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Darwinists Spin ENCODE Findings More Than Even I Thought Possible

I was certain the Darwinists would spin the ENCODE findings, but even I am stunned at their sheer audacity. In response to my previous post, Critical Rationalist says that the ENCODE findings, which falsify a prediction Darwinists have been making for decades, far from being a crushing defeat for the theory and its proponents is a positively good thing for Darwinists.

CR writes: “all theories contain errors of varying degree and that finding them is how knowledge grows . . . Surviving criticism and *not* surviving criticized is a win win situation, which doesn’t represent a blow to human intellect.”

Then CR makes the outlandish suggestion that ENCODE is somehow a loss for ID. He writes: “[When ID] Merely assum[es] the entire genome ‘should be functional’ [it] does not stick its neck out in a way that allows itself to be criticized.”

CR is wrong on both counts. Yes, Darwinism will survive ENCODE as he suggests, but not because it is the best explanation for the data. It will survive because materialists have hegemonic control of the academy and for them Darwin is quite simply the only game in town. That’s what Dawkins means when he says he would choose Darwinism even if there were no evidence for it.

No, CR, ID proponents did not merely say that the code “should be functional.” They made a testable prediction in the teeth of the overwhelming opposition from Darwinists. They said, “Darwinists are wrong when they say the vast majority of DNA is junk. We predict that function will be found.” And that prediction was confirmed.

Sorry CR. No matter how you try to spin ENCODE, it is a crushing defeat for Darwinism.

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65 Responses to Darwinists Spin ENCODE Findings More Than Even I Thought Possible

  1. The whole issue is damaging to evolutionist activists.
    They always demand creationists must accept conclusions from ‘scientists” and here it seems they are not doing that.
    Are these people not doing doing science?
    How could they be wrong?
    Somebody is wrong about something!

    If they reject these findings then they are rejecting science?
    Yes or no!?

    If these researchers had found Junk DNA as evolutionists desired they would be demanding ID etc creationists submitt to the findings!
    What changed?
    If the findings can be questioned then all findings can be questioned including evolution stuff!
    Degrees and papers isn’t settling things after all.

    As a YEC i have no interest and disagree that DNA is in any way a trail of biology.
    Its just a grand presumption that has griped to many.
    Another error.
    Whether junk or not it still is all about assumptions about DNA and biology that has never been proven.

    It is however a embarrassment to not just some idea on DNA and evolution but to the whole universe of confidence in investigative abilities of researchers in these very slippery things.

    who predicted this?

  2. Nick, you are embarrassing yourself

  3. Darwinism, and materialism in general, the atheistic philosophy which undergirds Darwinism, is certainly not ‘hard’ science in the normal sense of engineering and physics in that there is a rigid falsification criteria that can be applied to it to see if it is true or not (at least not a rigid criteria that Darwinists will accept),,,

    Science and Pseudoscience – Imre Lakatos
    “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture

    ,,, Moreover, Darwinism does not make daring predictions such as the predicted bending of starlight by a certain degree around the sun during an eclipse, which was perhaps the most famous stunning confirmed prediction in the history of science that brought General Relativity overnight prominence in science (and made a household name out of Einstein):

    Gil Dodgen – Something that continues to frustrate me is that Darwinists would like people to believe that their “science” is in the same category as mine and that of my colleagues who are working on the development of hypersonic inflatable aerodynamic decelerators. We must get stuff right. There is accountability.
    If the thing burns up, is aerodynamically or structurally deficient, and falls apart and goes down in flames, we are proven to be wrong and incompetent.
    There is no such standard for Darwinists. They just make up stories and call it science. When their theories/stories go down in flames (e.g., junk DNA) they just proclaim victory, that Darwinian theory is still incontrovertible and fully intact, and walk away.
    It would be as though the scientists and engineers who designed and built the hypersonic inflatable aerodynamic decelerators, after they crashed and burned, proclaimed that the project was actually a success, and that their theories predicted this outcome from the start.
    If our team did such a thing, and made such a claim, we would be laughed out of the science and engineering community and never be awarded another penny of funding from anyone for anything.
    Yet, Darwinists do exactly what I have described, and are not only never held to account, but are awarded endless funding to make up stories that have nothing to do with legitimate science.
    This is a travesty.
    http://www.uncommondescent.com.....ustration/

    “In science’s pecking order, evolutionary biology lurks somewhere close to the bottom, far closer to [the pseudoscience of] phrenology than to physics.”
    Jerry Coyne – ardent and ‘angry’ neo-Darwinist

    neo-Darwinian evolution simply has no rigorous mathematical foundation with which one can rigorously analyze it.

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.

    The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology
    Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation..
    http://www.biosignaling.com/co.....X-9-30.pdf

    The Fate of Darwinism: Evolution After the Modern Synthesis – January 2012
    Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.
    http://www.springerlink.com/co.....03g3t7002/

    This lack of mathematical rigor in Darwinism is clearly exposed by supposed ‘Evolutionary Algorithms’, which have been ‘intelligently designed’ by computer programmers to simulate Darwinian evolution (please explain that huge non-sequitur to me!):

    Refutation of Evolutionary Algorithms
    https://docs.google.com/document/pub?id=1h33EC4yg29Ve59XYJN_nJoipZLKIgupT6lBtsaVQsUs

    Accounting for Variations – Dr. David Berlinski: – video
    http://www.youtube.com/watch?v=aW2GkDkimkE

    “No human investigation can be called true science without passing through mathematical tests.”
    Leonardo Da Vinci

    Yet despite this lack of scientific/mathematical clarity in Darwinism, it is still possible, by the criterion laid out by Lakatos in the following audio lecture, to see that Darwinism is, in reality, a ‘degenerating science program’, i.e. a ‘pseudoscience’;

    Science and Pseudoscience – Lakatos – audio lecture
    http://richmedia.lse.ac.uk/phi.....nce128.mp3

    Science and Pseudoscience (transcript) -
    “In degenerating programmes, however, theories are fabricated only in order to accommodate known facts” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture
    http://www2.lse.ac.uk/philosop.....cript.aspx

    Even some ‘honest’ Darwinists are now admitting that their theory has suffered major renovations (fabricated ‘epicyclic’ theories) in order to fit what the evidence is now saying:

    EMBO workshop focuses on “phenomena that are not part of the traditional narrative of molecular evolution … ” August 2012
    Excerpt: It is impossible to deny that our ideas on evolution are shifting from the simple and rigid ‘random mutation–selective fixation’ scheme epitomized in the Modern Synthesis, to a much more complex, nuanced picture. Under the new view, the interplay between stochasticity and adaptive mechanisms is extensive and essential, both in the generation of variation and in the fixation of the changes.
    http://www.uncommondescent.com.....evolution/

  4. Here is how neo-Darwinists avoid falsification from ‘anomalous’ genetic evidence by ‘fabricating theories’:

    A Primer on the Tree of Life – Casey Luskin – 2009
    Excerpt: The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified.
    http://www.discovery.org/a/10651

    How to Play the Gene Evolution Game – Casey Luskin – Feb. 2010
    http://www.evolutionnews.org/2.....32141.html

    Evolution Falsified Yet Again: They Are So Complicated “That it’s Stunning” – Cornelius Hunter – April 2012
    Excerpt: These similarities between the Euglenids and Dinoflagellates, of very odd and peculiar traits, disproves evolution yet again. It’s just another example of how the evidence explains evolution rather than evolution explaining the evidence. Evolution is a tautology. It is contorted to fit whatever we find in nature, no matter how absurd the theory must become.
    http://darwins-god.blogspot.co.....y-are.html

    The following article goes through a bit of the history of how neo-Darwinists have come to use horizontal gene transfer to ‘explain away’ contradictory patterns in the genetic evidence;

    Evolutionists Celebrated This Prediction But When it Later Failed They Didn’t Care – Cornelius Hunter – April 2012
    Excerpt: Sometimes their use of this lateral or horizontal gene transfer mechanism is a real stretch. And in any case, their story calls for evolution to have created this incredible mechanism which then was so important for adaptation and the supposed subsequent evolution. In other words, evolution created evolution.,,, In some cases evolutionists have no idea, beyond pure speculation, about how it could have happened. As they admit in one paper: “An alternative and more plausible possibility is that the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism.”
    http://darwins-god.blogspot.co.....-this.html

    Here’s the Latest Just-So Story: Recurrent Evolution – Cornelius Hunter – April 2012
    Excerpt: The first step to explaining something away is to give it a name. And so evolutionists have labeled this awkward evidence as recurrent evolution.,,, If the pattern fits the evolutionary tree, then it is explained as common evolutionary history. If not, then it is explained as common evolutionary forces. Heads I win, tails you lose.,, Common descent has always been an auxiliary hypothesis for the simple reason that evolution’s theoretical core does not mandate common descent, or anything else for that matter, aside from its insistence that the species arose naturally. Beyond that, anything goes.,, Evolutionists insist the species arose naturally, their religion requires it.
    http://darwins-god.blogspot.co.....rrent.html

    Pattern pluralism and the Tree of Life hypothesis – 2006
    Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.
    http://www.pnas.org/content/104/7/2043.abstract

    Another Evolutionary Just-So Story Was Just Refuted (But Another One Replaced it) – Cornelius Hunter – March 2012
    Excerpt: as one evolutionist explained:
    “Our most significant findings reveal not only differences between the species reflecting millions of years of evolutionary divergence, but also similarities in parallel changes over time since their common ancestor.”
    You remember learning that with evolution species split and move apart. Now, amazingly, we know they also evolve together. Differences, similarities, whatever. In any case, it’s Evidence 1, Evolution 0:
    http://darwins-god.blogspot.co.....y-was.html

    Here are articles that clearly illustrate that the protein evidence (extreme rarity of functional proteins), no matter how crushing against Darwinism, is always crammed into the Darwinian framework by Evolutionists:

    The Hierarchy of Evolutionary Apologetics: Protein Evolution Case Study – Cornelius Hunter – January 2011
    http://darwins-god.blogspot.co.....etics.html

  5. Here is how neo-Darwinists avoid falsification from the fossil record;

    “What Would Disprove Evolution?” – July 10, 2012
    Excerpt: Fossils are found in the “wrong place” all the time (either too early, or too late). Paleontological theory, however, allows for such devices as “ghost lineages” to repair the damage; see ENV’s coverage here and here. (links on the site)
    Again, discordance between molecular and anatomical phylogenies is commonplace in systematics; see here.(link on the site)
    But we expect Coyne is able to handle these anomalies via his shock-absorbing adjective “complete,” which allows an indefinitely large range of possibilities, short of “complete” discordance (whatever that means).
    http://www.evolutionnews.org/2.....61891.html

    Seeing Ghosts in the Bushes (Part 2): How Is Common Descent Tested? – Paul Nelson – Feb. 2010
    Excerpt: Fig. 6. Multiple possible ad hoc or auxiliary hypotheses are available to explain lack of congruence between the fossil record and cladistic predictions. These may be employed singly or in combination. Common descent (CD) is thus protected from observational challenge.
    http://www.evolutionnews.org/2.....31061.html

    The Fossil Record and Falsifiable Predictions For ID – Casey Luskin – Audio
    http://intelligentdesign.podom.....6_42-07_00

    Here is how evolutionists avoid falsification from the biogeographical data of finding numerous and highly similar species in widely separated locations:

    More Biogeographical Conundrums for Neo-Darwinism – March 2010
    http://www.evolutionnews.org/2.....32471.html

    The Case of the Mysterious Hoatzin: Biogeography Fails Neo-Darwinism Again – Casey Luskin – November 5, 2011
    Excerpt: If two similar species separated by thousands of kilometers across oceans cannot challenge common descent, what biogeographical data can? The way evolutionists treat it, there is virtually no biogeographical data that can challenge common descent even in principle. If that’s the case, then how can biogeography be said to support common descent in the first place?
    http://www.evolutionnews.org/2.....52571.html

    Let’s not forget another prevalent means in which neo-Darwinism avoids falsification; the fraudulent, and very deceptive, practice of literature bluffing;

    In this following podcast, Casey Luskin interviews microbiologist and immunologist Donald Ewert about his previous work as associate editor for the journal Development and Comparitive Immunology, where he realized that the papers published were comparative studies that had nothing to do with evolution at all.

    What Does Evolution Have to Do With Immunology? Not Much – April 2011
    http://intelligentdesign.podom.....9_03-07_00

    The deception (literature bluffing), from neo-Darwinists at Dover, did not stop with immunology;

    The NCSE, Judge Jones, and Bluffs About the Origin of New Functional Genetic Information – Casey Luskin – March 2010
    http://www.discovery.org/a/14251

    A very good site with many references exposing many more instances of Darwinism avoiding falsification from the empirical data, by ad hoc models (rationalizations), is found in this following site:

    Darwin’s Predictions – Cornelius Hunter PhD.
    http://www.darwinspredictions.com/

    Quote of note:

    “But how could it be otherwise that Darwinism would fail to make accurate predictions? It is simply impossible for a materialistic theory which denies the reality of ‘mind’ to have have any real predictive power with any sort of integrity since it clearly takes a ‘mind’ to foresee the future and predict it fairly accurately in the first place!”
    Blogger

    Music and verse:

    Hold Us Together (w. lyrics) — Matt Maher
    http://www.youtube.com/watch?v=Ut0ENzQcjrM

    Matthew 7:16
    By their fruit you will recognize them. Do people pick grapes from thornbushes, or figs from thistles?

  6. Nick Matzke,

    The problem is that your version of “evolution” can explain lots of junk, some junk or no junk DNA. And THAT is the problem if it can “explain” everything as it explains nothing.

  7. 8

    One of the greatest scientific revolutions in history is occurring before our eyes and the cultural and psychological aspects are almost as fascinating as the discoveries themselves. While scientists who seek design in the genome are finding it, others desperately continue clinging to a steam-age myth that has put blinders on biologists for a century and a half. This is going to be fun.

  8. Casey Luskin has a article up on the Darwinian spin, oops, I meant Darwinian response, to the ENCODE findings:

    What an Evolution Advocate’s Response to the ENCODE Project Tells Us about the Evolution Debate – Casey Luskin September 10, 2012
    http://www.evolutionnews.org/2.....64101.html

  9. From the New York Times reporting on the ENCODE announcement:

    “There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter [a.k.a. junk] DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.” Emphasis mine.

    Based on the above text, it seems that the dark matter DNA segments act as both “spacers” and controllers of their respective genes. Taking into account the 3D structure of DNA and its arrangement of genes proximate to the DNA that controls them, “junk” DNA wound around histones functioning as a “spacer” for the controlling of genes should be considered sufficiently functional to disqualify it as “junk”. Acting as spacers may not be as gloriously functional as a gene but is essential nonetheless.

  10. The ‘denialism’ of these ENCODE findings by Darwinists is reminiscent of the ‘denialism’ Darwinists went through with the finding of digital information in DNA. I’ve lost count of how many times Darwinists have denied that the coded information we find in DNA is not really coded information. Here is one such episode of denial by, of all people, a software engineer at Google:

    Every Bit Digital: DNA’s Programming Really Bugs Some ID Critics – March 2010
    http://www.salvomag.com/new/ar.....uskin2.php

    But as with Junk DNA now, ID has recently been vindicated with big time proof that the information we find in DNA is in fact ‘digitally encoded’ information:

    Information Storage in DNA by Wyss Institute – video
    https://vimeo.com/47615970

    Quote from preceding video:
    “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.”
    Sriram Kosuri PhD. – Wyss Institute

    Harvard cracks DNA storage, crams 700 terabytes of data into a single gram – Sebastian Anthony – August 17, 2012
    http://www.extremetech.com/ext.....ingle-gram

    This is simply completely insane,,,

    you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.

    ,,,just how far beyond this is for the capacity of anything man has designed to store information in computers! ,,, And yet Darwinists, without even a batting a eye, think nothing of declaring the information that is stored in this astonishing DNA molecule to be mostly junk. It would be absolutely hilarious, on par with a modern scientist believing in a flat earth, if it were not for the fact that, in much of America, these Darwinists are allowed to teach impressionable young minds without restraint!.

  11. The article Nick linked to makes an interesting suggestion. Create an entirely random sequence of DNA and see if it gets transcribed (what he calls the null hypothesis against the ENCODE results). The author suggests that it will. And on its face, this may not be a bad idea nor a bad expectation of the transcription outcome.

    However — and these are the kinds of caveats you’ll rarely hear from someone who is enamored of the idea of pervasive junk DNA — we have to consider the following:

    - The idea of pervasive transcription itself is a surprise for the evolutionary story. Oh, sure, it is now being accommodated, but let’s remember that it was a surprise (i.e., certainly not predicted or expected by the theory). This isn’t a knock-down proof one way or another, but it is a failure of expectations based on the theory, and on the other hand a vindication of expecations based on design, and we should be honest enough to admit as much.

    - DNA is a 3D structure, with positioning of elements important in some cases, with more cases almost surely to be found. Thus, it is possible that certain portions of DNA are there solely for structural positioning, without regard to specific sequence.

    - Some studies have started to discover that timing is important. Thus, there may be strings withing DNA that get transcribed purely as a timing element (and without any specific sequence needed), similar to a ‘wait loop’ in a computer program. Based on our own computer design experience, in fact I would expect to see such timing elements. We’ll see if more of these get found.

    - The cell still has to deal with expenditure of resources in DNA replication during cell replication, identifying and breaking down unneeded RNA transcripts, and so forth. As we’ve been noting on another thread the last few days, this is not an insignificant use of resources, particularly for those who claim that somewhere betwen 60-90% of DNA is junk. The Darwinist response to date is simply that selection works sometimes and doesn’t work other times. Stuff happens.

    - The real null hypothesis for the junk DNA claims is to get rid of all the alleged ‘junk’ and see if the organism can thrive, reproduce through multiple generations, fend off disease, respond to environmental pressures, etc. without the alleged junk. Even then it would not be definitive proof of non-function, but I would view it as evidence that needs to be seriously considered (unlike the current claims, which essentially amount to: “well it looks strange, and anyway we haven’t found a function for it yet”).

  12. 13
    critical rationalist

    Barry,

    Is there a particular reason why you did not include a link to my actual comment?

    BA: The ID community, including many writers here at UD, has been predicting for years that so-called junk DNA would be found to be functional. The Darwinists have scoffed. Now ID proponents are being vindicated. My prediction: The Darwinists will change their story to “we’ve been saying this all along.”

    The assumption that Darwinists will change their story suggests finding errors in a theory is somehow a bad thing. This is illogical, as it conflicts with our current, best explanation for the growth of knowledge. Namely, all theories contain errors of varying degree and that finding them is how knowledge grows. It also assumes some ultimate explanation can be found.

    For example, even when found to be in error as a whole, as it was in this case, a theory that only roughly 2% of the genome has a specific purpose is better than the vague claim that 100% of the genome “should be functional”. This is because it encompasses the theory that roughly 2% of the genome a specific function, rather than some other specific function, which can be found in error.

    Merely assuming the entire genome “should be functional” does not stick its neck out in a way that allows itself to be criticized. Furthermore, if we do not conjecture a specific theory of what specific function they do perform, then we do not know what tests to run. And without tests, we do not know what observations to make. So, merely saying “all genes should be functional” doesn’t tell us where we should look or what we should look for.

    In addition, a replicators, we know that genes to serve a purpose. They play a casual role in getting copied. So, of course, they “do something”. The question is, what hard to vary role do they play in adaptations of biological organisms.

    IOW, proposing the remaining 98% of the genome did not play a role in building biological adaptations means that the 2% should play the entire role. That’s a testable prediction that can be criticized.

    Surviving criticism and *not* surviving criticized is a win-win situation, which doesn’t represent a blow to human intellect. In fact, it’s just the opposite. Our ability to devise specific tests that would falsify one theory, but not the other, is an example of human intellect. This is what allows us to make progress.

    Furthermore human designers regularly make things that are merely cosmetic or inadvertently end up creating things that serve no purpose. In addition, a designer could make genes non functional in an attempt to obscure its role in the process. IOW, it’s not clear why you would expect an abstract designer with no defined limitations to make all genes functional.

  13. For those interested, 10 of the ENCODE scientists are currently accepting questions on reddit’s r/askscience:

    http://www.reddit.com/r/asksci.....opedia_of/

  14. 15
    critical rationalist

    BA writes…

    CR writes: “all theories contain errors of varying degree and that finding them is how knowledge grows . . . Surviving criticism and *not* surviving criticized is a win win situation, which doesn’t represent a blow to human intellect.”

    Then CR makes the outlandish suggestion that ENCODE is somehow a loss for ID. He writes: “[When ID] Merely assum[es] the entire genome ‘should be functional’ [it] does not stick its neck out in a way that allows itself to be criticized.”>

    CR is wrong on both counts.

    Now the missing link becomes more apparent, as you’ve taken my comment out of context.

    I wrote:

    The assumption that Darwinists will change their story suggests finding errors in a theory is somehow a bad thing. This is illogical, as it conflicts with our current, best explanation for the growth of knowledge. Namely, all theories contain errors of varying degree and that finding them is how knowledge grows. It also assumes some ultimate explanation can be found.

    several paragraphs later I wrote…

    Surviving criticism and *not* surviving criticized is a win-win situation, which doesn’t represent a blow to human intellect. In fact, it’s just the opposite. Our ability to devise specific tests that would falsify one theory, but not the other, is an example of human intellect. This is what allows us to make progress.

    Also, I wrote:

    For example, even when found to be in error as a whole, as it was in this case, a theory that only roughly 2% of the genome has a specific purpose is better than the vague claim that 100% of the genome “should be functional”. This is because it encompasses the theory that roughly 2% of the genome a specific function, rather than some other specific function, which can be found in error

    Merely assuming the entire genome “should be functional” does not stick its neck out in a way that allows itself to be criticized. Furthermore, if we do not conjecture a specific theory of what specific function they do perform, then we do not know what tests to run. And without tests, we do not know what observations to make. So, merely saying “all genes should be functional” doesn’t tell us where we should look or what we should look for.

    In addition, [as] replicators, we know that genes to serve a purpose. They play a casual role in getting copied. So, of course, they “do something”. The question is, what hard to vary role do they play in adaptations of biological organisms?

    The key point I was illustrating is how even different theories that have been shown wrong, *as a whole*, via observations can be closer to the truth than others because they have more informational content that can be found false. This is a property Popper called “Verisimilitude”.

    IOW, I said no such thing about ENCODE being a loss for ID. And it’s out ability to devise specific tests that would falsify one theory, but not the other, that is a example of human intellect, which is independent of Darwinism. Having developed a universal theory of how knowledge grows is yet another such an example.

  15. 16
    critical rationalist

    Here are a few additional examples from a comment on another thread

    …even the statement that “all swans are white”, which is found in conflict with observations and therefore false as a whole, is better than merely “all swans have a color” as the former has more ways to be found wrong. All theories usually contains errors to some degree. In my example, the error is “all”, but it does bring us closer to the truth than merely “all swans have a color” because it encompasses the theory that there are *white* swans. Popper called this property Verisimilitude.

    [...]

    …it’s logically possible one or more designers intentionally went out of its way to obscure its role in designing biological organisms. Even if this was the case, Darwinism would still be the best explanation because it encompasses the theory that the biosphere appears *as if* adaptations of organisms were created by genetic variation that was random to any specific problem to solve and natural selection. IOW, the theory encompasses a specific means by which the designer set out to obscure it’s role, which could also be found false as compared to some other specific means of obscuring its role. As such, this too represents a better theory than merely an abstract designer with no defined limitations.

    This is one example of what I mean when I say the current crop of ID is a bad explanation.

  16. Looks like Larry Moran found the reddit thread also:

    http://www.reddit.com/r/asksci.....of/c667vqi

    Could each of you please give me your personal opinion on how much of our genome has no biological function? In other words, how much of our genome is composed of junk DNA? Please don’t quibble about “biochemical function.” That’s not a biological function. You don’t need an elaborate answer. Something like 10% or 50-60% will do nicely.

  17. Taken together with evidence of pervasive genome transcription, these data indicate that additional protein-coding genes remain to be found.

  18. semi OT:

    Harvard Scientists Write the Book on Intelligent Design—in DNA – Dr. Fazale Rana – September 10, 2012
    Excerpt: One gram of DNA can hold up to 455 exabytes (one exabyte equals 10^18 bytes). In comparison, a CD-ROM holds about 700 million (7 x 10^8) bytes of data. (One gram of DNA holds the equivalent amount of data as 600 billion CD-ROMs. Assuming a typical book requires 1 megabyte of data-storage capacity, then one gram of DNA could harbor 455 trillion books.)
    http://www.reasons.org/article.....ign-in-dna

  19. Larry Moran asked one of the ENCODE researchers:

    How about we define junk DNA as the DNA that could be deleted without affecting the survival of the individual or the species.

    How much of the genome is junk by that definition?
    http://www.reddit.com/r/asksci.....of/c667vqi

    Don’t know if Dr. Moran was being sarcastic in that question (it’s hard to tell with him), but if that definition he suggested is used then we find that the percentage for ‘junk’ drops to far less than the 20% he is so upset about,,,

    Jonathan Wells on Darwinism, Science, and Junk DNA – November 2011
    Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin?] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.”
    But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler? said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued.
    In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances.
    http://www.uncommondescent.com.....-junk-dna/

    Moreover, there is ‘redundancy’ considerations to deal with:

    Minimal genome should be twice the size – 2006
    Excerpt: “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath. “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product. “When you knock out one gene, the genome can compensate by using an alternative gene. “But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead. “Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.
    http://www.news-medical.net/ne.....16976.aspx

    Mouse Genome Knockout Experiment
    http://www.uncommondescent.com.....ent-374647

  20. @ba77: 1mb from a mouse genome is about .03%, not 1%. The mouse genome has about 2.8 billion base pairs.

    It looks like an error in the original nature article: http://www.nature.com/news/200.....018-7.html

  21. Thanks JoeCoder, will make a note correcting the error. Thanks for the correction since it is certainly ‘non-trivial’ as to the topic.

  22. Barry, thanks for the OP. It’s all a hoot. I hope I’m not taking advantage of your hospitality by posting this link. But back in the 1990s on a nationally syndicated TV show I sparred with anti-ID gal Eugenie Scott for one hour. The best (only?) evidence she offered for evolution was Junk DNA. I challenged her to retract. She didn’t :) It’s at http://realsciencefriday.com/eugenie-scott

  23. OT:

    Michael Denton: Remarkable Coincidences in Photosynthesis – podcast
    http://www.idthefuture.com/201....._coin.html

  24. I wish we had a forum here so we didn’t have to hijack threads for interesting topics and announcements.

  25. The ENCODE team’s answers to Larry Moran don’t seem to confirm the idea that they accidentally spun their results to suggest more function in DNA than there actually is. The word “putdown” comes to mind.

  26. I especially liked this response to Dr. Moran’s question by rule_30:

    “That said, I can’t help but notice a trend: over time, “junk DNA” is disappearing. Good riddance: this is just a term for DNA that we don’t have any guesses about its function. The more we learn about the genome, the more functions we uncover, thus fewer unknowns and a more seemingly “useful” genome. Where will it end? I have no idea,,,”
    http://www.reddit.com/r/asksci.....of/c667vqi

    that comment reminds me of this video from ENV a while back:

    Francis Collins, Darwin of the Gaps, and the Fallacy Of Junk DNA – video http://www.evolutionnews.org/2.....40361.html

  27. notes:

    Time to Redefine the Concept of a Gene? – Sept. 10, 2012
    Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins!
    While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25.
    Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance.
    http://networkedblogs.com/BYdo8

    Junk DNA Not Junk After All Sept. 9, 2012
    http://www.medicalnewstoday.co.....250006.php

    8 Important Facts You Didn’t Know about ENCODE and the Human Genome Sept. 7, 2012
    http://www.medicaldaily.com/ar.....-human.htm

    The title of this following paper is catchy :)

    ENCODE Project Writes Eulogy for Junk DNA – Sept. 7, 2012
    http://www.sciencemag.org/cont.....59.summary

  28. The real null hypothesis for the junk DNA claims is to get rid of all the alleged ‘junk’ and see if the organism can thrive, reproduce through multiple generations, fend off disease, respond to environmental pressures, etc. without the alleged junk. Even then it would not be definitive proof of non-function, but I would view it as evidence that needs to be seriously considered (unlike the current claims, which essentially amount to: “well it looks strange, and anyway we haven’t found a function for it yet”).

    What you guys aren’t getting is that nature has basically already done this experiment, and we know it works. Closely related species — same genus, hard to tell apart — are often known to have drastically smaller genome sizes than their relatives.

  29. 14
    JoeCoderSeptember 10, 2012 at 12:28 pm

    For those interested, 10 of the ENCODE scientists are currently accepting questions on reddit’s r/askscience:

    http://www.reddit.com/r/asksci.....opedia_of/

    Heh. The very first thing an ENCODE person said on the 80% functional claim, was that he likes the post I linked to here on this thread, which you guys instantly ignored/dismissed:

    [–]langoustine 34 points 1 day ago

    How do you feel the PR for this was handled? There’s some blowback over claims that 80% of the genome has some sort of function, the trope that “we’ve refuted ‘junk’ DNA”, etc. In a similar vein, do you agree with your work being distilled into these claims?

    permalink

    [–]mlibbrechtENCODE Consortium 28 points 1 day ago

    Regarding the 80% claim, I like this post: http://selab.janelia.org/people/eddys/blog/?p=683

    permalink
    parent

  30. Nick Matzke:

    Closely related species — same genus, hard to tell apart — are often known to have drastically smaller genome sizes than their relatives.

    That is not a prediction of the theory of evolution.

  31. Nick you state:

    What you guys aren’t getting is that nature has basically already done this experiment, and we know it works. Closely related species — same genus, hard to tell apart — are often known to have drastically smaller genome sizes than their relatives.

    Well Nick now this should be a snap for you since you already got a blueprint from the smaller genome. All you have to do to verify your +50% junk claim is snip out all, or lots, of the ‘extra junk’ (close to 50% or thereabouts) of the larger genome and see if your hypothesis holds up. Do you care to take any wagers on your experiment that you will never get anywhere near deleting 50%???

  32. Eric Anderson says,

    The idea of pervasive transcription itself is a surprise for the evolutionary story. Oh, sure, it is now being accommodated, but let’s remember that it was a surprise (i.e., certainly not predicted or expected by the theory). This isn’t a knock-down proof one way or another, but it is a failure of expectations based on the theory, and on the other hand a vindication of expecations based on design, and we should be honest enough to admit as much.

    That’s an untrue statement, otherwise known as a lie.

    We’ve been running an undergraduate lab experiment on RNA polymerase for 25 years. Students isolate RNA polymerase from bacteria (E. coli) then add the purified enzyme to DNA from cows (calf thymus DNA). They get lots of transcription even though there are no bacterial promoters in the cow genome.

    That’s because RNA polymerase is known to bind nonspecifically and initiate transcription at many, many, sites in cow DNA. We know this because the binding constants for RNA polymerase were worked out over thirty years ago.

    The same thing is true for human RNA polymerase and human DNA. There will be specific transcription from strong fnctional promoters but there will also be tons of low-level nonspecific transcription (pervasive transcription).

    Those of us who understood basic biochemistry EXPECTED pervasive, nonspecific transcription and we demonstrate it in undergraduate labs. The explanation is in all the textbooks on biochemistry and molecular biology. It’s been there for decades. Look on pages 636-643 of my textbook.

    It’s not nice to lie no matter who you do it for.

  33. Larry,

    That it is known does not mean it was expected- you know a prediction of the theory made BEFORE the biochemstry was known- ie before your undergraduate labs and even before you. And as you just provided evidence for, the observation is now being accomodated.

  34. Larry Moran @33:

    It’s not nice to lie no matter who you do it for.

    Let’s think through the logic for a minute. There is nothing in evolutionary theory that would suggest pervasive transcription. Indeed, we can see this by simply looking at how many were surprised at the results of the ENCODE work.

    Now, it is possible that you are a lot smarter than many other people and that you previously predicted nearly all of human DNA would be transcribed. Did you? If so, congratulations. Either way, you certainly would not have gained that expectation from evolutionary theory itself. Perhaps from some good bench science; but not from evolutionary theory.

    Further, it is one thing to place some RNA polymerase from bacteria into cow DNA and notice that transcription takes place (which is very good and interesting science, by the way). Indeed, we might not even be particularly surprised that transcription takes place as soon as we insert the new material. It is quite another thing to have a genome in a population undergo pervasive transcription for millions of years without selection doing anything about it.

    Some of us note, rightly so, that it is a little bit too convenient for the evolutionary story to say that selection is so very capable when it suits the story and so very inept when it suits some other aspect of the story, as I noted on the other thread here:

    http://www.uncommondescent.com.....ent-432893

    Part of what we have been discussing on these threads is what selection is alleged to be able to do and not do, coupled with the position some are taking that the vast majority of the genome is junk. We’re being asked to believe that: (i) the vast majority of the genome is pure junk (way more than 50%, perhaps as high as 80-90%); (ii) significant cellular resources are spent in transcription, identification, breakdown, and, upon replication, copying all this junk, all without a single hitch to normal cellular function; (iii) selection hasn’t done anything much about this tremendous waste of resources for millions of years (while at the same time selection has just happened to fix numerous other genomic changes in the population; whew, what a lucky accident for us); and (iv) this was all expected by evolutionary theory.

    Sorry, some people may be interested in buying that bridge, but others of us are not that gullible.

    I’ll be more charitable than you and not say that you are intentionally lying. I think it is just a case of being stuck in a broken paradigm that clouds one’s thinking.

  35. Larry Moran, 09/11/2012: “It’s not nice to lie no matter who you do it for.”

    Larry Moran, 10/16/2011:

    Yes, in a sense I am “afraid” to debate the issue raised by Upright BiPed. When he/she/it said …

    These observations establish that the entailed objects (and dynamic relationships) exist the same in the translation of genetic information as they do in any other type of recorded information (in every example from human language, to computer and machine code, to a bee’s dance).

    … that goes well outside of my area of expertise. I don’t know anything about how the word “information” is used in human language and in computer code.

    I know that most IDiots are expects in almost everything so they are completely fearless about plunging into debates on all kinds of topics.

    Scientists like me, however, are much less intelligent. We tend to be experts on only a few things and we try to avoid pretending otherwise.

    I guess that means I’m a coward.

    You “don’t know anything about” how the word “information” is used in human language?

    You touch the pretty little letters on a keyboard and giggle when those same letters magically appear on the screen?

    Bullshit…er…lie.

  36. as to:

    The idea of pervasive transcription itself is a surprise for the evolutionary story.

    to which Dr. Moran states:

    That’s an untrue statement, otherwise known as a lie.

    and yet:

    A ‘scientific revolution’ is taking place, as researchers explore the genomic jungle: – 2007
    “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.”
    http://www.boston.com/news/glo.....ed/?page=1

    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.
    http://www.sciencedaily.com/re.....131932.htm

    Concluding statement of the ENCODE study 2007:
    “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.”
    http://www.genome.gov/Pages/Re.....e05874.pdf

    Astonishing DNA complexity demolishes neo-Darwinism – Alex Williams
    Excerpt: Not only has the ENCODE project elevated UTRs out of the ‘junk’ category, but it now appears that they are far more active than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes.
    http://creation.com/images/pdf.....11-117.pdf

    Larry you state:

    It’s not nice to lie no matter who you do it for.

    And please tell me exactly where you have derived this moral virtue from???:

    Stephen Meyer – Morality Presupposes Theism (1 of 4) – video
    http://www.youtube.com/watch?v=uSpdh1b0X_M

    The Knock-Down Argument Against Atheist Sam Harris’ moral landscape argument – William Lane Craig – video
    http://www.youtube.com/watch?v=xL_vAH2NIPc

    At Emory University, Consternation over Ben Carson, Evolution, and Morality – Richard Weikart – May 10, 2012
    Excerpt: If Emory University (biology) professors want to argue that evolution has no ethical implications, they are free to make that argument (I wonder how many of them actually believe this). However, if they do, they need to recognize that they are not just arguing against “benighted” anti-evolutionists, but against many of their cherished colleagues in evolutionary biology, including Darwin himself.
    http://www.evolutionnews.org/2.....59491.html

    Hitler & Darwin, pt. 2: Richard Weikart on Evolutionary Ethics – podcast
    http://intelligentdesign.podom.....3_04-08_00

    The Moral Impact Of Darwinism On Society – Dr. Phil Fernandes – video
    http://www.nwcreation.net/vide.....ciety.html

  37. 38
    critical rationalist

    I’m still unclear why this ID makes this particular prediction or why it relevant either way.

    Surely, you’re not suggesting an abstract designer with no defined limitations couldn’t make nonfunctional DNA? Are you? Having no defined limitations, it wouldn’t need to make all genes functional. And, we as designers, do not make everything functional either.

    Furthermore, observations are neutral until you have an explanatory theory by which to extrapolate them. OPERA’s “observations” of faster than light neutrinos are just one such example.

    So, what we’re looking for is an *explanatory theory* as to why the genome is the way it is. It’s unclear how “abstract designer with no defined limitations must have wanted it that way” is a good explanation, for reasons I’ve pointed out.

  38. I’m still unclear why this ID makes this particular prediction or why it relevant either way.

    We agree on something. However the point is that some evos were using the existence of junk DNA as evidence against ID and it ain’t.

  39. BA,

    You’re quoting news reports. News reports almost always over play the novelty of “new results”. It appears to be a particular problem in molecualr biology/biochemesitry because those fields seems to have very little respect for their on history (though Larry may have more to say on that)

  40. You touch the pretty little letters on a keyboard and giggle when those same letters magically appear on the screen?

    Stretches credulity, doesn’t it?

    I bet the concept of bioinformatics is completely foreign as well.

    I wonder where Dr. Moran’s results get published, and how and why? I’m sure he thinks that’s just as magical.

    And then I wonder how it is that what Dr. Moran publishes becomes available to other scientists to access and use.

    In the 1980′s my lab cloned and sequenced several members of the HSP70 multigene family from Drosophila, mouse and yeast cells. We have combined these sequences with hundreds of other HSP70 sequences to create an HSP70 Sequence Database. By aligning these sequences we are able to construct phylogenetic trees that reveal the deepest relationships of all living species.

    There’s no recorded information in that there database!

  41. CR @38:

    You have a valid question and perhaps I can provide my perspective in the following terms.

    I have stated elsewhere on this forum, and will repeat now, that both materialistic evolution and design can admit to some amount of functional and some amount of non-functional DNA. Thus, the issue is not one of absolute “all functional” or “all non-functional,” and no deductive proof can result from whatever percentage the evidence ultimately supports.

    However, it is not the case that we are just talking about a minor quibble over a couple of percentage points. Evolutionists have loudly and publicly proclaimed for years that the vast majority of DNA is nonfunctional (historically stated as something around 90%+; now some are backpedaling to maybe 80% or even two-thirds). In direct contrast, several prominent IDists have stated publicly that they expect much and perhaps the majority of DNA to be functional. Again, this is not driven by deduction from the principles of the theories; but it highlights very starkly the near opposite expectations arising from the two theories. We are now beginning to glimpse a bit more clearly which theory provided the most accurate expectations for understanding DNA.

    Having some occasional exposure to computer systems design, I have publicly stated on this forum that I do not expect more than 10% to be non-functional (note this is essentially diametrically opposed to the figure typically put forward by evolutionists). Other ID proponents may not be so bold and might hedge for a higher percentage of non-functionality, but as a group will typically still expect a much higher percentage of functionality than their materialist-minded friends. I have outlined my reasons in some detail previously and won’t bore you with the details again, but in short it has to do with our understanding of how highly-integrated functional systems operate.

    Additionally, there are a couple of reasons the discussion merits attention: (i) prominent evolutionists have long proclaimed (and several notable personalities continue to proclaim) in the most juvenile and disparaging way possible that the existence of large amounts of junk DNA is proof against design (which it isn’t, but it is used as a bully pulpit to disparage design and attempt to take the rhetorical advantage); (ii) design theorists have proposed that a much larger percentage of DNA will ultimately prove to be functional than was claimed by the evolutionists.

    So finding a bit more functional DNA here and there is not definitive proof against materialistic evolution or proof of design. No particular piece of DNA is going to settle the question. But the overall trajectory of the evidence is quite telling and it is important because (i) it demonstrates the inadequacy of the evolutionary expectation proclaimed by many notable evolutionary personalities; (ii) it puts the lie to their silly “proof” against design; and (iii) it demonstrates that a design perspective can yield insights and expectations that have long been missing in a paradigm that refuses to consider any possibility of intelligent involvement in the history of life.

    Is it a knock-down, deductive proof? Of course not. It is the overall trajectory of the evidence that supports the design perspective and should make thoughtful observers sit up and take notice.

  42. wd400 said:

    You’re quoting news reports.

    and ignored that I listed this paper:

    Concluding statement of the ENCODE study 2007 on page 20:
    “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.”
    https://docs.google.com/viewer?a=v&q=cache:4-lEzTYXwNEJ:archive-ouverte.unige.ch/vital/access/services/Download/unige:9143/ATTACHMENT01+&hl=en&gl=us&pid=bl&srcid=ADGEESga9Xv_vCtMcV76qmnEUkoQF9cLrp8qApPeJHS_Zt3_XwqtGkThaBMnSO8gGqtL7xKEJEzXV0K5JEAVaO0t_Di6XVecqQsbZI7ueq5b1Uor6OfGAdA-hFLD2ExSuHBVv2Lvdozh&sig=AHIEtbT4mW8FXJXQvXsM0eJyVU4bug_bOQ

  43. But the problems are much deeper than that, as listed previously the new study found:

    Time to Redefine the Concept of a Gene? – Sept. 10, 2012
    Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins!
    While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25.
    Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance.
    http://networkedblogs.com/BYdo8

    Thus these new studies strongly suggest that nobody really has a clue what the fundamental unit of inheritance is anymore. If Larry and you pretend like this is no big surprise to the entire Darwinian framework all I can say is dream on buddy, that is devastating!!!

    But actually this ‘overthrow of the gene as the fundamental unit of inheritance’ has been building for some time now:

    The Fate of Darwinism: Evolution After the Modern Synthesis – January 2012
    Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.
    http://www.springerlink.com/co.....03g3t7002/

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    The Mysterious Epigenome. What lies beyond DNA – video
    http://www.youtube.com/watch?v=RpXs8uShFMo

    Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video
    http://www.metacafe.com/watch/4187488

    “Live memory” of the cell, the other hereditary memory of living systems – 2005
    Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.
    http://www.ncbi.nlm.nih.gov/pubmed/15888340

    As well, as was pointed out to Dr. Moran by the ENCODE researcher who goes by the handle ‘rule_30′, ENCODE has revealed a ‘hierarchy of information’ in the genome that goes far beyond mere genetic text. A good glimpse of that hierarchy is here:

    Multidimensional Genome – Dr. Robert Carter – video (Notes in video description)
    http://www.metacafe.com/w/8905048

    as to the ‘pervasive overlapping transcription’ mentioned in the ENCODE studies, well that presents its own unique set of problems for neo-Darwinism that are insurmountable:

    Poly-Functional Complexity equals Poly-Constrained Complexity
    http://docs.google.com/Doc?doc.....Zmd2emZncQ

    further note:

    Modern Synthesis of Neo-Darwinism Is Dead – Paul Nelson – video
    http://www.metacafe.com/watch/5548184/

  44. More to add to the collection > http://sandwalk.blogspot.com/2.....-like.html WOW!!

  45. From the above-linked Sandwalk post:

    “Nothing has changed. The ENCODE consortium scientists were wrong in 2007 and they are still wrong—all of them.” Larry Moran

    WOW!! is right

  46. @ REX

    Or this:

    “I would never, ever, try to misrepresent science in order to strengthen the argument against creationism” Larry Moran

    Yet that is exactly what he seems to be doing.

    And: “I will fight that by continuing to present evidence that junk DNA exists and that our genome is mostly junk.” Larry Moran

    Double WOW!

  47. I wonder if that evidence would qualify as information.

    One hopes it can be stored and even transmitted.

    And one can surely assume that even Larry Moran himself believes that it ought to have some discernible effect.

  48. That exchange on reddit was amusing. I think one of the researchers made a good point when he stated that it can’t be known that something is nonfunctional until it is tested. That is the material point – assuming nonfunction a priori is just plain stupid. When we don’t know what something does, we should just test it and leave our assumptions at the door. It’s not even a natural assumption to make given what we know about the workings of biological systems. The only real reason why people are fighting ENCODE so much is that it undercuts a favorite anti-design argument, namely junk DNA. There’s an interesting pattern displayed by Darwin defenders: criticize some organ or biological system (appendix, eye, DNA, etc.), more research is done, criticize research ferociously or pretend that initial criticisms were never made, repeat as needed.

  49. This is an interesting bit of research, but I’ve got an issue with the claim made by many ID proponents that these results were predicted by ID.

    For example, Casey Luskin says:

    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.

    Does this mean that ID also predicts that most of the onion genome will have function?

  50. 51

    Genomicus, it is quite understandable that you want to change the subject after suffering such a massive defeat. But we decline to oblige you. The record is as plain as day. For years ID proponents have been saying junk DNA is wrong. Darwinists have been pushing it. It turns out the ID proponents were correct and the Darwinists were wrong. Now Darwinists say, “let’s talk about something else.” Why don’t you just admit you were wrong?

  51. Barry Arrington, I like you but I think it’s necessary to point out that I’m an ID proponent (I was the guy who wrote the front-loading articles for UD’s ID foundations series), although I don’t go along with a lot of what the mainstream ID community says.

    Having said that, I am genuinely interested as to whether or not ID predicts that most of the onion genome will turn out to be functional.

    Thoughts?

  52. For years ID proponents have been saying junk DNA is wrong. Darwinists have been pushing it. It turns out the ID proponents were correct

    Actually, no, as people have repeatedly made clear to you, ENCODE doesn’t do away with the idea of junk DNA. I’m still waiting to here someone make a defence of ENCODE’s 80% given that it includes every nucleotide of every intron…

  53. For years ID proponents have been saying junk DNA is wrong. Darwinists have been pushing it. It turns out the ID proponents were correct

    Actually, no, as people have repeatedly made clear to you, ENCODE doesn’t do away with the idea of junk DNA. I’m still waiting to here someone make a defence of ENCODE’s 80% given that it includes every nucleotide of every intron…

  54. “Nothing has changed. The ENCODE consortium scientists were wrong in 2007 and they are still wrong—all of them.” Larry Moran

    Hold on a second, what’s to be ‘wrong’ about? Surely the only confusion is over what is meant by ‘function’?

    I think Larry has just about thrown in the towel (or may as well).

  55. Ummm darwinists pushed junk DNA because they thought it refutes ID- “no designer would put junk dna in us” stupid strawman.

    That said ID does not say anything about it because we have no idea what tolerance our genomes have for junk. Not only that no one said the design had to be perfect nor that if it started out perfect that it had to remain that way.

    With that in mind there is a function that we are not even considering- that of just holding software. Ya see we know we cannot put more data on a disk than the disk can hold. But darwinists don’t ever consider software so they never consider that possibility.

    Then there are future functions that also need to be considered…

  56. James Shapiro weighs in on ENCODE (and Intelligent Design):

    Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin’ – James Shapiro – Sept. 12, 2012
    Excerpt: Last week, the ENCODE project (ENCyclopedia Of Dna Elements) released a tremendous amount of new information about our genomes. The results of literally hundreds of millions of experiments using the most current “high throughput” technologies provided the data for over a dozen scientific papers in the journals Nature and Genome Research. The conclusions about organization and expression of the human genome were so significant that they were the topic of a front-page story in The New York Times.
    The massive collaborative project examined how our genomes are copied into RNA, interact with regulatory proteins, and are compacted in chromatin, which organizes the genome for cellular differentiation. ENCODE examined DNA from dozens of cell types to find out if the results changed in specific ways from one kind of cell to another. Cell type specificity provides a strong indication that the data are biologically relevant.
    ENCODE described their most striking finding as follows:
    “One of the more remarkable findings described in the consortium’s ‘entrée’ paper is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly ‘junk DNA’. The authors report that the space between genes is filled with enhancers (regulatory DNA elements), promoters (the sites at which DNA’s transcription into RNA is initiated) and numerous previously overlooked regions that encode RNA transcripts that are not translated into proteins but might have regulatory roles. Of note, these results show that many DNA variants previously correlated with certain diseases lie within or very near non-coding functional DNA elements, providing new leads for linking genetic variation and disease.”
    In other words, the old idea of the genome as a string of genes interspersed with unimportant noncoding DNA is no longer tenable. Many eminent scientists had opined that the noncoding DNA, much of it repeated at many different locations, is nothing more than “junk DNA.” ENCODE revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information. Moreover, much of it was also copied into RNA with additional but still unknown functions.
    I had a longstanding, personal interest in the repetitive part of our genomes (up to as much as two-thirds of all our DNA) because it is composed of mobile genetic elements. I first discovered these elements in bacteria in my thesis research in 1968. I remember being scientifically offended by a 1980 article from Francis Crick and Leslie Orgel describing this DNA as “selfish” and functionless.

    My interest in the roles of repetitive and mobile DNA has continued since my thesis more than four decades ago. The initial sequencing of the human genome in 2001 found over 40% to be mobile repeats spread throughout our genomes, thirty times more than protein-coding DNA.
    In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled “Why repetitive DNA is essential to genome function.”
    These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for “guilt-by-association” claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.
    The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.
    “ABSTRACT: There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or
    boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the ‘functionalist ‘ perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.”
    Although we could not predict in detail all the ways repeated DNA would serve genome functions, I think our statements stand up well in light of the recent data. Without knowing the specifics, we were correct in asserting that the genome had to be highly formatted to serve as the marvelous information organelle it is in every living cell and organism.
    So, while Rick’s choice of evolutionary philosophies is different from mine, I am grateful to him for doing so much work on a paper that remains a source of justified scientific pride. Thinking of the genome informatically and of mobile DNA as a potent force for genome organization are central to the arguments presented on this blog and in my book.
    http://www.huffingtonpost.com/.....73935.html

  57. Anyone who seriously and logically thinks about evolution for more than ten minutes and still believes it is a moron. Sorry for pronouncing that hard truth. And I have found, through long experience, is that it is futile to argue with them. Granted, that is inductive and only gives a probable prediction. So it is possible that there is a committed darwinist out there who will respond to reason and evidence. I just haven’t found one yet. In fact, I’ve pretty much quit looking.

    p.s. Note to darwinists. The laws of physics explain physics and chemistry. Information (thought) explains biology. If you want to understand biology then continue to unpack the genetic language. I predict that it will be more complex than any human language by orders and orders of magninute. Why can’t physics ever explain biology? Because physics can’t explain language. It’s pretty simple, really.

  58. Hey Tom.

    Spot on, as usual.

  59. Regarding the Shapiro/ENCODE link, amusing to watch them still banging away with the onion test.

  60. It let’s them think it’s the onion that’s causing them to weep.

  61. Found this while reading Ewan’s thoughts on ENCODE:> http://www.blogger.com/comment.....7187001223 (Note; Nick seems very ‘worried’ about you guys:-P

  62. PeterJ @ 55:

    “Nothing has changed. The ENCODE consortium scientists were wrong in 2007 and they are still wrong—all of them.” Larry Moran

    Hold on a second, what’s to be ‘wrong’ about? Surely the only confusion is over what is meant by ‘function’?

    I think Larry has just about thrown in the towel (or may as well).

    Interesting, that the wedge which is dividing off, isolating, and setting up the Darwin Death Cult for its inevitable demise, is being driven by practitioners of mainstream science. Who are more interested in following the evidence where it leads than in curve fitting their science to fit the dogma of the cultists.

    The latter’s entertaining-to-watch, slow-mo slide into oblivion is going to continue to be a sight to behold. Erm, I just looked in my pantry, and yep. I need more popcorn.

  63. >”The latter’s entertaining-to-watch, slow-mo slide into oblivion is going to continue to be a sight to behold. Erm, I just looked in my pantry, and yep. I need more popcorn.” http://www.huffingtonpost.com/.....81788.html

    Note how the cultist’s are jumping all over Shapiro..

  64. My previous comment is not showing correctly. It was meant to to say:

    “The latter’s entertaining-to-watch, slow-mo slide into oblivion is going to continue to be a sight to behold. Erm, I just looked in my pantry, and yep. I need more popcorn”

    LoL!

    Michael White is defending Junk DNA over at Huffington Post; http://www.huffingtonpost.com/…..81788.html

    Note how the cultist’s are jumping all over Shapiro..

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