MINUTES

Biological and Environmental Research Advisory Committee (BERAC) Meeting
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy

 

DATE:  November 27-28, 2001

LOCATION: American Geophysical Union, Washington, D.C. The meeting was announced in the Federal Register.

PARTICIPANTS: Approximately 85 people were in attendance during the meeting. Fourteen BERAC members were present:

 

Keith Hodgson

S. James Adelstein

Eugene Bierly

Michelle Broido

David Burgess

Carlos Bustamante

Curt Civin

Jonathan Greer

Richard Hallgren

Steven Larson

Louis Pitelka

Lisa Stubbs

James Tiedje

Warren Washington

 

Tuesday, November 27, 2001

 

Jim Decker, Principal Deputy Director, Office of Science

 

Impacts of September 11, 2001

 

New management environment at DOE

 

SC Advisory Committees are to help SC evaluate performance measurement. BESAC to take the lead and will have representatives from all six SC advisory committees. They will evaluate -

 

FY02 – most requests were provided across SC. ASCR down 3%. BER funding is up due to a record number of 51 earmarks.

 

(DISCUSSION)

 

The performance criteria that have been developed to date for applied programs are really quite thoughtful so it can be assumed that similar care will be taken in developing criteria for basic research programs.

 

How is what SC is asking BESAC to do any different than what the National Academy of Sciences did over a much longer period of time in generating the COSEPUP report? Clearly we need to build on the previous work of others. We don’t want completely separate sets of goals and metrics for different people/programs. Everything should flow from a strategic plan so SC is kicking off a new strategic plan development activity in the near future. There is already much to build on from the FY02 and FY03 budgets. An initial draft is likely to be prepared and run through the programs and Advisory Committees.

 

What can BERAC do over next 6-9 months to help SC that is outside of activities already mentioned? Work with other committee chairs has been very valuable. Upcoming meeting with Deputy Secretary will be useful. Other suggestions may be provided later.

 

Thoughts/comments on the search for a new SC director? Can’t say anything at this point. The President is rumored to be close to announcing a new SC director.

 

 

 Keith Hodgson, BERAC Chair

 

·        Committee introductions

·        BERAC has two charges at this point -  one indirectly provided at this meeting  and a Structural Biology Charge (BESAC charge that will require input from others). That activity will need someone to represent BERAC.

·        Informal committee chair activities – DOE briefings, Marburger briefing, others.

·        Should BERAC form a small ad hoc working group to help BER and SC articulate biothreat opportunities and needs to which SC can contribute?

 

 

Gloria Sulton, DOE Office of General Counsel – advisory committee ethics

 

·        Financial conflicts of interest – recusal from discussion or public acknowledgement of potential conflict or appearance of conflict

·        General conflict of interest issues – appearance of using membership for private gain, use of position to benefit self or family

·        Handout provided on conflicts and gifts

·        Phone number at GC – 202-586-1522

·        Email at GC – standardsofconduct@hq.doe.gov

·        Do members have an obligation to disclose committee membership under other circumstances, e.g., Congressional testimony or grant applications? Unless reason not to disclose, probably better to do so.

 

Comments from Mike Holland – BER Budget Examiner at OMB

 

·        Focus on performance metrics. New OMB management is strongly committed to focus on and rewarding of good performance through a suite of performance metrics generated for specific programs.

·        Unfortunately the things that are easy to measure tend to be less relevant and the most relevant things are the hardest to measure. 

·        There will be additional consultation with NAS in the spring. NAS recommendations focused on quality, relevance, and leadership. These things represent broader looks at research portfolios versus day-to-day / annual types of metrics that will likely need to be run in parallel.

·        Small science done in small groups is one of the most difficult/challenging to measure.

·        Looking to get advisory committee input on this issue in the spring.

·        There is a need to knit together big portfolio metrics with nitty-gritty type metrics. Grand metrics are likely to be used more at an SC and even interagency level whereas annual type metrics unique to each program will also be developed.

·        The role of oversight committees like BERAC was emphasized in COSEPUP report.

 

 Ari Patrinos – The State of BER

 

 

(DISCUSSION)

 

 

 

Derek Lovely – Science talk

University of Massachusetts, Amherst

Dissimilatory Metal Reduction: Genomics Meets Bioremediation and Environmental Energy Harvesting

 

 

 

 Ari Patrinos – National Climate Change Technology Initiative

 

President’s June 11, 2001, Commission

 

A technology R&D call with climate change at its center – the first time for this focus. A new commitment to take this seriously. While this initiative may not appear in the FY03 request, the seeds for the future will be planted.

 

Deputy Secretary of Energy has lead with others involved – State, EPA, USDA, Commerce (co-lead), OSTP, OMB

 

Long term goal of stabilizing green house gases in the atmosphere in this century means that we need to get to zero net carbon emissions this century. Tall order given humanity’s reliance on fossil fuels.

 

There is a need for “innovative concepts along unconventional paths.” We don’t want to (and can’t) continue to do the same old thing as we move forward.

 

Jae Edmonds of Battelle Pacific Northwest Lab is one of the key drivers and authors in this initiative.

 

Carbon cycle research will be more important than ever – what are the sinks and sources? This will also underpin future need to measure and monitor, i.e., enforce carbon emissions, sequestration, etc.

 

Have still not agreed as a community on the stabilized level of green house gases in the atmosphere that will “prevent dangerous anthropogenic interference with the climate system.” Range of what constitutes a dangerous level can guide our path forward.

 

Overall, the initiative will have activities with short, medium, and long-range (50-60 year) impacts. Biotechnology is, in many ways, at the heart of the long-term solutions. Genomes to Life will be a major contributor.

 

(DISCUSSION)

 

What is the role of nuclear energy in the overall formula? It is part of the overall plan but don’t know what the mix will be 60-70 years from now. If we don’t solve the waste disposal problem it is hard to imagine that it will be a significant player but if we are innovative in developing new solutions for waste disposal it could be a significant player.

 

Coordination with others on energy R&D, e.g., Europeans? Certainly willing to do this but the European community has neglected energy R&D for a number of years so they are far behind in this area.

 

Interactions with and investments in developing countries? Likely to be in NOAA or NASA budgets next year especially in the monitoring area.

 

 

Update on Genomes to Life

 

 Mike Knotek

 

Current view of Genomes to Life is driven by 4 things –

 

Payoffs of GTL research within the next 10 to 50 years

 

Mike Colvin, LLNL/DOE

 

Computational workshops

 

August workshop recommendations

 

September workshop

 

Upcoming workshops

 

Close planning between BER and ASCR.

 

ASCR subgroup to collect information on mathematics and computational needs in biology

 

Bert Weinstein, LLNL

 

The current NNSA CBNP (Chemical and Biological National Security Program) is a very broad program that is not large (~$40M) by NNSA standards. Examples of current activities:

 

NNSA CBNP emphasis areas - biological foundations, detection, decontamination, modeling.

 

GTL links –

 

Jae Edmonds, PNNL

 

Global net emission of CO2 must be zero for any stabilization concentration. This requires more than business as usual. Need to start departing from business as usual emissions by 2010, with global emissions peaking in 2030 to stabilize atmospheric levels by 2090.

 

Technologies that could make a big difference are currently insignificant - carbon capture, geologic sequestration, hydrogen systems, energy storage systems, commercial biomass.

 

Biggest impacts on model runs (compared to ocean sequestration and hydrogen economy) was from commercial biomass – growing crops as a fuel to be used in place of current carbon based fuels. To be successful will need big improvement in growing crops and their conversion to fuel (also land availability). Still doing model runs but looks very promising. Can get zero net emissions by substituting for carbon based fuels but if used to generate hydrogen and sequester emissions can actually get into a negative carbon emission scenario.

 

Robin Graham, ORNL

 

Energy security and the carbon cycle. Even major oil companies are moving into renewable energy (Shell and British Petroleum).

 

Fossil fuel feedstock – petroleum, coal, natural gas – for energy and materials. 1.5 billion metric tons of carbon emitted principally from energy and transportation. Only 3% of US energy from biomass currently. Biofeedstocks can be used for anything that current fossil fuels used for and can also sequester carbon in soils in the process.

 

Carbon neutral feedstocks? Genomic technologies to improve biofeedstocks? Need to understand carbon fixation, allocation, partitioning, sequestration and the associated genes. Importance of understanding the whole nutrient cycle including role of microbes in plant growth. Populas attributes – First woody crop to be sequenced. Prediction that Populas could be domesticated in decades through understanding of critical genes. Projected doubling of Populas biomass yield through genomics. 55 million acres of biofeedstock could displace 30% of current US gasoline needs + 50 million tons of carbon sequestered in initial years of growth.

 

Could “crack” plant cell walls as we do for fossil fuels to isolate basic component for reconstitution into needed chemicals using microbial enzymes.

 

Identification of more efficient cellulases? Development of designer yeast that could ferment at higher temperatures using extremophile enzymes?

 

Use of microbes to produce more/better fossil fuel feedstocks as well.

 

Blaine Metting, PNNL

 

Potential impacts on cleanup costs. DOE cleanup problem estimated at $230-280 billion over 75 years – metals and radionuclides in chlorinated solvents (out of $1.7 trillion nation wide).

 

Bio-based clean up strategies:

 

Overarching challenges/problems:

 

Potential cost savings?

 

 

Dan Rokshar

DOE Joint Genome Institute

Report on the Sequencing and Assembly of FUGU at the Joint Genome Institute

 

·        Fugu has a small (365 million bases) and cost effective genome to sequence for comparison with other, larger genomes. “Reader’s Digest version of the human genome” (Sydney Brenner).

·        Interesting note – a bacterium (not the fish itself) makes the infamous Fugu toxin.

·        Fugu sequence complements the rat and mouse genome projects funded by NIH.

·        Fugu team - JGI; Sydney Brenner; Institute for Molecular Biology (Singapore); Myriad and Celera Genomics; Institute for Systems Biology (Seattle); UK Human Genome Mapping Program and Cambridge University Department of Oncology (Cambridge)

·        5.4 x coverage of the genome was completed one year from date of project announcement (3X at JGI, 1.4X at Myriad, 1X at Celera). 95% DNA sequencing pass rate and 640 nucleotide read length – among the best of all sequencing centers – contributed to the success of the project.

·        Need for publicly available assembler analogous to nonpublic Celera assembler. Use of both sequence overlap and paired end information (unique to JGI approach). Needed to be useful with large genomes. Visualization tools needed.

·        JAZZ (JGI Assembler)

·        Tens of minutes per microbe. Parallelized for larger genomes. 6X Drosophila 120 Mbp tokk 22 h; 6X 30 Mbp microbe took 7 hours; 7X 1.65 Mbp microbe took 20 minutes using 800 MHz Pentium III with 2 GB RAM. Use if 6-8 processors gave comparable speed up. Being parallelized for use on NERSC.

·        1 gene per 10-11 kb implies 31,000 – 32,000 genes which is comparable to current estimates for human genome. Shorter introns and intergenic sequences than in human. For most genes find conservations of intron-exon structure between Fugu and human. BLAST hits for most human genes.

·        Goal to have a single scaffold for all microbes sequenced.

 

 

Public Comment – None

 

Meeting Adjourned

 

Wednesday, November 28, 2001

 

 

Keith Hodgson

 

 

Jim Tiedje – NABIR Subcommittee Report

 

June 21-22 meeting.

 

October 8-9 meeting

 

(DISCUSSION)

 

Where are we in terms of FRC development versus actual use? ORNL folks have done a good job. Two field studies in place have actually done studies at the FRC already. This seems to be going well. FRC actually ‘opened for business’ about a year ago so research is being conducted. 25 of NABIR projects are using FRC samples in addition to the large scale experiments at the site.

 

What sort of person would fill the FRC leader position? How would the person be selected? Analogous to scientific leaders on ship cruises. Up to DOE to decide how to implement.

 

Reports accepted unanimously by voice vote.

 

 

Richard Moss, Executive Director USGCRP (US Global Change Research Program – Margaret Leinen, NSF, Chair)

 

Commerce has the lead Federal role in developing the Presidentially mandated US Climate Science Research Initiative. 60% of Commerce’s budget resides in NOAA – the National Oceanographic and Atmospheric Administration. The specific relationship of this initiative with the USGCRP remains to be determined but clearly many of the needed capabilities exist within this program. Handout of Our Changing Planet – The FY 2002 Research Program.

 

We have a lot to be proud of as a community and we need to do a better job of getting this information out.

 

The USGCRP was established in 1989 by President Bush (senior) and was codifed in 1990 by the Global Change Research Act. The FY 2002 budget is $1.7 billion.

 

The original 1990 plan emphasized a decade of research  - Earth system changes, understanding basic processes, developing a predictive understanding. Overall, the program had an Earth sciences disciplinary organization. The program is now looking ahead to develop a new vision for the next decade to integrate and apply knowledge. From OMB’s perspective the USGCRP is an applied science program not just doing research for research sake. The current planning process began in June 2000 using multiple reports from the National Research Counsel (NRC). The group is currently awaiting a review of a draft plan by the NRC. The Bush Administration is involved in a planning process for the Climate Change Research Initiative (CCRI). These two processes have been closely linked and many of the same people have been involved in both.

 

The overall goal of the USGCRP is to provide information and tools needed to make informed decisions in light of persistent uncertainties.

 

Three goals:

 

Inputs to CCRI

 

USGCRP starting point

 

Integrating and enabling activities also part of the USGCRP planning process, e.g., modeling, human dimensions

 

Criticisms of the USGCRP

 

Looking for improved external guidance from the scientific community for each program area. Need for a detailed science plan for each program area. Goal to have stronger interagency participation in planning each area like the carbon cycle group has already done. Would like to have this coordination prior to agency budget submissions to OMB. Will develop implementation plans for each area. Plan to use the Subcommittee on Global Change Research more actively as an oversight group for integration and management.

 

Science doesn’t necessarily (need to) happen in isolation from its useful applications.

 

(DISCUSSION)

 

Ari – Activities like the National Assessment really need to be supported and carried out as part of the core, basic research programs. Carrying out these types of activities as set-aside or earmarked type processes tend to fragment the management and conduct of the programs.

 

We had a thorough review of the DOE Global Change Research Program last March. Would be appropriate for BERAC to take another look next spring when the FY03 budget details are known and when the details of the Administration’s new initiative(s) for climate change research have been published. BERAC could comment on the whole package.

 

 

Michael Viola – Update on BER Advanced Medical Technologies Research

 

BER is the only player in the imaging instrumentation business. For example, MicroPET and the future development of technology for imaging of awake animals are all from DOE research. NIH is aware of DOE role and continues to rely of DOE for its contributions.

 

Examples of current research portfolio -

 

 

(DISCUSSION)

 

Future role of radiopharmaceutical development programs? BER funds five relatively small programs that result in very large leveraging of BER funds to attract NIH funds. There are too few programs in the US and too few radiochemists. There is a growing need for these reagents for disease diagnosis and normal function analysis that NIH is not likely to develop. It would be desirable to expand this aspect of the BER program. Perhaps time for some workshops in this area to identify and highlight current needs and opportunities. We need to advance the development of radiotracers and general compound development.

 

DOE interactions with new NIH Institute for Bioimaging and Bioengineering that has a technology rather than a disease focus. This institute is not likely to have an intramural research program. DOE’s role in this new institute repeatedly comes up in planning discussions about the institute. DOE lab roles clearly viewed as critical to the success of the institute. DOE viewed as part of this institute’s future. DOE is written into the institute’s mission. The institute will likely be tied into traditional NIH funding and review mechanism