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Research glossary
Evolving terminology for emerging technologies  Suggestions? Comments? Questions? mchitty@healthtech.com
Last revised November 29, 2001
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Related glossaries include Applications Business of the life sciences, Clinical genomics, Drug discovery & development, Drug approvals, Informatics  Algorithms & data management Advances in technologies often enable research breakthroughs Technologies overview

applied research: Aimed at gaining knowledge or understanding to determine the means by which a specific, recognized need may be met. In industry, applied research includes investigations oriented to discovering new scientific knowledge that has specific commercial objectives with respect to products, processes, or services. [National Science Foundation,  Directorate for Social, Behavioral & Economic Sciences, US definitions for resource surveys 1996] http://www.nsf.gov/sbe/srs/seind96/ch4_defn.htm

basic research: The objective of basic research is to gain more comprehensive knowledge or understanding of the subject under study, without specific applications in mind. In industry, basic research is defined as research that advances scientific knowledge but does not have specific immediate commercial objectives, although it may be in fields of present or potential commercial interest. [National Science Foundation,  Directorate for Social, Behavioral & Economic Sciences, US definitions for resource surveys 1996] http://www.nsf.gov/sbe/srs/seind96/ch4_defn.htm

bottom-up: The classical reductionist approach to biology which aims to examine the smallest units to gain insight into the larger ones. Mendelian genetics, which looks at single genes, is a bottom- up approach. Compare top- down. Narrower term Miniaturization glossary nanofabrication- bottom- up

clinical trials:  Clinical trials, drug approvals glossary

determinism: Clinical genomics glossary

development: The systematic use of the knowledge or understanding gained from research directed toward the production of useful materials, devices, systems, or methods, including the design and development of prototypes and processes.  [National Science Foundation, Directorate for Social, Behavioral & Economic Sciences, US definitions for resource surveys 1996.] Related terms applied research, basic research  http://www.nsf.gov/sbe/srs/seind96/ch4_defn.htm

discovery driven research: High throughput techniques in DNA sequencing and gene expression have led to a vast increase in quantitative data. This data is extensive and widely available on the internet. By all accounts there is a wealth of information in the data that has not been completely investigated. 

Traditional biology research is hypothesis driven. However, the best way to exploit the vast databanks is discovery driven. The difference is that for hypothesis driven research you need an encyclopedic knowledge of a very specific area (a particular protein, for example) to be able to suggest and perform unique and interesting experiments. Discovery driven research requires a much broader knowledge, along with the ability to rapidly read the relevant literature and get up to speed on a specific area.  [James P. Brody, Assistant Professor, Center for Biomedical Engineering, University of California, Irvine jpbrody@uci.edu ] http://brodylab.eng.uci.edu/~jpbrody/comp.html

forward genetics Functional genomics glossary.

glue grants: NIGMS [National Institute of General Medical Sciences, NIH, US] has two initiatives that seek to promote the integrative and collaborative approaches that are increasingly needed to solve complex problems in biomedical science. Because these programs are meant to provide resources to bring people together, they have been nicknamed "glue grants." http://www.nigms.nih.gov/funding/gluegrants.html

holism: The idea that ``the whole is greater than the sum of the parts.'' Holism is credible on the basis of emergence alone, since reductionism and bottom-up descriptions of nature often fail to predict complex higher-level patterns. Related term top- down.  [Gary William Flake, Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems, and Adaptation, MIT Press, 1998] http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-intro.html

Coined by General J. C. Smuts (1870-1950) to indicate the tendency of nature to produce wholes. First recorded 1926 in Holism & Evolution. [OED]

hypothesis driven research:  The traditional approach of moving from a hypothesis to a specific understanding through research. The era of high- throughput and systematic functional analysis of genes has not rendered hypothesis- or problem driven biological research obsolete or outmoded. Instead, it has created a vast set of new problems to be solved by the traditional biological research approach, centered on human researchers rather than automated systems. However, biologists carrying out hypothesis- or problem driven research often do so utilizing new tools made possible by genomics and other cutting edge systemic technologies (e.g., bioinformatics databases, model organisms for which there are extensive genomics information, and array technology). [CHI Functional Genomics] Related terms discovery driven research, problem driven research; forward genetics Functional genomics glossary.

Institutional Review Board: Clinical trials, drug approvals glossary

longitudinal research: Studies done over time, with data collected from the same population.

problem driven research: Applied research, contrast with basic research and discovery- driven, hypothesis- driven.  Are there other nuances?  Technologies & instrumentation overview

R&D research & development: Narrower terms applied research, basic research, development; pre- competitive R&D Business of the life sciences glossary

reductionism: The development of molecular genetics on the heels of Mendelian genetics has raised the inevitable philosophical question of whether the discovery of DNA represents the ultimate reduction of biological to physicochemical processes. Numerous philosophers of science have approached the issue, especially the basic question of what exactly is meant by "reductionism." A useful exploration of this issue, specifically in relation to genetics, is by Kenneth Schaffner in "Approaches to Reduction," Philosophy of Science, 1967, 34:137-147. In another paper Schaffner argues that molecular biology was not built on a conscious attempt to reduce Mendelian to molecular genetics: "The Peripherality of Reductionism in the Development of Molecular Biology," Journal of the History of Biology, 1974, 7:111-139. On a slightly different track, David Hull maintains that molecular genetics is not logically deducible from Mendelian genetics: see "Reduction in Genetics - Biology or Philosophy?" Philosophy of Science, 1972, 39:491-499. Contrary to Schaffner and Hull, William K. Goosens maintains that Mendelian genetics was reduced to the chemical level by molecular genetics: "Reduction by Molecular Genetics," Philosophy of Science, 1978, 45:73-95. Although this topic moves from history into philosophy, students find it challenging. Because of the centrality of molecular genetics to modern biology, it is particularly relevant to raise these philosophical questions in the context of the history of genetics. [Garland E. Alen "Life Sciences in the Twentieth Century" History of Science Society Newsletter, 17 (5) Supplement 1988] http://depts.washington.edu/hssexec/newsletter/1997/allen.html    

"Often used as a term of abuse for those theories which simplify too much" [OED]

research diagnostics: Hard to predict the speed at which these will move into the clinic. The growing momentum of genomics and molecular analysis has enormous promise for earlier and non (or less) invasive diagnostics, novel therapeutics and more precise prognoses in cancer, cardiovascular and infectious diseases. Improved patient stratification holds the allure of faster, smaller clinical trials and fewer adverse effects for patients. Advances in gene sequencing and analysis have made these processes higher throughput, more scaleable and reproducible. Microarrays are revolutionizing basic research. Proteomics and protein chips further broaden the range of possibilities. Molecular Analysis for Research and Diagnostics:  Single Cells, Biomarkers, Clinical Applications February 13-14  2002 • San Diego, CA   Related terms analysis - molecular Assays, signaling & detection glossary; diagnosis Clinical genomics glossary      

research informatics:  The explosion of genomic information, from sequences and gene expression to SNPs and protein structures, is of limited value for pharmaceutical researchers without powerful software capable of interpretation and comparisons. Case studies and experiences that companies have with both the problems and solutions in the areas of data mining, multiple location data sharing, and computational enhancements of biological and chemistry projects, as well as integration of these efforts, served as the focus of this meeting. Different approaches for overcoming the problems of legacy information systems, the very different language and perspectives of chemists and biologists, and the organizational issues of compartmentalization were among the key topics discussed.  Research Informatics  Nov. 29-30, 2000

research technologies: Technologies & instrumentation Overview

reverse genetics: Functional genomics glossary

top-down: A systems approach, which looks at the big picture and complexity. Genomics is essentially a top- down approach, the opposite of a bottom- up approach. Our ways of thinking have been so profoundly influenced by bottom- up, reductionist approaches that we are having to learn to think in very different ways to begin to fully exploit genomic data. Narrower term Miniaturization glossary nanofabrication- top- down

Bibliography

[IRB] Institutional Review Board Glossary, Office for Human Research Protection, US Dept. Health & Human Services, 2001. 150+ definitions.  http://ohrp.osophs.dhhs.gov/irb/irb_glossary.htm

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