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Geneticists shell-shocked by new discoveries? And little junk DNA? Some key comments …

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DNA double helix/Human Genome Research Institute

… from 2007, which could be useful:

Boston Globe:

A ‘scientific revolution’ is taking place, as researchers explore the genomic jungle: “The science of life is undergoing changes so jolting that even its top researchers are feeling something akin to shell-shock. Just four years after scientists finished mapping the human genome – the full sequence of 3 billion DNA “letters” folded within every cell – they find themselves confronted by a biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.” (Paywall)

National Institutes of Health:

BETHESDA, Md., Wed., June 13, 2007 -“An international research consortium (ENCODE) today published a set of papers that promise to reshape our understanding of how the human genome functions. The findings challenge the traditional view of our genetic blueprint as a tidy collection of independent genes, pointing instead to a complex network in which genes, along with regulatory elements and other types of DNA sequences that do not code for proteins, interact in overlapping ways not yet fully understood.”

Encyclopedia Of DNA*: New Findings Challenge Established Views On Human Genome:

The ENCODE consortium’s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active. The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact.

*= ENCyclopedia Of DNA Elements (ENCODE)

From the concluding statement of the ENCODE study:

At the outset of the ENCODE Project, many believed that the broad collection of experimental data would nicely dovetail with the detailed evolutionary information derived from comparing multiple mammalian sequences to provide a neat “dictionary” of conserved genomic elements, each with a growing annotation about their biochemical function(s). In one sense, this was achieved; the majority of constrained bases in the ENCODE regions are now associated with at least some experimentally derived information about function. However, we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more “neutral” view of many of the functions conferred by the genome.

All from 2007, recall. Meanwhile, the ENCODE naysayers seem to be stuck in 2006 (as late as 2013), with statements like

“If ENCODE is right, then Evolution is wrong.”

Well, if you say so, buddy.

See also: Someone finally admits the real reason Darwin’s followers need junk DNA

Hat tip: Matthew Cochrane

6 Replies to “Geneticists shell-shocked by new discoveries? And little junk DNA? Some key comments …

  1. 1
    bornagain77 says:

    And the situation has only gotten far worse for Darwinists since 2007:

    Scientists go deeper into DNA (Video report) (Junk No More) – Sept. 2012

    Quote from preceding video:
    “It’s just been an incredible surprise for me. You say, ‘I bet it’s going to be complicated’, and then you are faced with it and you are like ‘My God, that is mind blowing.’”
    Ewan Birney – senior scientist – ENCODE

    ENCODE: Encyclopedia Of DNA Elements – video

    Quote from preceding video:
    “It’s very hard to get over the density of information (in the genome),,, The data says its like a jungle of stuff out there. There are things we thought we understood and yet it is much, much, more complex. And then (there are) places of the genome we thought were completely silent and (yet) they’re (now found to be) teeming with life, teeming with things going on. We still really don’t understand that.”
    Ewan Birney – senior scientist – ENCODE

    Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin September 5, 2012
    Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well:
    “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.””
    We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let’s simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called “junk” DNA. ENCODE researchers use words like “surprising” or “unprecedented.” They talk about of how “human DNA is a lot more active than we expected.” But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.

    ENCODE: The Encyclopedia of DNA Elements (Interviews with members of the ENCODE Project) – video

    Quotes from preceding video:
    “Very little of our genomes are junk. 80% of our genome is engaged in at least one biochemical activity. For a large fraction of our genome, not now 5%, but 80% of the genome, we can (now) say that we know that it does something.”
    “This metaphor about Junk DNA has become very entrenched. It has been entrenched publicly and entrenched scientifically. And ENCODE totally challenges that. We just don’t have big, blank, boring, bits of the genome. All the genome is alive at some level.”
    “There are about 2000 DNA binding proteins in the genome. We looked at about 100 of those, 115 of those, so there is a long way to go yet, there is a lot more to study.”

    Landscape of transcription in human cells – Sept. 6, 2012
    Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,,
    Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line.

    Here is a recent paper (July 2013) that defends the Sept. 2012 ENCODE findings, of pervasive functionality across the genome, from Darwinian attempts to discredit the findings:

    The extent of functionality in the human genome – John S Mattick and Marcel E Dinger – July 2013
    Excerpt of abstract: Finally, we suggest that resistance to these (ENCODE) findings is further motivated in some quarters by the use of the dubious concept of junk DNA as evidence against intelligent design.

  2. 2
    Johnnyfarmer says:

    A nice clean genome free of debris is not what you would expect evolution to produce. For example one of the proposals for providing new genetic material is the double duplication of a gene during replication. One gene functions normally and the other is not needed and is free to mutate until a chance event finds a non detrimental use for it. Then maybe natural selection will prefer it.

  3. 3
    humbled says:

    Dawkins, 2009: on “ junk-DNA”
    “it’s full of junk, which is just as Darwinism predicted… how embarrassing for those creationists who say it shouldn’t be!”

    Dawkins, 2012: on non-junk-DNA…
    “it’s not full of junk, which is just as Darwinism predicted… nothing for the creationists to take advantage of here, move along!”

  4. 4
    Axel says:

    Dawkins seems to have become a major embarrassment to the adult atheists.

  5. 5
    Johnnyfarmer says:

    For going from no function to multiple functions …

  6. 6
    Axel says:

    Shell-shocked? I would say, ‘chocolate-shocked’.

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