Another Science Hurricane: A Massive Survey of the Genome

By Carl Zimmer | September 5, 2012 6:45 pm

Every now and then we science writers come face to face with how much science there is to write about–and how limited our powers to write about it are. This week, I’m on the road to report a magazine feature–a week that just so happens to be the one that a team of scientists chose to publish dozens of papers at once on the nature of the human genome. The purpose of the project, called ENCODE, is to systematically measure the function of every bit of the human genome. ENCODE has been going on for quite some time. In 2008, I wrote about the first chunk of results from ENCODE in the New York Times, and I followed up in 2010 here with a report on the work of some skeptics who challenged some of ENCODE’s results. If I wasn’t already insanely busy with another story, I’d be all over this one.

If you’re interested in the debate over how our DNA works, let me direct you to some coverage:

Brendon Maher at Nature News

Ed Yong blogs the story, then updates with responses from skeptics

University of Toronto biochemist Larry Moran explains why he doesn’t buy the results.

 

CATEGORIZED UNDER: Writing Elsewhere

Comments (5)

  1. John Kwok

    I respectfully disagree, gaddeswarup. The best scientific journalism account I have seen is from John Farrell at Forbes:

    http://www.forbes.com/sites/johnfarrell/2012/09/07/reports-of-junk-dnas-demise-have-been-greatly-exaggerated/

    And the most extensive scientific critique is from T. Ryan Gregory:

    http://www.genomicron.evolverzone.com/2012/09/a-slightly-different-response-to-todays-encode-hype/

  2. John Kwok

    There’s a better scientific journalism account from Faye Flam, which discusses the history of science behind the ENCODE paper and emphasizes that some of the authors recognize that this paper doesn’t refute the existence of junk DNA:

    http://www.philly.com/philly/columnists/faye_flam/20120910_Planet_of_the_Apes__What_is_that_big_hunk_of__junk__DNA_up_to__.html

  3. 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.

    The ENCODE project has produced high quality and valuable data. There is no question about that. Also, the micro-interpretation of data was fair. The problem was 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: http://sandwalk.blogspot.com/2012/06/tributre-to-stephen-jay-gould.html; also, see a recent comment in Science, that I posted at Sandwalk: http://sandwalk.blogspot.com/2012/09/science-writes-eulogy-for-junk-dna.html ).

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

    #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 ( http://www.genomicron.evolverzone.com/2007/04/onion-test/), 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?

  4. 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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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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