The NSF Directorate for Biological Sciences has published a Dear Colleague Letter seeking ideas from the community on Integration Institutes for cross-cutting biology. These institutes would support collaborative teams of researchers to address questions that span multiple levels of organization in living systems and require expertise from diverse biological subdisciplines.
This is not a call for research proposals, but rather for high-level ideas about the types of questions and resources that would benefit from NSF investment in a truly integrated research environment.
The deadline for submissions is March 1. Please see the Dear Colleague Letter (NSF 19-027) for details on how to submit your ideas.
In August, the BIO directorate released new solicitations to its proposal submission process to eliminate deadlines and limit the number of proposals that could be submitted to a given division annually by a PI or co-PI. As BIO was receiving far more worthy proposals than it has money to support, this submission cap was established with a view to ensuring that BIO’s merit review process would not be overwhelmed with the move to no deadlines.
In the ensuing three months, the community expressed serious concern that this new policy would hinder collaboration as well as limit funding prospects for new investigators. BIO places a high value on collaboration and on fostering careers of new investigators; thus, we held internal discussions to consider ways to address these concerns. In addition, relatively few proposals have been submitted to BIO since the release of the solicitations.
Having listened to community concern and tracked the current low rate of submission, and following extensive internal consultation, BIO is lifting all PI or co-PI restrictions on proposal submission for FY 2019, effective immediately.
BIO recognizes that it is important to track the effects of the no-deadline policy on proposal submission patterns, to ensure that a high-quality review process is sustained. Therefore, we are seeking approval from the Biological Sciences Advisory Committee to establish a subcommittee to assist in developing the evidence base for any future policy changes that may be needed.
Solicitations for proposals will be amended and released over the next few weeks to reflect these changes.
Joanne Tornow, PhD
Acting Assistant Director for the Biological Sciences
The BIO advisory committee will hold a special meeting on Friday, November 16th from 2:30-4:30 PM to discuss immediately establishing a subcommittee to consider different options for addressing community concerns with the BIO proposal submission limits.
This meeting will be held via teleconference among the Advisory Committee members. Public visitors will be able to attend the meeting in person at NSF headquarters; please contact Alexis Patullo at firstname.lastname@example.org to request a visitor badge.
Accelerating Research through International Network-to-Network Collaborations (AccelNet) supports strategic linkages among U.S. research networks and complementary networks abroad that will leverage research and educational resources to tackle grand scientific challenges that require significant coordinated international efforts. AccelNet invites proposals, submitted by U.S.-based researchers, for the creation of international networks of networks in research areas aligned either with one of the NSF Big Ideas or a community-identified challenge with international dimensions.
For the first competition, Letters of Intent for are due December 21, 2018 and Full Proposals due February 28, 2019. The NSF Office of International Science and Engineering (OISE) funded several workshops that will take place in 2019, and we will offer webinars for the community.
The first webinar will be this Monday, November 5 – visit the event page for webcast info. Updates on future webinars will be posted on the program page.
The National Science Foundation (NSF) has taken the next steps in its agency-wide effort to protect the research community from harassment, publishing a term and condition that requires awardee organizations to report findings and determinations of sexual harassment, as well as establishing a secure online portal for submitting harassment notifications.
This is an exciting time for the biological sciences. The way we do science is rapidly changing; it is increasingly collaborative, interdisciplinary, and enhanced by new capability to collect and analyze more complex data than ever before. We at the National Science Foundation Directorate for Biological Sciences (BIO) are committed to creating funding opportunities that foster collaboration and innovative research to advance biological knowledge. As part of this effort, we have recently made changes to enable us to respond to this changing research environment and continue to meet the needs of our community – early career and senior scientists alike – as it progresses into the future.
We have just released a set of solicitations designed to support the biological sciences community broadly and to take advantage of emerging research opportunities. In addition to retaining all core and special funding programs, we have added a new funding opportunity: a Rules of Life track, which provides new mechanisms for review and funding of ambitious, integrative research projects addressing questions across scales that would not ordinarily fit well within a single BIO division. With these solicitations, we have also completed our initial transition to a BIO-wide no deadline submission process. By accepting proposals at any time, BIO aims to encourage submission of creative, well-developed, interdisciplinary projects by providing investigators with greater flexibility to prepare their proposals.
Given that BIO already receives many more excellent, funding-worthy proposals than we have money to support, more submission opportunities do not equate to more awards. Thus, with a shift to no deadlines, it was clear there needed to be some restrictions to limit submission and resubmission of similar proposals within a given year. After extensive consideration, conversations with key community stakeholders, and analysis of past submission patterns, we determined the most balanced way to do this was to limit annual submissions as PI or co-PI. Each year, researchers may submit one proposal each to MCB, IOS and DEB core programs, and two proposals to DBI infrastructure programs. In addition, researchers may submit one proposal to the Rules of Life track each year. Further, to ensure that this cap does not harm collaborative projects, we have removed previous restrictions on submissions as subaward PIs. We sought an objective way to limit proposal submissions to carefully considered, unique research ideas, while removing barriers to collaboration by allowing unlimited involvement on proposals with potential to receive budgets.
We recognize concerns have been expressed about potential negative impacts of this shift, and I can assure the community that we have extensively considered these same issues. We have paid particular attention to the possible impacts on early career researchers. We are confident these caps will not harm their opportunities to receive research funding; in addition to the funding opportunities open to all researchers within BIO, early career researchers will remain eligible to apply for CAREER awards. Nurturing the next generation of biologists is a priority for BIO program staff, and we will continue to monitor progress closely. I encourage the community to read the FAQs and blogs posted by each division on the new submission cap and shift to no deadlines for answers to common questions and more details on the opportunities available within BIO. As we go through this first year under the new submission system, BIO will track these and other areas of concern and will evolve as necessary.
Collectively, these new solicitations offer many opportunities for innovative, challenging and potentially transformative science. I am eager to see how our new solicitations will move forward BIO’s mission to enable discoveries for understanding life and advance the frontiers of biological knowledge.
Joanne Tornow, PhD
Acting Assistant Director for the Biological Sciences
BIO recently welcomed a new Acting Assistant Director, Dr. Joanne Tornow. Though she is coming to BIO after six years in NSF’s Directorate for Social, Behavioral and Economic Sciences and the Office of Information and Resource Management, Dr. Tornow is no stranger BIO, having spent more than a decade in a variety of roles across the Directorate. We sat down with Dr. Tornow to get to know her a little better and welcome her back to her first home at NSF.
When did your interest in the sciences first begin?
I trace back my falling in love with biology and genetics to my 9th grade biology class. It all just made perfect sense and I loved it, so from then on, I was a biology person. At the time that I was in college, molecular biology did not really exist as a discipline, but microbial biology and microbial and molecular genetics was just starting, so I concentrated on what was then a very emerging area of microbial genetics. As I progressed, there was really very little debate in my own mind about what I was interested in. I love biology and knew I wanted to pursue it as a career.
Can you tell us a little bit about your journey from a career as a traditional, academic researcher to science administrator?
I did the traditional academic path – graduate school, postdoc, faculty position – and then there was an opportunity during my sabbatical to do something completely different that I was really interested in.
At the time, Dolly had just been cloned the year before and we were in the middle of the Human Genome Project. I was teaching genetics to undergraduates and molecular genetics graduate students, and these events were raising all of these questions about the intersection of science and policy, genetic privacy, cloning – it was really a fascinating time. So when I stumbled on the AAAS policy fellowship, I thought it would be a great opportunity to go and see how the policy side intersected with the science and then bring that back to the classroom.
I spent a year working on the Senate Veterans’ Affairs committee, getting experience working on the Hill and understanding how that process worked – how the federal budget is generated and how it drives policy. Then an opportunity came up to go to OSTP [the White House Office of Science and Technology Policy] for a year, and there I was able to work on things that were a little bit more relevant to my science.
What was your favorite part of working on the policy side of things?
Just a month or two after I started my fellowship in OSTP, the first papers on isolating human embryonic stem cells came out. Every month or so, something else was getting cloned. It created some really great policy questions, and so it was a wonderful time for me to be at OSTP – that was a fabulous year.
How did you ending up coming to NSF?
At the end of that year, I was getting ready to go back to my institution. I had been in contact with NSF because I knew that when I had initially planned to come to DC on my sabbatical that NSF had been an option. A position was available as a rotator and they reached out to me. By that time, after two years in DC I had sort of made the switch in my mind from doing the academic life to thinking about science in the bigger context, and it was really appealing to me both personally and professionally to stay in this area, so I took the position.
You and BIO have a long history together! When were you last here, and what projects were you involved with?
Starting in the Fall of 1999, I was program director for gene expression in the division of Molecular and Cellular Biosciences (MCB). The portfolio for gene expression was much broader than understanding the control of transcription, which was my area of expertise. I was a program director in MCB for about six and a half years before leaving for a little bit to do a detail in the Directorate for Education and Human Resources (EHR) front office.
After that, I came back to be senior advisor in the BIO front office, but as it turned out, I went up to the Director’s office for about 8 months on a detail to work on a particular project for the Deputy Director, and so spent very little time in the front office. After that, I returned to BIO and was the Acting Division Director for MCB for two years.
By that time [former BIO AD] Jim Collins was finishing up his tenure and left, and I moved in to be the acting Executive Officer [equivalent to the current Deputy Assistant Director]. When a new AD was found two years later, there were a variety of vacancies in the Deputy AD spots, so I applied for those and that’s when I moved to the Directorate for Social, Behavior and Economic Sciences (SBE) as Deputy AD.
Each of these jobs – that whole path, including my details in EHR and in the OD, and my time in OIRM – all gave me different perspectives and really helped me when I came back to be an Acting Division Director and now Acting Assistant Director in BIO. Having spent the time at OSTP, on the Hill, in the OD – all of those experiences helped me be more effective here at NSF.
What are you most looking forward to for your time as Acting Assistant Director for BIO?
There are a couple of things that I’m really looking forward to. One is that it’s been six years since I’ve been in BIO and I’m just really loving getting back in touch with BIO and catching up on all that’s happened – all the ways that the science and the programs in BIO have advanced. So that’s probably the best part about this – I’m really just getting back to my first love.
On January 10, 2018, Dr. Jim Olds’ term as Assistant Director for Biological Sciences came to an end. Since taking up the post in September 2014, Dr. Olds has led BIO through many big changes, including the conception of the Rules of Life Big Idea and implementation of a no-deadline submission mechanism for receiving and reviewing proposals. All of us at BIO would like to thank Dr. Olds for his excellent leadership over the past three and a half years, and wish him the best as he returns to George Mason University.
Dr. Joanne Tornow, Head of the Office of Information and Resource Management (OIRM) and former BIO Acting Deputy Assistant Director, will be taking up the mantle as Acting Assistant Director for BIO while the search for Dr. Olds’ successor is underway. Stay tuned to learn more about Dr. Tornow and the exciting things she has planned for the directorate in the coming months!
“Karma” means a lot of things to a lot of different people. For Rob Martienssen, a pioneer in epigenetics and professor at Cold Spring Harbor Laboratory, it refers to a specific transposon – a DNA sequence that can change its position within a genome – that can mean the difference between a plentiful crop and ten years of wasted labor.
Some of the biggest names in plant science have guided Martienssen throughout his career, from his Cambridge University doctoral mentor David Baulcombe – who, with Andrew Hamilton, discovered small interfering RNA – to his postdoctoral mentors, William Taylor and Michael Freeling, at the University of California, Berkeley. As a junior faculty member at Cold Spring Harbor Laboratory, Martienssen even had the chance to work with Barbara McClintock, whose discovery of mobile genetic elements won her the Nobel Prize in 1983.
Today, Martienssen, who has received several NSF awards for his work, is building on that legacy as a professor at Cold Spring Harbor and Howard Hughes Medical Institute. Martienssen recently discussed his lab’s research on epigenomic modification of Karma transposons in the African oil palm in a BIO distinguished lecture titled, “Germline reprogramming and epigenetic inheritance: How to avoid BadKarma.” Afterward, he spoke to us how epigenetics shapes the world around us and just what “bad Karma” means to a plant scientist.
OAD: What is “epigenetics”? How is it different from the genetics we learn about in high school biology?
A: The concept of epigenetics actually has a really long history. Throughout most of the Middle Ages there was this controversy about developmental biology: you could either imagine a germ cell as being very naïve and having to be programmed to make the next generation, or in those days, there was also this idea that maybe there was a homunculus in the sperm that was fully formed and simply had to grow into a baby. Aristotle was very much in the former camp and William Harvey used the term “epigenesis” as a way to talk about this programming that happened to very naïve germ cells to allow them to become a new body – and of course, that’s how we think about development now.
Then in the 1940s, Conrad Waddington wrote a famous article and subsequently a book on something he called “epigenetic landscapes.” He went a bit further with this idea, saying that there was this underlying genetic program, but that depending how it was interpreted in every cell, you would get different fates for those cells. So, this was the idea that you don’t access all the information in the genome in every single cell, you only access some of it – and that was determined by epigenetics. He was using the term because it was sort of superimposed on genetics – it was “above” genetics.
OAD: Did he have a concept of how we interpret epigenetics today?
A: He’s often regarded as the father of epigenetics – he really did have a good idea of what was going on. He had done experiments in Drosophila where he’d selected different wing shapes over multiple generations and was able to select new forms without making mutations – or without making mutations that he could readily identify as a geneticist. So, he really did get it, and was the first person to propose this sort of transgenerational inheritance being based on genes.
At the same time, Barbara McClintock and Alexander Brink were maize geneticists working in the 1940s and 50s, and they actually came up with real examples of traits controlled by genes affecting plant color – like the color of kernels on a corn cob – that were under epigenetic control. They could go in one direction or another from one generation to the next, and Barbara was convinced that all of this was controlled by her “controlling elements” – transposable elements. So those were really the first definitive examples of “transgenerational” epigenetics.
OAD: So, epigenetics led to changes in these traits – wing shape and corn kernel color – without any mutations in the genes that encode them. And even though the change wasn’t genetic, it was able to be shared from one generation to the next. Do we know how this happens?
A: With the discovery of DNA as the genetic material and the composition of chromosomes over the next several decades, mechanisms that might explain this started to come forward and that’s how we really think about epigenetics today. These mechanisms are ways of modifying the chromosomes without changing the DNA sequence. Primary among these – at least in plants and mammals – is DNA methylation, which is very widespread. You can methylate and demethylate DNA chemically using enzymes in the cell, and you can also just replicate DNA without methylation and that will remove methylation passively.
This turned out to be one of the major mechanisms of epigenetic inheritance, but it wasn’t the only one. Chromosomes are not only composed of DNA but also histones, which are the proteins that DNA is wrapped around – you can think of it like a spool of string or wool – and those histones can also be chemically modified in a reversible way. Those modifications are just as important as the ones on DNA, but they have to be associated with specific genes, and so how these modifications only end up on specific genes has been a major part of research in the last few decades.
OAD: What are the prevailing theories for how that happens – how does the cell know where to put those modifications?
One of the things I was involved in about 15 years ago was the realization that some of that instruction about where these modifications were made – both DNA methylation and histone modifications – was through RNA, and in particular small RNA, which David Baulcombe discovered in plants. It’s not the only way – there are lots of DNA-binding proteins that also instruct the cell where to make these epigenetic modifications – but RNA turns out to be very important. More and more we believe that in plants and in some animals like C. elegans, this RNA can actually pass from generation to generation, and could actually have this transgenerational epigenetic effect.
OAD: Much of your work focuses on the African oil palm. Why that plant specifically? What are the “real world” ramifications of the questions you study?
A: The African oil palm is propagated by cloning, and this was done starting in the 1970s. There are some very good reasons for that – it allows you to clone elite germplasm [living seeds or tissues kept as genetic resources for breeding plants or animals] without having to breed it any further, because the clones are all supposedly the same and they’re all going to have the same elite properties. But it turns out that epigenetics raises its ugly head, and in fact these clones are not identical. The reason they’re not is because of transposons that lose DNA methylation in the cloning process – and we’re trying to understand why that happens. When they lose methylation in the cloning process, the next generation has really nasty phenotypes that are really important economically – they develop abnormal flowers and dry, shriveled fruit that yield much less oil.
The reason the oil palm is so important from this point of view is that it only grows in very sensitive parts of the world where it competes with rainforest, and if you transplant an oil plant from the nursery into the plantation, you have to do that before it fruits. It isn’t until 10 years later that you realize there’s a problem – that it has fruit that won’t yield any oil because of this epigenetic change – and you’re sort of stuck, so the temptation is to burn down a bit more of the rainforest and plant a bunch more. Now for big palm oil companies, they can afford to not do that, but for a small holder, it’s a different matter altogether. This is a major problem in Malaysia and Indonesia, and so I’ve been very fortunate to work with the Malaysian government, with the MPOB – the Malaysian Palm Oil Board – and some biotech companies in the U.S. – and I should say in full disclosure that I’m a founder of one – for the last ten years to figure out what was going on.
OAD: What does “bad Karma” mean in this context?
A: We discovered that there was indeed a single transposon that’s responsible for this phenotype. It’s in a gene that is very well known in other plants – and I should say if we hadn’t had all of that basic research in Arabidopsis [a flowering plant used as a model organism in plant biology], we would have no idea what this gene actually does. We were able to develop a very simple test that can predict the phenotype of palm trees that are cloned. The test is based on a transposon called “Karma”, so we call it “good karma” when it’s methylated and you have normal fruit, and “bad Karma” when it’s unmethylated and you have this horrible phenotype. It’s a nice story that goes from really basic principles in epigenetics in model systems to a real-world consequence.
OAD: You work in a field that has – like many others – evolved rapidly over the course of your career, due in no small part to significant technological advances over the last few decades. What is it like to work in your field now versus when you were a graduate student at Cambridge?
A: I’m sure everyone has stories like this, but I got my Ph.D. based on about 1.5 kilobases of DNA sequence, and it’s just amazing when you think about it. The idea of doing a whole genome wasn’t really seriously discussed until the 1990s, and now an individual graduate student or postdoc can easily knock off a genome. It’s amazing. Having the genome sequencing projects¬ has really changed how we do epigenetics and that’s been very exciting. We used to have to grind up a whole plant to get enough DNA to do anything, and now you can literally look at a single pollen grain and really get a good idea of what the epigenetic and genetic makeup of that pollen grain is.
But at the same time, it’s interesting that the same questions are still there and despite all of this fabulous technology, we don’t have a unified concept of what epigenetics really means. And I think that’s very exciting – that’s why we do it.
In 2016, NSF Director France Córdova unveiled ten “Big Ideas” to shape NSF’s priorities for investment at the frontiers of science and engineering, and drive American science into the future. One in particular – “Understanding the Rules of Life” – has reshaped how we at the BIO Directorate think about scientific inquiry in the biological sciences. The Rules of Life Big Idea seeks discoveries that will allow us to accurately predict change and outcomes in biological systems, and to develop infrastructure and innovative tools to help us ask more complex questions than ever before.
NSF has now published a Dear Colleague Letter (“DCL”; NSF 18-031) catalyzed by this Big Idea, titled, “Rules of Life: Forecasting and Emergence in Living Systems.” This DCL solicits research proposals to develop a better understanding of complex interactions within biological systems, and identify causal, predictive relationships across scales, levels of organization and layers of complexity – so-called “rules” for how life functions.
This DCL describes an initial opportunity to identify areas where such rules may exist, to drive progress toward their discovery, and to focus efforts on using these rules for prediction and design of biological systems. Activities supported through this DCL include conferences, EArly-concept Grants for Exploratory Research (EAGERs) and Research Advanced by Interdisciplinary Science and Engineering (RAISE) grants to create opportunities for enabling predictive capability.