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".

Would you like to meet a Tardigrade?

In the Canopy with Water Bears and Wheelchairs

We’ve already met tardigrades (or water bears) virtually. If you are an undergraduate with an ambulatory disability, you also have an opportunity to meet tardigrades in the tops of trees.

At ScienceOnline 2014 I learned from Meg Lowman & Rebecca Tripp during a very impressive keynote presentation about a research program to study tardigrades in forest canopies that was specifically focused on making field research accessible to individuals with ambulatory disabilities. Not only was the research fascinating (water bears are EVERYWHERE), but it also represents an important effort to help the social practice of knowledge building that we call science actually include the diversity of our society.

The project is organized through the lab of William Miller at Baker University in Kansas. If you or someone you know might be interested, contact check-out the announcement flyer below, the information sheet below that, and contact the Miller lab. The application deadline is 14 March 2014. Act quickly while supplies last.REU-2014-AnnouncmentFlyer-2 (1)

REU-Canopy-InfoSheet2014-1 (1)


Filed under: Items of Interest Tagged: accessibility, ambulatory disability, Baker University, disability, field research, meet the, Meg Lowman, NSF, Rebecca Tripp, reu, Tardigrade, Water Bear, William Miller

Science in the “national interest”

LS

Representative Lamar Smith supports legislation to make NSF ensure each grantee is pursuing science in the national interest. Image courtesy of Wikipedia.

A particularly concerning piece of legislation is making its way around the House of Representatives. This bill would require that the National Science Foundation (NSF) justify each grant it awards with respect to its contributions to protect the “national interest”. Earlier in the year, a similar bill was proposed with an extremely limited definition of what would meet “national interest” criteria. While the current bill has expanded its definition of national interest to include economic competitiveness, health and welfare, scientific literacy, partnerships between academia and industry, promotion of scientific progress and national defense, legislation like this should be getting all scientists up in arms.

Predicting which avenues of science will lead to major breakthroughs in health or energy is almost impossible. This bill would severely limit early exploratory work that has yet to prove it is in the national interest. This political interference in the operation of the scientific enterprise  is a very dangerous door to open. Decisions of what is in the national interest can very quickly become influenced by party politics and the interests of lobbyists. While it is important that NSF funds good proposals of sound science, requiring immediate association with national interest will lead to exaggerated claims by scientists and the exclusion of some of the future’s greatest breakthroughs.

Whether you are a scientist or not, reach out to your representative and let them know how this qualifier will negatively affect the scientific enterprise in the United States. If you don’t know who your representative is, you can find that information here.


Filed under: Follies of the Human Condition Tagged: grant funding, house of representatives, lobbyists, national interest, NSF, Politics

Science in the “national interest”

LS

Representative Lamar Smith supports legislation to make NSF ensure each grantee is pursuing science in the national interest. Image courtesy of Wikipedia.

A particularly concerning piece of legislation is making its way around the House of Representatives. This bill would require that the National Science Foundation (NSF) justify each grant it awards with respect to its contributions to protect the “national interest”. Earlier in the year, a similar bill was proposed with an extremely limited definition of what would meet “national interest” criteria. While the current bill has expanded its definition of national interest to include economic competitiveness, health and welfare, scientific literacy, partnerships between academia and industry, promotion of scientific progress and national defense, legislation like this should be getting all scientists up in arms.

Predicting which avenues of science will lead to major breakthroughs in health or energy is almost impossible. This bill would severely limit early exploratory work that has yet to prove it is in the national interest. This political interference in the operation of the scientific enterprise  is a very dangerous door to open. Decisions of what is in the national interest can very quickly become influenced by party politics and the interests of lobbyists. While it is important that NSF funds good proposals of sound science, requiring immediate association with national interest will lead to exaggerated claims by scientists and the exclusion of some of the future’s greatest breakthroughs.

Whether you are a scientist or not, reach out to your representative and let them know how this qualifier will negatively affect the scientific enterprise in the United States. If you don’t know who your representative is, you can find that information here.


Filed under: Follies of the Human Condition Tagged: grant funding, house of representatives, lobbyists, national interest, NSF, Politics

Science Caturday: Antarcticat

penguincat

Bad news kept coming for US scientists this week, as the National Science Foundation announced that they would cancel the U.S. Antarctic research program for this year because of the ongoing government shutdown.  The cancellation will directly affect over 50 scientists, grad students and support staff, and Stanley, a cat conducting important research on Antarctica’s penguins.  Sorry, buddy. 


Filed under: Science Caturday Tagged: antarctic cat, antarctic research, NSF, penguin cat, science cat

The dark side of running a lab

Image courtesy of Ludie Cochrane

Image courtesy of Ludie Cochrane

A lucky few scientists make it through graduate school and a post-doctoral fellowship AND manage to secure a position running their own lab. Once they begin the day-to-day grind of operating a research enterprise they often realize there’s way less time for science and more administrative tasks to do. This administrative burden can be a drain on creativity and scientific productivity. The National Science Foundation (NSF) issued a request for information (RFI) to learn what aspects of administration are affecting scientists at work, and hear their suggestions for change. The Federation of American Societies for Experimental Biology (FASEB), a coalition of many scientific societies, administered a survey sent out to all 26 member societies to collect the data for NSF. The answers they received painted a picture of what it’s like to be a scientific investigator.

Parts of the data are not THAT new. A large percentage of respondents ranked grant related activities as their largest administrative burden. In this time of tight funding, it’s not surprising scientists are spending more time writing more grants for different funders. However, I was surprised to read that many had complaints about their administrative staff regarding grant submission. The staff’s inexperience with the scientific enterprise was a serious handicap to many researchers and essentially created even more work for the scientists. Is this a problem that is fixed by more training for administrators? Or by moving people with scientific training into those roles?

Another major area of burden and complaint was animal care regulations and oversight. While I personally haven’t worked with animals needing special protections and protocols, I’ve heard about the headaches it can cause. No scientist wants to harm their animals or violate regulations but when a tiny revision (even a spelling change) can take months to be approved it puts scientists in a position where they violate their approved protocol just to prevent a huge disruption in their experiments. Many suggested streamlining the review process and having certain changes fast-tracked with an approved protocol. They also suggested having certain approved protocols available to be cited instead of rewritten by each researcher performing that particular protocol.

A last area of concern is personnel management. It’s often overlooked that scientists become managers without any training on how to hire, manage the budget, and deal with administrative issues. Many requested personnel management training as part of starting their labs. There were complaints surrounding the administrative personnel in this area as well, in that HR agents were ill-equipped for the hiring needs and complexities of staffing research labs.

So what will the outcome of this survey be? Many of the issues raised are institution specific and I highly doubt many administrators of public research institutions are reading up on this surveys results. Some of the issues require collaboration between funding agencies to simplify requirements and generate a common system. Based on my current experience working for the man (National Institutes of Health, NIH) I think the likelihood of that happening is extremely low. NIH has certain reporting requirements and systems and unless outside agencies are willing to just adopt what they do, it’s doubtful that they will come up with a new simplified system.

It’s interesting to see what burdens scientists face in operating their own labs. Will this just be one of many reports presented, but not used to improve the system?


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

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.
And got some responses

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.
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.  
  • 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. 
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.