Home » 'Junk DNA', Darwinism » Anyone else for the myth of junk DNA? Richard Dawkins, for one

Anyone else for the myth of junk DNA? Richard Dawkins, for one

The Selfish Gene

He certainly drew the desired Darwinian conclusion:

“The amount of DNA in organisms,” Dawkins wrote in 1976, “is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the ‘purpose’ of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA. “

- Jonathan Wells, author of The Myth of Junk DNA, p. 20

And he was wrong as a result. Just like these folk:

Jerry Coyne and Michael Shermer. Oh, and Francis Collins, though he may be coming round.

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65 Responses to Anyone else for the myth of junk DNA? Richard Dawkins, for one

  1. “The amount of DNA in organisms,” Dawkins wrote in 1976, “is more than is strictly necessary for building them”

    Probably true-deletion of fairly large swaths of DNA shows no apparent negative effect.

    “A large fraction of the DNA is never translated into protein.”

    True. A large amount of it doesn’t even seem to get transcribed, or is rarely transcribed as background noise.

    “The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”

    True. Transposons, ERVs, and other genome parasites, for example show this behavior.

    I don’t see the obviously false statement.

  2. 2

    Dawkins is right. Many very similar species have very different genome sizes. For example, onions. Many “simpler” species, like lungfish and ferns, have genomes up to 100 times bigger than the human genome.

    Thus, it really is true that many species have way more DNA than is needed to build them.

    This has been known for decades. This is the primary data in support of the idea that a lot of the genome is junk. Why do creationists/ID guys never mention this overwhelmingly important observation?

  3. Does Sternberg plan on presenting his research on mRNA splicing as it relates to the issue of junk DNA at the pertinent Cold Spring Harbor Meeting in August? Just wondering.

  4. Thus, it really is true that many species have way more DNA than is needed to build them.

    So. What.

    This is the primary data in support of the idea that a lot of the genome is junk.

    Why?

    Why do creationists/ID guys never mention this overwhelmingly important observation?

    Perhaps we’re waiting for an argument that consist of more than a non-sequitur.

  5. Actually, one scientist maintains that junk DNA plays a vital role in yielding special forms of RNA.

    Article: http://www.lifescientist.com.a.....etworking/

  6. 6

    Thus, it really is true that many species have way more DNA than is needed to build them.

    So. What.

    So the OP, and Jonathan Wells, are wrong, and Dawkins was right. Seems like a relevant point to make on this thread, don’t you think?

  7. NickMatzke_UD,

    You say:

    Dawkins is right. Many very similar species have very different genome sizes. For example, onions. Many “simpler” species, like lungfish and ferns, have genomes up to 100 times bigger than the human genome.

    Thus, it really is true that many species have way more DNA than is needed to build them

    This is a non-sequitur. First one has to show that the particular species can indeed be built using a smaller genome. In your example, drasctically smaller genome with the same fitness as the wild version. “Simpler” species may have to cope with a plethora of inputs from the environment that jolly well may need larger genome than humans.

    “Simpler” species and the assumed smaller genome size are evolutionary predictions, am I not right?

    Unfortunately, today we do not even know what is needed to build a single cell, so speculation about what is needed for a lungfish is, well, just speculation…

    By the way, this is an extremely exciting area of research. If the current trend goes on, we will continue to discover complexity upon complexity in the way the genome, proteins and the environment interact.

  8. To piggyback on Alex73′s comment:

    This disparity of genome sizes is found throughout life. 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 somewhat paradoxical to the materialistic, neo-Darwinian, point of view, from a design point of view we would expect genome sizes to vary with design constraints imposed in trying to achieve ‘optimal design’ in any particular life-form; For instance:

    “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

  9. Also of note: The is consistent scaling, of genome length to gene number, that is certainly not expected from the neo-Darwinian framework of Junk DNA:

    Scaling graph
    Excerpt under graph: Total number of nucleotides (above) and number of different genes (below) scale with identical slopes of 0.35, consistent with our hypothesis that scaling of metabolic power in prokaryotes reflects the number of genes and the complexity of the biochemical network.
    http://www.pnas.org/content/10.....nsion.html

  10. Of further note:

    THE ALLOMETRIC RELATIONSHIP BETWEEN GENOME SIZE (C-VALUE) AND TOTAL METABOLIC ENERGY PER LIFESPAN, PER UNIT BODY MASS IN ANIMALS
    http://www.sustz.com/Proceedin.....ANASOV.pdf

  11. excerpt from previous paper:

    Excerpt: this show that,,, the higher total life energy per unit body mass leads to smaller C-value.

  12. Nick – what did you think of the link I posted where a scientist belives that junk DNA isn’t all junk? Thoughts?

  13. Some discussion for Barb – there’s more to the RNA Underworld than just transcription:

    http://aghunt.wordpress.com/20.....promoters/

    http://aghunt.wordpress.com/20.....ond-power/

  14. Maybe you unknown evo-guys are right, but what about this (just to mention a brief part)?

    2003, Scientific American, introns are genetic junk?

    “The failure to recognize the
    importance of introns ‘may well go down as one of the biggest mistakes in the history of molecular biology.’”

    Wayt T. Gibbs, “The Unseen Genome: Gems among the Junk,” Scientific American (Nov., 2003).

    2010, Nature:

    “Biology’s new glimpse at
    a universe of non-coding DNA—what used to be called ‘ junk’ DNA—has
    been fascinating and befuddling. Researchers from… ENCODE showed
    that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA.”

    Erika Check Hayden, “Life Is Complicated,” Nature, Vol. 464:664-667 (April 1, 2010).

    Papers indicating huge portions of DNA transcribed and hinting at function:

    John S. Mattick & Igor V. Makunin, “Non-coding RNA,” Human Molecular Genetics,
    Vol. 15: R17–R29 (2006); Shao-Yao Ying, Donald C. Chang & Shi-Lung Lin, “MicroRNA
    (miRNA): Overview of the RNA Genes that Modulate Gene Function,” Molecular Biotechnology,
    Vol. 38:257-268 (2008); Marcel E. Dinger, Paulo P. Amaral, Timothy R. Mercer
    & John S. Mattick, “Pervasive transcription of the eukaryotic genome: functional indices and
    conceptual implications,” Briefings in Functional Genomics and Proteomics, Vol. 8: 407-423
    (2009); Aristotelis Tsirigos & Isidore Rigoutsos, “Alu and B1 Repeats Have Been Selectively
    Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes,” Vol.
    5(12):e1000610 (December 2009); Rodrigo Louro, Anna S. Smirnova & Sergio Verjovski-Almeida,
    “Long intronic noncoding RNA transcription: Expression noise or expression choice?,
    Genomics, Vol. 93: 291-298 (2009); Noam Shomron & Carmit Levy, “MicroRNA-Biogenesis
    and Pre-mRNA Splicing Crosstalk,” Journal of Biomedicine and Biotechnology, Vol. 2009:
    594678 (2009).

    Maybe it’s time to awake on this, don’t you think?

  15. …Oh, I’ve forgot this:

    What can you say about another “correct” prediction of ET?

  16. 16
    Elizabeth Liddle

    Is anyone here claiming that all DNA is necessary for the organism to survive and reproduce?

    If not, what are people claiming?

  17. Other confirmations about ET correct predictions…Ah-ah-ah, ih-ih-ih, uh-uh-uh..(thanks to http://www.evolutionnews.org)

    “..In particular, she found that repeated tracts of one base, adenosine, were more likely to form kinks than other sequences..”

    http://www.newscientist.com/ar.....works.html

    “..Pseudogenes have long been labeled as “junk” DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation..”

    http://rnajournal.cshlp.org/co.....1.abstract

    “..The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms as well as in genome evolution..”

    http://jvi.asm.org/cgi/content/abstract/85/10/4761

    “..Repetitive sequences, including transposable elements, are now believed to play a significant role in genomic differentiation and evolution. Some are also expressed as regulatory noncoding RNAs. Vast DNA databases exist for higher eukaryotes..”

    http://www.ncbi.nlm.nih.gov/pm.....MC2851119/

    “..Thus transposable elements, far from being “junk”, have one of the most important roles in multicellular biology..”

    http://arxiv.org/abs/1005.4896

  18. To Elizabeth Liddle (15):

    >Is anyone here claiming that all >DNA is necessary for the organism >to survive and reproduce?

    We’re just saying, as opposite to what the most prominent evo-tists had as an inevitable result for epochs of evolution “noise” [i.e. another evolutionary false prediction] that the majority of DNA isn’t “junk”, but maybe is designed for a purpose.

    Don’t try to “change railway”..

    >If not, what are people claiming?

    See the above.

  19. Thus, it really is true that many species have way more DNA than is needed to build them.

    So. What.

    So the OP, and Jonathan Wells, are wrong, and Dawkins was right.

    I read Wells’s book and I don’t recall it containing an argument about how much DNA it takes to build a species. Nor does the OP.

    Dawkins: If the ‘purpose’ of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing.

    Let’s just ignore that mighty big if shall we? Perhaps DNA serves multiple purposes. Oh, wait, but that would mean Wells and the OP are right, and Dawkins was wrong.

  20. Elizabeth Liddle:

    If not, what are people claiming?

    Dawkins is claiming all DNA is there to build bodies and that’s it’s only purpose.

    How stupid is that, yeah?

  21. 21
    Elizabeth Liddle

    Jonin:

    We’re just saying, as opposite to what the most prominent evo-tists had as an inevitable result for epochs of evolution “noise” [i.e. another evolutionary false prediction] that the majority of DNA isn’t “junk”, but maybe is designed for a purpose.

    Yes, it would be surprising, given the likely low metabolic cost of producing DNA, if there were not to be substantial stretches of “junk” – and we know that there are – pseudo genes, bits of old virus etc. And they are really useful to researchers because as they are not used for anything, they acquire mutations readily (mutations to them are not purged) and so help with the construction of genetic phylogenies.

    Of course it’s possible that DNA may be more “expensive” to maintain than we think, and that therefore there may be a selective advantage to mutations that omit useless sections, reducing the amount of “Junk” likely to accumulate.

    But there does seem to be a fair bit of junk in there, as predicted.

    But also a fair bit of stuff which we are now discovering uses for – which is really exciting. Protein coding genes are fairly boring really. What is much more exciting are genes that control which proteins are produces when under what conditions, because that’s what makes organisms develop and function.

  22. 22
    Elizabeth Liddle

    Mung:

    Dawkins is claiming all DNA is there to build bodies and that’s it’s only purpose.

    How stupid is that, yeah?

    Pretty stupid. But did he really claim that?

  23. Well, I suppose he could have just been using it as a straw-man for his selfish gene theory.

    You know, if you want to make your theory look better than another theory make up a really stupid other theory to compare your theory with and then declare yours the victor.

    But surely Dawkins wouldn’t do that.

  24. 24

    Re: c-value enigma. Ah! Brilliant! That’s exactly what I was talking about (and have been for years).

    Regarding your extremely vague suggestions that all of that extra DNA has some important function…

    Really? To avoid the conclusion that a lot of DNA is nonfunctional, you’re really going to argue that onions, of all things, *need* drastically different amounts of functional DNA to build themselves?

    Go take the Onion Test. It was devised by T. Ryan Gregory — the very same scientist who coined the term “c-value enigma”, actually!

    http://pandasthumb.org/archive.....unk-s.html

    Re: the correlation between cell volume and genome size. This is well-known. There are several proposed explanations, e.g. “skeletal DNA” (genome size physically determines nucleus size, which determines cell size which is under selection for growth rate) and “not costly enough to remove” (slow-growing species have low population sizes and generation times, thus selective pressure against extra DNA).

    What all the explanations have in common is that most of the DNA of large genomes has no sexy “information” or “coding” function. At best it has a function in bulk, i.e. the “function” is taking up space, where the actual sequence doesn’t matter as long as it doesn’t cause problems. None of this is what the ID guys are talking about.

  25. Nick, Let’s skip your theologically based ‘bad design’ argument for a minute and take your atheistic presuppositions to their logical conclusion. If neo-Darwinism and materialism are true then science would be impossible in the first place!! Thus, neo-Darwinism defeats itself with its own internal inconsistency towards first principles of science;

    Should You Trust the Monkey Mind?
    Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties.
    http://www.firstthings.com/ont.....onkey-mind

    What is the Evolutionary Argument Against Naturalism? (‘inconsistent identity’ of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) – video
    http://www.youtube.com/watch?v=5yNg4MJgTFw

    Can atheists trust their own minds? – William Lane Craig On Alvin Plantinga’s Evolutionary Argument Against Naturalism – video
    http://www.youtube.com/watch?v=byN38dyZb-k

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?” – Charles Darwin – Letter To William Graham – July 3, 1881

    It is also interesting to point out that this ‘inconsistent identity’, pointed out by Plantinga, which leads to the failure of neo-Darwinists to make absolute truth claims for their beliefs, is what also leads to the failure of neo-Darwinists to be able to account for objective morality, in that neo-Darwinists cannot maintain a consistent identity towards a cause for objective morality;

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

    “Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth.
    As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain.” Creation-Evolution Headlines
    http://creationsafaris.com/cre.....#20110227a

    This following video humorously reveals the bankruptcy that atheists have in trying to ground beliefs within a materialistic worldview;

    John Cleese – The Scientists – humorous video
    http://www.youtube.com/watch?v=-M-vnmejwXo

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

    Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:

    Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video
    http://www.metacafe.com/watch/5318486/

    This following site is a easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.

    Proof That God Exists – easy to use interactive website
    http://www.proofthatgodexists.org/index.php

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes.
    http://www.faqs.org/periodical.....27241.html

    etc.. etc.. etc..

    Nick, perhaps you think this is all trivial, but I beg to differ!!! If you cannot establish a firm foundation onto which to make ‘truth’ claims in the first place, why in blue blazes should I pay any attention, whatsoever, to what you have to say about science???

  26. But to bring this back a little to the topic Nick, it is important to note just what you have chosen to ignore to focus on your theologically based ‘bad design’ argument: You have chosen to ignore the fact that we are dealing with a level of complexity that exceeds anything man has ever done in his most advanced computers by several orders of magnitude:

    Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information – David L. Abel and Jack T. Trevors – Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8
    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?”
    http://www.biomedcentral.com/c.....2-2-29.pdf

    First-Ever Blueprint of ‘Minimal Cell’ Is More Complex Than Expected – Nov. 2009
    Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae’s transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation.
    “At all three levels, we found M. pneumoniae was more complex than we expected,”
    http://www.sciencedaily.com/re.....173027.htm

    There’s No Such Thing as a ‘Simple’ Organism – November 2009
    Excerpt: In short, there was a lot going on in lowly, supposedly simple M. pneumoniae, and much of it is beyond the grasp of what’s now known about cell function.
    http://www.wired.com/wiredscie.....s-of-life/

    Scientists Map All Mammalian Gene Interactions – August 2010
    Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome.
    http://www.sciencedaily.com/re.....142044.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

    And on top of this staggering complexity, complexity that should make any sane man drop to his knees and praise God, you have also chosen to ignore the sheer poverty that neo-Darwinian processes have in generating any functional complexity whatsoever:

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe, Jay Richards – audio
    http://intelligentdesign.podom.....9_03-07_00

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    etc.. etc.. etc..

    Brooke Fraser – Lord of Lords(Legendado Português) – music video
    http://www.youtube.com/watch?v=rkF3iVjOZ1I

  27. Hey, bornagain77, in spite of our precise citations, in which it is clear the ET false prediction about the vast majority of “junk” DNA (not only a little amount), the can only appeal to an “onion”..

    Is this not called “argument from ignorance”?

    Committing the same error over and over..

    “We don’t know why onions DNA is longer than ours, so the vast majority of it must be junk, i.e. the origin of life must be chance and necessity and we must have evolved..”

    To Elizabeth Liddle:

    We’re addressing ET false predictions (and ET bishop’s false claims too) about the ***vast part*** of junk DNA in all species, not some strings of *apparent* “junk” value that seem to exist in DNA.

  28. To avoid the conclusion that a lot of DNA is nonfunctional, you’re really going to argue that onions, of all things, *need* drastically different amounts of functional DNA to build themselves?

    STRAWMAN!

  29. 29
    To avoid the conclusion that a lot of DNA is nonfunctional, you’re really going to argue that onions, of all things, *need* drastically different amounts of functional DNA to build themselves?

    STRAWMAN!

    What? Why? Look, it’s very simple.

    1. You guys say junk DNA is a myth.

    2. I point out that one onion species has 5 times more DNA than humans.

    3. I further point out that another onion species has ~25 times more DNA than humans.

    4. I argue that it is therefore plausible that those onions have a lot of DNA they don’t need. I.e., this is strong evidence for junk DNA, and for Dawkins’s initial statement being correction.

    In response? You guys do nothing but shout “STRAWMAN”, with no rebuttal argument, or just blatantly try to change the subject (bornagain77).

    This is why creationism/ID eventually loses in schools, courtrooms, etc., again and again and again. The actual details of the science do not support the endless-repeated and never-checked ID talking points.

  30. Hey Nick, speaking of details of science being ignored by Darwinists: Please tell me where the DNA code came from in the first place, this is a fairly significant detail:

    “an attempt to explain the formation of the genetic code from the chemical components of DNA… is comparable to the assumption that the text of a book originates from the paper molecules on which the sentences appear, and not from any external source of information.”
    Dr. Wilder-Smith

    DNA Enigma – Chemistry Does Not Create Information – Ashcraft
    http://www.metacafe.com/watch/5542033/

    Stephen C. Meyer – The DNA Enigma
    http://www.metacafe.com/watch/yt-AmnVNc7jcFk/

    A New Design Argument – Charles Thaxton
    Excerpt: “There is an identity of structure between DNA (and protein) and written linguistic messages. Since we know by experience that intelligence produces written messages, and no other cause is known, the implication, according to the abductive method, is that intelligent cause produced DNA and protein. The significance of this result lies in the security of it, for it is much stronger than if the structures were merely similar. We are not dealing with anything like a superficial resemblance between DNA and a written text. We are not saying DNA is like a message. Rather, DNA is a message. True design thus returns to biology.”
    http://www.arn.org/docs/thaxto.....gn3198.htm

    The DNA Enigma – Where Did The Information Come From? – Stephen C. Meyer – video
    http://www.metacafe.com/watch/4125886/

    The DNA Code – Solid Scientific Proof Of Intelligent Design – Perry Marshall – video
    http://www.metacafe.com/watch/4060532

    Codes and Axioms are always the result of mental intention, not material processes
    https://docs.google.com/document/pub?id=1PrE2Syt5SJUxeh2YBBBWrrPailC3uTFMdqPMFrzvwDY

    “A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107.”
    (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

    Shannon Information – Channel Capacity – Perry Marshall – video
    http://www.metacafe.com/watch/5457552/

    “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
    Donald E. Johnson – Bioinformatics: The Information in Life

    “In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10].
    Donald E. Johnson – Programming of Life – pg.51 – 2010

    etc.. etc..

  31. Nick, the ‘onion test’ is addressed on pg 85-87 in Wells’s book ‘The Myth Of Junk DNA’,,, If you don’t have a copy you may order it here:

    The Myth of Junk DNA
    http://www.amazon.com/Myth-Jun.....1936599007

    The ‘wrap up’ by Wells on page 87 is this;

    ‘So the onion test is a red herring. Why onion cells have five times as much DNA as human cells is an interesting question, but it poses no challenge to the growing evidence against the myth of junk DNA.’

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

    Notes:

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

    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

  32. Nick Matzke:

    In response? You guys do nothing but shout “STRAWMAN”, with no rebuttal argument, or just blatantly try to change the subject (bornagain77).

    Find someone here who thinks the sole purpose of DNA is for building the organism that contains it.

    I’m not that person.

    If you cannot find someone here who believes that, it’s a strawman indeed. So yes. That’s the appropriate response.

  33. 33

    The Myth of Junk DNA
    http://www.amazon.com/Myth-Jun…..1936599007

    The ‘wrap up’ by Wells on page 87 is this;

    ‘So the onion test is a red herring. Why onion cells have five times as much DNA as human cells is an interesting question, but it poses no challenge to the growing evidence against the myth of junk DNA.’

    This provides no answer, except mere assertion, against the points I raised. Some onions have 20 human genomes worth of DNA that appears to be completely unnecessary for building an onion.

    If Wells **explains** why this hard, empirical data doesn’t support the pro-junk DNA side, then quote that! Otherwise, you’ve got nothing.

  34. 34

    Mung writes,

    Find someone here who thinks the sole purpose of DNA is for building the organism that contains it.

    I’m not that person.

    If you cannot find someone here who believes that, it’s a strawman indeed. So yes. That’s the appropriate response.

    I’m not the one defending the position that “junk DNA is a myth”, and that most/all DNA is functional and “Darwinists” were stupid for ever thinking otherwise.

    If you agree with me, that junk DNA is NOT a myth, well then, welcome to my side! And too bad for Wells and the ID movement, that they can’t convince even a sympathetic listener once the listener has been informed of the basic facts.

  35. Tell you what Nick, since you think you can design a genome better than the one we find in life, lay it all out for me. I am a willing listener. But something tells me you are not going to be embarrassing God anytime soon!!!

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.
    http://www.sciencedaily.com/re.....142957.htm

  36. 36

    Correction on my figures, although they don’t change the argument:

    human genome = 3.5 picograms of DNA (about 3 Megabases)

    onion genome sizes range from 7 pg (twice the human genome size) to 31.5 (9 times the human genome size)

    So: why do some onions take *7 human genomes worth of DNA* **more** to build an onion that is basically similar to another onion?

  37. 37

    Born: “Hey Nick, speaking of details of science being ignored by Darwinists: Please tell me where the DNA code came from in the first place, this is a fairly significant detail:”

    Yes, do tell.

  38. 38

    Tell you what Nick, since you think you can design a genome better than the one we find in life, lay it all out for me. I am a willing listener. But something tells me you are not going to be embarrassing God anytime soon!!!

    *You ID guys* are the ones saying that the genome is like computer code, it’s information-dense, and it’s mostly functional, and that scientists were stupid for thinking that a lot of it was junk. In fact, “we predicted junk DNA wasn’t junk” is the single leading talking point IDists have about how ID can allegedly be useful science.

    Now, the ID claims can be right or wrong. I am pointing out simple facts that indicate that the ID claims are wrong, because an awful lot of the DNA in many genomes looks like, basically, junk. It’s unnecessary. We know this because nearly identical organisms don’t have it and are just fine.

  39. 39
    Elizabeth Liddle

    Jonin:

    We’re addressing ET false predictions (and ET bishop’s false claims too) about the ***vast part*** of junk DNA in all species, not some strings of *apparent* “junk” value that seem to exist in DNA.

    Can you find me a citation in which somebody representing “ET” makes the claim that ET predicts that the vast part of DNA in all species will be junk?

    I would be intrigued to see the reasoning behind such a bizarre claim.

  40. Arthur :
    Thank you for the links; they made for some deep but interesting reading. I did note, however, that as much as the blogger touted the fact that this discovery didn’t reflect favorably on ID, he did write that, “the supposed functional swaths of non-coding junk DNA may be nothing more than parts of the genome that encode, and lead to the production of, “junk” RNA (if I may so bold as to coin a phrase).” Notice the word “may”. In other words, it’s not entirely supportive of Darwinian evolution, either, simply because we don’t have all the answers right now.
    Also, the first linked essay noted that there might be some “hitherto hitherto overlooked aspects of promoter and chromatin structure and function.” In other words, it might not all be junk piling on top of junk; that’s an unwarranted assertion.

    Nick writes, “…because an awful lot of the DNA in many genomes looks like, basically, junk. It’s unnecessary. We know this because nearly identical organisms don’t have it and are just fine.”
    You do not know for a fact that it is unnecessary. What works for an onion will not necessarily work for a penguin, a head of cabbage, or a human being. This is another unwarranted assertion. Also, there still is no evolutionary explanation of where the DNA came from in the first place.

  41. 41

    “You do not know for a fact that it is unnecessary. What works for an onion will not necessarily work for a penguin, a head of cabbage, or a human being.”

    True. But we see similar wide variations in genome size in many, many groups.

    “You do not know for a fact that it is unnecessary.”

    True, we don’t know it for a fact. But a lot of very basic, very simple data points that way. Yet for some reason the IDists are trumpetting from the hilltops the idea that junk DNA is pure myth, that evolutionists were dumb to believe it, etc., etc., when in fact the actual data and actual science still say a huge amount of DNA lacks any very sexy informational “function.”

    “This is another unwarranted assertion.”

    This is far, far more true about the ID side’s statements on the junk DNA issue.

    “Also, there still is no evolutionary explanation of where the DNA came from in the first place.”

    We know where those huge variations in genome size came from: replication of repetitive elements, genome duplications, deletion events, etc. The origin of life itself? Different topic entirely, start a new thread for that.

  42. Nick claims;

    ‘We know where those huge variations in genome size came from: replication of repetitive elements, genome duplications, deletion events, etc.’

    And yet real world data states:

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2....._edge.html

    Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution” – Michael J. Behe – December 2010
    Excerpt: In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.
    http://www.journals.uchicago.e.....086/656902

    Again I would like to emphasize, I’m not arguing Darwinism cannot make complex functional systems, the data on malaria, and the other examples, are a observation that it does not. In science observation beats theory all the time. So Professor (Richard) Dawkins can speculate about what he thinks Darwinian processes could do, but in nature Darwinian processes have not been shown to do anything in particular.
    Michael Behe – 46 minute mark of video lecture on ‘The Edge of Evolution’ for C-SPAN
    http://www.uncommondescent.com.....ent-361037

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    Epistasis between Beneficial Mutations – July 2011
    Excerpt: We found that epistatic interactions between beneficial mutations were all antagonistic—the effects of the double mutations were less than the sums of the effects of their component single mutations. We found a number of cases of decompensatory interactions, an extreme form of antagonistic epistasis in which the second mutation is actually deleterious in the presence of the first. In the vast majority of cases, recombination uniting two beneficial mutations into the same genome would not be favored by selection, as the recombinant could not outcompete its constituent single mutations.
    http://www.uncommondescent.com.....ach-other/

    further note as to functionality of ‘junk’ DNA:

    Gene Regulatory Networks in Embryos Depend on Pre-existing Spatial Coordinates – jonathan Wells – July 2011
    Excerpt: The development of metazoan embryos requires the precise spatial deployment of specific cellular functions. This deployment depends on gene regulatory networks (GRNs), which operate downstream of initial spatial inputs (E. H. Davidson, Nature 468 [2010]: 911). Those initial inputs depend, in turn, on pre-existing spatial coordinate systems. In Drosophila oocytes, for example, spatial localization of the earliest-acting elements of the maternal GRN depends on the prior establishment of an anteroposterior body axis by antecedent asymmetries in the ovary. Those asymmetries appear to depend on cytoskeletal and membrane patterns rather than on DNA sequences,,,
    http://www.evolutionnews.org/2.....48301.html

    etc.. etc.. etc..

    So Nick, what am I to believe the actual evidence or what you dogmatically want the evidence to say so as to conform to your atheistic worldview????

  43. Nick Matzke:

    Some onions have 20 human genomes worth of DNA that appears to be completely unnecessary for building an onion.

    Strawman. Repeating it more than once and saying ‘onion’ instead of ‘human’ doesn’t make it not a strawman.

    ok, so back to basics. Nick, do you know what a strawman is?

  44. Nick, do you know what a strawman is?

    Silly me. Of course you do! That’s why you’re doing it. DOH!

  45. Nick Matzke:

    So: why do some onions take *7 human genomes worth of DNA* **more** to build an onion that is basically similar to another onion?

    Straw-man, Straw-man.

    Nick, do you seriously want us to believe that the sole purpose of all onion DNA is to build an onion and that the sole purpose all of human DNA is to build a human?

    Why would we believe such a thing?

  46. Nick Matzke:

    Re: c-value enigma. Ah! Brilliant! That’s exactly what I was talking about (and have been for years).

    Hi nick,

    Certainly you understand that the c-value enigma didn’t arise because of intelligent design?

    I mean, it’s an enigma for you. Why should it be an enigma for ID theory?

    Oh, can i, can i? Puleeeeeze!!!

    IT’S NOT.

  47. Elizabeth Liddle:

    I would be intrigued to see the reasoning behind such a bizarre claim.

    Says the lady who insists that “junk DNA” is a prediction of evolutionary theory.

  48. Nick Matzke:

    We know where those huge variations in genome size came from: replication of repetitive elements, genome duplications, deletion events, etc.

    Well, we think that might be where they come from. But why would events like that occur more often in an onion than in a human?

    Is this true of all onions?

    Is this something that seems to happen more often in plants than in animals?

    You’re not comparing onions and humans again are you?

  49. 49

    Nick, do you seriously want us to believe that the sole purpose of all onion DNA is to build an onion and that the sole purpose all of human DNA is to build a human?

    Why would we believe such a thing?/

    Oh really? IDists have proposed a different purpose for DNA? What is it, pray tell?

  50. 50

    Oops, hit send too soon. Trying again:

    Nick, do you seriously want us to believe that the sole purpose of all onion DNA is to build an onion and that the sole purpose all of human DNA is to build a human?

    Why would we believe such a thing?

    Oh really? IDists have proposed a different purpose for DNA? The ID focus, ever since they started talking about junk DNA has been *entirely* on the premise that “junk DNA” is “chock-full” of information that codes for stuff — gene regulation mostly, which is allegedly necessary for building and maintaining an organism.

    Based on the table of contents of Wells’s book, Wells might have finally realized the problem that wild genome size variation poses for standard ID claims about junk DNA, and tried to paper it over, probably by acknowledging the genome-size vs. cell size correlation, which “Darwinists” have been talking about for decades and which I already addressed.

    But apart from that? I’ve read pretty much all of the ID literature and blogs etc. I bet you can’t find a single instance of an IDist proposing some function for junk DNA other than hidden coding information for building and maintaining and organism.

  51. 51

    Mims/Dembski: “As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science against assuming that ‘junk’ DNA was ‘useless.’” Science wouldn’t print Mims’ letter, but soon thereafter, in 1998, leading ID theorist William Dembski repeated this sentiment in First Things: “[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. Design encourages scientists to look for function where evolution discourages it.”

    Nick: At best it has a function in bulk, i.e. the “function” is taking up space, where the actual sequence doesn’t matter as long as it doesn’t cause problems.

    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

  52. 52
    Elizabeth Liddle

    Mung @ 47:

    Can you re-read, please, the post of mine you half quoted?

    Here it is:

    Can you find me a citation in which somebody representing “ET” makes the claim that ET predicts that the vast part of DNA in all species will be junk?

    I would be intrigued to see the reasoning behind such a bizarre claim.

    Also please link to where I apparently “insist… that “junk DNA” is a prediction of evolutionary theory.”

    Thanks.

  53. 53
    Elizabeth Liddle

    Mung:

    Straw-man, Straw-man.

    Nick, do you seriously want us to believe that the sole purpose of all onion DNA is to build an onion and that the sole purpose all of human DNA is to build a human?

    Why would we believe such a thing?

    I have no idea, Mung. It’s patently untrue. A lot of DNA is for ensuring that an organism actually functions. Our brains wouldn’t work, and we’d be unable to remember anything unless genes in neurons were being expressed to modify neural connections.

    But I’m not aware that onions do a lot of remembering.

  54. Nick, I remember a few years back when many neo-Darwinists denied that information was even in DNA!!! ,,,But then again it never was about science in the first place was it Nick???,, Especially since you cannot even justify doing science within your neo-Darwinian worldview!!!!,,, as clearly noted here:

    http://www.uncommondescent.com.....ent-390161

    And Nick exactly how does finding multiple layers of overlapping functional complexity, in the genome, help your neo-Darwinian case in the least??? Would not finding complexity stacked on top of complexity provide exponentially larger levels of constraint on neo-Darwinism???

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

    “There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns – which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture – which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
    Dr. John Sanford; Genetic Entropy 2005

    notes as to higher level functionality:

    On Not Reading Signature in the Cell: A Response to Francisco Ayala
    Excerpt: In general, SINEs (and thus Alus) allow genetic information to be retrieved in multiple different ways from the same DNA data files depending on the specific needs of different cell types or tissues (in different species-specific contexts). In particular, Alu sequences perform many taxon-specific lower-level genomic formatting functions such as: (1) providing alternative start sites for promoter modules in gene expression–somewhat like sectoring on a hard drive (Faulkner et al., 2009; Faulkner and Carninci, 2009); (2) suppressing or “silencing” RNA transcription (Trujillo et al., 2006); (3) dynamically partitioning one gene file from another on the chromosome (Lunyak et al., 2007); (4) providing DNA nodes for signal transduction pathways or binding sites for hormone receptors (Jacobsen et al., 2009; Laperriere et al., 2004); (5) encoding RNAs that modulate transcription (Allen et al., 2004; Espinoza et al., 2004; Walters et al., 2009); and (6) encoding or regulating microRNAs (Gu et al., 2009; Lehnert et al., 2009).

    In addition to these lower-level genomic formatting functions, SINEs (including Alus) also perform species-specific higher-level genomic formatting functions such as: (1) modulating the chromatin of classes of GC-rich housekeeping and signal transduction genes (Grover et al., 2003, 2004; Oei et al., 2004; see also Eller et al., 2007); (2) “bar coding” particular segments for chromatin looping between promoter and enhancer elements (Ford and Thanos, 2010); (3) augmenting recombination in sequences where Alus occur (Witherspoon et al., 2009); and (4) assisting in the formation of three-dimensional chromosome territories or “compartments” in the nucleus (Kaplan et al., 1993; see also Pai and Engelke, 2010).
    Moreover, Alu sequences also specify many species-specific RNA codes. In particular, they provide: (1) signals for alternative RNA splicing (i.e., they generate multiple messenger RNAs from the same type of precursor transcript) (Gal-Mark et al., 2008; Lei and Vorechovsky, 2005; Lev-Maor et al., 2008) and (2) alternative open-reading frames (exons) (Lev-Maor et al., 2007; Lin et al., 2008; Schwartz et al., 2009). Alu sequences also (3) specify the retention of select RNAs in the nucleus to silence expression (Chen et al., 2008; Walters et al., 2009); (4) regulate the RNA polymerase II machinery during transcription (Mariner et al., 2008; Yakovchuk et al., 2009; Walters et al., 2009); and (5) provide sites for Adenine-to-Inosine RNA editing, a function that is essential for both human development and species-specific brain development (Walters et al., 2009).
    Contrary to Ayala’s claim, Alu sequences (and other mammalian SINEs) are not distributed randomly but instead manifest a similar “bar-code” distribution pattern along their chromosomes (Chen and Manuelidis, 1989; Gibbs et al., 2004; Korenberg and Rykowski, 1988). Rather like the distribution of the backslashes, semi-colons and spaces involved in the formatting of software code, the “bar-code” distribution of Alu sequences (and other SINEs) reflects a clear functional logic, not sloppy editing or random mutational insertions. For example, Alu sequences are preferentially located in and around protein-coding genes as befits their role in regulating gene expression (Tsirigos and Rigoutsos, 2009). They occur mainly in promoter regions–the start sites for RNA production–and in introns, the segments that break up the protein-coding stretches. Outside of these areas, the numbers of Alu sequences sharply decline. Further, we now know that Alu sequences are directed to (or spliced into) certain preferential hotspots in the genome by the protein complexes or the “integrative machinery” of the cell’s information processing system (Levy et al., 2010). This directed distribution of Alu sequences enhances the semantic and syntactical organization of human DNA. It appears to have little to do with the occurrence of random insertional mutations, contrary to the implication of Ayala’s “sloppy editor” illustration and argument. (page down for 33 references of ALU functionality)
    http://www.stephencmeyer.org/n.....art_2.html

    And let’s not forget Nick,,,

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

    Human Genome “Infinitely More Complex” Than Expected – April 2010
    Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said,,,, Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.”
    http://www.creationsafaris.com.....#20100405a

    Contrary to Darwinian expectations for ‘simplicity’ at the basis of life, the complexity being uncovered in genomes keeps increasing dramatically as our resolution increases:

    Most Detailed Annotation of Fruit-Fly Genome Points Way to Understanding All Organisms’ Genomes – December 2010
    Excerpt: “We also found an order-of-magnitude increase in the ways that genes are spliced and edited to produce alternate forms of known proteins, thus significantly increasing the complexity of the proteome.”,,, Despite the scrutiny to which the Drosophila genome has been subjected, the researchers found new or altered exons or splice forms in almost three-quarters of Drosophila’s previously annotated genes,,,
    http://www.sciencedaily.com/re.....131131.htm

    Astonishing DNA complexity update
    Excerpt: The untranslated regions (now called UTRs, rather than ‘junk’) are far more important 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/astonishin.....ity-update

    etc.. etc.. etc…

  55. 55

    LOL, Mung vs. other pro-ID commentators:

    Mung:

    Straw-man, Straw-man.

    Nick, do you seriously want us to believe that the sole purpose of all onion DNA is to build an onion and that the sole purpose all of human DNA is to build a human?

    Why would we believe such a thing?

    If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. Design encourages scientists to look for function where evolution discourages it.”

    And Nick exactly how does finding multiple layers of overlapping functional complexity, in the genome, help your neo-Darwinian case in the least??? Would not finding complexity stacked on top of complexity provide exponentially larger levels of constraint on neo-Darwinism???

    If the latter arguments are made, then Mung can’t claim it’s a strawman to say that ID expects “junk DNA” to have informational function.

  56. 56

    Dembski 1998: “If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function…Design encourages scientists to look for function where evolution discourages it.”

    Nick: …“Mung can’t claim it’s a strawman to say that ID expects “junk DNA” to have informational function.

    Wiggle it in there baby.

  57. LOL, Elizabeth Liddle vs. Nick Matzke.

    I have no idea, Mung. It’s patently untrue. A lot of DNA is for ensuring that an organism actually functions.

    Yes Nick, it’s patently untrue. That means it’s obviously untrue. One hardly needs an argument to see so.

    Yet that doesn’t stop you.

    And perhaps at least a teeny bit of DNA is there for the purpose of reproduction.

    And I think it’s also funny how the silly claim relied on purpose.

    Come back when you’ve left the strawman at home Nick. Others may fall for it, I won’t.

  58. Nick Matzke:

    Mung can’t claim it’s a strawman to say that ID expects “junk DNA” to have informational function.

    That would be just stupid. By definition junk DNA has no function.

    But that’s not what I was claiming, so it’s a red herring.

    So Nick.

    Straw man.

    Red herring.

    So typical of “arguments” against ID.

  59. Time for review:

    Dawkins is right. Many very similar species have very different genome sizes. For example, onions. Many “simpler” species, like lungfish and ferns, have genomes up to 100 times bigger than the human genome.

    Thus, it really is true that many species have way more DNA than is needed to build them.

    Oh my. Therefore, ID must be false.

  60. Time for review:

    Dawkins is right. Many very similar species have very different genome sizes.

    Therefore, ID must be false.

  61. 61
    Elizabeth Liddle

    Mung:

    1. DNA does more than build an organism – it also ensures it functions
    2. Not all DNA codes for proteins
    3. Some DNA is junk, i.e. does nothing, including pseudogenes, ervs and huge repeats
    4. Onions appear to have a large amount of junk
    5. Evolutionary theory suggests that unless there is an organismal cost to making DNA, junk will tend to accumulate.
    6. The existence of junk DNA is consistent with Darwinian evolution
    7. It is possibly consistent with ID too.

    What is your point?

  62. 62

    “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”

    –I’ve seen this quoted a number of times, apparently as an argument against junk dna, although I’m not sure why. Isn’t this exactly what we’d expect if much of the genome is junk dna? If there is selective pressure to increase metabolism, consequently there is selective pressure to decrease cell size, and consequently selective pressure to decrease the genome size. If the genomes of animals with higher metabolism didn’t shrink, despite the selective pressure to do so, than presumably that would mean there isn’t much room for their genomes to shrink, which would hardly square with the idea that much of the genome is junk.

  63. goodusername you ask:

    ‘Isn’t this exactly what we’d expect if much of the genome is junk dna?’

    Actually no, but failed predictions never stopped neo-Darwinists before so I don’t it will bother you now.

    Darwin’s Predictions
    http://www.darwinspredictions.com/

    Darwin’s Predictions With Cornelius Hunter – podcast with Cornelius Hunter
    http://intelligentdesign.podom.....3_23-08_00

  64. a more recent podcast:

    Failed Predictions of Evolutionists – Cornelius Hunter – audio
    http://intelligentdesign.podom.....0_49-08_00

  65. 65

    ba77:

    I listened to the podcasts and looked over the website, but couldn’t find anything regarding this topic.

    But about the “failed prediction”. Are you saying that given a) that junk dna is real and b) selective pressure to shrink the genome, that the genome shouldn’t shrink? What do you think the prediction should be given those premises? That the genome should grow? Stay the same size?

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