Empowering 21st Century Biology

Roundtable Empowering 21st Century Biology Gene E. Robinson, Jody A. Banks, Dianna K. Padilla, Warren W. Burggren, C. Sarah Cohen, Charles F. Delwiche, Vicki Funk, Hopi E. Hoekstra, Erich D. Jarvis, Loretta Johnson, Mark Q. Martindale, Carlos Martinez del Rio, Monica Medina, David E. Salt, Saurabh Sinha, Chelsea Specht, Kevin Strange, Joan E. Strassmann, Billie J. Swalla, and Lars Tomanek Keywords: ecology, genomics, bioinformatics, cell biology, biological infrastructure B iology is confronted with the need to answer fundamental questions about how life and natural systems evolve, are governed, and respond to changing environments. We need to understand the basic biological processes that drive life on this planet—those common to all organisms as well as those that provide unique adaptation to different environments. We also urgently need to identify all the life forms on this planet and understand their interrelationships and geographic distributions. Biology must also apply new and existing knowledge to solve the pressing problems of our times, which include the environmental crises of global climate change, ocean acidification, biodiversity loss and the introduction of nonnative species, serious concerns for human health, emerging and pandemic diseases, and critical needs for agricultural and biofuel production. The urgency of these fundamental and practical needs has prompted scientists to begin to identify sets of “grand challenges” in biology (Denver et al. 2009, NRC 2009, Satterlie et al. 2009, Schwenk et al. 2009). To succeed in addressing the challenges of 21st century biology, scientists must generate, have access to, interpret, and archive more information than ever before. This effort will involve analyses that span scales of time and space, from decoding information from genomes to extracting information from the environment on how organisms survive and reproduce (NRC 2009). Scientists need to learn how complex biological systems work across levels of organization, from cells to ecosystems, and across time scales, from the millisecond response of neural systems to the long-term response of evolutionary change. We need to be able to trace the effects of changes in DNA sequence or epigenetic regulation on multiple organismal phenotypes, understand how these changes affect ecological relationships, and have sufficient examples of these to begin to articulate new theories of organismal function and evolution. Addressing the challenges of 21st century biology requires integrating approaches and results across different subdisciplines of biology, such as genetics, development, physiology, ecology, and evolution, as well as technologies, information, and approaches from other disciplines, such as engineering, computer science, physics, chemistry, mathematics, and the geological and atmospheric sciences (figure 1). However, biologists do not have the tools required to achieve this vision. For many important questions in biology, progress is stymied by a lack of the essential instruments to make rapid advances. In some cases, certain devices or technologies exist in other fields but are currently unavailable to biologists. In other cases, we need tools that scientists have not yet imagined. Developing those tools may require new technologies, applications of existing technologies, software, model organisms, and social structures to promote tool building, tool sharing, research collaboration, and interdisciplinary training. This article presents examples of what we believe to be the most important needs for tools to address critical questions in biology. We focus on the tools and the social structures needed to enable such tools; for an in-depth treatment of biology’s grand challenges, see Denver and colleagues (2009), the National Research Council report A New Biology for the 21st Century (2009), Satterlie and colleagues (2009), and Schwenk and colleagues (2009). Tools Researchers need tools to enable high-throughput acquisition and synthesis of information at all levels of the hierarchy of biological organization, and across all biologically relevant BioScience 60: 923–930. ISSN 0006-3568, electronic ISSN 1525-3244. © 2010 by American Institute of Biological Sciences. All rights reserved. Request permission to photocopy or reproduce article content at the University of California Press’s Rights and Permissions Web site at www.ucpressjournals.com/ reprintinfo.asp. doi:10.1525/bio.2010.60.11.8 www.biosciencemag.org December 2010 / Vol. 60 No. 11 • BioScience 923 Several lists of grand challenges in biology have been published recently, highlighting the strong need to answer fundamental questions about how life evolves and is governed, and how to apply this knowledge to solve the pressing problems of our times. To succeed in addressing the challenges of 21st century biology, scientists need to generate, have access to, interpret, and archive more information than ever before. But for many important questions in biology, progress is stymied by a lack of essential tools. Discovering and developing necessary tools requires new technologies, applications of existing technologies, software, model organisms, and social structures. Such new social structures will promote tool building, tool sharing, research collaboration, and interdisciplinary training. Here we identify examples of the some of the most important needs for addressing critical questions in biology and making important advances in the near future. Roundtable spatial and temporal scales. These include technologies, software, and devices related to “omics”; informatics and systems biology; sensors and imaging; and information archiving. Omics, informatics, and systems biology. The ability to sequence the genomes of microbes, plants, and animals has led to remarkable advances in biology. But this “first genomic revolution” has been based on the genome sequences of only a relatively small number of organisms: hundreds of microbes, and just a few dozen plant and animal species (www.genomenewsnetwork. org/). The relentless push to lower DNA sequencing costs for biomedical purposes will continue, and will soon make it possible to sequence the genomes of most species of interest for any biological question. Lower sequencing costs will usher in a “second genomic revolution,” having a transformative effect on all areas of biology because genome sequence information can be used to illuminate questions at all levels of biological organization; we present just a few examples here. DNA-based tools can have profound interdisciplinary impacts, beginning with faster and cheaper field identification of species and extending to assessments of genomewide patterns of genetic variation in different environments to determine what allows or limits the ability of individuals to 924 BioScience • December 2010 / Vol. 60 No. 11 www.biosciencemag.org Figure 1. Tools for 21st century biology. To solve grand challenge (...truncated)