere ...

 Are you a healthy adult, 18-50 years old? (Massachusetts General Hospital)

Fecal Microbiota Transplant
Healthy adult volunteers 18-50 years old
Involves donation of stool samples and medical screening
Blood draws, complete medical exam
No medical problems
5-7 out-patient visits at MGH
Compensation up to $700 for completion of study
617-724-8625

• Location: Massachusetts General Hospital
• it's NOT ok to contact this poster with services or other commercial interests

Posting ID: 4050676649

Posted: 2013-09-06, 4:04PM EDT

Updated: 2013-09-06, 5:09PM EDT