Encode Project Leads to Revolutionary Ideas in Genetics as Well as Contorversy

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The unique insight brought by the ENCODE project has lead to several revolutionary ideas for the inter workings of genetics on the molecular scale; however, there has been much controversy over the projects findings throughout the scientific community. The ENCODE project states “The vast majority (80.4%) of the human genome participates in at least one biochemical RNA-and/or chromatin-associated event in at least one cell type” (The ENCODE Project Consortium). This statement claims the functionality of the human genome as a whole and is the core theme that will be analyzed.
The human genome was mapped for RNA transcribed regions (functional RNA’s other than protein coding), protein coding regions, transcription factor binding sites, chromatin structure and DNA methylation sites (including histone modifications). (The ENCODE Project Consortium)
Controversy has arisen through multiple facets of the scientific community how this 80.4% has no empirical proof. The grounds for these arguments begin with the definition of function vs. functionality. ENCODE does not take this consideration into the relevancy of function and use the second meaning of function, called casual role. The problem with ENCODE using this definition means that this type of function, from an evolutionary stance, has no protection against mutation or deleterious causes that would leave it non-functional. Because ENCODE decided it was too difficult to find all of these evolutionary conserved protections they used the incorrect definition of function, difficulty in identifying selection does not justify ignoring it. (Dan Graur)
The incorrect use for the meaning of functionality by the ENCODE project has brought more controversy. Functionality according to the ENCOD...

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...a Boychenko,1 Toby Hunt,1 Mike Kay,1 Gaurab Mukherjee,1 Jeena Rajan,1 Gloria Despacio-Reyes,1 Gary Saunders,1 Charles Steward,1 Rachel Harte,2 Michael Lin,3 Ce´dric Howald,4 Andrea Tanzer,5 Thomas Derrien,4 Jacqueline Chrast,4 Nathalie Walters,4 Suganthi Balasubramanian,6 Baikang Pei,6 Michael Tress,7 Jose Manuel Rodriguez,7 Iakes Ezkurdia,7 Jeltje van Baren,8 Michael Brent,8 David Haussler,2 Manolis Kellis,3 Alfonso Valencia,7 Alexandre Reymond,4 Mark Gerstein,6 Roderic Guigo´ ,5 and Tim J. Hubbard1,9 1Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom and 2University of California. "GENCODE: The reference human genome annotation for The ENCODE Project." Genome Research (2012): 1760-1774.

The ENCODE Project Consortium. "An integrated encyclopedia of DNA elements in the human genome." Nature 489.11247 (2012): 57-74.
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