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cartoon genomic function

See also my blog:
Genomics & Philosophy
Philosophy of Genomics
This project critically examines the ways that functions are assigned to genetic elements. I am particularly interested in non-coding or "Junk" DNA and the claim that it has some function that benefits the organism. A related interest concerns transposable elements and the suggestion that their abundance and distribution are best understood by viewing the genome as a mini-ecosystem. 

Publications

Linquist, S. Cottenie, K. Elliott, T.A. Saylor, B. Kremer, S.C. and Gregory, T.R. (2015) Applying ecological models to communities 
of genetic elements: the case of neutral theory. Molecular Ecology, 24(13): 3232-3242.

Elliott, T.A., S. Linquist and T.R. Gregory (2014).   Conceptual and empirical challenges of ascribing functions to transposable elements.  The American Naturalist, 184 (1), 14-24.

Doolittle, W. F., T. Brunet, S. Linquist, & T.R. Gregory (2014). Distinguishing between function and effect in genome biology.   Genome Biology and Evolution, 6, 1234-1237.

Linquist, S., B. Saylor, K. Cottenie, T.A.. Elliott, S.C. Kremer & T.R. Gregory (2013). Distinguishing ecological from evolutionary approaches to transposable elements. Biological Reviews, 88(3): 573-584.

Saylor, B. T.A. Elliott, S. Linquist. S.C. Kremer, T.R.. Gregory & K Cottenie (2013). A novel application of ecological analyses to transposable element distributions in the Bos taurus genome. Genome, 56: 521-533.

Recent Presentations
"Four decades debating junk DNA and the Phenotype Paradigm is (somehow) alive and well."  Evolutionary Roles of Transposable Elements: the Science and the Philosophy. Dalhousie University. October 20, 2018.

"Does junk DNA provide habitat for transposable elements? A simulation model for genome-level ecology." At the Philosophy of Biology week in Halifax. July, 2018.

"The genome as ecosystem: Clarifying a novel approach to jumping genes." Philosophy of Biology at the Mountains (POBAM), Salt Lake, Utah. May 18, 2018.


Current Work
Transposons accumulate through genome-level ecosystem engineering.
We are currently developing a simulation model to determine whether TEs can accumulate in large numbers while remaining deleterious to their host. Our findings suggest that this is possible, provided they engage in genome-level ecosystem engineering.

Evolution of the concept of Junk DNA.  
I am working with Ryan Gregory on a paper about the evolution of the concept of junk DNA. We argue that changes in meaning reflect its use as a framing device and for purposes of research promotion. Such  adaptations are contrary to its use as an explanatory concept, but arguably no less important.

Genomics, philosophy and the F-word.
Working with participants in the 2018  Workshop on the Science and Philosophy of Mobile DNA, this paper reviews some of the theoretical and empirical issues surrounding the ascription of functions to transposable elements.