New peer-reviewed paper in Nature falsifies Darwinian junk DNA prediction

First, let’s see what Darwinian evolutionists say about junk DNA, before we look at what the experiments show.

Here’s biologist John Timmer to explain the orthodox Darwinian view of DNA from 2007:

Personally, I fall into the “it’s all junk” end of the spectrum. If almost all of these sequences are not conserved by evolution, and we haven’t found a function for any of them yet, it’s hard to see how the “none of it’s junk” view can be maintained. There’s also an absence of support for the intervening view, again because of a lack of evidence for actual utility. The genomes of closely related species have revealed very few genes added from non-coding DNA, and all of the structural RNA we’ve found has very specific sequence requirements. The all-junk view, in contrast, is consistent with current data.

Got that? According to Darwinists, DNA is almost entirely junk – this is what is consistent with the view that creatures have evolved through a process of random mutation and selection. The estimates that I’ve seen from evolutionary biologists range from 95% to 99% junk. Now let’s compare the religion with the lab experiments and separate myth from fact.

Now let’s compare that with intelligent design theorist William Dembski’s view of “junk” DNA, from 1998:

Even if we have a reliable criterion for detecting design, and even if that criterion tells us that biological systems are designed, it seems that determining a biological system to be designed is akin to shrugging our shoulders and saying God did it. The fear is that admitting design as an explanation will stifle scientific inquiry, that scientists will stop investigating difficult problems because they have a sufficient explanation already.

But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function… Design encourages scientists to look for function where evolution discourages it.

Now let’s look at the experimental evidence and see whose prediction was right.

Evolution News reports on a new peer-reviewed paper published in Nature, the top peer-reviewed science journal. (H/T ECM)


A groundbreaking paper in Nature reports the results of the Encyclopedia of DNA Elements (ENCODE) project, which has detected evidence of function for the “vast majority” of the human genome. Titled “An integrated encyclopedia of DNA elements in the human genome,” the paper finds an “unprecedented number of functional elements,” where “a surprisingly large amount of the human genome” appears functional. Based upon current knowledge, the paper concludes that at least 80% of the human genome is now known to be functional:

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.

(The ENCODE Project Consortium, “An integrated encyclopedia of DNA elements in the human genome,” Nature, Vol. 489:57-74 (September 6, 2012) (emphasis added))

If you doubt Evolution News, we can always turn the ultra-leftist Los Angeles Times, reporting on the same study. (H/T Wes from Reason to Stand)


The $123-million effort involved more than 400 scientists and more than 1,600 experiments during five years of work. If presented graphically, the data generated so far would cover a poster 30 kilometers wide and 16 meters high, Birney has estimated.

This is still just a start — akin to “grainy images beamed back to Earth by the first satellite,” said Dr. Eric Green, director of the National Human Genome Research Institute, which funded ENCODE. But already, it’s throwing up surprises.

Strikingly, the data overturn old ideas that the bulk of DNA in our cells is useless — albeit inoffensive — junk just carried along for the evolutionary ride. Back in 2003 when the human genome was published, scientists estimated that less than 2% of it carries instructions for making proteins, and many of them thought the rest didn’t do very much.

But the new analysis shows that more than 80% of the human genome is active in at least one biological process that the ENCODE team measured. Nearly every part of it could end up being active when the data are more complete.

Here’s the ultra-left-wing New York Times, confirming the statement I made earlier about the dogma of the Darwinians:

The discoveries were published on Wednesday in six papers in the journal Nature and in 24 papers in Genome Research and Genome Biology. In addition, The Journal of Biological Chemistry is publishing six review articles, and Science is publishing yet another article.

[…]The thought before the start of the project, said Thomas Gingeras, an Encode researcher from Cold Spring Harbor Laboratory, was that only 5 to 10 percent of the DNA in a human being was actually being used.

The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.”

It’s just another prediction of Darwinian orthodoxy falsified by experimental evidence published in the top scientific peer-reviewed journal. Will this cause Darwinians to revise their theory to fit the evidence? Not likely. Their motivations for clinging to naturalism, the religion that undergirds Darwinism, are entirely beyond correction by evidence.

I wonder what people like P.Z. Myers and Larry Moran do when their religion comes into conflict with scientific evidence from lab experiments? Do they bitterly cling to their mythology from the 19th century? Or do they adjust their worldview to be in line with the progress of science?

Let Richard Dawkins explain evolution and the role of evidence:

“My argument will be that Darwinism is the only known theory that is in principle capable of explaining certain aspects of life. If I am right it means that, even if there were no actual evidence in favour of the Darwinian theory (there is, of course) we should still be justified in preferring it over all rival theories.” — p. 287, Blind Watchmaker” (1986)

Or Richard Lewontin:

“Our willingness to accept [naturalistic]  scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world but, on the contrary, that we are forced by our own a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, not matter how counterintuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a divine foot in the door.” (Richard Lewontin in New York Review of Books, January 9, 1997, p. 28)

Junk DNA isn’t the only battle in the long war between atheism and scientific evidence. Naturalists fought the Big Bang tooth and nail, trying to save their eternal universe from the progress of science. Naturalists invented the now discredited oscillating model of the universe in order to “explain” the evidence for a cosmic beginning. Naturalists invented the unobservable, untestable multiverse to “explain” the cosmic fine-tuning. Aliens are posited in order to “explain” the origin of life. Precursor fossils are invented without evidence in order to “explain” the Cambrian era explosion in complexity. And so on.

Evidence doesn’t matter to people who are motivated by naturalistic faith. Like belief in a flat-Earth, the delusion of naturalism is not accountable to scientific evidence. They believe what they want to believe. It’s not up for debate. For some people like Richard Dawkins, a prior lifestyle commitment makes theism (and the moral law!) an impossibility a priori. But rational people know that believing something just so that your actions are “justified” doesn’t make what you believe true.

For the intelligent design take on junk DNA, check out this article. To see who was right about predicting whether “vestigial organs” like the appendix have function, check out this post. You can find more predictions that follow from intelligent design right here.

18 thoughts on “New peer-reviewed paper in Nature falsifies Darwinian junk DNA prediction”

  1. I fail to see how this rebuts Darwinism. It always seemed strange that there would be all this “junk” DNA that didn’t have a purpose. Why would it have evolved without a purpose? The new information is quite interesting and indicates that it has a regulatory function.

    No doubt, individual scientists can be dogmatic about particular aspects of how they see evolution working, and may be loath to abandon them. I think this applies to Dawkins and Lewontin. But the though the details change, the overall picture of evolution by natural selection looks quite solid to me, and nothing in this news threatens it.


    1. Well, for a Darwinist, predictions about 98% junk DNA falsified by experimental evidence published in Nature showing 20% or less “junk” DNA don’t falsify Darwinism. It’s your religion, that’s my whole point.

      And it not limited to evolution, it’s a general aversion to science. For example, secular humanists are committed to an eternal universe, according to the Secular Humanist Manifesto. You have to believe in an eternal universe, and you’re holding out hope that some day the big Flying Spaghetti Monster in the sky (Parmesan Be Upon Him) is going to roll back the helium/hydrogen abundance predictions, the cosmic microwave background radiation, the redshift, etc. with his noodly appendage. That’s what it means to be an atheist. You hate science. I’m not surprised that your delusions would be insulated from the progess of science.

      Now go on and threaten to burn me at the stake for being a witch, and put Nature on the index of banned books. Pope Dawkins would expect no less.

      Note: I am picking on him because he is a friend.


  2. You should become a DJ wintery, you’re excellent at spinning things!! I think you ignore the last quote of the unknown biologist: “The all-junk view, in contrast, is consistent with current data.”

    I know what I’m about to say is considered biblical heresy, but if you open a science book it will teach you about the scientific method. Prior to this current research, science did hold the belief that a great deal of the DNA sequence was junk. Does that mean that science will no longer believe this – not quite yet…do you know why that is? According to the science books, it has to be verified. Scientists, unlike the religious masses, don’t read one article (or book, say the bible) and take it’s word for granted, the science has to be verified.

    You’re making the same mistake many of the non-scientific masses do – you grab on to an initial scientific study, take it as scientific fact, and then attempt to bash those that hold a different view or those that hold/held the prior view before new scientific evidence came out!

    Here’s how this will roughly progress. Many scientists will read the study. They will evaluate if there are any flaws in the study. If there are, they will write papers on the flaws and possibly debunk the theory, though not always. If there are no flaws, they start to re-evaluate their scientific views. Many/some will attempt to validate the original authors findings and publish their findings. Once this is all done, science will update its view on DNA!!

    Out of curiosity, what does the bible say about DNA? Maybe we can just skip the whole scientific progress thingy if the bible can tell us how it works (aside from “god did it”)

    Note: I’m picking on you because you’re wrong…and a friend!


    1. The whole point of me quoting that scientist in 2007 was to show that his prediction was FALSIFIED in 2012 at the highest possible level, with experimental evidence. It’s important to show the Darwinian speculative prediction by quoting them, and then show how the evidence falsified the speculation. He never had any evidence for his assertion – it was just ideology. Now we know in full, and his speculation is revealed as religious belief. Mythology, as it were. That quote of him might as well have been from a praise-hymn to the Flying Spaghetti Monster (Parmesan Be Upon Him).

      Just to re-cap, in favor of intelligent design, we have a massive peer-reviewed study published in the top science journal Nature.

      On the other side, we have primitive pre-scientific speculations about DNA being the product of random processes (“all junk”)and the “evidence” offered for this naturalistic Darwinian view is that people like Dawkins don’t want to be judged for their curious views on promiscuity and infanticide ( He has to be able to justify his immorality by saying he’s a monkey, and therefore evolution is true? I think not.

      Do we have to twist science to justify promiscuity and infanticide, or should we just agree to go where the evidence from lab experiments leads? Do we have to twist science to save the religion of naturalism from critical inquiry, or can we just believe what the progress of science tells us? I prefer to make my worldview on lab experiments, not Flying Spaghetti Monsters (Parmesan Be Upon Him).

      Since you’re my friend, I am allowed to pick on you! :)


      1. What study in Nature supports ID?

        Prior to this study, it was widely theorized among scientists that it was junk and unused – they could find no proof that the living organisms needed it – it was a scientific theory. New research has advanced science and invalidated an old, incorrect theory. We couldn’t call it useful DNA when we couldn’t explain what it was useful for (now we can, but prior to this we couldn’t).

        As for promiscuity, we have studies for that: (or just google “promiscuous mice”). As for infanticide…that’s a whole different can of worms. Science follows the evidence, humans don’t always do. You’re trying to impugne(sp?) science when you should be attacking those who misuse science to further personal beliefs.

        Your worldview is dictated to you by the GOP and the bible and only where science supports those two. I can worship the spaghetti monster and eat a little of him like last night to get his noodly goodness that much closer to my soul!!


    2. That is how it will progress. And that’s how it’s supposed to work. But the general public (including the satisfied atheist non-scientists) won’t hear about this progression and will cling to Dawkins’ blustery proclamations from years ago and feel confident in their opinion that anyone who questions that “randomness and nothingness did it” is nothing more than an idiot bible-thumper.


      1. No we won’t. because people like me, who straddle the general public/scientific world* will publicize this article & many others like it. At my church, scientists are teaching high school kids chemistry & physics using the classical method. They’ll be very interested in this article. I know a number of home schooling parents who will be interested & will share this. Ditto theologians & others in professional fields who will be interested. In short, God has provided a few, well educated persons who will use modern communication tools to share the truth. Those who reject truth are to be pitied but they won’t stop its dissemination to, at least, a critical mass.

        *I learned how to learn & either understand the scientific world or know how to learn to understand it


  3. I like to ask people who have bought the evolution schtick about death. Our DNA is programmed for death and decay – how in the world did that sneak into ours and just about everything else’s chromosomes? And how did the first living thing that was programmed to die survive against those organisms that were not so modified? How is this a beneficial evolutionary change that would enhance the survivability of any living thing? Isn’t that what evolution is all about?


    1. Well, my guess is that an immortal species would not evolve as fast as a mortal one. Death is an important part of evolution, after all.

      And if the immortal species reproduced, they would quickly consume all local resources (because of exponential growth) and die off.

      What’s best for the individual isn’t always what is best for the species. From a darwinistic point of view, it is the DNA which is immortal. It slowly evolves over time. We (as in humans and other life forms) are short term carriers.

      We can react to short term events (the tree is falling towards me!) to protect our DNA and allow it to continue to evolve, which occurs over a longer time span.


  4. Yes, some Darwinists have made false assumptions based on their somewhat (Godless) religious view, just as others have on the other side for various scientific issues. It is true for example, that (mostly atheists) initially opposed the Big Bang theory on grounds that it appeared to support a creation-story like beginning to the universe (and it was initially discovered / promoted by a Catholic priest), but how many modern Christians now take the Old Testament literally and have turned against the Big Bang? How many historical examples can be posted of various churches opposing science?

    Clearly, parts of modern evolutionary theory are true, and I don’t think much (or all) of it is entirely inconsistent with the idea of a God or creator. It may have been the way a God wanted to bring us into existence.

    Further, this idea that a creator must give purpose to the entire DNA sequence / organ is absurd. Imperfect humans are born everyday, yet this doesn’t mean the designer is imperfect or that there must not be a designer. You can’t selectively acknowledge that a designer would allow for imperfection and also argue that a lack of junk DNA demonstrates a designer.

    From my perspective, whether our DNA is 2% or 98% junk provides no persuasive answer as to whether or not there is a creator. And as has been reported, media coverage of this study has been greatly overblown…


  5. Timmer was explaining probably the most rational view we could have taken of things back in 2007, given the evidence we had back then.

    In now way was he claiming Darwinism predicts 98% junk dna. He was simply saying that that was how it appeared to be. Based on the availaible evidence at the time.

    Try finding *one* reputable scientist who claims “this new lower figure for junk DNA refutes Darwinism! It must be false!”

    Sorry Wintery, the scientists are absolutely interested in the evidence. OTOH, a high junk dna % is very bad news for the creationists – and when the evidence we had was pointing towrad that it didn’t slow them down at all. So the creationists, unlike the scientists, can’t really make a claim to be that interested in the evidence. They just cling to bits they think suits them. Open your eyes to the bias! Ditch this silly idea that Darwinism is a religion and take a critical look at how selectively the ID crowd actually view things.


  6. Here is more evidence of ENCODES contribution to the progression of science concerning this so called junk. Question. What has PZ Myers done to contribute to these new findings? Answer. Absolutely nothing.

    In fact in telling young people, that those who look for function, are only interested in job security he is doing more harm than good. Another words, lets just give up on research since we already know its junk. This is the same PZ Myers who told me to perform a certain sexual act on myself for simply asking a question. So please forgive the passionate tone in my post. I’m only human.

    The dynamic epigenomeNature Structural & Molecular Biology 20, 258 (2013) doi:10.1038/nsmb.2534Published online 05 March 2013

    Article tools

    The dynamic nature of functional information present in the genome—such as DNA methylation, histone modifications and chromatin organization—is beginning to be uncovered, along with the relationship between epigenomic patterning and developmental decisions or disease.Chromatin is a dynamic structure that must respond to myriad stimuli to regulate access to DNA.

    The epigenetic processes that modulate access to DNA in response to upstream signals include DNA methylation, covalent modification of histones, nucleosome remodeling, nuclear dynamics and chromatin interaction with regulatory noncoding RNAs. In recent years epigenetic processes have been extensively studied at a mechanistic level, but their dynamic nature in genomes is only beginning to be uncovered—thanks in part to herculean efforts by the Encyclopedia of DNA Elements (ENCODE) Consortium and others to generate hundreds of genome-wide datasets to map the human ‘epigenome’ and that of other organisms.

    Genome-wide studies are also being extended to analyze the relationship between epigenomic patterning and developmental decisions or disease, and the crosstalk between different epigenetic processes. In this issue, we present a special Focus on Epigenetic Dynamics………


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