On 2017 Jun 21, Misha Koksharov commented:

For those curious - an excellent response from Dan Graur: http://judgestarling.tumblr.com/post/67599627086/a-pre-refuted-hypothesis-on-the-subject-of-junk

On 2013 Nov 25, Claudiu Bandea commented:

Junk DNA and the skewed perspective of Graur et al. on biological function and genome size evolution

In their article “On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE” (1), Graur et al. dismantle ENCODE’s evidence and suggestion that 80% of the human genome is functional (2), which would render the traditional concept of junk DNA (jDNA) obsolete (3).

I agree with many assertions made by Graur et al. about the poor rationale behind some of ENCODE’s experimental approaches and the overall interpretation of the results; indeed, it has been known for decades that, by its bare presence in the genome, so called junk DNA (jDNA) gets replicated and undergoes repair, recombination, non-specific transcription, transposition, etc., and that all these biochemical activities involve various DNA-binding proteins.

However, the article by Graur et al. contains assumptions and statements that are questionable. For example, the authors limit their evaluation of genomic DNA’s biological functions to informational roles, which are based on sequence specificity. Although Graur et al. recognize, apparently as an afterthought, that: “It has been pointed to us that…some parts of the genome may be functional but not under constraint with respect to nucleotide composition”, the paper sidesteps the significance of non-informational roles for genomic DNA.

In a recent paper (4), I discussed this and some the other weaknesses of Graur et al. and expanded on an old hypothesis (5) that might explain the evolution of genome size and jDNA, and solve the long-standing C-value enigma.

References

(1) Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E. 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol., 5(3):578-90. Graur D, 2013

(2) ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. 2012. Nature, 489:57–74. ENCODE Project Consortium., 2012

(3) Pennisi E. 2012. ENCODE project writes eulogy for junk DNA. Science, 337:1159–1161. Pennisi E, 2012

(4) Bandea CI. 2013. On the concept of biological function, junk DNA and the gospels of ENCODE and Graur et al. bioRxiv doi: 10.1101/000588 (http://biorxiv.org/content/early/2013/11/18/000588)

(5) Bandea CI. 1990. A protective function for noncoding, or secondary DNA. Med Hypotheses, 31(1):33-4. Bandea CI, 1990

On 2013 Nov 25, Claudiu Bandea commented:

None

On 2013 Nov 25, Claudiu Bandea commented:

None

On 2013 Nov 25, Claudiu Bandea commented:

Junk DNA and the skewed perspective of Graur et al. on biological function and genome size evolution

In their article “On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE” (1), Graur et al. dismantle ENCODE’s evidence and suggestion that 80% of the human genome is functional (2), which would render the traditional concept of junk DNA (jDNA) obsolete (3).

I agree with many assertions made by Graur et al. about the poor rationale behind some of ENCODE’s experimental approaches and the overall interpretation of the results; indeed, it has been known for decades that, by its bare presence in the genome, so called junk DNA (jDNA) gets replicated and undergoes repair, recombination, non-specific transcription, transposition, etc., and that all these biochemical activities involve various DNA-binding proteins.

However, the article by Graur et al. contains assumptions and statements that are questionable. For example, the authors limit their evaluation of genomic DNA’s biological functions to informational roles, which are based on sequence specificity. Although Graur et al. recognize, apparently as an afterthought, that: “It has been pointed to us that…some parts of the genome may be functional but not under constraint with respect to nucleotide composition”, the paper sidesteps the significance of non-informational roles for genomic DNA.

In a recent paper (4), I discussed this and some the other weaknesses of Graur et al. and expanded on an old hypothesis (5) that might explain the evolution of genome size and jDNA, and solve the long-standing C-value enigma.

References

(1) Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E. 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol., 5(3):578-90. Graur D, 2013

(2) ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. 2012. Nature, 489:57–74. ENCODE Project Consortium., 2012

(3) Pennisi E. 2012. ENCODE project writes eulogy for junk DNA. Science, 337:1159–1161. Pennisi E, 2012

(4) Bandea CI. 2013. On the concept of biological function, junk DNA and the gospels of ENCODE and Graur et al. bioRxiv doi: 10.1101/000588 (http://biorxiv.org/content/early/2013/11/18/000588)

(5) Bandea CI. 1990. A protective function for noncoding, or secondary DNA. Med Hypotheses, 31(1):33-4. Bandea CI, 1990