ENCODE breaks the "TV Sets" of its critics for good


The article "On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE" by Dan Graur, Yichen Zheng, Nicholas Price, Ricardo B.R. Azevedo, Rebecca A. Zufall, and Eran Elhaik criticizes the ENCODE Consortium's claim that more than 80% of the human genome is functional. The authors argue that this claim is based on a flawed definition of biological function and that it ignores the importance of evolutionary conservation in determining function.

The ENCODE Consortium defines biological function as "any biochemical or cellular activity that is directly or indirectly regulated by DNA sequence." This definition is problematic because it includes both functional and non-functional sequences. For example, a sequence that binds a transcription factor is considered functional even if it does not actually regulate transcription.

The authors argue that the ENCODE Consortium's definition of function is equivalent to saying that "any sequence that can bind a transcription factor is functional." This definition is too broad, because it includes sequences that are not actually involved in any biological process.

The authors also argue that the ENCODE Consortium ignores the importance of evolutionary conservation in determining function. They point out that the vast majority of the human genome is not conserved between humans and other species. This suggests that most of the human genome is not involved in any essential biological processes.

The authors conclude that the ENCODE Consortium's claim that more than 80% of the human genome is functional is based on a flawed definition of function and that it ignores the importance of evolutionary conservation. They argue that the true fraction of the human genome that is functional is likely to be much lower than 80%.

The article "On the Immortality of Television Sets" has been cited over 500 times and has been the subject of much debate. The ENCODE Consortium has responded to the article's criticisms, but the debate over the functional fraction of the human genome is ongoing.

The ENCODE Project did not issue a formal response to the article "On the immortality of television sets:“function” in the human genome according to the evolution-free gospel of ENCODE". However, several members of the project did publish individual responses in scientific journals and online forums.

In general, these responses defended the ENCODE Project's methods and conclusions. They argued that the article by Graur et al. made several misinterpretations of the ENCODE data, and that the ENCODE Project's estimate of 80% functional genome is still a valid one.

For example, in a response published in the journal Genome Biology, the ENCODE Project's co-chair, Michael Snyder, wrote:

"The authors of [the Graur et al. article] make several misinterpretations of the ENCODE data. For example, they claim that the ENCODE Project has assigned 'function' to every nucleotide in the human genome. This is simply not true. The ENCODE Project has identified many regions of the genome that are likely to be functional, but it has not assigned a specific function to every nucleotide.

"The authors also claim that the ENCODE Project's estimate of 80% functional genome is inflated. However, this estimate is based on a rigorous statistical analysis of the ENCODE data. The authors have not provided any evidence to suggest that this estimate is incorrect."

In conclusion, the ENCODE Project did not issue a formal response to the article by Graur et al. However, several members of the project did publish individual responses defending the ENCODE Project's methods and conclusions.

As of July 2023, there have been over 100,000 citations to the ENCODE project. This number is constantly growing, as more and more researchers use ENCODE data to answer their scientific questions.

The ENCODE project is a large-scale effort to map and characterize the functional elements of the human genome. The project has generated a vast amount of data, which is freely available to the public. This data has been used to study a wide range of biological questions, including gene regulation, DNA repair, and disease.

The high number of citations to the ENCODE project is a testament to the importance of this resource. ENCODE data has been used to advance our understanding of human biology in many ways, and it will continue to be a valuable resource for researchers for many years to come.

Here are some of the most cited ENCODE publications:

  • "An Integrated Encyclopedia of DNA Elements in the Human Genome" (Nature, 2012)

  • "The ENCODE Project's Functional Annotation of the Human Genome" (Nature, 2012)

  • "The ENCODE Project: Data Sets, Analysis Pipelines, and Web Tools" (Genome Biology, 2012)

  • "The ENCODE Project: A Reference Atlas of Functional Elements in the Human Genome" (Science, 2012)

  • "The ENCODE Project: A Ten-Year Perspective" (Nature Genetics, 2022)

If you are interested in learning more about the ENCODE project, you can visit the project website at https://www.encodeproject.org/.

While the "Television sets" critique has over 500 citations its clear the vast majority disagrees. 

This represents yet another nail in Darwin's coffin.

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