Home » Intelligent Design » Review: The Myth of Junk DNA

Review: The Myth of Junk DNA

Myth of Junk DNAJonathan Wells’ The Myth of Junk DNA, is a well-written book that manages to accomplish two separate tasks: to silence the Darwinists who had claimed that recent genomic discoveries supported their dystopic version of The Signature in the Cell; and to bring all of us up-to-date on the breath-taking mysteries being decoded from this most ancient script.

He begins by picking up where Stephen Meyer left off, telling us that within each cell is this memory chip, this software program that directs everything we are and ever meant to be. When Watson and Crick decoded the DNA, there was great expectation that soon we would find the gene to every talent and attribute we had ever wished we had been born with. Sci-fi was filled with stories about a DNA pill that would turn you into a concert pianist, a ballerina, or a nuclear physicist, because the genes for all these talents could manually remedy what evolution had denied you. Soon a billion-dollar government program was begun to decode the human genome, after which, it was widely touted, we would find the cure to cancer and the common cold. The three billion base pairs of the human genome, it was thought, would hold genes stacked up cheek-to-jowl, together encoding some 100,000 different proteins. We knew how to count genes because we had already decoded the way the cell made protein, first by making RNA copies of the DNA, and then sending the RNA to the ribosome factory, which could identify the unique “start” and “stop” codes among the 64 different 3-letter “words” of the RNA software that marked the beginning and end of each gene.

After a decade of work and to everyone’s great surprise, the human genome project found only 10,000 such start-stop pairs, suggesting that you and I are made out of fewer proteins than an amoeba! Furthermore, over 90% of the missing genes were DNA that apparently did nothing. Much of this “dark matter” was in long “stutter repeats” that couldn’t even make a useful protein if you inserted the start and stop codons yourself. All that work, and nothing to show for it! Neither cancer nor the common cold was cured, and instead an even greater mystery was uncovered.

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70 Responses to Review: The Myth of Junk DNA

  1. 1
    Elizabeth Liddle

    Time someone wrote a book called “The Myth of the Myth of Junk DNA” :)

    Your OP sets up a quite extraordinary straw man.

    Regulatory genes (non-coding genes) have been posited and known about pretty well since the dawn of genetics. If they didn’t exist, multicellular organisms would be impossible, and organisms wouldn’t function.

    The idea that any geneticist thought that all there was to genes was the code for proteins is absurd. There has been a text book called “Gene Expression” on our bookshelf for the 37 years of our marriage.

    How would it even be have been the subject of a textbook if the only functional genes had been assumed to be coding genes?

    I do see why you guys think that “Darwinism” is junk.

    If it were what you thought it was, it would be!

  2. Morning Lizzie,

    It was Dawkins who said in The Greatest Show on Earth, that “the greater part…of the genome might as well not be there, for all the difference it makes,” and that this fact is “useful for…embarrassing creationists.”

    And Dawkins is not alone in claiming that Junk DNA is abundant in our genome and exactly what evolution predicts. In recent years, many evolutionists have pointed to Junk DNA as major evidence for their beliefs.

    If you’re trying to claim, Lizzie, that evolutionists didn’t really believe in junk DNA after all then that is demonstrably false. Maybe we are the ones who know what “Darwinism” really is and you are the one who is mistaken about it!

  3. Here is Jonathan Well’s index of references from his book:

    Reference Notes For Jonathan Wells’ Book – The Myth Of Junk DNA – Hundreds of Studies Outlining Function for ‘Junk’ DNA
    http://docs.google.com/viewer?.....xHdM_e731g

    =================

    Jonathan Wells: On Francis Collins and Junk DNA – video
    http://www.youtube.com/watch?v=hksGZcqJ5h4

  4. 4
    Elizabeth Liddle

    No, I’m not claiming that, Chris!

    I suspect that there are substantial parts of the genome that are, in fact, Junk (pseudo genes, for instance), that neither code for proteins nor regulate the expression of genes that code for proteins. But while all junk is non-coding, all non-coding DNA is not junk, and could never be.

    The OP implied that “it was thought” that DNA was all about coding for tens of thousands of proteins. Well, obviously it wasn’t, because if that was what DNA was supposed to be all about, where were we supposed to find the regulatory genes that determine when and where the protein-coding genes are expressed?

    So non-coding DNA had to be there, and indeed it was. And some of it is probably left over junk. But the idea that every time a function is found for a stretch of non-coding DNA that Darwinism takes a mortal blow, is just silly. There have to be highly functional stretches of non-coding DNA in the genome or biology wouldn’t work. Multicellular organisms would develop, and wouldn’t even function.

    Every second of your life, non-coding DNA is busy ensuring that the right proteins are made, in the right places, in response to the right signals. Without it, you wouldn’t be able to think, heal, or even maintain homeostasis. Non-coding DNA is at the heart of biology.

    And we keep identifying more of it.

    The interesting thing, from a Darwinian point of view, is indeed how few proteins are made by living things and how widely they are shared. This suggests that the way that evolution works is largely by finding (“finding”) new uses for existing proteins rather than new proteins. This makes sense – a longer leg is much more likely to evolve because of an allele that causes leg-making proteins to be expressed for longer during development than because of an allele that codes for a new “long-leg-making protein”. Indeed, new body plans are much more likely to evolve from a change to a regulatory gene that alters when, say, a limb-bud forming protein is expressed than from a new protein, and so on down the cascade.

    Again and again I see bad ideas about biology expressed on this blog and (rightly!) exposed as nonsense. The trouble is that almost none of them bear much resemblance to actual biology!

  5. Elizabeth, so your OK with Junk DNA as long as it doesn’t make Darwinism look bad, and your not OK with Junk DNA when it does??? Glad you cleared up your ‘unbiased’ starting point for evaluating the evidence!!! Hmmm, with such a ‘unbiased’ starting position I wonder what conclusion will you possibly reach no matter what the evidence says??? :)

  6. 6
    Elizabeth Liddle

    No, ba77. That is not a good paraphrase of what I wrote.

    Try reading it again!

    Or, here’s a tl:dr version:

    All junk DNA must be non-coding DNA.
    Non-coding DNA is essential for gene expression.
    Therefore not all non-coding DNA can be junk.

    I assume you agree?

  7. So why do you think Dawkins and Co keep expressing “bad ideas about biology”, Lizzie?

    The point about the myth of Junk DNA is that the majority of evolutionists still believe that most of our DNA is junk based on the fact that only 2% of our DNA codes for genes and only a similar percentage perform other functions.

    As Larry Moran says: “It’s true that there have been lots of examples of of novel functions for small pieces of the genome that were previously lumped into the junk DNA category. These dozens of functional parts of the genome may amount to as much as 1-2% of the genome (probably less).”

    You even say yourself that “I suspect that there are substantial parts of the genome that are, in fact, Junk (pseudo genes, for instance)!”

    To dismiss *any* part of our DNA as “junk” is an argument from ignorance (or even an “evolution in the gaps” argument!) and it is made for purely non-scientific reasons.

    As “The Myth of Junk DNA” demonstrates, we have found function in ALL of the various categories of Junk DNA: including the so-called “pseudogenes”. And remember, research in the area of non-coding DNA has been restricted by the prevailing attitude that “it would be folly in such cases to hunt obsessively” for functions in it.

    So scientists should merely be saying:

    We don’t yet know what most of our DNA does. Will we keep investigating.

  8. Elizabeth, for prime example of how ‘non-scientific’ you can be, Let’s take a little look at the c-value enigma, which you have defended for neo-Darwinism, and see if you will accept the direction the evidence is actually pointing in or if you will, once again, make up lame ‘pseudo-scientific’ excuses for why it does not match neo-Darwinian expectations:

    ,,,There is no logical ‘evolutionary progression’ to be found for the amount of DNA in less complex animals to the size of genomes found in more complex animals. In fact the genome sizes are known to vary widely between Kinds/Species despite their differences in complexity and this mystery is known as the c-value enigma:

    C-value enigma
    Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical;
    http://en.wikipedia.org/wiki/C-value_enigma

    And yet, even though this C-value enigma is paradoxical to the materialistic, neo-Darwinian, point of view, which falsely holds information to merely be an ‘emergent’ property from a material bases, from a design point of view we would expect genome sizes to vary within the parameters of design constraints. Design Constraints which are realized in achieving ‘optimal design’; And the evidence says,,,:

    “There is strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus – which effects the rate of cell growth and division. Furthermore, in mammals there is a negative correlation between genome size and rate of metabolism. Bats have very high metabolic rates and relatively small genomes. In birds, there is a negative correlation between C-value and resting metabolic rate. In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration.”
    Jonathan Wells – The Myth Of Junk DNA – page 85

    Thus Elizabeth, the evidence points in a ‘design’ direction, and a true ‘scientist’ will not be satisfied with lame ‘excuses’ until he has sufficient empirical merit to disregard it.,,, What will you do??? What will you do???

  9. Hello bornagain77,

    You know I’m a fan of yours and, contrary to the claims of one or two people here, find your postings containing links elsewhere very informative and interesting.

    However, I’d like to stick up for Lizzie here because it strikes me that attacks on her position are overspilling into attacks on her person and that is absolutely wrong. We are all trying to be logical and scientific here but sometimes non-scientific a priori commitments affect each and every one of us.

    Lizzie is one of the best opponents I have ever come across on any forum and I do not doubt her impressive scientific credentials for a second. Lizzie deserves our utmost respect, not unpleasant personal remarks.

    We can disagree strongly and still make this an equally pleasant experience for people from all sides.

  10. As to solidify the proposition that ‘transcendent’ information is found within life which is not reducible to the matter-energy space-time basis of neo-Darwinism;

    First, there is a enigmatic higher dimensional component to life,,,

    4-Dimensional Quarter Power Scaling In Biology – video
    http://www.metacafe.com/w/5964041/

    ,,, a enigmatic component which is not expected from a neo-Darwinian framework which holds information to be merely ‘emergent’ from a 3-Dimensional material basis:

    “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79

    The ‘Fourth Dimension’ Of Living Systems
    https://docs.google.com/document/pub?id=1Gs_qvlM8-7bFwl9rZUB9vS6SZgLH17eOZdT4UbPoy0Y

    ,,,Moreover we have direct empirical evidence for this ‘transcendent component’ to life;

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum Action confirmed in DNA by direct empirical research;

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    And we have direct empirical evidence that this ‘transcendent information component’ to life is not reducible to the 3-D material framework:

    The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

  11. Chris, I’ll try to keep it on evidence, but one observation as to Elizabeth’s prideful claim to being a ‘scientist’, If I call myself a chicken does that mean I will suddenly start laying eggs?

  12. 12

    Liz: “But the idea that every time a function is found for a stretch of non-coding DNA that Darwinism takes a mortal blow, is just silly.”

    Not a mortal blow, just another example of a dogma driven prediction based on an ideological craving rather than prudent scientific circumspect. I think when the phrase, “embarrass creationists” enters the non-coding dna/pseudogene narrative, as Chris Doyle noted in 2, that this becomes a food fight and not a scientific discussion, which it seems is what Dawkins is more interested in anyhow. So of course you should attempt to spin doctor the “Myth of Junk DNA”, any neo-darwinist worth her weight in mutations should try to muddy the water.
    That being said, I believe you stated before you were once were once on team Jesus, and now you are a free agent, that’s too bad, you would be a good debater to have back on the squad.

  13. continued from 10; moreover ‘life’ is ‘screaming’ for an explanation as to why it is so far out of thermodynamic equilibrium:

    Dr. Morowitz did another probability calculation working from the thermodynamic perspective with a already existing cell and came up with this number:

    DID LIFE START BY CHANCE?
    Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias)
    http://members.tripod.com/~Black_J/chance.html

    Does DNA Have Telepathic Properties?-A Galaxy Insight
    Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to. Explanation: None, at least not yet.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
    http://www.dailygalaxy.com/my_.....ave-t.html

    i.e. From a ‘scientific’ point of view the question that is screaming at us is ‘exactly what is the component that constraining life to be so far out of thermodynamic equilibrium?” ,,, And as noted previously the resounding answer is ‘non-reducible’ transcendent information!!!

  14. 14

    Hi bornagain77,

    I suspect that Lizzie advances this claim because she actually is a scientist (ie. someone who has been paid to do scientific work).

    I understand where you’re coming from though. I usually object to the phrase “I am a scientist” because people only tend to use it when they are stating their beliefs and want us to take their word for it that those beliefs are true.

    The beauty of science is that it belongs to everyone: if the observational and experimental evidence is on your side then no amount of disagreement can change the truth: even if those who disagree are all scientists.

  15. 15
    Elizabeth Liddle

    ba77:

    Chris, I’ll try to keep it on evidence, but one observation as to Elizabeth’s prideful claim to being a ‘scientist’, If I call myself a chicken does that mean I will suddenly start laying eggs?

    No, but if you train for several years as a chicken, and successfully master (mistress?) the skilled art of egg-laying, then you will be entitled to call yourself a fully credentialled chicken :)

    I simply meant, ba77, that being a scientist is what I do for a living.

    (And I’m finding it just as much fun as playing the viola da gamba :))

  16. 16
    Elizabeth Liddle

    junkdnaforlife:

    Liz: “But the idea that every time a function is found for a stretch of non-coding DNA that Darwinism takes a mortal blow, is just silly.”

    Not a mortal blow, just another example of a dogma driven prediction based on an ideological craving rather than prudent scientific circumspect. I think when the phrase, “embarrass creationists” enters the non-coding dna/pseudogene narrative, as Chris Doyle noted in 2, that this becomes a food fight and not a scientific discussion, which it seems is what Dawkins is more interested in anyhow.

    tbh, I partly agree with that last point. It should be pointed out more often that Dawkins hasn’t been an active scientist for many years, and when he was, he was an ethologist. He’s a smart guy, of course, but he gets a lot of stuff wrong, particularly when he’s in polemical mode. When he is simply being informative, he’s pretty good to read IMO. But he has an axe to grind, and would certainly not be my choice of source for what evolutionary theories actually posit.

    And the fact is that protein coding is a minor part of what genes do, and has to be. It is one thing for a cell to produce proteins. It’s quite another to produce the right proteins in the right place at the right time. So a huge amount of what DNA does has be regulatory, i.e. non-coding.

    I’m sure Dawkins knows this, but somehow the idea has got around that “Darwinism predicts” that any DNA sequence that doesn’t code for protein must be evolutionary junk. Yes, we would expect to find evolutionary junk in the genome, such as pseudogenes, as well as other kinds of junk (ERVs, for instance) and we do. But we would also expect to find large sequences of non-coding DNA that regulate gene expression. If we didn’t, something really would be wrong with our science!

    So of course you should attempt to spin doctor the “Myth of Junk DNA”, any neo-darwinist worth her weight in mutations should try to muddy the water.

    Quite the reverse. I’m trying to clear the water, by distinguishing between “junk” (i.e. pseudogenes, ERVs and stuff) which must be a subset of all “non-coding DNA”. We don’t know how small a subset, but it’s certainly exciting to identify regulatory functions in non-coding DNA, because we predict it must be there! (That’s not a Darwinian prediction btw, merely a prediction based on our understanding of the mechanisms of gene expressing, but it has important implications for evolutionary theory).

    That being said, I believe you stated before you were once were once on team Jesus, and now you are a free agent, that’s too bad, you would be a good debater to have back on the squad.

    aw, I’m touched :)

    But I’m better at debating for what I think is supported by evidence and argument! If you want me back on “team Jesus” you’ll have to convince that you are right :)

  17. Elizabeth, there is no ‘convincing’ you of anything for you ignore evidence that disagrees with your ‘chosen’ worldview, instead of follow the evidence to the truth.

  18. 18
    Elizabeth Liddle

    ba77: I agree it is hard for you to convince me of what you want to convince me of. But that isn’t because I “ignore evidence that disagrees with [my] ‘chosen’ worldview” but because I don’t find the evidence you present persuasive! Often it is to videos of someone telling me something, rather than actual evidence, and when you do reference actual scientific evidence, I don’t find that it rebuts my case!

    But I do admit I don’t follow all that many of your links. You present a great many, and the relevance of most of them to the point at issue often seems to me to be tenuous.

    Anyway, I’m sure other people here enjoy them, but I suggest that simply posting a list of links, especially to videos of power point presentations, isn’t a very efficient way of making a persuasive argument, or even more, attempting to rebut one.

  19. Elizabeth, and now you make excuses for why you ignore evidence, just lovely!

  20. 20
    Elizabeth Liddle

    They aren’t excuses ba77.

    I’m not ignoring “the evidence”, I’m just ignoring most of your links!

    Because I haven’t yet found that any of your links actually lead to evidence!

    But I have to hand it to you: you’ve got me in a double bind.

    If I follow your links and say I don’t think they support your case, you say I’m ignoring the evidence.

    If I don’t follow your links, you say I’m ignoring the evidence.

    What’s a girl to do?

  21. For instance Elizabeth of ‘excuse making’ instead of ‘following the evidence’, the following ‘proof’ you have simply ignored repeatedly instead of honestly trying to supply a sufficient cause to explain the effect:

    Falsification of neo-Darwinism;

    First, Here is the falsification of local realism (reductive materialism).

    Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:

    The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (reductive materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    (of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)

    And yet, quantum entanglement, which rigorously falsified local realism (reductive materialism) as the complete description of reality, is now found in molecular biology on a massive scale!

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    The relevance of continuous variable entanglement in DNA – July 2010
    Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix.
    http://arxiv.org/abs/1006.4053v1

    Quantum Information confirmed in DNA by direct empirical research;

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH
    Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.
    http://journals.witpress.com/paperinfo.asp?pid=420

    i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself
    not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!
    ,,,To refute this falsification of neo-Darwinism, one must falsify Alain Aspect, and company’s, falsification of local realism (reductive materialism)!

    ,,, As well, appealing to ‘non-reductive’ materialism (multiverse or many-worlds) to try to explain quantum non-locality in molecular biology ends up destroying the very possibility of doing science rationally;

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com.....arguments/

    ,,,Michael Behe has a profound answer to the infinite multiverse (non-reductive materialism) argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever.

    “The multiverse idea rests on assumptions that would be laughed out of town if they came from a religious text.” Gregg Easterbrook

    =================

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007

    =========================

  22. And to further dovetail into Dembski and Marks’s work on Conservation of Information and make the ‘proof’ that much stronger ‘scientifically’;,,,

    LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information
    William A. Dembski and Robert J. Marks II
    http://evoinfo.org/publication.....ation-law/

    ,,,Encoded classical information, such as what we find in computer programs, and yes as we find encoded in DNA, is found to be a subset of ‘transcendent’ quantum information by the following method:,,,

    This following research provides solid falsification for Rolf Landauer’s contention that information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it;

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy.
    Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    ,,,And here is the empirical confirmation that quantum information is ‘conserved’;,,,

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

  23. 23
    Elizabeth Liddle

    In what sense does “the falsification of local realism” falsify “neo-Darwinism”?

    And what possible relevance does it have to the issue of whether non-coding DNA is, or is not, junk?

  24. And, Elizabeth, exactly how does finding ‘non-local’ information not present an insurmountable difficulty to the ‘local’ material causes of neo-Darwinism???,,, Your question is simply ludicrous!!!

    as to this question:

    ‘And what possible relevance does it have to the issue of whether non-coding DNA is, or is not, junk?’

    Seeing that ‘non-local’ quantum information is infused throughout the entire DNA structure, ‘holding the DNA together’, I would say this has direct relevance to the neo-Darwinian claims of Junk DNA,,,

    ”’Please note this ‘unanswered question””

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    i.e. not only HOW does it do it, but exactly WHY would neo-Darwinism go to such Herculean efforts to protect DNA??? Sorry Elizabeth no excuse making and ignoring allowed!!!

    Although evolution depends on ‘mutations/errors’ to DNA to make evolution plausible, there are multiple layers of error correction in the cell to protect against any “random changes” to DNA from happening in the first place:

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.”
    http://www.arn.org/blogs/index....._contradic

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    =====================

    further note to ‘non-local’ quantum information;

    DNA Caught Rock ‘N Rollin’: On Rare Occasions DNA Dances Itself Into a Different Shape – January 2011
    Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code,
    http://www.sciencedaily.com/re.....104244.htm

    Systems biology: Untangling the protein web – July 2009
    Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
    http://www.nature.com/nature/j.....0415a.html

  25. 25
    Elizabeth Liddle

    ba77

    And, Elizabeth, exactly how does finding ‘non-local’ information not present an insurmountable difficulty to the ‘local’ material causes of neo-Darwinism???,,, Your question is simply ludicrous!!!

    Well, humour, me, ba77. You want to convince me, right?

    Well, explain to me where the difficulty lies, because right now I’m not seeing it.

  26. Sorry Elizabeth I don’t ‘want to convince you’, I gave up on that weeks ago,, I merely want to show others how unreasonable you are!!!

  27. 27
    Elizabeth Liddle

    Well, that seems a little unreasonable on your part ba77!

    I mean, here am I, sitting here, wanting to be enlightened, and you won’t try to explain to me why violation of non-locality is a problem for evolutionary theory!

    :(

  28. An ethnologist? I thought Dawkins was an evolutionary biologist.

  29. Regulatory genes (non-coding genes) have been posited and known about pretty well since the dawn of genetics

    Since the dawn of genetics eh? Like how far back was that? Mendel?

    I fail to see how this claim can be even remotely true.

  30. I do see why you guys think that “Darwinism” is junk.

    Darwinism is junk because it is junk science. It’s largely guesswork and story telling.

  31. Elizabeth:

    …where were we supposed to find the regulatory genes that determine when and where the protein-coding genes are expressed?

    So non-coding DNA had to be there, and indeed it was.

    There has been a text book called “Gene Expression” on our bookshelf for the 37 years of our marriage.

    Can you quote from your book how they reasoned in this way and came to the same conclusion?

    But why could regulatory genes not code for proteins that control the expression of other proteins?

    A regulator gene, regulator, or regulatory gene is a gene involved in controlling the expression of one or more other genes. A regulator gene may encode a protein, or it may work at the level of RNA, as in the case of genes encoding microRNAs.

    Now if it is in fact the case that regulatory genes can and do encode proteins, how does it follow that there must be non-coding DNA?

    It doesn’t. Another non prediction of evolutionary theory.

  32. Elizabeth:

    This suggests that the way that evolution works is largely by finding (“finding”) new uses for existing proteins rather than new proteins.

    So what happened to the old use? Not needed any more? So the protein went on to do other things? How does that happen?

    If proteins descend from other proteins by descent with modification shouldn’t there be a nested hierarchy? If not why not?

    If not, why is a nested hierarchy a prediction of Darwinism?

  33. Elizabeth, it does seem like you raise more questions than you answer when you post your answers to questions. :)

  34. All junk DNA must be non-coding DNA. Non-coding DNA is essential for gene expression. Therefore not all non-coding DNA can be junk.

    Why do Darwinians fail at logic?

  35. So scientists should merely be saying:

    “Junk DNA” is the null hypothesis.

  36. Elizabeth:

    ‘here am I, sitting here, wanting to be enlightened,’

    yep, here you are,,, wanting to be ‘enlightened’:

    http://1rico.files.wordpress.c.....e-sand.jpg

    Your ‘enlightenment’ theme song:

    Pure Imagination
    http://www.youtube.com/watch?v=RZ-uV72pQKI

  37. 37
    Elizabeth Liddle

    Pah. A lot of help you are, ba77!

    Ah well.

    At least we are having fun :)

  38. You know I’m a fan of yours and, contrary to the claims of one or two people here, find your postings containing links elsewhere very informative and interesting.

    For the record, I’m not opposed to informative quotes and links. I’m opposed to cut and paste as a style of argument.

    I’ve shown in the past a case where 90% of the links posted had nothing to do with the claim that was supposedly being addressed. This does not mean they were not in some way informative about something.

    No one here on the other side of the debate is going to want to sift through all that material to try to figure out if there’s something relevant there.

    Just wanted to clear that up.

  39. 39
    Elizabeth Liddle

    Mung:

    Since the dawn of genetics eh? Like how far back was that? Mendel?

    I fail to see how this claim can be even remotely true.

    OK OK OK OK.

    Not back to Mendel. I meant since we knew about DNA and how it coded for proteins. As soon as we knew that, we had to ask: so how does the cell “know” which protein to produce?

    The answer itself had to lie in non-coding regulatory sequences. But you are quite right, I’m not sure when the hypothesis was first mooted. I just know that “gene expression” had made it to a text book at least 37 years ago because I seemed to have married it :)

    You are a lawyer aren’t you?

    It’s OK, I won’t hold it against you. Some of my best friends…oh, wait….

  40. … If I call myself a chicken does that mean I will suddenly start laying eggs?

    I’ve seen you lay a few eggs. :)

  41. Thanks mung for your continued stabs in the back. I’m building quite the knife collection.

  42. But I’m better at debating for what I think is supported by evidence and argument! If you want me back on “team Jesus” you’ll have to convince that you are right

    God is love. Jesus was the expression of that love. That’s not a matter of logic and reasoning. It’s a person, demonstrating love.

  43. Elizabeth, there is no ‘convincing’ you of anything for you ignore evidence that disagrees with your ‘chosen’ worldview, instead of follow the evidence to the truth.

    It wasn’t easy, but I think I convinced Elizabeth of a thing or two. So I think it can be done.

    I think I convinced her that I am a complete jerk, for example. ;)

  44. What’s a girl to do?

    Have a beer. Show that cat some loving. Set off a few fireworks in celebration of American independence.

    Go yanks!

    :)

  45. You are a lawyer aren’t you?

    Actually, no. I’m an engineer, of a sort. But I probably could have been a lawyer. Can you believe I started out wanting to be a doctor? Ah, how life gets in the way of plans :)

    I got my start in electronics in the Navy. I work in the mobile telephone industry and have since 1985. Mobile telephone switches have to be told what do do, and I basically write the stuff that tells them what to do. I also write software that makes my job and the job of my team easier. Why do it manually if you can get a computer to do it!

    So I do have to think in a certain way to be good at what I do.

  46. 46
    Elizabeth Liddle

    Mung:

    Can you quote from your book how they reasoned in this way and came to the same conclusion?

    Well, I’ll see if I can dig it out. It was mostly fairly heavy biochemistry. And may still be on one of our cardboard boxes :( But I’m fairly sure I’ve seen it on the shelf in recent times, so I will take a look.

    But why could regulatory genes not code for proteins that control the expression of other proteins?

    A regulator gene, regulator, or regulatory gene is a gene involved in controlling the expression of one or more other genes. A regulator gene may encode a protein, or it may work at the level of RNA, as in the case of genes encoding microRNAs.

    Now if it is in fact the case that regulatory genes can and do encode proteins, how does it follow that there must be non-coding DNA?

    You know, I guess you have a point there. Perhaps non-coding DNA really is useless junk.

    Seriously, you do have a point. Perhaps you are right that early on, people postulated that regulation was done by all done by suppressor proteins.

    I will double check :)

    It doesn’t. Another non prediction of evolutionary theory.

    Well, no. That would be (if it was) a non prediction of biochemical theory, or even genetic theory.

    I’m just aware that throughout my (earlyish) life, people talked about what DNA did apart from code proteins, because there must be some mechanism for determining which proteins should be produced. i.e. which genes should be expressed. It was fun being a nerdy teenager in the sixties!
    And the general principle (Crick’s “Central dogma”) was that the information flow goes DNA-> RNA -> Protein rather than the other way round. But in fact of course, that is not correct, because as you point out, proteins do play a role in regulating gene expression.

    Thanks for keeping my toes to the fire :)

  47. Mung,
    When I was in grad school in physics, we all posted cartoons on our doors. One door had a picture of fellow standing underneath a car on a lift, messing with the muffler or something, and he’s answering the owner of the car. “Well I wanted to do Quantum Mechanics, but I must have made a wrong turn somewhere”

    I tell people I started out wanting to be a physician but had some sort of difficulty with the spelling…

  48. 48
    Elizabeth Liddle

    Mung:

    I also write software that makes my job and the job of my team easier. Why do it manually if you can get a computer to do it!

    I hear you. I’d never coded anything until I hit my half-century, but boy has it been useful since! The way I started was I had a really tedious job to do, and it was going to take me about eight weeks and give me an SRI. So I figured if I spent seven weeks learning to code, I could use the eight to write a program that would do it in about an hour!

    And I did it.

    So I do have to think in a certain way to be good at what I do.

    Yes, me to. But we seem to have different operating systems :)

  49. 49
    Elizabeth Liddle

    to = too

    oops.

    Now you know why my code is buggy.

  50. 50
    Elizabeth Liddle

    SRI = RSI.

    lol

  51. 51
    Elizabeth Liddle

    Mung:

    God is love. Jesus was the expression of that love. That’s not a matter of logic and reasoning. It’s a person, demonstrating love.

    I’ll still bat for that team. With the odd caveat.

  52. lol

  53. ok, so an interesting question is, how did junk dna get it’s start?

    How did it ever come to gain a foothold in any genome?

    Is it common to all life, and if so to what extent?

  54. 54
    Elizabeth Liddle

    Mung:

    Elizabeth:

    This suggests that the way that evolution works is largely by finding (“finding”) new uses for existing proteins rather than new proteins.

    So what happened to the old use? Not needed any more? So the protein went on to do other things? How does that happen?

    Well, as I said, “this suggests”, not “this is because”. But I can tell you where we’d look for answers.

    First of all, it wouldn’t mean that the old use “wasn’t needed any more”. It could mean that the gene that coded for it was expressed under more than one condition (e.g. to in response to a developmental cellular signal that says “we need a bit more ear stuff here” and also, elsewhere to a signal that says “we need a bit more nose stuff here”. A change to the regulatory genes might mean that in one individual, more nose got made, even though the same amount of ear got made. And it might even happen that organisms with long noses and small ears were better adapted for survival in their current environment, and so the old ear & nose protein finally emerges just as a nose protein.

    Silly example, but you can extrapolate to something more sensible.

    If proteins descend from other proteins by descent with modification shouldn’t there be a nested hierarchy? If not why not?

    Interesting point. There may be. But Crick was mostly right about the information flow direction (DNA -> RNA -> protein) so phylogenies based on proteins alone are more likely to be blurred – you can deduce a protein (or at least the sequence of amino acids) from a DNA sequence but you can’t deduce a DNA sequence from the sequence of amino acids, because some amino acids are coded by more than one codon. Also, coding sequences tend, obviously, to be highly conserved, so you often get more phylogenetic information from non-coding sequences (especially “junk” sequences!) because they can accumulate mutations without phenotypic effects.

    If not, why is a nested hierarchy a prediction of Darwinism?

    Well, it’s not, exactly. Darwinism is an explanation of the observed nested hierarchies. Linnaeus’s hierarchies (which he mostly got right, if not entirely) preceded Darwin’s theory – it was a non-random pattern requiring an explanation.

    But Darwinian evolution was not the only possible explanation. Lamarckian evolution was another contender (and even Darwin thought that Lamarckian mechanisms might be responsible for the variation that is subject to natural selection…um… I mean for heritable differential reproductive success).

    It still isn’t. But Design, to me, doesn’t seem like a good alternative contender, because it doesn’t explain the nested pattern. Most (human) Design lineages are highly cross-referenced.

    Elizabeth, it does seem like you raise more questions than you answer when you post your answers to questions.

    Yes indeed. A lovely example of a nested hierarchy, in fact! But one not readily explained by Darwinian mechanisms :)

    And I really am going to get that response back to Upright Biped this weekend….

  55. 55
    Elizabeth Liddle

    Mung:

    ok, so an interesting question is, how did junk dna get it’s start?

    How did it ever come to gain a foothold in any genome?

    Is it common to all life, and if so to what extent?

    Well, as you pointed out above, “junk” is best set up as the null :)

    In other words, if we can find a function for a sequence, we can reject the null of “junk”, but if we fail to find a function, all we can do is “retain the null” – we cannot conclude the null is true.

    It is very hard to see how you could tackle the issue the other way round. So it’s a very poor flagship for Darwinian “predictions”, and I think Dawkins( (if it was he) was silly to put it further. Predictions are far better expressed as H1s rather than H0s.

    In fact, you could argue that Dawkins is making a “Darwin of the gaps” argument!

    Not a good idea (which is why Dembski sensible casts Design as H1, heh).

    But the expectation would certainly be, under a Darwinian scenario, that junk would tend to accumulate, and may even have been present in the earliest proto-genomes.

    The reason is because DNA isn’t very resource-consuming. Sure you need stuff to make it with, but not nearly as much as you need to make a continuous supply of proteins, for instance, because once it’s made, it is pretty cheap to maintain, so having extra footage isn’t going to cost the organism much.

    So if there’s no penalty at phenotypic level for having a extra footage, then there’s no selective pressure to delete stuff that isn’t doing any harm, even if it isn’t doing any good either.

    As for where it comes from: well, obviously we know very little about the very earliest genomes, so this is pure speculation, but it’s possible (if abiogenesis is possible at all :) that the earliest DNA molecules were mostly random sequences of bases, but that one or two fortuitously happened to code for a protein that fortuitously happened to increase longevity (yes I know, RNA, ribosomes tRNA yadda yadda, but I’m not going there right now). So that genome gets replicated more often than non-coding genomes.

    If a mutation happens to that bit of sequence, if it results in a less effective protein, that mutation will be “selected out”, but if, by chance, it selects a better one, then it will be reproduced more often etc etc.

    However, mutations that happen in the restof the sequence won’t result in differential reproduction, so they will just accumulate, until one of them hits a lucky protein.

    Fast forward …. We now have populations with lots of coding sequences, maybe still a fair bit of junk (imagine WEASEL half way through), then one of the coding sequences that happens not to be important in the current environment gets broken, or a virus comes along and leaves a bit of its DNA in your sequence, or a bit of junk sequence gets duplicated (repeated sequences very common in alleles, so it seems that the replication process lends itself to mistakes like mistakes like mistakes like this.)

    Leaving more junk.

    Fast forward again, and we have lots of remnants of old genes, no longer functional, ERVs, repetitive bits of code that never got weeded out because once a bit of code does nothing, further mutations to it, including repeats, don’t have any selectable phenotypic effects.

    And so, you end up with lots of “junk DNA”.

    So the apparent presence of junk sequences is certainly in accord with Darwinian theory, and it would indeed be surprising if there were none.

    But as you can’t prove a null, it’s a very poor prediction to cite as evidence for Darwinian theory. And if IDists can find a use for every single sequence, then Darwinian theory is in trouble (reject the null!)

    We’d certainly have to look for reasons why it should not be there (for example, it’s possible that it’s more “expensive”, phenotypically, to maintain than we currently think). But that would still be weird – it would mean all those virus sequences all proved functional. Perhaps the Designer uses Designer Viruses!

    As for your last question: I don’t know, but I don’t think anyone does, for the reasons given above.

    Null hypotheses are the very devil to support :)

  56. And I really am going to get that response back to Upright Biped this weekend….

    That thread is now closed to comments.

  57. Elizabeth Liddle:

    But Design, to me, doesn’t seem like a good alternative contender, because it doesn’t explain the nested pattern.

    Please hearken back to a previous discussion about when ID theory and evolutionary theory do and do not collide.

    afaik, design theory does not even attempt to offer an explanation for the nested hierarchy. So saying some other explanation is a better explanation than the one offered by design is just ludicrous.

    So again, you misrepresent ID by suggesting it offers a competing explanation for some phenomenon what it does not even address. Please stop.

    When in doubt, ask.

  58. 58
    Elizabeth Liddle

    OK, now my turn to be the lawyer!

    Mung, I did not even attempt to represent (or misrepresent) ID.

    That’s why I didn’t use the term. I said “Design”.

    I do not think Design is a good explanation for nexted hierarchies, because human design hierarchies tend not to be deeply nested.

    I was not talking about “ID”. I don’t actually think IDist inferences are sound, but not because I don’t think it accounts for nested hierarchies. Design could be implement within common descent, for instance, by some “frontloading” mechanism. That’s not how human design works, but it could well be how celestial Design works.

    I’m just saying that the specific pattern of nested hierarchies is not well explained by a Design hypothesis, e.g. the hypothesis espoused, for example, by baraminologists.

    Go have a beer.

    I’m off to find my cat.

  59. I have to disagree that the DNA being junk is the null hypothesis prima facie. It is now considered the null by many due to the knowledge about its origin. I would expect that when the DNA was initially discovered the null hypothesis was that most of it had a function.

  60. Go have a beer.

    I’m off to find my cat.

    I don’t drink beer. Can I have a cider instead?

    My cat’s sleeping on top of the DVR where it’s nice and toasty.

    Do you know what a vacuous claim is Dear Lawyer?

    It’s saying that Design doesn’t explain something without any statement of what Design consists of.

    So if you want to trade misrepresent for meaningless it’s ok with me.

  61. 61

    Liz: “maybe still a fair bit of junk (imagine WEASEL half way through),”

    The example you give is an intelligently designed program programmed to model non-intelligently designed Darwinian evolution that Darwinian evolutionists concede does not model Darwinism evolution because of its design, is an example of accumulation of Junk dna via non-design?

  62. 62
    Elizabeth Liddle

    Yes, but it was clear, surely, that I wasn’t using it as a model of evolution, just as a mental picture of what a string that was still half junk but had a few words in it that had been selected by some fitness function (say one that gave fitness points for any English word).

    It was just an image. Don’t use it if it doesn’t help.

  63. Yes, but it was clear, surely, that I wasn’t using it [Dawkins' WEASEL program] as a model of evolution,

    You can’t be serious.

    I will go back and harvest your comments if necessary.

    Dawkins’ sim includes all the relevant aspects.

    Reproduction
    Variance
    Selection

    What exactly is it about Dawkins simulation that did not model Darwinian evolution?

  64. I recently received a copy of Jerry Coyne’s Why Evolution Is True.

    In the index there is no entry for dysteleology.

    In the index there is no entry for junk dna.

    In the glossary there is no entry for dysteleology.

    In the glossary there is no entry for junk DNA.

    The closest I can see is in the index under DNA:

    dead genes and

    And under the entry for genes:

    dead (pseudogenes)

  65. Chris said:

    “To dismiss *any* part of our DNA as “junk” is an argument from ignorance (or even an “evolution in the gaps” argument!) and it is made for purely non-scientific reasons.

    As “The Myth of Junk DNA” demonstrates, we have found function in ALL of the various categories of Junk DNA: including the so-called “pseudogenes”. And remember, research in the area of non-coding DNA has been restricted by the prevailing attitude that “it would be folly in such cases to hunt obsessively” for functions in it.

    So scientists should merely be saying:

    We don’t yet know what most of our DNA does. Will we keep investigating.”

    Excellent point Chris. And if anything, it seems the evidence lies on the side of function as opposed to junk. But the default position of the Darwinists is that it is junk because that fits best with their Darwinian hypothesis about the world.

  66. But the default position of the Darwinists is that it is junk because that fits best with their Darwinian hypothesis about the world.

    I have to disagree. The Darwinian position is that anything can happen, no matter how improbable, because improbable things happen all the time.

  67. p.s. There has been no evidence that there is a limit to improbable things.

  68. 68
    Elizabeth Liddle

    Mung:

    Yes, but it was clear, surely, that I wasn’t using it [Dawkins' WEASEL program] as a model of evolution,

    You can’t be serious.

    I will go back and harvest your comments if necessary.

    Dawkins’ sim includes all the relevant aspects.

    Reproduction
    Variance
    Selection

    What exactly is it about Dawkins simulation that did not model Darwinian evolution?

    In that post, Mung!!!!!

    Sheesh.

    Yes, I think the WEASEL program models those three evolutionary processes. But I asn’t talking about that, I was attempting to explain why, under a Darwinian hypothesis, junk DNA could arise.

    I have to disagree. The Darwinian position is that anything can happen, no matter how improbable, because improbable things happen all the time.

    No. The “Darwinian position” is that even things that happen rarely are quite probable given enough opportunities.

    Which is precisely why Dembski attempt to refute the position by saying that even given all the events in the universe, the thing is improbable.

  69. Yes, but it was clear, surely, that I wasn’t using it [Dawkins' WEASEL program] as a model of evolution,

    ok Elizabeth, let’s see if I understand you. You do think Dawkins’ WEASEL models evolution, correct?

    But in this thread you were not using Dawkins’ WEASEL program as a model of evolution.

    Do I have it right so far?

  70. The “Darwinian position” is that even things that happen rarely are quite probable given enough opportunities.

    I don’t know if that’s the Darwinian position or not. It doesn’t make much sense to conduct trials without an end in sight, without a goal or target, does it?

    Take the trilobite eye. It’s hardly Darwinian to say that the trilobite, given enough opportunities, would eventually evolve the trilobite eye is it?

    Rather the Darwinian reasoning goes, there’s the trilobite eye. ergo, there must have been enough time and trials for it to come about by Darwinian means.

    It hardly matters whether such a thing is even possible.

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