Updating segmentation schemes
For example, we may have a large number of points in space at certain distances from a central reference/origin point.
Suppose we have to lookup the points which are in a certain range of distances from our origin.
To illustrate this, we review the evolution of operational definitions of a gene over the past century—from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks.
We then summarize the current ENCODE findings and provide a computational metaphor for the complexity.
This project represents a major milestone in the characterization of the human genome, and the current findings show a striking picture of complex molecular activity. The discrepancy between our previous protein-centric view of the gene and one that is revealed by the extensive transcriptional activity of the genome prompts us to reconsider now what a gene is.
While the landmark human genome sequencing surprised many with the small number (relative to simpler organisms) of protein-coding genes that sequence annotators could identify (∼21,000, according to the latest estimate [see ENCODE highlighted the number and complexity of the RNA transcripts that the genome produces. Here, we review how the concept of the gene has changed over the past century, summarize the current thinking based on the latest ENCODE findings, and propose a new updated gene definition that takes these findings into account.
Horton Memorial Lectureship, American Meteorological Society, 2006 William Nordberg Memorial Lectureship, NASA Goddard Scientific Colloquium, 2004Group Honor Award for Excellence, U. Department of Agriculture, 2001Fellow, American Association for the Advancement of Science (AAAS), 1997Fellow, American Meteorological Society (AMS), 1995Fellow, American Geophysical Union (AGU), 1994 Fellow, International Water Resources Association (IWRA), 2001Life Member, Phi Kappa Phi, 1988Life Fellow, Indian Association of Hydrologists, Roorkee, India Hearings and Testimonies Testimony for the hearing before the National Ocean Policy Study of the Committee on Commerce, Science, and Transportation, U. Senate on: Authorizations for the National Oceanic and Atmospheric Administration's Atmospheric and Satellite Programs, Chaired by Senator Kerry of Massachusetts, May 19, 1987. DOE)2006-2010: Chairman, Climate Change Science Program Product Development Advisory Committee Los Alamos National Laboratory (LANL)2006-2011 Member, LANL Earth and Environmental Science (EES) Division Review Committee National Academy of Engineering (NAE)2006-2009: Special Fields and Interdisciplinary Engineering Peer Committee The National Academies - National Research Council (NRC)2007: Member, Water Science and Technology Board2007-2009: Member, Space Studies Board National Science Foundation (NSF-STC) Sustainability of semi-Arid Hydrology and Riparian Areas (SAHRA)2003-2010: Member, Executive Committee Pacific Northwest Hydrologic Observatory (PNWHO)2005-2009: Member, Science Advisory Board US Department of Energy (US DOE), 2006-2008: Chairman, Climate Change Science Program Product Development Advisory Committee External Examining & Assessment Panels2008: Member, evaluation committee Institute of Observational Research for Global Change (IORGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)2009: Member, Review Panel, National Severe Storm Laboratory (NSSL), University of Oklahoma, Norman, OK2009: Member, Review Panel, Desert Research Institute, Division of Hydrologic Services, NV2009: Member, Review Panel, St. of Earth and Atmospheric Sciences2010: Member, Review Panel, University of Colorado at Boulder, Cooperative Institute in Environmental Science (CIRES)2010: Member, Review Panel, University of New Mexico, Water Resources Program2011: Member, Review Panel, EPFL ENAC School, Lausanne Switzerland2012: Member, Site visit team, NSF CISE Expeditions program at University of Minnesota2013: Member, Review Panel, DK proposal application to the Board of the Austrian Science Fund (FWF), Vienna, Austria2013: Member, Expert Review Panel on Water and Green Growth (WGG) joint research project of the Ministry of Land, Infrastructure, and Transport of the Republic of Korea (MOLIT), Korea Water Resources Corporation (K-water), and the World Water Council (WWC).
This can be a tedious and slow process, especially if the number of queries is large and repetitive.
While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is.
In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene.
Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products.
Our definition sidesteps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene.