Supercomputers: Speeding up medical discovery

October 18, 2010

At the Arizona Science Center, experts will explain how a powerful high-speed data-processing link based at ASU promises speedier progress in the battle against debilitating diseases

Large supercomputers and high- bandwidth networking are enabling researchers to accelerate efforts to discover more effective treatments for people afflicted by diseases such as diabetes, cancer and Alzheimer’s disease.
One of the fastest computer data-processing links dedicated to aid such biomedical research has been implemented between laboratories at the Translational Genomics Research Institute (TGen) in Phoenix and the facilities of the High">">High Performance Computing Initiative (HPCI) of the Arizona State University’s Ira A. Fulton Schools of Engineering.
TGen medical researchers and an ASU computer engineering expert will describe how it all works and answer questions about the system at Biotech Talk from 5:30 to 6:30 p.m. Nov. 10 at the Arizona">">Arizona Science Center.
HPCI research scientist Gil Speyer will be joined by James Lowey, director of TGen’s High Performance Biocomputing Center, and Amol Tembe, leader of the Collaborative Bioinformatics Center at TGen.
Using a supercomputer called Saguaro 2, ASU computer engineers are moving voluminous amounts of information to TGen researchers at as much as 100 times faster than previous systems.
The new system is capable of quickly processing of trillions of bits of DNA information. It will allow TGen scientists to accelerate the analysis of next-generation whole genome sequences — readouts of the entire three billion chemical letters in an individual’s DNA.
That information can be used by medical specialists to develop treatment for people with debilitating diseases more effectively, and may move scientists more quickly along the path to discovering cures.
Admission to Biotech Talk is free. The Arizona Science Center is at 600 W. Washington Street in downtown Phoenix, at the corner of Washington and Seventh Street. The Light Rail line has a stop at Fifth Street and Washington. Download Full Image

Joe Kullman

Science writer, Ira A. Fulton Schools of Engineering


Biodiversity experts address conservation goals for 2020

October 18, 2010

While not an outright failure, a 2010 goal set by the Convention on Biological Diversity (CBD) for staunching the loss of the world’s species fell far short of expectations for “The International Year of Biodiversity.”

What does this mean for the 20 proposed 2020 goals being considered by the 10th conference of parties at the Convention on Biological Diversity in Nagoya, Japan, on Oct. 18-29, 2010? Download Full Image

In the article “Ecosystem Services for 2020,” published Oct. 15, 2010 in the journal Science, some of the world’s foremost biodiversity experts assembled by the Paris-based international program of biodiversity science, DIVERSITAS, offer a strategic approach to the 2020 goals – one that incorporates trade-offs, timing and complexity.

Feasible goals

“While there is still time, it is critical to design the 2020 targets and their indicators in ways that give them a reasonable chance of success,” said Charles Perrings, ecosystem services expert at ASU. The DIVERSITAS team, led by Perrings, includes ASU scientist Ann Kinzig and 16 other leading biodiversity experts from the United States, Argentina, Sweden, Chile, Japan, England, France and Germany (the full list is appended).

The team lauds the convention for increased efforts to address the most serious aspects of global change, climate and biodiversity, through pursuit of 20 “SMART” (specific, measurable, ambitious, realistic and time-bound) targets to be achieved by 2020.  However, the group also argues that it is not enough for the targets to be SMART.

“The 2010 CBD goal was unrealistic,” said Perrings, a professor in ASU’s School of Life Sciences and co-director of the ecoSERVICES group in ASU’s College of Liberal Arts and Sciences.

“And while the 20 proposed goals for 2020 are more specific about where to go to reduce the rate of loss of biodiversity, there are critical oversights that need to be considered by the Nagoya conference delegates and beyond.”

For example, the 2020 target that “all people are aware of the values of biodiversity and the steps they can take to conserve and use it sustainably” seems unrealistic. In addition, a 2020 target for the sustainability of agriculture, aquaculture and forestry asserts that doing this will automatically assure conservation of biodiversity, yet scientific evidence does not support this, according to the authors. Both the extensive and the intensive growth of agriculture  – expansion of the area committed to the production of crops or livestock, increased use of pesticides and herbicides – come at a cost to non-farmed species.

One issue with the 2020 targets, the authors point out, is that many of them are interdependent. Some are likely to be mutually inconsistent, meaning achieving one compromises achievement of another. Others are contingent, meaning achieving one is conditional on achievement of another. It will be important to adopt indicators that recognize the interdependence of targets.

“We are also fishing out oceans, one stock at a time," Perrings said. "Often there are no real instruments for protection and those that do exist have no teeth. There are lots of reasons, reasonable ones, for people making private decisions that lead to biodiversity loss, but they cost us all collectively.”

The journal article points out that the proposed 2020 CBD targets also need to tap into the benefits that biodiversity provides to humanity, in addition to recognizing trade-offs between benefits. 

Codes for success

The DIVERSITAS team assessed the 2020 targets and challenges to their implementation using the ecosystem services framework developed by the Millennium Ecosystem Assessment, an effort led by the United Nations in 2001-2005 to “analyze the capacity of the world’s ecosystems and assess the consequences of ecosystem change for human well-being.” 

The authors’ resulting roadmap for 2020 recommends a hierarchical approach, one that is sensitive to the timing and sequence of targets. Some targets concern issues that need to be addressed before 2020 (DIVERSITAS codes urgent targets “red”), and other targets concern issues that need to be implemented in sequence (“enabling conditions” are coded “blue”). Moreover, many of the traditional conservation targets (coded “green”) involve trade-offs with red and blue targets that will play out over much longer timescales.

The 2020 targets to be negotiated at the Nagoya convention are a significant improvement over the 2010 target. They address the international community’s traditional conservation goals – to reduce the pressures on biodiversity and to safeguard ecosystems, species and genetic diversity. But they also address the underlying causes of biodiversity loss, its sustainable use, and the capacity and knowledge building that need to be done to if the targets are to be successfully implemented. 

The scientists argue that while the 2020 targets could be strengthened, Nagoya could well be a turning point for the Convention on Biological Diversity.

“The development of a strategic plan supported by targets, indicators and actions is a very positive step,” Perrings said.

The convention, together with the United Nations Framework Convention on Climate Change (UNFCCC), also established in 1992, represent the commitment of nations to secure global commitments to address the most serious aspects of global change: climate and biodiversity. The UNFCCC was the focus of much attention in 2009. Combined with the establishment of an Intergovernmental Science Policy Platform for Biodiversity and Ecosystem Services (IPBES), to be brought before the U.N. General Assembly later this year, Perrings and his team believe that the gathering in Nagoya, Japan, may mark the first serious attempt by the international community to deal with the second of the world’s two greatest environmental problems: biosphere change. 

Margaret Coulombe

Director, Executive Communications, Office of the University Provost