BERAC Meeting Minutes November 27-28, 2001


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

  • Technical assistance to other agencies
  • DOE laboratories have a lot to offer
  • Ron Walters (PNNL) is coordinating counter terrorism activities for SC
  • Science and technology pervade all parts of the war on terrorism
  • There are new costs associated with increased DOE security needs
  • Seeing a shift of federal budget priorities
  • Gov. Ridge was at DOE on November 15 for a display of laboratory capabilities. Very impressive display. ANL, BNL, JGI, LBNL, ORNL, and PNNL represented SC. NNSA laboratories were also represented.

New management environment at DOE

  • Deputy Secretary and Chief of Staff provide policy oversight for the Secretary’s policy responsibility. The Deputy Secretary is also DOE’s Chief Operating Officer. The two Under Secretaries are the line managers for DOE’s 4 major business units – National Security, Energy, Science, Environment
  • Chief Financial Officer is now responsible for management, evaluation, and budget
  • Deputy Secretary Blake initiated operational reviews with a focus on setting top priorities and methodologies used for tracking progress and measuring performance, e.g., each program is being asked to identify its top 10 goals. Decker to meet with Blake on December 10.
  • Blake will hold quarterly reviews on major projects – SNS is the only SC project to be reviewed
  • October speech by Secretary on DOE missions and priorities emphasized a common objective – national security. Our energy and science programs should be judged by whether they advance this Nation’s energy needs and hence national security.
  • Performance, planning, and accountability now a priority. Funding decisions will now consider how well programs are managed. A strategic mission review is underway – much of this flows from GPRA (Government Performance and Results Act) that has been in place for a number of years – just a step up from what we have done in the recent past.

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 -

  • current methods used
  • appropriateness and comprehensiveness of methods
  • effects on science programs
  • integration as required by GPRA

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


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 –
  • 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
  • Public thanks to Bob Marianelli for his contributions to SC and OSTP as he plans to retire at the end of 2001
  • The state of BER reasonably good especially in a period of considerable uncertainty. New SC leadership is certainly one uncertainty. Tight budgets – the surplus is gone. Serious and significant focus by new DOE leadership on R&D relevance at DOE, SC, BER. Our job is to sharpen the connections to DOE mission areas. BER is well positioned to do this. Lots of relevance to DOE missions and priorities. Some areas of BER will receive lots of scrutiny and may have tougher times in terms of justification, but knowing which areas these are may not be obvious at this time. I don’t consider any part of the BER portfolio as an outlier or irrelevant. Our minority status across all areas we fund allows us to be flexible and to take risks.
  • Staff – several recent additions to stop outflow – Noelle Metting, Brendalyn Faison, Jeff Amthor
  • Importance of inter- and intra- agency efforts. Strongly encouraged within BER and through BERAC. Importance of ties with private sector. Examples – Human Genome (NHGRI), Microbial Genomics (NSF and interagency Microbe Project), Genomes to Life (ASCR – Advanced Scientific Computing Research), Global Change (8 agencies), NABIR (EM and Office of Naval Research), Medical Research (NIH connections)
  • New and emerging opportunities. Need to seize these with or without new funds. Climate change  - higher profile now within Administration and public. Genomes to Life as a vehicle and mechanism for addressing global change and post September 11 needs. Acknowledgement to colleagues in NNSA for interactions on biothreat reduction collaboration.
  • Stewardship of scientific user facilities. Have taken previous criticisms of our minimal role in this area seriously and over past few years have bolstered our attention in this area. Still don’t have many large facilities but do support a growing infrastructure for the biological needs of tomorrow. We support not just conventional facilities (beamlines and EMSL) but facilities in a more general sense. Gene Bierly has spearheaded BERAC efforts to define these, e.g., Ameriflux, ARM, FACE, new ORNL Laboratory for Comparative and Functional Genomics, Joint Genome Institute.
  • We got our request for FY 02 plus ~$2M undesignated that we will use for interagency activities to sequence biothreat agents. In addition, we received an extras - $5M for low dose, $3.5M for EMSL computer, $1.3M for ORNL construction
  • Beneficiary of record number of earmarks (51 earmarks worth ~$72M). Most of these are likely to be construction, but some will be research activities that may directly benefit BER goals.
  • Structural Biology plans – Small Angle Neutron Scatter facility for structural biology at ORNL’s HFIR and a SPEAR III upgrade.
  • Genomes to Life plans this year – fund a few large collaborative grants that are partnerships between labs, universities and even industry.
  • Low dose solicitation planned jointly with NASA.
  • Microbial genomics – USDA partnership for sequencing, microbial carbon sequestration research – solicitation planned for this year
  • Poplar sequencing for biomass and carbon sequestration
  • Human Genome – committed to finishing our human chromosomes (5,16,19), review of finishing activities underway; Fugu sequencing announcement (Rokshar will describe assembler later today – best available in public sector); Ciona sequencing underway - important for comparative genomics.
  • Global Change – DOE program ideally poised to play role however things go politically; role in USGCRP 10 year plan; player in all different topical areas of program to develop future plans
  • Climate modeling - ~$8M part of Scientific Discovery through Advanced Computing (SciDAC) through ASCR; ARM – scrubbed last summer by JASON and did very well; science program solicitation planned this year
  • UAV – some delays since planes diverted to Afghanistan, Gene Bierly will lead a BERAC effort to take close look at this program early next year
  • Carbon cycle and carbon sequestration programs likely to grow in general since carbon science is at the center of global change concerns and challenges. BER is a player in both the ocean and terrestrial sides of this issue. The ocean side will have a solicitation this year. We have disbanded the LLNL/LBNL ocean center though not because of a change in our emphasis or priorities.
  • The ecology program has just received proposals from a recent solicitation.
  • A NABIR solicitation is planned jointly with EM through Savanna River Operations Office. We are excited about the additional funds we received for the upgrade of the EMSL computer.
  • We have struggled for some time with the need to redefine our budget categories to give BER a more logical program and financial organizational structure.
  • The Medical Sciences program has been restructuring over past few years through series of workshops and in parallel with its key interactions with NIH. This program has benefited from expertise and capabilities at the National Labs. It is now emphasizing early diagnosis capabilities.
  • You will hear more tomorrow from Mike Vioal on our imaging and medical photonics efforts that have resulted in several large, multi institutional, high risk, high payoff grants.
  • The transition of our Boron Neutron Capture Therapy is complete. The Brookhaven Medical Research Reactor has been shut down and our clinical trials work has stopped (a role we never should have had in the first placed). We hope that NIH will pick up the slack in this area including drug development and they have started funding some of these trials. BER has started a modest new program looking at novel isotope therapies.


  • BER not directly funding any Anthrax work though several labs (e.g., LLNL and LANL) are involved in activities without direct BER funds. BER facilities were used to solve the structure of the Anthrax toxin recently. It has been reassuring to not have seen any turf issues at the labs or among agencies in the biothreat reduction area as everyone is just doing what needs to be done.
  • Bioterrorism role for BER? Unique and distinct from NNSA? $2.2M in undesignated funds proposed for use through JGI. The JGI labs have been discussing a proposal for biothreat agent sequencing and analysis. We hope that the NNSA will be able to invest in this as well. We may even delay other sequencing priorities as needed. We are currently engaged in discussions with other agencies (NIAID, NSF, CIA, DARPA, USDA) on sequencing, databases, private sector involvement, and customers for biothreat agent characterization. What about tools to be developed beyond sequencing as in Genomes to Life? Genomes to Life is already adapting to this need. What can/should BERAC do to help? BERAC’s genome or bioremediation subcommittees will hopefully provide feedback on the proposed interagency collaboration. It would be helpful to have this discussion/review by the next BERAC meeting. This interagency effort to look at long range research needs is very important.
  • Role of environmental processes type research – transport, diffusion, aerosols, inner cities, complex terrains – in post September 11 activities as well.
  • An ASCAC subcommittee is looking at how to best address SC computing needs including those for data distribution. BERAC was asked to provide a member for this subcommittee. Charles DeLisi will likely represent BERAC.

Derek Lovely – Science talk

University of Massachusetts, Amherst

Dissimilatory Metal Reduction: Genomics Meets Bioremediation and Environmental Energy Harvesting
  • Dissimilatory iron reduction likely the first form of microbial respiration on Earth
  • Important influence on soil chemistry and water quality
  • Role in carbon cycle and bioremediation
  • Geobacter role in conversion of organic matter back to C02 (in the absence of oxygen) with iron serving as the electron acceptor. Example shown of different colored sediments from jet fuel contaminated site due to iron reduction through process of organic contaminant degradation.
  • Uranium can be used as electron receptor to reduce acetate, uranium precipitation following reduction. Can use technicium, cobalt, and other metals as electron receptors – value for clean up of contaminated water or subsurface environments to immobilize metal.

Ari Patrinos – National Climate Change Technology Initiative

President’s June 11, 2001, Commission

  • Evaluate current state of US climate change technology research
  • Provide guidance on strengthening basic research including development of advanced mitigation technologies to reduce green house gas emissions
  • Develop opportunities to enhance public-private partnerships
  • Make recommendations for funding demonstration projects for cutting edge technologies
  • Develop improved technologies for measuring and monitoring greenhouse gas emissions

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

  • Workshops held and white papers developed
  • Integration paper being written to serve as center of recommendation from Secretary to President in January 2002.

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.


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 –

  • NCCTI activity
  • New front office in DOE
  • Partnership with ASCR
  • September 11 as a new driver not only for biothreats but for energy independence

Payoffs of GTL research within the next 10 to 50 years

  • Bioterrorism
  • Cleanup
  • Carbon sequestration
  • Energy independence
Mike Colvin, LLNL/DOE

Computational workshops

  • August/September 2001
  • January-March 2002

August workshop recommendations

  • Modeling of cells and microbial communities – research needed to accelerate progress
  • Functional annotation of genomes – automated methods needed for structural and functional annotation of whole genomes
  • Biological data management – large and heterogenous data sets and associated data mining and visualization methods needed
  • Data distribution policy – who owns the data – policy needed prior to making research awards
  • Scope of computational biology research – projects need to have sufficient scope to attract biologists to computational biologists to mathematicians to computer scientists

September workshop

  • General excitement about model driven biology
  • Wide range of topics from computer infrastructure needs to training for computational and systems biologists to organizational structures for data-driven biology

Upcoming workshops

  • Essential computational biology applications areas needed to enable GTL
  • Determine computer and network infrastructure needs for GTL

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:

  • Development of assays for CDC, e.g., candidate signatures/assays for microbes
  • Infrastructure to turn DNA sequence data into tailored assays
  • Field laboratory to support security at 2002 winter Olympics (BASIS- Biological Aerosol Sentry and Information System)

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

GTL links –

  • Identify protein machines – virulence factors and targets
  • Regulatory networks – virulence pathways
  • Microbial communities - signaling mechanisms  and host-pathogen interactions
  • Computational tools – countermeasure target and strategy development

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:

  • Intrinsic remediation (natural attenuation) – let nature takes its normal course - or accelerated bioremediation by stimulation or bioaugmentation of natural communities.
  • Ex situ treatment of waste

Overarching challenges/problems:

  • Characterization of microbial communities and their potential/capabilities – bioavailability and toxicity of contaminants and control over critical metabolic pathways
  • Monitoring and verification – biosensors
  • Long-term consequences for site stewardship – gene transfer in the environment
  • Industrial scale waste treatment – cell free systems, new technology & protein machines

Potential cost savings?

  • Examples of a few biotreatment approaches that have given 1/3 to 20 fold savings at Savanna River site or at EPA sites

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

  • Ad hoc subcommittee on Biodefense R&D to be led by Jim Tiedje. To help BERAC and BER formulate appropriate plans and strategies in this area.  
Jim Tiedje – NABIR Subcommittee Report

June 21-22 meeting.

  • Review of NABIR strategic plan draft document. Program now to be focused on biostablization in situ and a limited set of DOE unique metals and radionuclides. General organization model for NABIR also applicable for bioterrorism research strategies.
  • BASIC (Bioremediation and its Societal Implications and Concerns) review. Not a particular focus other than general issue of cleanup initially so BASIC projects didn’t match very well. Now with focus on biostablization there is a specific issue for BASIC to focus on. What are the societal concerns associated with this cleanup strategy. This should now be a central BASIC goal. Also need to attract a broader sector of the social science community to get involved in NABIR.  

October 8-9 meeting

  • Field Research Center (FRC). A highlight of the FRC is that the site conditions are more complex than initially imagined. Very high levels of nitrate in situ though target is still uranium. PH is low and lots of aluminum present. These are all things that need to be dealt with in doing research and studies at the FRC. Importance of having an overall intellectual leader at the FRC. This position can rotate over time but important to drive and focus research.
  • Biomolecular Science & Engineering. Most fundamental of NABIR elements. Closest interface with Genomes to Life program.  


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:

  • Regional scale predictions of human impacts on the environment
  • Vulnerabilities and options for enhancing the resilience of vulnerable natural resources
  • Government and private sector decision making capabilities  

Inputs to CCRI

  • Carbon forcings and feedbacks
  • Carbon cycle
  • Modeling
  • Observations
  • Regional impacts of climate change  

USGCRP starting point

  • Atmospheric composition
  • Climate variability and change
  • Carbon cycle
  • Water cycle
  • Terrestrial and marine ecosytems
  • Land use and land cover changes  

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

Criticisms of the USGCRP

  • Not all necessary observations were/are included within the program. However, the program didn’t have a mandate for everything, e.g., Weather Service responsibilities are outside the program.
  • No mechanism to enforce budgetary priorities. This is a real challenge given the distributed nature of the program across many agencies.
  • Inadequate follow through to gauge progress towards interagency deliverables – OMB concern
  • Progress in reducing some key uncertainties not rapid enough, e.g., climate sensitivity  

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. 


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 -  

  • Development of an artificial retina. If successful would allow patients with macular degeneration and retinitis pigmentosum to see. Project centered at ORNL but involves 5 labs, 2 universities and a private company. The nerve-device interface is a key to this development. Microengineering challenge.
  • Imaging brain function without anesthesia. BNL lead. PET and MRI technologies. Future value for imaging infants and to detect changes in brain function. Large computational challenge for motion correction for example.
  • Imaging the moving patient. Thomas Jefferson lead. Continuous tracking of motion for computational deconvolution of moving animals (patients). Importance for patients with motion disorders or for infants to avoid anesthesia.
  • Using astronomy to diagnose eye diseases and to correct human vision. LLNL lead. Use of adaptive optics developed for correction of the blurring of astronomical images by the atmosphere to correct for comparable blurring due to fluid in the eye. Use of deformable optics. Likely that every US ophthalmologist will have one of these devices within 5-10 years.
  • Using astronomy to improve medical imaging. LLNL lead. Goal to develop an x ray detection system that will allow high resolution imaging of small animals using radioactive tracer technology. Very high-risk project that would never be funded by NIH system. Innovation in the mirror system for image correction.
  • Biosensing research in collaboration with NNSA. Small optical sensors for the diagnosis of disease. LNL lead. Development of a handheld device using an antibody based detection system to diagnose tuberculosis in the field using a sputum sample.
  • Ultrasensitive devices to measure medically important molecules. ORNL lead. Use of microcantilevers whose deformation by molecular interactions can be detected using lasers. Extraordinary potential as a sensitive detection technology.
  • A previous commercial success story. Precise eradication of cancer with radiotherapy. LLNL lead.  Peregrine – an improved computational program to direct radiation to cancer at high doses to avoid damage to normal tissue. Has gone through clinical trials at NCI. No doubt that this will be the standard in radiation oncology in the coming years.  


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 mechanisms. It is unlikely that any or many of the projects described above would be successful in an NIH type peer review. 

BER Facilities Overviews 

Wanda Ferrell – Atmospheric Radiation Measurement (ARM) sites 

The ARM program operates highly instrumented field sites to collect data for understanding the role of clouds in climate and in seeing this understanding reflected in the improvement of the appropriate models in General Circulation Models. 

The sites measure:

  • Water vapor column and profile
  • Aerosol optical depth
  • Cloud properties
  • Radiation budget components
  • Meteorology
  • Soil water and temperature 

Sites spanning global climate variability are located at:

  • Southern Great Plains (Oklahoma) – since 1994
  • Tropical Western Pacific – 3 sites started in 1996, 1998, and 2002
  • North Slope of Alaska – 2 sites since 1998 

These sites are both onsite user facilities for investigators and instrument developers and generators of data used by large numbers of investigators.  The Southern Great Plains and North Slope of Alaska sites both had 140 to 150 visitors in 2001 while the more remote Tropical Western Pacific sites only had about 50 visitors in 2001. Periodic intensive observation periods (principally at the Southern Great Plains Site) were initiated by the BER ARM program 66% of the time and by external users the remainder of the time. The program has also seen an exponential increase in cumulative data storage over the past two years. 


The program has and uses its capability to reprocess/reanalyze old data sets when instruments, etc. change. We now have enough data so that trend analyses are possible and useful. 

Comment on the interface with the modeling community. There is not as much success interfacing with the general climate modeling community as desired though the European Centre for Medium-Range Weather Forecasts does use the data. There are just different community mindsets that need to be and are being addressed. For some in the General Circulation Modeling community it has been an instrument calibration problem that has been resolved from earlier problems.  

Roger Dahlman, Free-Air CO2 Experiment (FACE) Sites 

FACE sites support long-term field biology studies on macrobiology, studying the effects, on plants, of CO2 concentrations that are assumed will be found in 50 years. The FACE program supports a network of six large field experiments using protocols and technology originally designed by BNL. FACE sites are located in a range of different ecosystems:

  • Managed pine forest (Duke Forest)
  • Natural desert ecosystem (Nevada Test Site)
  • Eastern deciduous forest (ORNL)
  • Sub-boreal deciduous forest (Wisconsin)
  • Grassland/prairie (Minnesota)
  • Cotton, wheat, sorghum (Arizona) 

Each FACE site consists of control plots with ambient CO2 concentrations and experimental plots where CO2 concentrations are elevated by the introduction of CO2 from a ring of CO2 towers surrounding the plot. Typical studies include:

  • Molecular-level studies on the control of the enzyme Rubisco
  • Plant and canopy photosynthesis for gross and net carbon gain
  • Role of soil micro biota in carbon cycling and nutrient dynamics
  • Controls on ecosystem production associated with limiting soil dynamics
  • Ecosystem-level community dynamics 

To date, the FACE studies have shown variable ecosystem response to elevated CO2 ranging from increases in invasive species at the desert site to growth stimulation that is offset by ozone at the Wisconsin site to increased crop yield at the Arizona site. 

These sites and the FACE data are used by hundreds of scientists. The BER FACE network has also led to international collaborations with the development of sites in Switzerland, Germany, and New Zealand. 

The cost of operating and potential expanding the number of these sites is not trivial principally due to the high costs of CO2 and power required. Expansion of these sites to other ecosystems would provide information needed to understand the broad, long-term impacts of elevated CO2 on our Nation’s diverse ecosystems.  

Roland Hirsch, Structural Biology User Facilities 

BER supports the use and development of a range of user facilities for structural biology from beam lines at BES operated synchrotron and neutron sources to novel microscopies to high field nuclear magnetic resonance and mass spectrometry. BER’s largest investments are in development and operation of user stations at synchrotron and neutron sources:

  • 12 x-ray crystallography stations
  • 1 neutron crystallography station
  • 2 x-ray spectroscopy stations
  • 2 small angle x-ray scattering stations
  • 1 small angle neutron scattering station 

Many of these user resources have been developed in partnership with NIH’s National Center for Research Resources or the Institute of General Medical Sciences. 

At DOE synchrotrons, life sciences users have increased from 31% of total users in 1997 to 40% of all users in 2001. About 60% of the structures reported in  ‘high profile’ journals were determined at US synchrotrons. The total number of structural molecular biology beam lines in operation or under development has increased from about 30 in 1997 to about 60 in 2001. 

Paul Bayer, Environmental Molecular Sciences Laboratory (EMSL) 

EMSL is BER’s one official ‘bricks and mortar’ user facility. Located at PNNL in Richland, Washington, BER provides ~$27million in operating funds to EMSL annually. EMSL provides advanced and unique instrumentation and computational resources to scientists at universities, national laboratories, and industry principally in the environmental sciences related to PNNL’s and DOE’s environmental cleanup mission. EMSL scientists also conduct fundamental research and provide educational opportunities for students and scientists.  

EMSL provides over 100 state-of-the-art instrumentation and computation systems including:

  • A molecular sciences computing facility that is being upgraded to a 2-3 Tflp system in FY02
  • A high field magnetic resonance with a suite of machines including the anticipated 900 MHz wide-bore NMR scheduled for delivery in 2002
  • A high field mass spectrometry facility with a suite of machines including the world’s largest, an 11.5 Tesla Fourier Transform Ion Cyclotron Resonance mass spectrometer 

Since its dedication in 1997, the number of EMSL users has increased dramatically from a total of 834 in 1999 to 1415 in 2001. More than half of all users are remote users with the vast majority from academia. 

A more detailed description of EMSL’s capabilities and a description of some of its impressive accomplishments are available on the web at http://www.emsl.pnl.govExternal link

Public Comment – None 

Meeting Adjourned

Last modified: 3/18/2013 10:27:47 AM