Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

First multiple "Overselling the microbiome award": the Daily Mail article on Germs

At the recent “Future of Genomic Medicine” meeting, George Church gave me some grief over my “Overselling the microbiome award” because he thinks (rightly) that some people also undersell the microbiome.

So I set out today to find an example to give out such an award.  And within seconds I bumped into this: Germs: There are bugs that cure infections, protect against stroke and even keep your skin clear | Mail Online in the Daily Mail.

 Wow.  And not in a good way.  Oh well, so much for the underselling award.  Just the title made me cringe.  And so so so so many of the details are so so bad.

Where to start.  I guess from the beginning.

“.The secret lies in the balance of the bugs, which exist in a fragile ecosystem. Knock one out and the system goes haywire.”

Umm.  No.  Not that I know of.  Knock one out?  What evidence is there for this?  None.

“Imbalances in gut bacteria, for instance, have been linked with diabetes, obesity, autism, eczema, psoriasis, asthma and inflammatory bowel conditions such ulcerative colitis and Crohn’s disease”

“…. may even … cause … multiple sclerosis “

Holy crap.  That sounds awesome.  Except that there are all correlations so far with no known causative role at least in humans.

Then they list some of the other good things microbes apparently have been proven to do:

“ANXIETY-BUSTING GUT BACTERIA”
“It seems that the type of bugs you have in your body can affect mood.”

Though at least in this section they do refer to a mouse study but clearly imply this is true in humans too.  It may be.  But I am unaware of any studies proving it.

“BUGS ARE GOOD FOR YOUR SKIN”
“It’s a common misconception that the cleaner the skin, the better — and the bacteria that live on our skin have an important role.”

I am all for not killing all microbes willy nilly but their is certainly one part of the body that you probably do want to wash a lot – your hands.  So As long as they don’t say “Don’t wash your hands” this could be OK.

So what do they say next:

‘If you wash your hands repeatedly, they dry out — this is partly because you wash away all the oils but also because you remove a large number of the bacteria that help maintain the skin’s condition,’ says Professor Mark Fielder, a medical microbiologist at Kingston University.

Oh FFS now they are basically telling people to not wash their hands.

“SHARE A KISS… AND BACTERIA”
‘Every time you kiss, for example, you exchange a million bacteria. ‘So your gut microbiology becomes close to that of your loved ones.’

Sounds great.  I could not find any references on the topic but sounds great.

“SOME TYPES MAY PREVENT STROKE”
Wherein the tell a story based on a press release which had led me to post the following: “Award: Ridiculous, absurd, offensive overselling of the microbiome from Chalmers & Gothenburg”.  Any idea if I think this is an accurate press release?

TRANSFUSION TO BEAT INFECTIONS
Wherein they discuss fecal transplants for C. difficile infections, which seem to work quite well and I have written about a lot (e.g. Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively).  But then they kill their positive mojo on the topic by writing:

Lawrence Brandt, a professor of medicine and surgery at New York’s Albert Einstein College of Medicine, believes the treatment could work for other, non-gastro conditions, such as obesity and Parkinson’s.

Seriously?  Fecal transplants for Parkinson’s?

And it goes on and on including:
“SOME BACTERIA KEEP YOU SLIM”
“BUGS THAT HELP MEDICINE WORK”
“COULD THEY WARD OFF CANCER?”
“KEY TO BABIES’ IMMUNITY”

I mean – I really really do think the microbiome plays roles in many many parts of our lives.  But those who promote it this much are the snake oil sellers of the modern era.  A slight of hand here and soon they will be selling us some specific brand of probiotic or way to protect our microbiomes.  So for this article the Daily Mail is getting my first multiple “Overselling the microbiome award.”  They could get 3 or 4 just from this article if not more.  But I will just give them two.  And I will keep searching for an underselling the microbiome recipient.

——–
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.

——–

Just out from TED – Jessica Green on buildings and microbes

Go microbes:

  http://embed.ted.com/talks/jessica_green_good_germs_make_healthy_buildings.html

——–
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.

——–

HeLa genome sequenced w/o obtaining permission/consent from family – some comments and background

Last week David Coil in my lab reminded me that he had been wanting to borrow a copy of “The Immortal Life of Henrietta Lacks” by Rebecca Skloot.  I have read the book many many times and had told David I even had a preprint that Skloot or her publicist sent me before the book came out (I did not know Skloot then – I just got it because of my blog).  As I went to grab the preprint off my shelf in my office he said he wanted to read it know because the genome of the HeLa cells which had been taken from Mrs. Lacks had been published a few days before.  I was shocked.  I asked him if he knew if the authors of said paper had gotten consent before publishing it.  So I opened a web browser and googled and found the paper and some news stories and a press release from the group who did the sequencing.

Holy fuck.  They did not seem to have permission.  Uggh.  I had thought about this a lot because a few years ago I was thinking of writing a review of “The Immortal Life of Henrietta Lacks”. As part of that started to write about the possibility of sequencing the HeLa genome and what that might mean.  I also did an April Fools joke relating to the topic: http://therealhela.blogspot.com.  And every time new sequencing technology comes along I have thought about – and discussed with others – the possibility of sequencing the HeLa genome.  And every time I got to this point I decided that it would be unethical, inappropriate, and downright stupid to do this without consent.  Note – my original plans for the book review involved a focus on the strange balance between openness and sharing in the history of HeLa and the lack of consent (e.g., see this blog post).

I was so angry about the lack of consent here that I took to Twitter.

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And after that there was remarkably little discussion of the issue by others. What the fuck? People get up in arms about all sorts of minor things so why not get up in arms about this? Where were all the supposed genomic ethicists out there? How did this happen? Thankfully, yesterday a piece on the topic came out from Rebecca Skloot (it was in this mornings New York Times) and it has launched this issue into a much more public discussion. So much discussion that I decided to storify it. See below.

//storify.com/phylogenomics/hela-genome-sequenced-w-o-consent.js[View the story “#HeLa genome sequenced w/o consent (by Jonathan Eisen)” on Storify]

Lots of discussions going on out there. And I think Rebecca deserves credit for writing this piece and bringing the story out more. I tried to get people going on Twitter and it was a slog — people did not seem that interested to be honest. Now – everyone seems interested. Including some who say they agree with Rebecca (and me) that it was a mistake to publish this genome.

Alas, am wondering what these people thought before the Skloot article. Why did so many people just stand by and say nothing? Too busy? Did not occur to them that this could be an issue? Or something else.  Oh – and why did it not occur to Francis Collins and all the people behind encode that this could be an issue. They published a lot of genomic data from HeLa cells and never once asked for consent or apparently even thought about it.

Anyway – it’s about time we as a community got off our butts and started discussion how to deal with the ethics of personal genome data.  This data will be coming out more and more.  We need to figure out how to handle it and the consent issues around it.  And we also need to do a better job of figuring out what to do with samples for which consent was not given but which are used.  Should we stop using HeLa cells?  Possibly.  If we want consent to use them – who will give it?  I don’t know the answers.  But I do know one thing – science should not simply proceed forward just because these questions are hard to answer.  Publishing the genome without consent or talking to the family was a very very very bad idea given that the ethical issues around consent here are murky.

UPDATE – 5 PM 3/24/13

Adding some notes about the press release and genome publication
Genome paper: – some key quotes of interest
  • Abstract
    • “To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome”
    • “Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins.”
  • Results
    • “produced nearly 1 billion reads of length 101 nt” (thus they produced 101 billion bases of DNA sequence information).
    • The read data are available in the European Nucleotide Archive (ENA) database under the accession number ERP001427. 
    • We report a compendium of genomic variation (CN, SNVs and SVs) as well as the first HeLa genome draft, which are available as VCF and FASTA files respectively 
    • We provide a tool to perform the translation of coordinates between GRch37 and our HeLa reference, 
    • Most variants in these HeLa cells thus represent common variants in the human population. The African-American population (to which Henrietta Lacks belonged) is spread between the African and European clusters, with the HeLa sample overlapping both. This demonstrates that although the genomic landscape of HeLa is strikingly different from that of a normal human cell, the population-specific SNV patterns are still detectable. 
  • Discussion
    • Since the establishment of the HeLa cell line in 1952, it has been used as a model for numerous aspects of human biology with only minimal knowledge of its genomic properties. Here we provide the first detailed characterization of the genomic landscape of one HeLa line relative to the human reference genome 
Original press release (a copy of which I found here). 
  • “The results provide the first detailed sequence of a HeLa genome,” explain Jonathan Landry and Paul Pyl from EMBL, who carried out the research. “It demonstrates how genetically complex HeLa is compared to normal human tissue. Yet, possibly because of this complexity, no one had systematically sequenced the genome, until now.”
  • “The HeLa genome had never been sequenced before, and modern molecular genetic studies using HeLa cells are typically designed and analysed using the Human Genome Project reference. This, however, misrepresents the sequence chaos that characterises HeLa cells, since they were derived from a cervical tumour and have since been adapting in laboratories for decades.”
  • “The study provides a high-resolution genetic picture of a key research tool for human biology. It highlights the extensive differences that cell lines can have from the human reference, indicating that such characterisation is importahttp://www.nytimes.com/2013/03/24/opinion/sunday/the-immortal-life-of-henrietta-lacks-the-sequel.html?_r=0nt for all research involving cell lines and could improve the insights they deliver into human biology.”
  • Can we infer anything about Henrietta Lacks or her descendants from this sequencing?
    • No, we cannot infer anything about Henrietta Lacks’ genome, or of her descendants, from the data generated in this study. Firstly, the subtype of HeLa cells sequenced in this study has spent decades in labs, dividing and thus undergoing mutations and changes – they are very different from the original cells that started growing in 1951. Secondly, these initial HeLa cells were taken from Henrietta Lacks’ cervical cancer tumour – as cancer is a disease of the genome, the DNA of cancer cells is usually different to that of the patient. Without any genetic information from the http://www.genomeweb.com/blog/learnt-lessonsoriginal tumour or from Henrietta Lacks, it is impossible to distinguish which parts of the genome sequenced here originate from Mrs. Lacks, her tumour, or laboratory adaptation. The goal of this study was not to gain insights into Henrietta Lacks’ cancer or personal biology, but rather to provide a resource for researchers using HeLa cells.

UPDATE 3: 11: 40 PM 3/25/13 Presidential Commission

Rebecca Skloot has unearthed a report from the Presidential Commission on for the Study of Bioethical Issues which few people seem to have been aware of (I have heard nothing about it). 

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The report was release on October 2012 but got very very little coverage and I have never seen/heard it mentioned anywhere. But it covers a lot of ground of direct relevance to this HeLa story. The whole report is available here. Here are some choice statements (bolding by me)

“Large-scale collections of genomic data raise serious concerns for the indi- viduals participating. One of the greatest of these concerns centers around privacy: whether and how personal, sensitive, or intimate knowledge and use of that knowledge about an individual can be limited or restricted (by means that include guarantees of confidentiality, anonymity, or secure data protec- tion). Because whole genome sequence data provide important insights into the medical and related life prospects of individuals as well as their relatives— who most likely did not consent to the sequencing procedure—these privacy concerns extend beyond those of the individual participating in whole genome sequencing. These concerns are compounded by the fact that whole genome sequence data gathered now may well reveal important information, entirely unanticipated and unplanned for, only after years of scientific progress.”

“Whole genome sequencing dramatically raises the privacy stakes because it necessarily involves examining and sharing large amounts of biological and medical information that is not only inherently unique to a single person but also has implications for blood relatives. Genomic information is inherited and determines traits like hair and eye color. Unlike a decision to share our hair or eye color, which does not reveal anything about our relatives that is not observable, a decision to learn about our own genomic makeup might inadvertently tell us something about our relatives or tell them something about their own genomic makeup that they did not already know and perhaps do not want to know. More than other medical information, such as X-rays, our genomes reveal something both objectively more comprehensive and subjectively (to many minds) more fundamental about who we are, where we came from, and the health twists and turns that life might have in store for us.”

“Because whole genome sequence information directly implicates relatives, psychological harms often are not limited to the person whose genome is voluntarily being sequenced and publicly disclosed. Even individuals who learn that they do not carry a harmful variant may experience “survivor’s guilt” if another family member is affected.”

“At the same time, individuals have a responsibility to safeguard their privacy as well as that of others, by giving thoughtful consideration to how sharing their whole genome sequencing data in a public forum might expose them to unwanted incursions upon their privacy and that of their immediate relatives. To be indifferent to the implica- tions of disclosure of sensitive data and information about one’s self is to act irresponsibly. That being said, it can be good and virtuous to share sensitive data about oneself in appropriate circumstances, for example, for the good of public health research or public education.”

“Risks might also fall to blood relatives of these individuals who carry similar genomic variants, thereby raising the stakes of privacy concerns in whole genome sequencing compared with most other types of research.”

UPDATE 4: 3/26/13 – Some new stories / links

UPDATE 5: 3/26/13 – Rebecca Skloot on Morning Edition

UPDATE 6: 3/26/13 – Some more stories / discussion

UPDATE 7: 3/26/13 2 PM PST Still waiting for ENCODE to say something about whether they are going to take down their #HeLa data. See for example my Tweet from a few days ago

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UPDATE 3/27

UPDATE 3/28
UPDATE 3/29
——–
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.

——–

American Academy of Microbiology Postdoctoral Fellowship in Science Communication

The American Academy of Microbiology (Academy) is accepting applications for its next Colloquium Fellow. This is a one-year fellowship for a recent microbiology Ph.D. recipient to develop skills in science policy and communication. If you can think of former students or others you’ve encountered who would be a good fit, please consider encouraging them to apply. Applicants for the fellowship should have a broad interest in the field and a willingness to learn about topics outside their own area of expertise. The fellowship will provide salary and some benefits.

In addition to academic researchers and clinicians, the field of microbiology needs individuals who are skilled in science communication and public outreach. The goal of the AAM Colloquium fellowship is to provide an opportunity for a recent microbiology Ph.D. graduate to develop these skills. Each year the Academy convenes five to six colloquia to address critical issues in microbiology. The fellow will work closely with the Academy Director on the colloquium program, participating in the entire process from choosing appropriate topics through proposal development and fund-raising to writing colloquium reports to publicity and dissemination.

Applications are due May 15, 2013. Please visit here for a full job description, and here for application instructions.

Symposium on ADVANCEing STEM Faculty at #UCDavis 4/25 1-4 PM

UC Davis Consortium for Women and Research •
UC Davis Advance Program
Distinguished Women in Science Lecture Series

ADVANCEing STEM Faculty at UC Davis

A public symposium about the National Science Foundation ADVANCE program

Welcome by Provost Ralph Hexter Keynote by Chancellor Linda Katehi

Thursday April 25, 2013

1-4pm, with reception to follow ARC Ballroom A, UC Davis

For the past 20 years, the Distinguished Women in Science Lecture Series has showcased the work of top-ranking women scientists and explored the challenges facing women in STEM disciplines. This year the CWR is proud to partner with the UC Davis ADVANCE Program to present the 2013 Distinguished Women in Science Lecture Series in the form of a half-day symposium, “ADVANCEing STEM Faculty
at UC Davis.” The symposium will convene faculty, administrators, and students to discuss the national imperative for a diverse STEM faculty, the role the NSF ADVANCE Program plays in meeting that challenge, and the specific aims of the recently-established UC Davis ADVANCE Program lead by Chancellor Linda Katehi. Please join us to learn more about these issues and to welcome the ADVANCE effort to our campus.

Panel 1. “NSF ADVANCE: Goals, Impact, and Future”

  • Abigail Stewart, Sandra Schwartz Tangri Distinguished University Professor of Psychology and Women’s Studies, and Director of University of Michigan ADVANCE
  • Susan Carlson, UC Office of the President Vice Provost for Academic Personnel, Professor of English at UC Davis, PI of the NSF ADVANCE grant “Meeting the California Challenge”
  • Ruth Zambrana, Professor of Women’s Studies and Director of the Consortium on Race, Gender, and Ethnicity, University of Maryland, College Park

Panel 2. “ADVANCE Institutional Transformation at UC Davis”

  • Kim Shauman, Professor of Sociology, Co-PI and Faculty Director of UC Davis ADVANCE
  • Adela de la Torre, Interim Vice Chancellor of Student Affairs, Professor of Chicana/o Studies,
  • Director of the Center for Transnational Health at UC Davis, and Co-PI of UC Davis ADVANCE
  • Maureen Stanton, Vice Provost for Academic Affairs, Professor of Evolution and Ecology, and Co-PI of UC Davis ADVANCE

DWSLSFinalFlyer.pdf

Crosspost: New papers from our undergraduate “microbiology of the built environment” genome sequencing project

Crossposting from microBEnet.

We have two new papers out from our lab as part of our microBEnet supported undergraduate genome sequencing project:

Congratulations to all involved especially Jonathan Lo and Zack Bendiks, the undergrads who are first authors, and to David Coil who coordinated all the work.

More information about the project can be found on blog posts from my lab blog (https://phylogenomics.wordpress.com/category/undergraduate-genome-project/) and on a page here on microBEnet (http://www.microbe.net/undergraduate-research-built-environment-genomes/) and the YouTube video below:

 

.

In summary, the point of the project was to (1) start generating some reference genomes for microbes from the built environment and (2) to engage undergraduates at UC Davis in genome sequencing and microbiology of the built environment projects.

The papers are published in a new open access journal from the American Society for Microbiology called “Genome Announcements”.

Thanks also to the Alfred P. Sloan Foundation which funds microBEnet and to the UC Davis Genome Center DNA Technologies Core facility which ran the sequencing.  More papers are coming.  Stay tuned.

——–
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.

——–

A must read: Edge Principal Components and Squash Clustering paper from Matsen and Evans

Had no idea this paper was coming out: PLOS ONE: Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison.

Full citation: Matsen IV FA, Evans SN (2013) Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison. PLoS ONE 8(3): e56859. doi:10.1371/journal.pone.0056859

And it is very very cool.  My lab has been working with / collaborating with / wanting to be like Erik Matsen for a few years now and this paper is one of the reasons why.  In this paper Matsen and Evans detail some really powerful and fascinating tools for phylogeny driven analysis of microbial communities.

Edge principal component analysis (edge PCA)

  • “enables the detection of important differences between samples that contain closely related taxa“.  (from the abstract)
  • “applies the standard principal components construction to a “data matrix” generated from the differences between proportions of phylogenetic placements on either side of each internal edge of the reference phylogenetic tree.” (from the Introduction)

Squash clustering:

  •  “outputs a (rooted) clustering tree in which each internal node corresponds to an appropriate “average” of the original samples at the leaves below the node. Moreover, the length of an edge is a suitably defined distance between the averaged samples associated with the two incident nodes, rather than the less interpretable average of distances produced by UPGMA, the most widely used hierarchical clustering method in this context“.  (from the Abstract)
  • is hierarchical clustering with a novel way of merging clusters that incorporates information concerning how the data sit on the reference phylogenetic tree (from the Introduction)
Some nice figures tell the story of the methods pretty well:
Figure 1. A graphical representation of the operation of edge principal components analysis (edge PCA).
The phylogenetic distribution of reads for a given sample determines its position in the principal components projection. For the first axis, reads that fall below edges with positive coefficients on that axis’ tree (marked in orange on the tree) move the corresponding sample point to the right, while reads that land on edges with negative coefficients (marked in green on the tree) move the corresponding sample point to the left. The second axis is labeled with a subtree of the first tree (the position of which is marked with a star on the first principal component tree): reads below edges with positive coefficients move sample points up, while reads below edges with negative coefficients move sample points down. The principal components shown here are the actual principal components for the example shown in Figures 4, 5, and 6.

Figure 3. How the edge PCA algorithm works.
(a) For every edge of the tree, the difference is taken between the number of reads on the non-root side the number of reads on the root side (root marked with a star). (b) The results of this are put into a matrix corresponding to the sample number (row) and the edge number (column). (c) The standard PCA algorithm is then applied, resulting in a collection of eigenvectors (the principal components) and eigenvalues. (d) These eigenvectors are indexed by the edges of the tree, and hence they can be mapped back onto the tree.
Figure 2. A visual depiction of the squash clustering algorithm.
When two clusters are merged, their mass distributions are combined according to a weighted average. The edges of the reference tree in this figure are thickened in proportion to the mass distribution (for simplicity, just a subtree of the reference tree is shown here). In this example, the lower mass distribution is an equal-proportion average of the upper two mass distributions. Similarities between mass distributions, such as the similarity seen between the two clusters for the G. vaginalis clade shown here, are what cause clusters to be merged. Such similarities between internal nodes can be visualized for the squash clustering algorithm; the software implementation produces such a visualization for every internal node of the clustering tree. Note that in this figure only the number of reads placed on each edge is shown, although each placement has an associated location on each edge when performing computation.
Anyway – check out the paper.  And follow their work – this is some pretty cool stuff.

UPDATE 3/21 – switched the captions for Figure 2 and 3 as per Matsen’s comment that the legends were switched in production of the paper.

——–
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.

——–

Seminar at #UCDavis – Jeffrey Lawrence “Action of Natural Selection on Pentuplet Codons” 3/21 4 PM

Jeffery G Lawrence

Department of Biological Sciences University of Pittsburgh

Action of Natural Selection on Pentuplet Codons
(in bacteria and yeast)

LSB 1022 4PM

THURSDAY March 21, 2013

Open source software tool for the week: AXIOME: automated exploration of microbial diversity

Just found this paper via Google Scholar Updates:
GigaScience | Abstract | AXIOME: automated exploration of microbial diversity

From Josh Neufeld’s lab this paper describes a series of tools for automation of microbial diversity analyses.

Abstract:
BackgroundAlthough high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.
FindingsAXIOME streamlines and manages analysis of small subunit (SSU) rRNA marker data in QIIME and mothur. AXIOME also implements features including the PAired-eND Assembler for Illumina sequences (PANDAseq), non-negative matrix factorization (NMF), multi-response permutation procedures (MRPP), exploring and recovering phylogenetic novelty (SSUnique) and indicator species analysis. AXIOME has a companion graphical user interface (GUI) and is designed to be easily extended to facilitate customized research workflows.
ConclusionsAXIOME is an actively developed, open source project written in Vala and available from GitHub (http://neufeld.github.com/axiome) and as a Debian package. Axiometic, a GUI companion tool is also freely available (http://neufeld.github.com/axiometic). Given that data analysis has become an important bottleneck for microbial ecology studies, the development of user-friendly computational tools remains a high priority. AXIOME represents an important step in this direction by automating multi-step bioinformatic analyses and enabling the customization of procedures to suit the diverse research needs of the microbial ecology community.

Workflows like this are what many many people need.  I note – I have not used this yet but it looks promising.  It has some parallels to the WATERS workflow package that came from my lab a few years ago (see more about it here: https://phylogenomics.wordpress.com/software/waters/.)  Alas WATERS is no longer being actively developed.  Anyway – AXIOME has additional features and certainly seems like it would be useful to many people.

——–
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.

——–

Wanted: examples of family friendly policies for tenure review

I am on a committee at UC Davis that is part of an National Science Foundation “ADVANCE” grant that UC Davis’ Chancellor Linda Katehi and others at UC Davis received last year.  The goal of the project is “increasing the participation of women, especially Latinas, in academic science, technology, engineering and mathematics careers.”

More about the UC Davis ADVANCE program

One of the things the committee I am on is charged with is looking into how the policies and practices of tenure review might differentially impact women and minorities.  So – related to that I am writing to ask if people out there have examples of what one might call “family friendly” policies relating to extending the amount of time one is allowed before tenure review occurs.  Some questions I would love answers to for various institutions:

  • What are the policy guidelines for tenure review?
  • Can the tenure clock be extended for family related issues (e.g., birth of a child, adoption of a child, dependent medical care, etc)?
  • What is the specific wording of such policies?
  • How are such policies explained to tenure review committees and letter writers?

For UC Davis here is what I have been able to find (well, with help from the other people on the committee)

I posted a quick request to Twitter earlier.

//platform.twitter.com/widgets.js And got some responses

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Any other information would be great.  I am hoping to make this an “open discussion” of such issues rather than just an internal UC Davis discussion …
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——–
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.

——–