The sequencing of the entire genome of many organisms, both simple and complex, has brought us to the threshold of a new era in biology. The human genome project is one of the greatest achievements of scientific reductionism, whose completion opens a new era of synthetic biology. Genome sequence data have grown exponentially over the past decade, and are still an unexplored wilderness where many great and small discoveries remain to be made. For the first time, we can begin to understand the structural, functional, dynamic, and evolutionary organization of entire genomes. The task at hand is to interpret the data, to discover the patterns and processes represented within it, and synthesize a new understanding of life, and of ourselves.
How do the tens of thousand of genes of the human genome interact to generate the developmental process leading from the fertilized egg to the mature human? How do patterns of gene expression change as organisms develop, or respond to environmental influences, or experience disease? What do the sequence relationships among genes within a genome reveal of the footprints of evolution? What will the comparisons of genomes of many organisms teach us about genome evolution? What can genomics tell us about patterns of human migration? What will comparison of the human genome to that of our closest living relatives teach us about what makes us human, and the unique nature of the human mind?
Along with providing answers to these questions in basic science, the era of genomics will permit tremendous advances in medicine, as we learn the functions of each gene, and the problems created by their mutations. As we answer the fundamental questions in genomic science, we will gain the knowledge to selectively and skillfully manipulate the structures and functions of living organisms, to cure and eventually to prevent disease and to enhance the quality and productivity of agriculture.
When we have come to understand the organization, function, and evolution of a variety of organisms, we can hope to understand how alterations in one organism cause co-evolutionary changes in other organisms, leading to a genomic basis for a science of evolutionary community ecology. This understanding can help us to manage and mitigate the impact of humans on the biosphere, leading to a future in which humans can live in balance with wild nature.
The exponential growth of genome databases creates new challenges in computational biology. These challenges go far beyond the simple management of complex databases. The creative interpretation of the data in discovering the higher levels of organization and dynamic function of enormously complex genomes will require fundamental advances in computational biology.