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Friday, January 04, 2013

Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012

The folks over at Evolution News & Views (sic) have selected the ENCODE papers as the Number 1 evolution-related story of 2012. Naturally, they fell for the hype of the ENCODE/Nature publicity campaign as you can see from the blog title: Our Top 10 Evolution-Related Stories: #1, ENCODE Project Buries "Junk DNA".

Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...
Editor's note: For the No. 1 slot among evolution-related news stories of 2012, this one was an easy pick. The publication of the ENCODE project results detonated what had been considered among the sturdiest defenses that Darwinian evolutionary theory could still fall back upon: "Junk DNA." Casey Luskin's initial reporting is featured below. See also our response to the ensuing controversy over ENCODE ("Why the Case for Junk DNA 2.0 Still Fails").
Normally I would make fun of the creationists for misunderstanding the real scientific results in the papers that were published last September but, in this case, there are lots of real scientists who fell into the same trap.

Even Science magazine selected the ENCODE results as a top-ten breakthrough and noted that 80% of the human genome now has a function [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. Oh well, I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists!

I can still mock the creationists for claiming that "Darwinian evolutionary theory" supports junk DNA.


  1. 1) I think you mean 2012
    2) Because of a communications foul-up the official report of the first US space probe to Venus said that the atmosphere had a lot of petroleum as "predicted" by uber-kook Velikovsky. The claim that he was right about oil on Venus became a permanent claim by his supporters. I guess ENCODE 80% figure will become an equally immortal and uncorrectable part of creationism

  2. Amazing that one of "Darwinian theory's sturdiest defenses" did not even appear in the literature until the late 1970's. DNA was not even known to be the genetic material until 1952. And most of the continuum from none to 100% junk (not quite as far as the latter, for obvious reasons), appears to be represented by some organism, somewhere. Yet evolutionary theory rests upon it?

  3. "It's likely that 80 percent will go to 100 percent," says Birney.

    Indeed. If the current rate of terminological develuation continues, "being there" will soon qualify as a kind of function.

  4. Ironic almost everybody else is wrong, except Larry and his disciples here.....

    1. Your deep and penetrating analysis successfully build the foundation for a brilliant exposition on the matter of scientific journalism and rigour with respect to the claims of ENCODE and junk DNA.

    2. Anonymous (show yer face, stranger!) wrote:
      Ironic almost everybody else is wrong, except Larry and his disciples here.....

      What (even if true) would be the irony in that situation? Who are all these 'wrong' people, and what do they say?

      But as to my contribution ... did junk DNA actually appear in the literature before the late 1970's? Was DNA in fact proven to be the genetic material prior to 1952? How much nonfunctional DNA, approximately, is there in the most 'junky' organism known to man - none? What would be the impact on evolutionary theory if that were true?

    3. Allan: To answer the questions in your last paragraph:

      1. Yes. 1972.
      2. Yes. Depending on what you mean by "proven". But I'd say 1943.
      3. I don't think this has been rigorously studied. But if we assume that an amoeba has no more functional DNA than a human, and even assuming that the human genome is 100% functional at 3.5pg for a haploid genome, then the 1400pg genome of Chaos chaos, must be around 99.7% junk. It may be that the haploid genome of Chaos has been overestimated by a factor of several; let's say 10 just to be safe. In which case, it would be only 97% junk.
      4. It would revive the C-value paradox as a major question for investigation.

    4. John - 1 & 2 - dang! I was going from (obviously shaky) memory. The error was the pointless inclusion of the word 'late' before '1970's'. On the second, I was taking the Hershey-Chase experiments as confirmation of its role (more accurately, they eliminated protein, but felt that further experimentation would be needed to confirm DNA). I don't think that's wrong, but I won't fight you over it.

      Be that as it may, I would still like Anonymous, or anyone else in that camp, to explain why the discovery of widespread function for junk would be a problem for 'Darwinism', however defined.

    5. Well, I wasn't there. But I imagine that Watson and Crick (and Pauling, for that matter) wouldn't have invested so much time into figuring out the structure of DNA unless they had thought it was important, so it must have been widely accepted before then that DNA was indeed the genetic material, even if the very last doubts hadn't been eliminated.

      As for the problem for "Darwinism", oddly enough nobody has responded to that question.

    6. John Harshman says,

      But I imagine that Watson and Crick (and Pauling, for that matter) wouldn't have invested so much time into figuring out the structure of DNA unless they had thought it was important, so it must have been widely accepted before then that DNA was indeed the genetic material ...

      Watson was closely connected to the 'phage group and Pauling was well aware of their thinking (through Delbruck). The 'phage group was convinced that DNA was the genetic material, partly because of Avery et al. and partly because of the ongoing experiments by Hershey and Chase.

      I think the wider community of biologists was still thinking that proteins were the essential components of chromatin and DNA was just a scaffold. As we know, even Rosalind Franklin was not convinced that her work could potentially solve the secret of life.

  5. Who exactly is "almost everybody else", and what is it that they're 'right' about? Just wondering.

  6. It's amazing how many resources our germ cells put into silencing all of these "regions of biochemical function". Why, if it wasn't for ENCODE, I'd be tempted to think that our silly germ cells are ungratful about all of this regulatory potential, and are treating them like some kind of invading parasite...


    Mouse primordial germ cells (PGCs) erase global DNA methylation (5mC) as part of the comprehensive epigenetic reprogramming that occurs during PGC development. 5mC plays an important role in maintaining stable gene silencing and repression of transposable elements (TE) but it is not clear how the extensive loss of DNA methylation impacts on gene expression and TE repression in developing PGCs. Using a novel epigenetic disruption and recovery screen and genetic analyses, we identified a core set of germline-specific genes that are dependent exclusively on promoter DNA methylation for initiation and maintenance of developmental silencing. These gene promoters appear to possess a specialised chromatin environment that does not acquire any of the repressive H3K27me3, H3K9me2, H3K9me3 or H4K20me3 histone modifications when silenced by DNA methylation. Intriguingly, this methylation-dependent subset is highly enriched in genes with roles in suppressing TE activity in germ cells. We show that the mechanism for developmental regulation of the germline genome-defence genes involves DNMT3B-dependent de novo DNA methylation. These genes are then activated by lineage-specific promoter demethylation during distinct global epigenetic reprogramming events in migratory (~E8.5) and post-migratory (E10.5-11.5) PGCs. We propose that genes involved in genome defence are developmentally regulated primarily by promoter DNA methylation as a sensory mechanism that is coupled to the potential for TE activation during global 5mC erasure, thereby acting as a failsafe to ensure TE suppression and maintain genomic integrity in the germline.

  7. Is it possible, however, that there are faults in the evolution theory? Is it possible that it is not true, but false? The supporters of this theory certainly deny this possibility, but it should be noted that weaknesses and inconsistencies in the theory can be found even in their own writings. These have been discussed, but the possibility of the doctrine's whole foundation being wrong and untenable has never been brought out. It has generally been denied. This is why we will now study this subject, which everyone should learn about.

    This article proves problems of the evolution theory;