NSF asks for comments on "genomes-phenomes" program; here's a comment - phenome is a silly #badomics term

Hmm.  Just got this in the emails.

BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO's future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link:Sign-up.  Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding.  Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to bio-gen-phen@nsf.gov.
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Nice that they are seeking input. But really - does NSF have to adopt "phenome" as a term? How exactly is this different from "phenotype"? This seems to be a case of exactly what I was criticizing in my Badomics article in Gigascience and in all my posts here (eg bad omics words of the day, Worst New Omics Word Award, badomics, etc). Blech. Genomics is really interesting. I have worked on it for many years. But there is no need to contaminate the literature by using new, uninformative, oversold terms like "phenome".

Storified tweets from the #UCDavisADVANCE Symposium on Increasing Diversity of STEM Faculty

I live tweeted a symposium at UC Davis yesterday that was part of the UC Davis ADVANCE project to increase diversity of STEM Faculty. Here are the notes.

 

For more on the project see

• Chancellor-led center aims to boost women's numbers in STEM ...
• 'ADVANCEing STEM Faculty' topic for symposium :: Dateline UC Davis
• NSF - ADVANCE - ADVANCE at a Glance
• nsf.gov - Funding - ADVANCE: Increasing the Participation and ...

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

• Press release about the UC Davis project
• NSF Award information

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)

• UC Davis Academic Personnel Manual 
• APM 210 has guidelines directly related to this
• UC Davis Work Life Balance

I posted a quick request to Twitter earlier.

Wanted: examples of wording / guidelines for tenure review that encourages / allows for family leaves to extend time clock #ADVANCE
— Jonathan Eisen (@phylogenomics) March 18, 2013

And got some responses

@phylogenomics Our wording is more on the 'allows' than 'encourages' end of the spectrum. Pg3 section 1.4 subsec 4 usu.edu/hr/files/uploa…
— weecology (@weecology) March 18, 2013

@phylogenomics Here's a page that describes cases of family leave for stopping tenure clock @uwmadison:secfac.wisc.edu/newfac/tenure/…
— Eve Emshwiller (@EveEmshwiller) March 18, 2013

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 ...

Digging around in National Science Foundation "news" is mostly a lesson in science by press release

Last week I wrote about how the National Science Foundation was involved in a painful press release about microbial genomics and evolution: Ugg - story about gene transfer/evolution based on NSF press release has a NASA-esque smell.  Today after getting some emails from people about this I decided to look to see if this was unusual or just what NSF press releases tend to look like.

I went to this site: News - US National Science Foundation (NSF) and decided to look at the links for stories I might know something about.  Here are some of them - a mix of NSF Press Releases and Links to outside PRs.

• Untangling Life's Origins
• Home Toxic Home
• Genetic Study of House Dust Mites Demonstrates Reversible Evolution
• How to Thrive in Battery Acid and Among Toxic Metals
• "True Grit" Erodes Assumptions About Evolution

Alas most of these have some issues - some more than others.  Going through them one by one

Untangling Life's Origins.  Link to an outside PR about work supported by NSF.  Not so bad - some painful stuff in the PR like the following:

• “They are not the standard trees that people see in phylogenetic analysis,” he said. “In phylogenetic analysis, usually the tips of the trees, the leaves, are organisms or microbes. In these, they are entire biological systems.”
• But overall reasonably tolerable compared to the others.

Home Toxic Home.  Link to an outside PR.  Filled with really painful stuff. Some examples

• "Most organisms would die in the volcanic sulfur pools of Yellowstone and Mount Etna. Robust simple algae call it home, and their secrets to survival could advance human medicine and bioremediation. "  Everything could advance human medicine and just about any other topic if you stretch it.  And it is a big stretch to find any connections here.
• "Michael Garavito, Michigan State University professor of biochemistry and molecular biology was part of a research team that revealed how primitive red algae use horizontal gene transfer, in essence stealing useful genes from other organisms to evolve and thrive in harsh environments. "  Ahh.  Back to the same general story that got me riled up to begin with.  This also has the fun "primitive" reference for algae which are not in any obvious way primitive. 
• "The algae’s membrane proteins are biologically quite interesting because they’re receptors and transporters, the same classes of proteins that play key roles in energy metabolism and human immune response,” said Garavito. “This has applications in human medicine because virtually all of the important pathways that contribute to disease treatment involve membrane proteins." So let me get this straight.  The algae has membrane transporters and receptors.  And therefore it is relevant to studies of human disease because many diseases are due to problems in transporters and receptors.  So - what organism on the planet then would not be relevant?  Uggh. 
• They then clarify "What makes the algae’s membrane proteins attractive as a model for humans is their robustness. Other traditional candidates, such as yeast, insect cell cultures and slime mold, are fragile. The algae give researchers extra time to manipulate and examine their membrane proteins."  Oh.  I see.  So nobody has ever thought of this before.  No work has ever been done on organisms that are "robust" as a model system.  Like - say - thermophiles?  Wouldn't that be cool (or hot) to work on.  
• There is more. I will not cover it.

Genetic Study of House Dust Mites Demonstrates Reversible Evolution.  Outside PR that is just completely full of crap.

• A few days ago I posted about this to Facebook and to Twitter.  

In idiotic evolution news: scientists "discover" reversible evolution (b/c we really all thought it was impossible) sciencerecorder.com/news/have-scie…
— Jonathan Eisen (@phylogenomics) March 10, 2013

• And it still riles me up.  Some lines to treasure:

• In evolutionary biology, there is a deeply rooted supposition that you can't go home again: Once an organism has evolved specialized traits, it can't return to the lifestyle of its ancestors. 

• And this led to some horrendous press coverage such as Have scientists discovered reversible evolution? - Signs of the Times.  Yup.  New discovery of reversible evolution ...

How to Thrive in Battery Acid and Among Toxic Metals.  This is the specific PR that got me riled up to begin with.  Awful.

"True Grit" Erodes Assumptions About Evolution.  Actually this one seems OK.

While most of what I looked at that seemed painful was from outside groups - I wonder whether NSF does any screening of outside press releases before posting them to their News site.  Given how bad some of the NSFs press releases are I am not so sure how they deal with outside PR.  But why aren't they linking to actual news stories by real journalists?  Instead they simply link to PRs from groups supported by NSF.  Yuck.

Ugg - story about gene transfer/evolution based on NSF press release has a NASA-esque smell

Well, this made me cringe many many times: Extreme Algae Thieves Its Genes From Bacteria - Science News - redOrbit: Science

The article discusses a new paper which itself sounds potentially interesting.  The paper itself sounds somewhat interesting.  But that is besides the point.  The parts that made me cringe are the inaccurate or overhyped statements about the novelty of this work.  Here are some of the statements I find troubling

• "While the ability to pilfer genes from another microorganism has been seen before, scientists have never observed this ability in a eukaryote – an organism with a nucleus."  
• Wow.  Completely ludicrous.  There are hundreds if not thousands of papers on lateral gene transfer to organisms with nuclei.  
• “The results give us new insights into evolution,” said co-author Gerald Schoenknecht of Oklahoma State University’s Department of Botany. “Before this, there was not much indication that eukaryotes acquire genes from bacteria.”
• Same complaint as above. 
• "The age of comparative genome sequencing began only slightly more than a decade ago, and revealed a new mechanism of evolution – horizontal gene transfer – that would not have been discovered any other way,” said co-author Matt Kane, program director in the National Science Foundation’s (NSF) Division of Environmental Biology. “This finding extends our understanding of the role that this mechanism plays in evolution to eukaryotic microorganisms."
• This quote is deeply troubling.  Genome sequencing did not reveal a new mechanism of evolution.  And it is thus also inaccurate to say 'it would not have been discovered any other way".  Lateral gene transfer was studies for many many many years before the first genome sequence was determined.  Certainly, comparative genome analysis helped reveal the extent of gene transfer but it is seriously inaccurate to say it "revealed a new mechanism of evolution".  Here for example is a link to a google search for the specific phrase "lateral gene transfer" in papers published prior to 1995.  And here is one for the phrase "horizontal gene transfer". 
• I hoped that this was a misquote because the person quoted is Matt Kane - an NSF program officer responsible for many areas related to microbial studies.  But alas I found the press release from NSF with the same quote.  Perhaps NSF PR people misquoted Matt.  I hope they misquoted Matt.  Because if not - the quote grossly oversells genome sequencing and what has been learned from it and rather than standing on the shoulders of giants it makes the giants of the past seem like ants.  
• "It's usually assumed that organisms with a nucleus cannot copy genes from different species--that's why eukaryotes depend on sex to recombine their genomes. "How has Galdieria managed to overcome this limitation? It's an exciting question. What Galdieria did is "a dream come true for biotechnology," says Weber."
• This is wrong in so so many ways.  Again, as discussed above, eukaryotes have been known to undergo gene transfer for many years.  
• And to say that the inability to acquire genes by LGT is why eukaryotes depend on sex to recombine their genes?  Really?  Uggh.  As far as I know there are no major theories out there that suggest sex is there because eukaryotes cannot undergo lateral transfer (although certainly some theories on the origin and maintenance of sex do indeed relate to increasing diversity by recombination).
• And what makes this a dream come true for Biotech exactly? 
• I note - this too was in the NSF press release.  Has NSF suddenly decided to become like NASA in terms of ludicrous PRs? 

I note - I do worry about the effect of calling out NSF on this in terms of my ability to get grants from them.  But this is just terrible stuff in this PR and story and it needs to be stopped.  I note further that I consider Matt Kane a friend and I hope that he clarifies his quote here and also manages to get NSF to be more rigorous in their PRs.

Request for input - are there any rules regarding posting text of one's own NSF (or other) grant proposals?

In response to a series of posts from Karen James (who is a biologist now in Maine and is director of the HMS Beagle Project) on Twitter, I am posting here to ask for input from the crowd.  On Twitter, Karen has been discussing her putting together an NSF proposal and was then celebrating a few days ago when it was done.

I have posted some of the twitter conversation below.  But to get directly to the point the question I have for everyone here is - are there any rules at the National Science Foundation that would prevent one from sharing with others a grant proposal that one has submitted?  Are there any rules against this at any agency?  I think there are none but apparently some are telling Karen otherwise.

Any information on this would be useful. Some of the twitter conversation is below:

NSF Cyber-Enabled Discovery and Innovation declares success, terminates self

Just got this email.  On the one hand it is nice to see that NSF is not keeping around programs when they may no longer be needed.  On the other hand, this somehow seemed melancholy ...

Dear Colleague,

The Cyber-Enabled Discovery and Innovation program has demonstrated the value of interdisciplinary computational and data-enabled science and engineering.  Increasingly, this research approach is being integrated into new and continuing NSF programs and solicitations.  As of fiscal year 2012, proposals will no longer be accepted by the CDI program.

Further proof of the ascendancy of microbes: 2011 NSF "biodiversity" grants mostly focused on microbes

As if the readers of this blog needing any more proof of the ascendancy of microbes and microbiology. Well, regardless, here is more. The NSF Announced recipients of the 2011 grants on "Dimensions of Biodiversity" - see The National Science Foundation (NSF) News Diversity of Life on Earth: NSF Awards Grants for Study of Dimensions of Biodiversity

And the recipients are strongly biased towards microbes relative to the general past patterns at many funding agencies.

Microbial focused awards:

Title: Pattern and process in marine bacterial, archaeal, and protistan biodiversity, and effects of human impacts
PI (Principal investigator): Jed Fuhrman, University of Southern California
Summary: Very little about marine microbial systems is understood, despite the fact that these diverse groups dominate cycling of elements in the oceans. Fuhrman and colleagues will compare heavily affected harbor regions with relatively pristine ocean habitat in the Los Angeles basin to understand patterns and relationships in marine microbial communities.

Title: Diversity and symbiosis: Examining the taxonomic, genetic, and functional diversity of amphibian skin microbiota
PI: Lisa Belden, Virginia Polytechnic Institute & State University
Summary: All animals host internal and external symbiotic microbes; most cause no harm and many are beneficial. This study seeks to understand the regulation of microbial communities on the skin of amphibian species, and how they may limit infection by a chytrid fungus that has decimated many amphibian populations around the globe.

Title: Lake Baikal responses to global change: The role of genetic, functional and taxonomic diversity in the planktonPI: Elena Litchman, Michigan State University
Summary: Microscopic plant- and animal-like plankton are the first links in aquatic food chains. This project will study the planktonic food web of the world's largest, oldest, and most biologically diverse lake--Lake Baikal in Siberia--to predict how native vs. non-native plankton in this ecosystem will respond to accelerating environmental change

Single annual cycle for the National Science Foundation's MCB, DEB and IOS Divisions.

Just received this from NSF and thought it might be of interest to some:

Dear Colleagues: The Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF) has initiated new procedures for the submission and review of regular research proposals to the core programs within the Division of Molecular and Cellular Biosciences (MCB), Division of Environmental Biology (DEB), and Division of Integrative Organismal Systems (IOS). The changes for MCB were previously announced in a new solicitation (NSF-11-545). Effective immediately, DEB and IOS will both operate on a single annual cycle of preliminary and full proposals. The initial deadlines for preliminary proposals will be in January, 2012 and the initial deadline for invited full proposals will be in August, 2012. New Solicitations NSF 11-573 (for DEB) and NSF 11-572 (for IOS) provide further details. Also see the Dear Colleague Letter NSF 11-078 and Frequently Asked Questions NSF 11-079 for additional information. Both DEB and IOS will be hosting webinars to provide further information, please see the Division websites, (DEB) and (IOS), for details and contact information if you have questions or concerns.

NSF requests for "conflicts of interest" lists drive me batty and seem to penalize collaborative, interdisciplinary researchers

OK, time to bitch and moan a bit.

I am working on a few proposals to the National Science Foundation where NSF asks one to include "lists of institutions, project personnel, and collaborators with Conflicts of Interest".

Seems simple I suppose.  But not when you get down to the details.  For example I found some guidance from the NSF about this where they ask one to list coauthors, collaborators, co-editors, students, advisors, advisees, friends, relatives, and many other affiliations.

To make a very long story short.  NSF wants you to make a list of anyone who possibly should not review your grant.  And if you are involved in many large collaborative projects or teach or train a lot of students.  Well, you are screwed.  For example, if they really want me to be thorough, I would probably have to list more than 500 people.  This would include a few hundred co-authors and hundreds of collaborators (e.g., on some projects I am working on with the Joint Genome Institute there are hundreds of people involved in some way).