Good reads about ENCODE.

For an antidote to the massive hype surrounding ENCODE, have a look at these excellent pieces:

The ever deepening mystery of the human genome by Linda Geddes (New Scientist)
and be sure to see this editorial: Don’t junk the ‘junk DNA’ just yet

Most of what you read was wrong: how press releases rewrote scientific history by John Timmer (Ars Technica)

Reports of Junk DNA’s Demise Have Been Greatly Exaggerated by John Farrell (Forbes)

ENCODE says what? by Sean Eddy

A genome-sized media failure by Michael White (Huffington Post)

Three reasons why junk DNA makes evolutionary sense by Ashutosh Jogalekar (Scientific American)

Junk DNA, junky PR by Athena Andreadis (Scientific American)

Scientists on what the ENCODE junk DNA study really said by Bradley J. Fikes (North County Times)

The ENCODE delusion by PZ Myers (Freethought Blogs)

Trashing junk DNA: the notorious 80% by David Kaye (Double Helix Law)
Trashing junk DNA: Alice in Genomeland by David Kaye (Double Helix Law)

ENCODE and “Junk DNA,” Part 1: All Good Concepts are Fuzzy by Dennis Venema (BioLogos Forum)
ENCODE and “Junk DNA,” Part 2: Function: What’s in a Word? by Dennis Venema (BioLogos Forum)

Junk DNA, the ENCODE Project, and Intelligent Design: Facts, Hype, and Spin by Scott Buchanan (Letters to Creationists)

Skeptical Takes on Elevation of Junk DNA and Other Claims from ENCODE Project by Faye Flam (Knight Science Journalism)

Publication of the ENCODE Encyclopedia: A Milestone in Genome Research by Bora Zivkovic (Scientific American)

The Encode Delusion League of Reason

And don’t forget that there’s a fair bit on this blog as well!


10 comments to Good reads about ENCODE.

  • Enezio E. de Almeida Filho

    Good grief! Are we still in the dark as to what function really means in Biology? There is no function???

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  • derwood

    I note that Shapiro is on the “I knew it all along – junkDNA is dead” bandwagon over on HuffPo.  

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  • Claudiu Bandea

    Five reasons why my theory on the function of ‘junk DNA’ is better than theirs

    I intend to submit the paper below for publication in a peer-reviewed journal. Before submitting it and have it reviewed by a handful (if that) of peers, I decided to post it here on the Blogosphere Preprint Server, which is rapidly becoming the front-line platform for transparent and comprehensive evaluation of scientific contributions.

    The ENCODE project has produced high quality and valuable data. There is no question about that. And, the micro-interpretation of the data has been of equal status. The problem is with the macro-interpretation of the results, which some consider to be the most important part of the scientific process.  Apparently, the leaders of the ENCODE project agreed with this criterion, as they came out with one of the most startling biological paradigm since, well, since the Human Genome Project has shown that the DNA sequences coding for proteins and functional RNA, including those having well defined regulatory functions (e.g. promoters, enhancers), comprise less than 2% of the human genome.

    According to ENCODE’s ‘big science’ conclusion, at least 80% of the human genome is functional. This includes much of the DNA that has been previously classified as ‘junk DNA’ (jDNA). As metaphorically presented, in both scientific and lay media, ENCODE’s results means the death of the jDNA. 

    However the eulogy of jDNA (all of it) was written more than two decades ago, when I proposed (and conceptually proven) that ‘jDNA’ functions as a sink for the integration of proviruses, transposons and other inserting elements, thereby protecting functional DNA (fDNA) from inactivation or alteration of its expression (see a copy of my paper posted here: <a href=http://sandwalk.blogspot.com/2012/06/tributre-to-stephen-jay-gould.html >http://sandwalk.blogspot.com/2012/06/tributre-to-stephen-jay-gould.html</a&gt;; also, see a recent comment in Science, that I posted at Sandwalk: <a href=http://sandwalk.blogspot.com/2012/09/science-writes-eulogy-for-junk-dna.html>http://sandwalk.blogspot.com/2012/09/science-writes-eulogy-for-junk-dna.html</a&gt; ).

    So, how does ENCODE theory stack ‘mano-a-mano’ with my theory?  Here are five reasons why mine is superior:

    #5.  In order to label 80% of the human genome functional, ENCODE changed the definition of ‘functional’; apparently, 80% of the human genome is ‘biochemically’ functional, which from a biological perspective might be meaningless. My model on the function of jDNA is founded on the fact that DNA can serve not only as an information molecule, a function that is based on its sequence, but also as a ‘structural’ molecule, a function that is not (necessarily) based on its sequence, but on its bare or bulk presence in the genome.

    #4. Surprisingly, ENCODE theory is not explicitly immersed in one of the fundamental tenets of modern biology: Nothing in biology makes sense except in the light of evolution. Indeed, there is no talk about how jDNA (which contain approximately 50% transposon and viral sequences) originated and survived evolutionarily. On the contrary, my model is totally embedded and built on evolutionary principles.

    #3. One of the major objectives of the ENCODE project was to help connect the human genome with health and diseases. Labeling 80% of these sequences ‘biochemically functional’ might create the aura that these sequences contain genetic elements that have not yet been mapped out by the myriad of genome wide studies; well, that remains to be seen.  In the context of my model, the protective function of jDNA, particularly in somatic cells, is vital for preventing neoplastic transformations, or cancer; therefore, a better understanding of this function might have significant biomedical applications. Interestingly, this major tenet of my model can be experimentally addressed: e.g. transgenic mice carrying DNA sequences homologous to infectious retro-viruses, such as murine leukemia viruses (MuLV), might be more resistant to cancer induced by experimental MuLV infections as compared to controls.

    #2. The ENCODE theory is a culmination of a 250 million US dollars project.  Mine, zilch; well, that’s not true, my model is based on decades of remarkable scientific work by thousands and thousands of scientists who paved the road for it.

    #1. The ENCODE theory has not passed yet the famous Onion Test (<a href=http://www.genomicron.evolverzone.com/2007/04/onion-test/> http://www.genomicron.evolverzone.com/2007/04/onion-test/</a&gt;), which asks: why do onions have a genome much larger than us, the humans? Do we live in an undercover onion world?  The Onion Test is so formidable and inconvenient that, to my knowledge, it has yet to make it through the peer review into the conventional scientific literature or textbooks.  So, does my model pass the Onion Test? I think it does, but for a while, I’m going to let you try to figure it out how!  And, maybe, when I’m going to submit my paper for publication, I’ll use your ideas, if the reviewers will ever ask me for an answer.  Isn’t that smart?

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  • Claudiu Bandea

    Ryan,
    In my comment above, I say that, to my knowledge, you have not published your Onion Test, because it is so formidable and inconvenient for the field that it can’t make it through the peer review system of reputable journals. Is that true?

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  • derwood

    And yet people die of cancer all the time.  Some protection…

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  • Claudiu Bandea

    @derwood
    Well, without the anti-cancer defense mechanism provided by the so called ‘junk DNA’ (jDNA) many more people would die of cancer. Possibly, without jDNA, neither we, nor our ancestors, would have survived evolutionarily.

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  • Claudiu Bandea

    In my parodic comment above, “Five reasons why my theory on the function of ‘junk DNA’ is better than theirs”,  I brought forward an old model (1) on the genome evolution and on the origin and function of the genomic sequences labeled ‘junk DNA’ (jDNA), which in some species represents up to 99% of the genome.

    Since then, I posted in Science five mini-essays outlining some of the key tenets associated with this model, which might solve the C-value and jDNA enigmas (http://comments.sciencemag.org/content/10.1126/science.337.6099.1159).

    As discussed in the original paper (1) and these mini-essays, the so called jDNA serves as a defense mechanism against insertional mutagenesis, which in humans and many other multicellular species can lead to cancer. 

    Expectedly, as an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the insertional mutagenesis activity and the evolutionary constrains on genome size.

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

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  • I just noticed that you sourced my blog-post from theLeagueOfReason. I guess I didn’t do that bad a job then, considering this thread is called “good reads”. :D

    Thanks so much.

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  • wonderful points altogether, you just received a new reader.
    What may you suggest in regards to your post that you just made a few days ago?
    Any positive?

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