On the immortality of television sets : "function" in the human genome according to the evolution-free gospel of ENCODE
Graur, Dan ; Zheng, Yichen ; Price, Nicholas ; Azevedo, Ricardo B R ; Zufall, Rebecca A and Elhaik, Eran LU
(2013)
In Genome Biology and Evolution
5(3).
p.90-578
- Abstract
A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be... (More)
A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.
(Less)
- author
- Graur, Dan
; Zheng, Yichen
; Price, Nicholas
; Azevedo, Ricardo B R
; Zufall, Rebecca A
and Elhaik, Eran
LU
- publishing date
- 2013
- type
- Contribution to journal
- publication status
- published
- keywords
- Animals, DNA Methylation, Databases, Nucleic Acid, Evolution, Molecular, Genome, Human, Human Genome Project, Humans, Primates/genetics, Selection, Genetic, Transcription Factors/genetics
- in
- Genome Biology and Evolution
- volume
- 5
- issue
- 3
- pages
- 90 - 578
- publisher
- Oxford University Press
- external identifiers
-
- pmid:23431001
- scopus:84875275808
- ISSN
- 1759-6653
- DOI
- 10.1093/gbe/evt028
- language
- English
- LU publication?
- no
- id
- 8f37a1f9-a2a8-41b5-a5c2-f4b648dbf95f
- date added to LUP
- 2019-11-10 16:59:43
- date last changed
- 2024-06-26 06:02:17
@article{8f37a1f9-a2a8-41b5-a5c2-f4b648dbf95f,
abstract = {{<p>A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.</p>}},
author = {{Graur, Dan and Zheng, Yichen and Price, Nicholas and Azevedo, Ricardo B R and Zufall, Rebecca A and Elhaik, Eran}},
issn = {{1759-6653}},
keywords = {{Animals; DNA Methylation; Databases, Nucleic Acid; Evolution, Molecular; Genome, Human; Human Genome Project; Humans; Primates/genetics; Selection, Genetic; Transcription Factors/genetics}},
language = {{eng}},
number = {{3}},
pages = {{90--578}},
publisher = {{Oxford University Press}},
series = {{Genome Biology and Evolution}},
title = {{On the immortality of television sets : "function" in the human genome according to the evolution-free gospel of ENCODE}},
url = {{http://dx.doi.org/10.1093/gbe/evt028}},
doi = {{10.1093/gbe/evt028}},
volume = {{5}},
year = {{2013}},
}