Tag: Misc.

How to keep up with microbial ecology and the built environment: microBEnet is your place

Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway – here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) — meeting reports from a Planetary Protection meeting

My posts:

Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

Elisabeth Bik from Stanford roundups from Microbiome Digest
David Coil (a staff scientist at UC Davis in my lab)
Linsey Marr of Virginia Tech
Rachel Adams – post doc at UC Berkeley
Ben Kirkup of the  Naval Research Laboratory
Embryete Hyde from UCSD

Brent Stephens of the Illinois Institute of Technology

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Curator, Professor, and Director of Comparative Biology Initiative Position at the American Museum of Natural History

Interesting …

Dear Colleague,

We are pleased to announce a search for a new senior scientific and leadership position (Curator, Professor, and Director of Comparative Biology Initiative) at the American Museum of Natural History. Please pass the attached posting along to anyone you think might be interested; applications and nominations are both encouraged.

Thank you,

John J. Flynn

Frick Curator, Professor, and Dean of the Richard Gilder Graduate School

On behalf of the AMNH Senior Curator-Director Search Committee

Senior Search:

Curator, Professor, and Director of Comparative Biology Initiative

American Museum of Natural History

The American Museum of Natural History (AMNH) in New York invites applications and nominations for an outstanding scholar at the Full Curator & Full Professor level with internationally-recognized research and leadership credentials, and demonstrated, ongoing high-impact research productivity and grantsmanship, to provide innovative leadership for a new museum-wide initiative in comparative biology. This initiative will incorporate the work of multiple investigators at the Museum and at collaborating institutions in genomics (including eukaryotic [including microbial] genomics, metagenomics, phylogenomics, transcriptomics, etc.), phenomics (large-scale phenotypic analysis) and bioinformatics/computational biology, aimed at understanding the evolution and relationships of organisms in ways that clarify and illuminate the architecture of life. The successful candidate for this position should show experience and interest in managing large–scale, interdisciplinary, collaborative, multi-institutional projects and is expected to qualify for and be appointed as a tenured full curator in either the Division of Invertebrate Zoology or Vertebrate Zoology, and as a full professor in the Richard Gilder Graduate School at the AMNH. We seek a creative, active, broad-based researcher and dynamic academic leader who interacts well with others and who will utilize the extensive resources the Museum has to offer in the way of collections, research instrumentation and laboratories, interactions with Museum colleagues and collaborations with area organizations (including the New York Genome Center, area universities, New York Botanical Garden, and others), teaching and mentoring, exhibition, and public education.

We particularly seek applications from, or nominations of, candidates with a compelling vision for the future trajectory of their science, and for comparative biology in general, and whose research addresses fundamental, cross-disciplinary questions. In addition to the above-noted expectations for high productivity and grantsmanship, the successful candidate will have outstanding communication skills in engaging diverse communities and demonstrated capabilities in management of collaborative projects and decision-making. Experience in interacting with governmental and non-governmental agencies and in fundraising are highly desirable, as are collection-based, field-based and/or computational research. Other responsibilities or opportunities include advising graduate students and postdoctoral fellows, offering courses in the Comparative Biology Ph.D. Program of the Museum’s Richard Gilder Graduate School, institutional service, development activities, and participating in Museum-sponsored exhibits and educational programs.

In addition to applications, we invite recommendations or nominations of potential candidates, and request that these include a resume and contact information for the nominee. Nominations or applications can be submitted to seniorcuratorsearch. Applicants should submit the following materials electronically, preferably as PDF files, via a single email message to seniorcuratorsearch (Subject line: 2015 Senior Curator IZ-VZ Search Committee: your name): 1) a cover letter in which you indicate your interest, experience, and qualifications for the position; 2) a curriculum vitae; 3) PDF files of up to five recent publications; and 4) names and contact information for five referees who can comment on leadership, scientific and other skills and accomplishments noted above (to be contacted by the Museum only at the time of arranging an interview or for the process of tenure review in the case of a potential appointment). Inquires should be directed to John Flynn, Chair of the Search Committee and Dean of the Richard Gilder Graduate School: dean-rggs. Applications or nominations should be received by April 2, 2015.

Employer Information:

The American Museum of Natural History is one of the world’s preeminent scientific and cultural institutions. Since its founding in 1869, the Museum has advanced its global mission to discover, interpret and disseminate information about human cultures, the natural world and the universe through a wide-ranging program of scientific research, education and exhibition. The Museum’s research collections include more than 33 million natural history and cultural objects, and AMNH scientists undertake more than 100 expeditions annually. Science at the Museum includes five academic divisions, the Richard Gilder Graduate School, Sackler Institute of Comparative Genomics, 1 million specimen-capacity Ambrose Monell Cryo Collection, Center for Biodiversity and Conservation, high performance computational facilities, Microscopy and Imaging Facility, Southwest Research Station, the largest independent natural history library in the Western Hemisphere, membership in the New York Genome Center, and an array of other scientific facilities and resources.

The American Museum of Natural History is an Equal Opportunity/ Affirmative Action Employer. The Museum encourages Women, Minorities, Persons with Disabilities, Vietnam Era and Disabled Veterans to apply. The Museum does not discriminate due to age, sex, religion, race, color, national origin, disability, marital status, veteran status, sexual orientation, or any other factor prohibited by law.

If special accommodations are needed in applying for this position, please contact the Office of Human Resources at hrdesk or 212-768-5108.

Senior curator-director job ad final for posting 2-17-15 .pdf

Calling attention to poor speaker gender ratio – even when it hurts

So I saw this Tweet earlier today

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And that sounded very interesting. So I clicked on the link to check out the Plant Breeding for Food Security: The Global Impact of Plant Genetics in Rice Production A symposium honoring Dr. Gurdev Khush symposium.  And, then I went to the program.  And sadly I saw something there that was not to my liking.  The speakers were almost all male (men labelled in yellow, women in green)

  • Welcome to the Khush Symposium (Alan Bennett)
  • The Plant Breeding Center (Charles Brummer)
  • The Confucius Institute (Glenn Young)
  • Global food production – challenges and opportunities (Ken Cassman) Food production, technology and climate (David Lobell)
  • Panel – Impact of Gurdev Khush on plant genetics and food security Tomato genetics
    • (Dani Zamir)
    • (Pam Ronald)
    •  (Gary Toenniessen)
    •  (Gurdev Khush)
  • Lunch; The California Rice Industry (Kent McKenzie)
  • The rice theory of culture (Thomas Talhelm)
  • Recent advances in rice productivity and the future (David MacKill)
  • Hybrid rice technology contributions to global food security (Sant Virmani)
  • Super green rice (Qifa Zhang)
  • Tackling the wheat yield barrier (Matthew Reynolds)
  • African Orphan Crops – inspiration and execution (Howard Shapiro/Allen Van Deynze)

If this was a symposium outside UC Davis the first thing I would do would be to post about it.  To Twitter or my blog or both.  And to critique them.  Why?  Because there is a bad history in STEM fields of having meetings and conferences have under-representation of women as speakers.  And this has become a passion of mine and I write about it a lot.  But I hesitated.  Why?  Because this was from UC Davis and many of the people involved are friends / colleagues.  I did not want to anger them, or embarrass them.  And I don’t think there is any intentional bias here by any means.  But, if I am going to critique people outside UC Davis, it seems like I should also apply the same standards to people inside UC Davis and to colleagues and friends.

So I posted to Twitter a response:

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But that did not seem sufficient.  So I wrote up this post.  Underrepresentation of women as speakers is a serious issue in STEM fields.  And it is solvable (e.g., see Some suggestions for having diverse speakers at meetings by myself and the wonderful Ten Simple Rules to Achieve Conference Speaker Gender Balance by Jennifer Martin).

Now – do I know who the possible speakers were for this symposium?  No – I don’t really know the field.  Is it possible that there just are no women in the field?  Sure.  But I would bet anything that is not the case here.  Having a meeting where the ratio of speakers is 16:1 male: female sets a bad example.  UC Davis and the organizers of this meeting can do better.  And though this will possibly hurt me in various ways (I already got grief from one person who I will not name for the Tweet), I think it is critical that we call out examples such as this.

And finally I note – I have taken on the issue of women at STEM conferences and meetings because, well, it is easy to identify cases where the numbers are anomalous and it is relatively easy to solve.  But it is also important that we consider other aspects of diversity of speakers (age, ethnicity, career stage, etc).  It is important to have diversity of speakers at meetings for many many reasons.  Speaking is a career building opportunity.  Speakers serve as role models for others.  Diverse points of view are important to have represented.  Bias – whether simplicity or explicit damages the whole practice of science.  And more.  Yes, we need to work on many aspects of diversity in STEM fields.  Improving the diversity of speakers at meetings is but one part of this.  But it is an important part and it is relatively easy to do.  So just do it.  And call attention to it.  Even if it hurts.

UPDATE 3/25 11:29 AM

The meeting organizers have responded on Twitter

Storify of some responses here

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//storify.com/phylogenomics/speaker-gender-ratio-at-ucdavis-meeting/embed?border=false//storify.com/phylogenomics/speaker-gender-ratio-at-ucdavis-meeting.js?border=false[View the story “Calling attention to poor speaker gender ratio – even when it hurts” on Storify]
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Treponema are not "ancient" but absence from some human’s guts is very interesting

So I saw some Tweets today that caught my attention, discussion news stories about “ancient” bacteria being missing from some human’s gut microbiomes:

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These refer to a sadly inappropriate headline in Science

What is wrong with this?  Well, there are no “ancient” bacteria around today.  They are all modern.  I am not even sure what they were trying to say.  Just a really bad evolution argument I guess.  I pondered giving Science a Twisted Tree of Life Award which I give out for exactly this kind of thing –  but decided first to dig into the science here and gloss over the bad evolution headline.

And it turns out – what the news story is about is in fact interesting – a new paper out in Nature Communications:  Subsistence strategies in traditional societies distinguish gut microbiomes.

The paper is freely available and has some really interesting material in it.  They key to me – at least related to this “ancient” bacteria claim is the following part of their abstract:

As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

And then some further detail in the paper:

Although Spirochaetes have been previously reported from the gut microbiome of non-human primates and ancient human populations, they have only been observed in high abundance among extant human populations with non-Western lifestyles, such as a traditional community in Burkina Faso and a hunter-gatherer community in Tanzania. As such, they may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes. 

So they don’t go into the full detail here but what I think they are saying is that they infer that human ancestors had Spirochaetes (based on the finding of it in non human primates and some human populations).  And thus they further infer that human populations (e.g., the people they studied in Oklahoma) that do not have these Spirochaetes have “lost” them.

I note – I think this terminology of “loss” they are using is not quite right here in a way.  Saying that these Spirochaetes have been lost implies to me that they are heritable.  But they do not in fact show that.  It could be that these are related to diet or environment in some way – something shared by some human populations and non human primates, for example.  And thus the absence from some “Westernized” populations could be more of an environmental thing than a “loss” in the past.


In a similar way, we could say that Westernized humans have “lost” the ability to be skinny (since obesity is high in many such populations).  Non human primates have such abilities and so do some non Westernized populations.  But “losing skinnyness” does not seem quite right since we do not know exactly why obesity is higher in Westernized populations.  I think it would be better in such cases to say something like “do not show an ancestral trait” (the ancestral trait here being skinnyness) and to not use “lost” until we know more about what is going on.  Similarly, I think saying some human populations have “lost” these Spirochaetes is not quite right.

Nevertheless, the absence (or at least, low levels) of these Spirochaetes from some human populations is certainly interesting.  And given that the presence of such Spirochaetes does appear to be an ancestral trait, the absence is even more interesting.  And thus this paper here, which details some of the genomic features of these “missing” Spirochaetes is definitely worth paying attention to.

In addition, I note – the findings in this paper serve as an additional justification for projects to generate genomic data from across the phylogenetic diversity of microbes.  Consider for example their Figure 6 and 7 which show that the most closely related Treponema species and the ones with the most similar genomes to these human Spirochaetes are those from Treponema succinifaciens and Treponema brennabornese.

Both of those genomes were generated by the Genomic Encyclopedia of Bacteria and Archaea project which I coordinated with the DOE-JGI and DSMZ.  See the paper on one of them: Complete genome sequence of Treponema succinifaciens type strain (6091T) and the posted data on the other.

We argued that we needed to sequence reference genomes from across the tree of life because this would help inform studies of uncultured microbes from diverse ecosystems.  Little did I know that one of the key ecosystems we would help inform would be the human gut.

Certainly more needs to be done in regard to these Spirochaetes.  Why are they at low levels or missing from some Westernized populations?  What do they do in other populations?  Would they be helpful if they were reintroduced to populations that do not have them?  So many questions actually.  But despite the misleading news article headline, this paper seems to me on first glace at least to in fact be quite interesting.

I made a Sorify of some comments

//storify.com/phylogenomics/not-ancient-bacteria-not-lost-but-interesting/embed?border=false//storify.com/phylogenomics/not-ancient-bacteria-not-lost-but-interesting.js?border=false[View the story “Not ancient bacteria, not lost, but interesting” on Storify]
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Horizontal gene transfer into humans? I am not convinced. Full text of my comments to reporters here

Some news stories about a new paper claiming evidence for horizontal gene transfer into humans and other chordates. I got asked by many reporters about it and some used some of my email comments in their articles.

See for example

 Here is the full text of my responses:

“got asked by another reporter to comment on this

so – have seen the paper 

it is interesting .. but I am not overwhelmed by what they present in the paper itself. For example, the HAS story seems really incomplete as presented (e.g., the Figure showing the tree does not have all the HAS1, HAS2, HAS3 genes even though they imply they studied that). “

I have been looking through the supplemental information. I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those. 

Without seeing the alignments I offer multiple alternative hypothesis for their findings

  1. They have identified genes for which they are unable to produce reasonable alingnments. Alignments are central to phylogenetic analysis and if their alignments are poor quality then the trees will show all sorts of anomalies that have nothing to do with phylogenetic history. By scanning through 1000s of genes and flagging those with unusual patterns they may be selectively identifying genes for which producing good alignments between species is tough. I note – clustalw is a bit notorious for not producing idea alignments in some cases.
  2. I do not buy their arguments for why gene loss is not a possible explanation. They need to present more detail on how many gene losses would be required for each gene family under consideration and then present some evidence for why that # of gene losses is less likely than HGT.
  3. They have not even considered as far as I can tell, the possibility of divergent evolution (as opposed to gene loss) in many taxa which could lead to them being unable to identify homologs in some species
  4. I am not convinced by the arguments against long branch attraction as an explanation for some of the tree patterns.
  5. Related to alignments they need to show which regions of alignments they excluded from phylo
  6. Convergent evolution could also explain some of the patterns they observe.
  7. I could go on. I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is up to them to exclude other MORE plausible alternatives and I just do not think they have done that.

Reporter: asking if it was OK to quote me

Yes it is OK to quote from me. I would like to reiterate – I am not saying they are wrong. Just that I would like to see (1) all the data (e.g., alignments) that unreels their conclusions and (2) them do more to exclude other possibilities.

Reporter asking what other analyses could they do

So – I don’t want to be difficult, but it is their job to figure out how to do such tests before claiming they have strong evidence for HGT. 

In general, this is pretty typical of claims of HGT. Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives. And I personally have grown a bit tired of pointing out how people can do better controls for their papers.

Reporter asking about initial impressions:

I see little here that is particularly convincing evidence for HGT …

My follow up email

Note – I am not saying that this is a bad paper — just that I am not overwhelmed by their evidence and especially by what they put in the paper. 

For example, the HAS1 gene story seems incomplete.  Figure 3 seems to show just HAS1 but in the text the say they show the same thing for all HAS genes.  And the tree they show shows a tiny subset of all the available sequences (e.g., HAS1 HAS2 HAS3 and fungal and bacterial homologs).  They claim that they now have proof that HAS1 was transferred near the base of chordates but I just don’t see how they tested alternative hypotheses …

Some related links:

Also here are some presentations from many years ago with some discussion of HGT

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Probiotics for athletes? Possible someday, but right now – I (and others) don’t think so

Nice article in Outside Magazine by David Despain: Should You Be Taking Probiotics? | Performance Plate | OutsideOnline.com.  The article has comments from me, Peter Turnbaugh and Ellen Silbergeld.  The article discusses some of the overhyped claims about probiotics and athletic performance and even mentions my Overselling the Microbiome award.  I like in particular the following paragraph:

The biggest issue scientists currently have with probiotics, however, doesn’t have to do with athletes. Instead, it has to do with the initial hypothesis that we need them in the first place, says Ellen Silbergeld, a professor of Johns Hopkins Bloomberg School of Public Health. Because there’s still no real understanding of what makes “healthy” or “poor” microbiomes, there’s no real understanding of how or if we should cultivate them.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

UC Davis Postdoctoral Research Symposium May 14

POSTDOCTORAL RESEARCH SYMPOSIUM

May 14th 2015
Memorial Union, UC Davis

We invite all UC Davis postdoctoral researchers to register for a 10-min talk or a poster. Awards will be given to the best talks and posters.

Deadline for abstract submission: March 27th

The entire campus community is welcome to attend for free. Lunch is provided for registered participants.

Register at
https://sites.google.com/site/ucdavisprs/home

PRS-poster.pdf

Teaching with Wikipedia 3/13 at #UCDavis

Teaching with Wikipedia

Friday March 13, 2-3pm

165 Shields Library (Shields Library Instruction Lab, http://lib.ucdavis.edu/dept/instruc/maps.php?map=lil)

Description:

Students use Wikipedia — but have you ever thought of asking them to contribute content to Wikipedia? In this short workshop, LiAnna Davis and Jami Mathewson from the Wiki Education Foundation (http://wikiedu.org) will explain best practices for using Wikipedia as a teaching tool. In contributing content to Wikipedia, students gain skills in media literacy, fact-based writing, research, collaboration, and critical thinking. You’ll learn how Wiki Ed can support you and your students in this innovative service learning assignment.

http://calendar.ucdavis.edu/event_detail.lasso?eventID=16650

Seminar at #UCDavis 3/11 4PM: Biogeography and ecological role of thermophillic archaeal nitrifiers

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Dr. Jose de la Torre
(San Francisco State University)

"Biogeography and ecological role of thermophillic archaeal nitrifiers"

Wednesday, March 11, 2015

4:10 pm

1022 Life Sciences

de la Torre 3-11-15.doc

New NSF funding opportunity: Cracking the Olfactory Code – An Ideas Lab Activity

Not that I do anything related to olfaction … but this NSF Ideas Lab system at least seems interesting … though not sure how well it actually works. See email I just received from NSF below:
Dear Colleagues,

A new NSF program solicitation (NSF 15-547) is now available:

Cracking the Olfactory Code
— An Ideas Lab Activity

Please see

http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504773&org=DMS

for details.

Due Date for Preliminary Proposals (required): May 1, 2015