'Junk DNA' Intelligent Design

Does Evolutionary Theory Really Help Scientists?

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For a number of years, many of us at UD have made the argument that evolutionary theory, in practice, is of almost no help whatsoever in getting at the secrets of biology. I’ve taken the position personally that it actually hurts, and that it is not a matter of indifference to the study of biology whether evolution is employed or not. ID is the way to go.

In this study reported on at Phys.Org, scientists looked at a particular portion of “non-coding” RNA in the zebra fish and found that it actually does code for a protein (which they call “Toddler”), and which turns out to be almost essential in the proper development of the embryo. Cutting out the sequence for “Toddler” results in improper development of, or the entire loss of, a heart, and subsequent death because the embryo fails to enter the gastrula stage of early embryonic development.

Here’s the important quote for the point I want to make:

“We have been interested in this question [of what triggers gastrulation] for 20 years,” Alexander Schier, the Leo Erikson Life Sciences Professor of Molecular and Cellular Biology and senior author of the study, said of discovering the new signal. “We’ve made a great deal of progress in understanding how these cells are made, but we could never really explain why these cells suddenly start to move. This new signal is part of the answer.”

They’ve studied this embryonic stage for 20 years, and couldn’t figure out the decisive signals for initiation of the gastrula. They had to look to “non-coding” RNA, i.e., “junk DNA,” in order to solve their new found secret.

And why didn’t they study “junk DNA” before? Well, evolutionary theory posits that it is “junk” (their word, not ours), so why investigate.

Meanwhile, ID would say this: the genes are the cells tools; how to use these tools and building materials MUST BE encoded in the “non coding” (nc) portions of DNA. IOW, from an ID perspective, one of the first moves one would make in studying why “cells suddenly start to move” would be look at the nc-DNA.

Has evolutionary theory put these scientists 20 years behind? I’ll let you be the judge of that.

Read more at: http://phys.org/news/2014-02-cells.html#jCp

53 Replies to “Does Evolutionary Theory Really Help Scientists?

  1. 1
    wd400 says:

    Except, of course, this myth that all non-coding DNA was once considered junk is absurd. From the very first mention of junk DNA regulatory sequences were considered functional, and functional RNAs have been known since the 1970s.

    On the other hand, this protein was identified in part due to it’s evolutionary conservation…

  2. 2
    Joe says:

    wd400-

    Just how does unguided evolution explain regulatory networks? How does the blind watchmaker make sense non-coding sequences having a function?

    From a design standpoint that is easily explained due to our knowledge of cause and effect relationships. However if you are looking at living organisms from a materialistic PoV, then such layers of information would not be expected and impossible to explain, scientifically.

  3. 3
    JGuy says:

    Except, of course, this myth that all non-coding DNA was once considered junk is absurd. From the very first mention of junk DNA regulatory sequences were considered functional, and functional RNAs have been known since the 1970s.

    Then why the discovery lag?

    On the other hand, this protein was identified in part due to it’s evolutionary conservation…

    That isn’t really on the other hand, because that is comparative anatomy – not evolution. Referring to observed homologies evolutionary conservation is begging the question.

  4. 4
    JGuy says:

    edit: Referring to observed homologies [as] evolutionary conservation is begging the question.

  5. 5
    bornagain77 says:

    as to:

    Does Evolutionary Theory Really Help Scientists?

    NO!!! Materialists like to claim evolution is indispensable to experimental biology and led the way to many breakthroughs in medicine, Yet in a article entitled “Evolutionary theory contributes little to experimental biology”, this expert author begs to differ.

    “Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming’s discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin’s theory was wrong. The responses were all the same: No.,,, In the peer-reviewed literature, the word “evolution” often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for “evolution” some other word – “Buddhism,” “Aztec cosmology,” or even “creationism.” I found that the substitution never touched the paper’s core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology.”
    Philip S. Skell – (the late) Emeritus Evan Pugh Professor at Pennsylvania State University,

    The Late Dr. Skell is hardly alone in this sentiment

    “In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, and physiology, have not taken evolution into account at all.”
    Marc Kirschner, Boston Globe, Oct. 23, 2005

    “While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that “Nothing in biology makes sense except in the light of evolution”, most can conduct their work quite happily without particular reference to evolutionary ideas. Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superflous one.”
    A.S. Wilkins, editor of the journal BioEssays, Introduction to “Evolutionary Processes” – (2000).
    Does Biology Make Sense Without Darwin? – Dr. David Menton – video
    https://www.youtube.com/watch?v=K9znyGQo2QE

    Science Owes Nothing To Darwinian Evolution – Jonathan Wells – video
    http://www.metacafe.com/watch/4028096

    Even the famed atheist Francis Crick, co-discoverer of the DNA helix, admitted as much:

    “Biologists must constantly keep in mind that what they see was not designed, but rather evolved. It might be thought, therefore, that evolutionary arguments would play a large part in guiding biological research, but this is far from the case. It is difficult enough to study what is happening now. To figure out exactly what happened in evolution is even more difficult. Thus evolutionary achievements can be used as hints to suggest possible lines of research, but it is highly dangerous to trust them too much. It is all too easy to make mistaken inferences unless the process involved is already very well understood.”
    Francis Crick – What Mad Pursuit (1988)

    At the 7:00 minute mark of this following video, Dr. Behe gives an example of how evidence is falsely attributed to Darwinian processes by using the word ‘evolution’ as a sort of coda in peer-reviewed literature for how a system came about with never an actual demonstration by Darwinian processes of how the system actually came about:

    Michael Behe – Life Reeks Of Design – video
    http://www.metacafe.com/watch/5066181/

    In fact, in so far as Darwinian presuppositions have influenced scientific research they have had a overwhelming tendency to mislead researchers. Nowhere is this more evident than in the recent Junk DNA fiasco,,,

    Matheson’s Intron Fairy Tale – Richard Sternberg – June 2010
    Excerpt: The failure to recognize the importance of introns “may well go down as one of the biggest mistakes in the history of molecular biology.”
    –John Mattick, Molecular biologist, University of Queensland, quoted in Scientific American,,,
    http://www.evolutionnews.org/2.....35301.html

    On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. – Richard Sternberg – 2002
    Excerpt: It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian “narratives” have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes.
    http://www.ncbi.nlm.nih.gov/pubmed/12547679

    Is Panda’s Thumb Suppressing the Truth about Junk DNA?
    Excerpt: Dr. Pellionisz sent me an e-mail regarding his recent experiences at Panda’s Thumb. Pellionisz reports that Panda’s Thumb is refusing to print his stories about how he has personally witnessed how the Darwinian consensus rejected suggestions that “junk” DNA had function. Dr. Pellionisz’s e-mail recounts how some rogue Darwinian biologists have believed that “junk” DNA had function, but it also provides historical proof that this went against the prevailing consensus, and thus such suggestions that “junk”-DNA had function were ignored or rejected by most Darwinian scientists.
    http://www.evolutionnews.org/2.....03947.html

    And please bear in mind that even though the information in the DNA, that researchers have barely been able to decode thus far, is orders of magnitude more sophisticated than anything man has yet devised in his most advanced computers and computer programs,

    ENCODE: Encyclopedia Of DNA Elements – video
    http://www.youtube.com/watch?v=Y3V2thsJ1Wc
    Quote from preceding video:
    “It’s very hard to get over the density of information (in the genome),,, The data says its like a jungle of stuff out there. There are things we thought we understood and yet it is much, much, more complex. And then (there are) places of the genome we thought were completely silent and (yet) they’re (now found to be) teeming with life, teeming with things going on. We still really don’t understand that.”
    Ewan Birney – senior scientist – ENCODE 2012

    ,,,and even with the leader of ENCODE 2012 declaring the metaphor of Junk DNA isn’t that useful for research,,,

    Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin – September 5, 2012
    Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well:
    “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.””
    http://www.evolutionnews.org/2.....64001.html

    ,,,in spite of all this unfathomed complexity in DNA, We still find hard core neo-Darwinists such as Coyne, Moran, Meyers, and even our own wd400 on UD, fighting tooth and nail for the concept of DNA. I would think the whole thing fiction if I had not witnessed them do it first hand!

  6. 6
    bornagain77 says:

    Moreover, ‘Junk’ DNA is hardly the only place where Darwinian presuppositions are useless for useful guidance. In medical diagnostics Darwinian presuppositions are useless:

    Darwinian Medicine and Proximate and Evolutionary Explanations – Michael Egnor – neurosurgeon – June 2011
    http://www.evolutionnews.org/2.....47701.html

    and even In the development of medicine itself with animal testing, the false Darwinian presupposition that we are all related to lower animals is useless and misleading for research (besides wasting billions of dollars of research money)

    The mouse is not enough – February 2011
    Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.”
    http://www.the-scientist.com/news/display/57986/

    What scientific idea is ready for retirement? – Mouse Models
    Excerpt: A recent scientific paper showed that all 150 drugs tested at the cost of billions of dollars in human trials of sepsis failed because the drugs had been developed using mice. Unfortunately, what looks like sepsis in mice turned out to be very different than what sepsis is in humans. Coverage of this study by Gina Kolata in the New York Times incited a heated response from within the biomedical research community.
    AZRA RAZA – Professor of medicine and director of the MDS Centre, Columbia University, New York
    http://www.theguardian.com/sci.....t-edge-org

    Animal Testing Is Bad Science: Point/Counterpoint
    Excerpt: The only reason people are under the misconception that animal experiments help humans is because the media, experimenters, universities and lobbying groups exaggerate the potential of animal experiments to lead to new cures and the role they have played in past medical advances.,,,
    The Food and Drug Administration (FDA) has noted that 92 percent of all drugs that are shown to be safe and effective in animal tests fail in human trials because they don’t work or are dangerous.,,,
    Physiological reactions to drugs vary enormously from species to species. Penicillin kills guinea pigs but is inactive in rabbits; aspirin kills cats and causes birth defects in rats, mice, guinea pigs, dogs, and monkeys; and morphine, a depressant in humans, stimulates goats, cats, and horses.
    http://www.peta.org/issues/ani.....ience.aspx

    In fact, as to the somewhat minor extent evolutionary reasoning has influenced medical diagnostics, it has led to much ‘medical malpractice’ in the past:

    Evolution’s “vestigial organ” argument debunked
    Excerpt: “The appendix, like the once ‘vestigial’ tonsils and adenoids, is a lymphoid organ (part of the body’s immune system) which makes antibodies against infections in the digestive system. Believing it to be a useless evolutionary ‘left over,’ many surgeons once removed even the healthy appendix whenever they were in the abdominal cavity. Today, removal of a healthy appendix under most circumstances would be considered medical malpractice” (David Menton, Ph.D., “The Human Tail, and Other Tales of Evolution,” St. Louis MetroVoice , January 1994, Vol. 4, No. 1).
    “Doctors once thought tonsils were simply useless evolutionary leftovers and took them out thinking that it could do no harm. Today there is considerable evidence that there are more troubles in the upper respiratory tract after tonsil removal than before, and doctors generally agree that simple enlargement of tonsils is hardly an indication for surgery” (J.D. Ratcliff, Your Body and How it Works, 1975, p. 137).
    The tailbone, properly known as the coccyx, is another supposed example of a vestigial structure that has been found to have a valuable function—especially regarding the ability to sit comfortably. Many people who have had this bone removed have great difficulty sitting.
    http://www.ucg.org/science/god.....-debunked/

    And then of course when we get to society at large, the horror from Darwinian presuppositions is almost unimaginable:

    How Darwin’s Theory Changed the World – Rejection of Judeo-Christian values
    Excerpt: Weikart explains how accepting Darwinist dogma shifted society’s thinking on human life: “Before Darwinism burst onto the scene in the mid-nineteenth century, the idea of the sanctity of human life was dominant in European thought and law (though, as with all ethical principles, not always followed in practice). Judeo-Christian ethics proscribed the killing of innocent human life, and the Christian churches explicitly forbade murder, infanticide, abortion, and even suicide.
    “The sanctity of human life became enshrined in classical liberal human rights ideology as ‘the right to life,’ which according to John Locke and the United States Declaration of Independence, was one of the supreme rights of every individual” (p. 75).
    Only in the late nineteenth and especially the early twentieth century did significant debate erupt over issues relating to the sanctity of human life, especially infanticide, euthanasia, abortion, and suicide. It was no mere coincidence that these contentious issues emerged at the same time that Darwinism was gaining in influence. Darwinism played an important role in this debate, for it altered many people’s conceptions of the importance and value of human life, as well as the significance of death” (ibid.).
    http://www.gnmagazine.org/issu.....-world.htm

    the body count for abortion is now well over 50 million unborn babies in America since it was legalized, by judicial fiat not by public decree, in 1973 (legislation by liberal justices from the bench!):

    Abortion Statistics
    http://www.voiceofrevolution.c.....tatistics/

    And let’s not forget the horror of the holocaust which, although Darwinists are in complete denial of this fact of history, Richard Weikart has done a excellent job in tying evolutionary reasoning directly to the ‘scientific justification’ behind the holocaust:

    From Darwin To Hitler – Richard Weikart – video
    http://www.youtube.com/watch?v=w_5EwYpLD6A

    Verse and Music:

    John 10:10
    The thief comes only to steal and kill and destroy; I have come that they may have life, and have it to the full.

    Avalon – I don’t want to go – lyrics
    http://www.youtube.com/watch?v=QOEOX_Rxm8E

  7. 7
    bornagain77 says:

    OT: Podcast – Dr. Michael Egnor: Do Humans Have Free Will?
    http://intelligentdesign.podom.....8_01-08_00
    Listen in as Dr. Egnor explains why the argument against free will is self-refuting and shows how determinism as a theory in physics is dead.

  8. 8
    sixthbook says:

    As I have posted before when Wd400 claims that no one has ever called non coding DNA junk:

    “From AP Biology Textbook by Campbell and Reece, 7th Edition page 374:

    “The bulk of most eukaryotic genomes consists of noncoding DNA sequences, often described in the past as ‘junk DNA’”

    Furthermore, Querius also posted in response to Wd400:
    “There certainly is! Why just look at what the idiots at Medical News wrote:

    Junk DNA – What is Junk DNA?
    In genetics, “junk DNA” or noncoding DNA describes components of an organism’s DNA sequences that do not encode for protein sequences.

    In many eukaryotes, a large percentage of an organism’s total genome size is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding versus noncoding DNA varies greatly between species.

    Much of this DNA has no known biological function. However, many types of noncoding DNA sequences do have known biological functions, including the transcriptional and translational regulation of protein-coding sequences.

    (snip)

    Junk DNA Term
    Junk DNA, a term that was introduced in 1972 by Susumu Ohno, is a provisional label for the portions of a genome sequence of a for which no discernible function has been identified.

    According to a 1980 review in ”Nature” by Leslie Orgel and Francis Crick, junk DNA has “little specificity and conveys little or no selective advantage to the organism”.

    The term is currently, however, a somewhat outdated concept, being used mainly in popular science and in a colloquial way in scientific publications, and may have slowed research into the biological functions of noncoding DNA.

    Emphasis added by Querius

    See http://www.news-medical.net/he…..k-DNA.aspx

    Also, Nature magazine . . .

    http://www.nature.com/scitable…..k-dna-1211

    Appalling, isn’t it!

    This kind of stuff is all over the internet and various scientific journals. Apparently, only wd400 is properly informed. ”

    Taking both of these from the comments section here: http://www.uncommondescent.com.....etes-risk/

    Wd400, you can keep denying that evolutionists have been calling most of the genome “junk” for years, but I for one refuse to believe you and would rather take the side of the facts.

  9. 9
    bornagain77 says:

    Junk DNA Predictions By Leading Evolutionists

    Haldane’s Dilemma
    Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160

    Walter ReMine on Haldane’s Dilemma – interview
    http://kgov.com/Walter-ReMine-on-Haldanes-Dilemma

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

    At the 2:45 minute mark of the following video, the mathematical roots of the junk DNA argument, that is still used by many Darwinists, can be traced through Haldane, Kimura, and Ohno’s work in the late 1950’s, 60’s through the early 70’s:

    What Is The Genome? It’s Not Junk! – Dr. Robert Carter – video – (Notes in video description)
    http://www.metacafe.com/w/8905583

    Carter: Why Evolutionists Need Junk DNA – Robert W. Carter – 2009
    Excerpt: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work. Without junk DNA, evolutionary theory cannot currently explain how everything works mathematically. Think about it; in the evolutionary model there have only been 3-6 million years since humans and chimps diverged. With average human generation times of 20-30 years, this gives them only 100,000 to 300,000 generations to fix the millions of mutations that separate humans and chimps. This includes at least 35 million single letter differences, over 90 million base pairs of non-shared DNA, nearly 700 extra genes in humans (about 6% not shared with chimpanzees), and tens of thousands of chromosomal rearrangements. Also, the chimp genome is about 13% larger than that of humans, but mostly due to the heterochromatin that caps the chromosome telomeres. All this has to happen in a very short amount of evolutionary time. They don’t have enough time, even after discounting the functionality of over 95% of the genome–but their position becomes grave if junk DNA turns out to be functional. Every new function found for junk DNA makes the evolutionists’ case that much more difficult.
    Robert W. Carter – biologist
    http://creation.com/junk-dna-slow-death

    Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional.

    Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, “they are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”

    Sternberg traces how the junk DNA argument developed through the mid 1970’s to the early 80’s and beyond in the following article:

    How The Junk DNA Hypothesis Has Changed Since 1980 – Richard Sternberg – October 8, 2009
    Excerpt: Two papers appeared back to back in the journal Nature in 1980: “Selfish Genes, the Phenotype Paradigm and Genome Evolution” by W. Ford Doolittle and Carmen Sapienza and “Selfish DNA: The Ultimate Parasite” by Leslie Orgel and Francis Crick. These laid the framework for thinking about nonprotein-coding regions of chromosomes, judging from how they are cited. What these authors effectively did was advance Dawkins’s 1976 selfish gene idea in such a way that all the genomic DNA evidence available up to that time could be accounted for by a plausible scenario. The thesis presented in both articles is that the only specific function of the vast bulk of “nonspecific” sequences, especially repetitive elements such as transposons, is to replicate themselves — this is the consequence of natural selection operating within genomes, beneath the radar of the cell. These junk sequences, it was postulated, can duplicate and disperse throughout chromosomes because they have little or no effect on the phenotype, save for the occasional mutation that results from their mobility.
    http://www.evolutionnews.org/2.....26421.html

    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.
    …. “creationists…might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.”
    Richard Dawkins – Selfish Gene (mid 1970’s)
    http://www.uncommondescent.com.....ent-374475

    Selfish DNA: the ultimate parasite. Orgel LE, Crick FH. – 1980
    The DNA of higher organisms usually falls into two classes, one specific and the other comparatively nonspecific. It seems plausible that most of the latter originates by the spreading of sequences which had little or no effect on the phenotype.
    http://www.ncbi.nlm.nih.gov/pubmed/7366731

    Dr. Wells gives some historical background as to why some neo-Darwinists are doing everything they can to discredit the recent (Sept. 2012) ENCODE findings:

    Why All the Fuss Over Some Junk? – Jonathan Wells – September 25, 2012
    Excerpt: Some historical context might help. After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found “the secret of life,” a popular formulation of which became “DNA makes RNA makes protein makes us.” But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term “junk” to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional).
    Why didn’t biologists simply call non-protein-coding sequences “DNA of unknown function” rather than “junk DNA?” For some, it was because “junk DNA” seemed more suited to the defense of Darwinism and survival of the fittest. In 1976, Richard Dawkins wrote in The Selfish Gene that “the true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] 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.”
    In 1980, W. Ford Doolittle and Carmen Sapienza wrote in Nature (284:601) that many organisms contain “DNAs whose only ‘function’ is survival within genomes,” and that “the search for other explanations may prove, if not intellectually sterile, ultimately futile.” In the same issue of Nature (284:604), Leslie Orgel and Francis Crick wrote that “much DNA in higher organisms is little better than junk,” and its accumulation in the course of evolution “can be compared to the spread of a not-too-harmful parasite within its host.” Since it is unlikely that such DNA has a function, Orgel and Crick concluded, “it would be folly in such cases to hunt obsessively for one.”
    Two biologists then wrote to Nature (285:617,618) expressing their disagreement. Thomas Cavalier-Smith considered it “premature” to dismiss non-protein-coding DNA as junk, and Gabriel Dover wrote that “we should not abandon all hope of arriving at an understanding of the manner in which some sequences might affect the biology of organisms in completely novel and somewhat unconventional ways.” Cavalier-Smith and Dover were not criticizing evolutionary theory; they were merely questioning the claim that non-protein-coding DNA is non-functional.
    After the rise of intelligent design (ID) in the 1990s, “junk DNA” became a favorite weapon against ID in the hands of some Darwinists, including Richard Dawkins and the four bloggers mentioned above. According to ID, it is possible to infer from evidence in nature that some features of the world, including some features of living things, are explained better by an intelligent cause than by unguided natural processes. The Darwinists’ argument was that an intelligent designer would not have filled our genomes with so much junk, but that it could have accumulated as an accidental by-product of unguided evolution. In 2004, Dawkins wrote in A Devil’s Chaplain that much of our genome “consists of multiple copies of junk, ‘tandem repeats,’ and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.” Dawkins suggested that creationists (among whom he included ID advocates) “might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.”
    Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. “It is a remarkable fact,” he wrote, “that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.” In particular, pseudogenes “are genes that once did something useful but have now been sidelined and are never transcribed or translated.” Dawkins concluded: “What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene… unless he was deliberately setting out to fool us.”
    But if most of our DNA is functional, as the ENCODE results suggest, then the “junk DNA” argument against ID collapses.
    So the four bloggers listed above are doing everything they can to discredit the ENCODE project’s estimate of functional DNA. Yet whatever the estimate may currently be, it is certain to increase with further research. In 2007, the ENCODE pilot project reported on the basis of about 200 datasets that our DNA is “pervasively transcribed,” suggesting functionality. The 2012 results, based on 1,640 datasets, documented that “the vast majority (80.4%) of the human genome” is biochemically functional in at least one cell type. But ENCODE has so far sampled only a fraction of the cell types in the human body.
    Clearly, we have a lot more to learn about our genome — but not if we start by assuming that most of it is junk.
    http://www.evolutionnews.org/2.....64721.html

    In 1994, the authoritative textbook, Molecular Biology of the Cell, co-authored by National Academy of Sciences president Bruce Alberts, suggested (incorrectly!) that introns are “largely genetic ‘junk'”: Unlike the sequence of an exon, the exact nucleotide sequence of an intron seems to be unimportant. Thus introns have accumulated mutations rapidly during evolution, and it is often possible to alter most of an intron’s nucleotide sequence without greatly affecting gene function. This has led to the suggestion that intron sequences have no function at all and are largely genetic “junk”

    Soon thereafter, the 1995 edition of Voet & Voet’s Biochemistry textbook explained that “a possibility that must be seriously entertained is that much repetitive DNA serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that, over many generations, has disseminated itself throughout the genome…”

  10. 10
    bornagain77 says:

    Will Darwinists try to Rewrite the History of Junk-DNA?
    In 1996, leading origin of life theorist Christian de Duve wrote: “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.” (Richard Dawkins makes similar pronouncements that DNA is junk in an article after 1998)
    http://www.evolutionnews.org/2.....ull_a.html

    Another leading biologist, Sydney Brenner argued in a biology journal in 1998 that:
    “The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it.”

    The Unseen Genome, Gems Among the Junk:
    “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.” (John S. Mattick Scientific American (November, 2003)
    http://www.evolutionnews.org/

    Casey Luskin response to Farrel – several quotes from Jonathan Wells book – ‘The Myth of Junk DNA’ – May 2011
    http://blogs.forbes.com/johnfa.....omment-153

    Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such – March 2011
    Excerpt: Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”
    This claim is easily disproved: Francis Crick and Leslie Orgel published an article in Nature in 1980 (284: 604-607) arguing that such DNA “is little better than junk,” and “it would be folly in such cases to hunt obsessively” for functions in it. Since then, Brown University biologist Kenneth R. Miller, Oxford University biologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design. National Institutes of Health director Francis Collins argued similarly in his widely read 2006 book The Language of God.
    It is true that some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) have long been skeptical of “junk DNA” claims, but probably a majority of biologists since 1980 have gone along with the myth. The revisionists are misinformed (or misinforming).
    http://www.uncommondescent.com.....more-18154

    Dawkins, 2009: on “junkDNA”
    “Junk DNA is just what a Darwinist would expect,”

    Dawkins, 2012: on non-junkDNA…
    “”junk DNA” isn’t junk at all but is instead “exactly what a Darwinist would hope for,”
    http://www.evolutionnews.org/2.....64521.html

    Richard Dawkins ENCODE 2013 “Junk DNA” – video
    http://www.youtube.com/watch?f.....pRB0#t=94s

    First Holistic View of How Human Genome Actually Works: ENCODE Study Produces Massive Data Set – ScienceDaily (Sep. 5, 2012)
    Excerpt: “During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong,” said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), a part of the National Institutes of Health. “ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms.”
    http://www.sciencedaily.com/re.....140913.htm

    Amazingly, many leading evolutionists as of 2010-11 (Ayala in 2010; Francis Collins in 2010) still insist that most of the genome, which does not directly code for proteins, is useless ‘Junk DNA’.

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

  11. 11
    bornagain77 says:

    PZ Myers argues for well over 50% junk DNA in the following video:

    PZ Myers, the self-described Paris Hilton of atheists, on junk DNA – December 2011 – video
    http://www.uncommondescent.com.....-junk-dna/

    Casey Luskin responds to a mean-spirited attack by a neo-Darwinist on ‘Junk DNA’ – July 2012
    Excerpt: (A) On the one hand, you try to rewrite history by arguing that evolutionary biologists never argued that the genome was full of junk (“Wells and Luskin have promoted the absurd falsehood that molecular biologists believed non-coding DNA was non-functional ‘junk.'”)
    (B) On the other hand, you then claim the genome is full of junk DNA. (“As for junk, it is between 65 to 91.3%.”)
    Do you not see how the fact that you’re making argument (B) makes it really hard for me to believe your argument (A)?
    In any case, your point (A) is an attempt to rewrite history, which is a predictable response to the overwhelming mass of evidence,,,
    http://www.evolutionnews.org/2.....t-15282571

    The human genome is littered with pseudogenes, gene fragments, “orphaned” genes, “junk” DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. . . . In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection. – Ken Miller

    Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution … we expect to find, in the genomes of many species, silenced, or ‘dead,’ genes: genes that once were useful but are no longer intact or expressed … the evolutionary prediction that we’ll find pseudogenes has been fulfilled—amply … our genome—and that of other species—are truly well populated graveyards of dead genes – Jerry Coyne

    We have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, gene fragments, tandem repeats, and pseudo¬genes, none of which are involved directly in the making of a human being. In fact, of the entire human genome, it appears that only a tiny percentage is actively involved in useful protein production. Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution. – Michael Shermer

  12. 12
    wd400 says:

    I can’t be responsible for other people’s mistakes. All I can say is read Ohno, who very clearly states that non-coding sequences sould be part of the non-junk. Or even better, think for yourself. Do you really think people thought all non-coding DNA was junk at the same time that detereming the basis fo gene regulation was a central topic in molecular biology? Or that peope tought all non-coding sequences where junk when functional RNAs have been known about since the 1970s?

    It’s true that most non-coding DNA is junk. Be informed pepole never claimed all non-coding sequences where junk, or that the absensce of known functions for sequences were the best argument for the junkiness of our genome. That myth, as your quotes show, extends far beyond the ID crowd, but it’s still dead wrong.

  13. 13
    bornagain77 says:

    wd400,

    Son get caught stealing cookies.
    “caught you boy!”
    http://www.youtube.com/watch?v=zagxOqIWmHc

  14. 14
    wd400 says:

    Excerpt: (A) On the one hand, you try to rewrite history by arguing that evolutionary biologists never argued that the genome was full of junk (“Wells and Luskin have promoted the absurd falsehood that molecular biologists believed non-coding DNA was non-functional ‘junk.’”)
    (B) On the other hand, you then claim the genome is full of junk DNA. (“As for junk, it is between 65 to 91.3%.”)
    Do you not see how the

    Can everyone spot Luskin’s mistake in A? It’s the one everyone keeps making here…

  15. 15
    bornagain77 says:

    wd400 you state:

    It’s true that most non-coding DNA is junk.

    I think anyone who has had a glimpse at the mind blowing complexity being dealt with in DNA, who still thinks that the vast majority of DNA is junk just because we don’t fully understand exactly what it all does, is a more than a few fries short of a happy meal,,

    Notes along that line:

    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

    DNA Packaging: Nucleosomes and Chromatin
    each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth’s equator 2.5 million times! How is this possible?
    http://www.nature.com/scitable.....omatin-310

    DNA – Replication, Wrapping & Mitosis – video
    https://vimeo.com/33882804

    ‘How good would each typists have to be, in order to match the DNA’s performance? The answer is almost too ludicrous to express. For what it is worth, every typists would have to have an error rate of about one in a trillion (conservatively a billion);.
    Richard Dawkins – The Blind Watchmaker – Page 123-124

    DNA: The Ultimate Hard Drive – Science Magazine, August-16-2012
    Excerpt: “When it comes to storing information, hard drives don’t hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare.”
    http://news.sciencemag.org/sci.....-code.html

    DNA Computer
    Excerpt: A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours.
    http://www.tech-faq.com/dna-computer.html

    Cells Are Like Robust Computational Systems, – June 2009
    Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,”We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail.”
    http://www.sciencedaily.com/re.....103205.htm

    “Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.”
    Edward N. Trifonov – 2010

    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

    “applying Darwinian principles to problems of this level of complexity is like putting a Band-Aid on a wound caused by an atomic weapon. It’s just not going to work.”
    – David Berlinski

    etc.. etc.. etc..

  16. 16
    wd400 says:

    I think anyone who has had a glimpse at the mind blowing complexity being dealt with in DNA, who still thinks that the vast majority of DNA is junk just because we don’t fully understand exactly what it all does, is a more than a few fries short of a happy meal,,

    Then I’ll repeat myself, as people find it hard to get past this myth: I do not think the most important argument for the proposition that most of our genome is junk is that most of the genome has no known function.

  17. 17
    wd400 says:

    (and again, can you see the mistake Luskin made in the passage quoted in #14, it should be instructive…)

  18. 18
    sixthbook says:

    Wd400:
    “Do you really think people thought all non-coding DNA was junk at the same time that detereming the basis fo gene regulation was a central topic in molecular biology? Or that peope tought all non-coding sequences where junk when functional RNAs have been known about since the 1970s?”

    Yes, based on what BA and I have both posted and you have completely ignored, I think we can be certain that evolutionists once believed that non coding sequences were junk. In fact it’s not just an ID mistake because it’s not an ID mistake at all! ID takes the pro-science, pro-progression of thought position that the non-coding sequences have function, just we don’t know what they do yet, and more research is important.

    When you contrast this to the evolutionist position that most of the genome is junk because we don’t know what it does and thus we don’t need to bother investigating it because we already don’t know what it does, it’s clear which side is impeding scientific progress.

    Wd400, I don’t care about whether or not you are taking the fault for others mistakes, I just think it is absolutely appalling that when an evolutionist has one of their favorite “evidences” of evolution shattered they just switch their position to the opposite and say the evidence still supports their position (Richard Dawkins). Evolutionists cannot be anything other than complete hypocrites when they constantly accuse creationists and ID advocates of moving the goal posts regarding micro vs macro evolution or information via mutations when they believe that everything is evidence for evolution, even things that directly contradict each other.

    That evolutionists have to employ these tactics to keep their theory alive (at least in their imaginations) should show that their beliefs are not based upon any sort of science.

  19. 19
    wd400 says:

    “When you contrast this to the evolutionist position that most of the genome is junk because we don’t know what it does a”

    Please, try and read what I have said. Here it is, one more time:

    1. Evolutoinary biologists have long thought most of the genome is junk
    2. The fact most of the genome has no known function is not the main reason they no this
    3. No one who knows the first thing aout molecular biology has argued all non-coding sequences are junk
    4. Most of the genome is, in fact, junk

  20. 20
    bw says:

    Wd400 I think the biggest problem is that while many scientists may have not thought that non-coding regions are junk just because they are not understood yet, they have been happy to let the illusion spread.

    This is worrying, happily let the media/public think one thing (which can been seen to be true from the many instances posted above) all the while knowing full well we don’t have the complete picture yet.

    It gives the impression (rightly or wrongly) that they want it to be junk… why?

    I find it frightening.

  21. 21
    CLAVDIVS says:

    A great many mainstream biologists explicitly said that non-coding DNA likely had function, right from the early days after it was discovered.

    Immediately after Ohno’s very first presentation at the conference proceedings where he coined the term “junk DNA” he gave an interview describing his expectation that Darwinian adaptation should remove non-functional DNA, and therefore by implication remaining DNA is likely functional, even if we don’t know what the function is. The transcript is published in Ohno, S. (1973) “Evolutional reason for having so much junk DNA” in Modern Aspects of Cytogenetics: Constitutive Heterochromatin in Man (ed. R.A. Pfeiffer), pp. 169-173. F.K. Schattauer Verlag, Stuttgart, Germany:

    Ohno: “If there is any gene which is doing some good for your general well-being, you will suffer when you lose that gene. For this very reason a fraction of randomly sustained mutations of that locus would be deleterious. There is simply no way of having a useful gene without paying a certain price for the cost of natural selection. If, on the other hand, there is a gene which is totally irrelevant, you will lose that gene sooner or later, for natural selection would not police that gene.”

    In fact, way back in 1971 before Ohno coined the term “junk DNA”, biologists were discovering large portions of the genome that did not code for proteins and/or was repetitive, and had no known function. Nonetheless, they were proposing numerous possible functions for such, and subsequent research has shown some of their proposals to be correct:

    Ever since the initial demonstration of the existence of repetitive DNA there has been no dearth of theories on the function of this material. … Following is a list of functions that have been proposed …

    1. Recognition of centromeres of common origin.
    2. Recognition between homologous chromosomes during pairing.
    3. Regions involved in the initiation of replication and/or transcription.
    4. Sites concerned with specifying the folding patterns of chromosomes.
    5. Recognition sites for the process of genetic recombination.
    6. Provision of raw material for genetic divergence.
    7. Reflection of similarities in the structure of different proteins.
    8. DNA concerned with the regulation of gene expression (regulatory DNA).
    9. Reflection of multiplicity of repeated genes, as for example, in the master and slave or multistranded chromosome hypothesis.

    None of the recognition functions, i.e., recognition of centromeres, initiation sites, pairing sites, recombination sites, folding sites, or regulatory sites, that we have discussed is mutually exclusive of the others. They all relate to cellular phenomena that have been demonstrated or inferred from other data. All these phenomena probably exist within every higher organism. Therefore, DNA involved in each of these functions could contribute in varying degrees to the repeated portion of the genome.

    – Bostock, C. (1971) “Repetitious DNA” Advances in Cell Biology 2: 153-223.

    And there are many, many more papers over subsequent decades describing the expectation that much “junk” DNA actually has function; some examples appear below.

    1974 — E. Southern, “Eukaryotic DNA” in MTP International Review of Science, Biochemistry Series One, Volume 6, Biochemistry of Nucleic Acids, (1974) University Park Press, Baltimore. pp. 101 – 139:

    “.. large variations in genome size could readily be accomodated if a high proportion of the DNA were used for functions other than coding for proteins. A number of such functions have been proposed and incorporated into hypothetical structures for the eukaryotic genome.”

    1977 — D.M. Skinner, “Satellite DNAs” BioScience 27 (1977) pp. 790-796:

    Satellites [tandemly repeating, non-coding DNA] constitute from 1% to 66% of the total DNA of numerous organisms, including that of animals, plants, and prokaryotes. Their existence has been known for about 15 years but, although it is thought that they must be biologically important … their functions are still largely in the realm of speculation.

    1980 — Orgel & Crick, Nature (284: 604-607), p. 606:

    Thus, some selfish DNA may acquire a useful function and confer a selective advantage on the organism.

    1982 — R. Lewin, “Repeated DNA still in search of a function” Science 217 (1982) pp. 621-623:

    Some repetitive DNA will undoutedly be shown to have a function, in the formal sense, some will likely be shown to exert important effects, and the remainder may well have no function or effect at all and can therefore be called selfish DNA. Repetitive DNA constitutes a substantial proportion of the genome (up to 90% in some cases), and there is considerable speculation on how it will eventually be divided between these three groups.

    Clearly, mainstream biologists have claimed for decades that non-coding DNA has functions, ever since the term “junk” DNA entered the scientific literature.

    Cheers

  22. 22
    kairosfocus says:

    WD400: Thanks for telling us just how sensitive the now collapsing Junk DNA claim is for Darwinists, by trying to project that citing the evidence of the claim being made and widely promoted by evolutionary biologists is a blunder. Shades of the Ministry of Truth in 1984. Sorry, WD, I was there to see the claim being used by Darwinists as a supposed definitive knockdown argument on a routine basis. Makes me wonder just what else is being revisionised beyond recognition by such. KF

  23. 23
    Joe says:

    Unguided evolution cannot account for regulatory networks. It cannot account for the genetic code.

    Unguided evolution is a useless heuristic.

  24. 24
    bornagain77 says:

    wd400 and CLAVDIVS, it is not that some evolutionary biologists, which did not have their brains completely scrambled by Darwinian thinking yet and still had a bit of common sense, predicted that some of the non-protein coding DNA might have function, it is the fact that Darwin’s theory itself predicts most of the DNA to be of little or no function i.e. junk!

    Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013
    Excerpt: We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as “Haldane’s Dilemma” is very real.
    Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon “Haldane’s Ratchet”.
    http://media.wix.com/ugd/a704d.....fa9c20.pdf

  25. 25
    wd400 says:

    The inability of people in this thread to actaully read what I’m saying, rather than persist in a convenient myth, is astounding.

    I’m not arguing that evolutionary biologists never said most of the genome was junk, or even that the junkiness of our genome. I’m saying people who conflat non-coding DNA for junk DNA are making a mistake. And, more importantly, that this is not a mistake that the peope who developed the argument for junk DNA made, and the fact most of genome has no known function is not the best evidence for the fact our genome is junk.

    It’s a shame that the myth of the myth of junk DNA is so widespread, but if IDists want to do better than the popular press an engaging in science they ought to learn a bit about the actual arguments for the presence of junk DNA.

  26. 26
    bornagain77 says:

    wd400, you accuse others of ‘persisting in a convenient myth’, when it is in fact the neo-Darwinists who refuse to concede even one inch of their ‘convenient myth’ that they believe in! Go figure!

    Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video
    http://www.metacafe.com/w/10395212

    ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”.
    Professor Denis Noble is President of the International Union of Physiological Sciences.

    Physiology is rocking the foundations of evolutionary biology – Denis Noble – 17 MAY 2013
    Excerpt: The ‘Modern Synthesis’ (Neo-Darwinism) is a mid-20th century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection.,,, We now know that genetic change is far from random and often not gradual.,,,
    http://onlinelibrary.wiley.com.....4/abstract

    At the 10:30 minute mark of the following video, Dr. Trifonov states that the concept of the selfish gene has ‘inflicted an immense damage to biological sciences’, for over 30 years:

    Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video
    https://vimeo.com/81930637

    Of note:

    Though the evidence against neo-Darwinian evolution is overwhelming, anyone who dares question the sufficiency of neo-Darwinism to explain all life on earth in the public school classroom, or academia in general, is persecuted, as the following clearly points out:

    EXPELLED – Starring Ben Stein – video
    http://www.youtube.com/watch?v=P-BDc3wu81U

    Slaughter of Dissidents – Book
    “If folks liked Ben Stein’s movie “Expelled: No Intelligence Allowed,” they will be blown away by “Slaughter of the Dissidents.” – Russ Miller
    http://www.amazon.com/Slaughte.....0981873405

    “In the last few years I have seen a saddening progression at several institutions. I have witnessed unfair treatment upon scientists that do not accept macroevolutionary arguments and for their having signed the above-referenced statement regarding the examination of Darwinism. (Dissent from Darwinism list)(I will comment no further regarding the specifics of the actions taken upon the skeptics; I love and honor my colleagues too much for that.) I never thought that science would have evolved like this. I deeply value the academy; teaching, professing and research in the university are my privileges and joys… ”
    Professor James M. Tour – one of the ten most cited chemists in the world

    Top Ten Most Cited Chemist in the World Knows That Evolution Doesn’t Work – James Tour, Phd. – video
    http://www.youtube.com/watch?v=JB7t2_Ph-ck

    Even atheists themselves, who break ranks with the ‘consensus’ party line, are severely castigated by Darwinian atheists:

    The Heretic – Who is Thomas Nagel and why are so many of his fellow academics condemning him? – March 25, 2013
    http://www.weeklystandard.com/.....07692.html

    The Altenberg 16: An Exposé of the Evolution Industry – book
    Excerpt: In the other camp are those challengers who want to steer evolutionary science in a more honest, scientifically accurate direction. However, the Darwinian theory has become a political powerhouse brand that is hard to unseat because of the money and power associated with it.
    The Altenberg 16 is about a group of evolution scientists who met in 2008 in Austria to discuss and attempt to tell the truth about this “brand.”,,,
    http://books.google.com/books/.....2FfQQ_DmsC

  27. 27
    SteRusJon says:

    wd400,

    You declare “4. Most of the genome is, in fact, junk.”

    How do you know that is a “fact”?
    What is your definition of “junk’ as pertains to the genome?
    How do you determine which parts are “junk” and which parts are not “junk”?
    What properties of a given section of DNA identify it as not “junk” as opposed to “junk”?

    Please elucidate.

    Stephen

  28. 28
    PaV says:

    wd400

    Except, of course, this myth that all non-coding DNA was once considered junk is absurd.

    Really. Why? Because you say so?

    BTW, when you throw in the modifier “all”, that does change the statement. I’m sure, from the very beginning, that there was some form of ncRNA that had function. But the argument was made, up until but a year or so ago, that the genome was littered with non-functional DNA, hence “junk”, and that this was a severe argument against ID. And it was made by Ph’Ds who worked with genetics.

    It’s not a myth. The only myth that now exists is the “myth” that Darwinists never made this kind of argument. Now that is a myth.

  29. 29
    PaV says:

    CLAVDIVS:

    Immediately after Ohno’s very first presentation at the conference proceedings where he coined the term “junk DNA” he gave an interview describing his expectation that Darwinian adaptation should remove non-functional DNA, and therefore by implication remaining DNA is likely functional, even if we don’t know what the function is.

    Ohno: “If there is any gene which is doing some good for your general well-being, you will suffer when you lose that gene. For this very reason a fraction of randomly sustained mutations of that locus would be deleterious. There is simply no way of having a useful gene without paying a certain price for the cost of natural selection. If, on the other hand, there is a gene which is totally irrelevant, you will lose that gene sooner or later, for natural selection would not police that gene.”

    At the end, CLAVDIVS adds:

    Clearly, mainstream biologists have claimed for decades that non-coding DNA has functions, ever since the term “junk” DNA entered the scientific literature.

    So, for forty years “mainstream biologists have claimed . . . that non-coding DNA has functions.” OK. And they’ve known for some time, now, that ncDNA is quite often “highly conserved.”

    Let’s, then, put this all together:

    (1) Since Ohno, “mainstream biologists” have reasoned if it’s there in the genome then there must be some function to it.

    (2) Not only that, since introns are so highly conserved, this gives every indication that it has a vital role to play.

    (3) And, yet, up until WGA (whole genome analysis) Darwinists have eschewed prying into this apparently vital DNA, and, instead, chose to continue to focus on coding DNA for almost forty years.

    You see, CLAVDIVS, what scientists may have said, and what they did, are two completely different things.

    And, BTW, here’s what Ohno also wrote:

    The chance of acquiring a new function by unrestricted accumulation of mutations, however, should be as small as that of an isolated population emerging triumphant as a new species. Degeneracy is the more likely fate. The creation of every new gene must have been accompanied by many other redundant copies joining the ranks of silent DNA base sequences, and these silent DNA base sequence may now be serving the useful but negative function of spacing those which have succeeded. Triumphs as well as failures of nature’s past experiments appear to be contained in our genome.”

    [From, “So much ‘junk’ DNA in our Genome”, Susumu Ohno, 1972]

    Notice the title of the paper: So much “junk” DNA in our Genome.

    This is 1984, and Newspeak: i.e., those in power attempting to re-write the past when their predictions prove wrong.

  30. 30
    Joe says:

    Neither Darwinism, neo-darwinism nor Intelligent Design predict a high % of junk DNA.

  31. 31
    Joe says:

    And only Intelligent Design would tell us to look for functionality in non-coding DNA, as opposed to stumbling across it.

    Just sayin’

  32. 32
    bornagain77 says:

    Semi OT: Excellent article up on ENV:

    (Dual Coding) RNA Shows Design, Too – February 4, 2014
    Excerpt: A paper in Nature describes how information is stored not only in RNA’s base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. “RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA’s ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures,” the authors begin (emphasis added). In their conclusion, they say, “We identify hundreds of specific mRNA regions that are highly structured in vivo, and we show for three examples that these structures affect protein expression.”
    In other words, the structure, not just the sequence, carries functional information. “Our studies provide an excellent set of candidate regions, among the truly enormous number of structured regions seen in vitro, for exploring the regulatory role of structured mRNAs.”,,,
    If RNAs show design, why not design them ourselves? In an experimental twist, researchers at Carnegie Mellon invited the public to be their design lab. In a “crowdsourcing” experiment, they found that volunteers could create new RNA designs better than computers could. The starting pool of 37,000 citizen scientists has grown to 130,000 members exercising their intelligent design skills.
    “An enthusiastic group of non-experts, working through an online interface and receiving feedback from lab experiments, has produced designs for RNA molecules that are consistently more successful than those generated by the best computerized design algorithms, researchers at Carnegie Mellon University and Stanford University report.”
    http://www.evolutionnews.org/2.....81841.html

    Of related note: This following peer-reviewed paper holds that there is ‘irreducible organizational complexity’ between the genetic (digital) information and the epigenetic (analog/structural) information:

    Refereed scientific article on DNA argues for irreducible complexity – October 2, 2013
    Excerpt: This paper published online this summer is a true mind-blower showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc.,,
    ,,,First, the digital information of individual genes (semantics) is dependent on the the intergenic regions (as we know) which is like analog information (syntax). Both types of information are co-dependent and self-referential but you can’t get syntax from semantics. As the authors state, “thus the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell”. In short, the linear DNA sequence contains both types of information. Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. This implies that the position and organization of genes on the chromosome is not arbitrary,,,
    http://www.christianscientific.....omplexity/

    To state what should be needless to say, these findings are not conducive to Darwinian presuppositions but are conducive to Intelligent Design presuppositions!

  33. 33
    wd400 says:

    Pab

    I’m sure, from the very beginning, that there was some form of ncRNA that had function.

    Yes, all the tRNAs and the rRNAs for a start. Much more non-coding DNA that doesn’t amke RNA has also been kown to serve a function for a long time. As Ohno made clear when he started talking about junk DNA.

    . But the argument was made, up until but a year or so ago, that the genome was littered with non-functional DNA, hence “junk”,

    Yes. This argument remains strong. The myth is that the best argument for junk DNA went something like “well, we don’t what this does so it must be junk”. That’s never been the case, so hauling out that story every time another fraction of a percent of genome is shown to have a function is silly.

    Not that this thread gives me any hope that this myth will die

  34. 34
    PaV says:

    wd400:

    You make no mention whatsoever of Susumu Ohno’s remark that the genome is filled with evolution’s “failures” as well as “successes.” You call it a “myth” that evolutionists/Darwinists made the claim that the genome is filled with junk, and this shows that it is the residue of random chance and NS. And, yet, I’ve had arguments online with scientists taking that very position, and in a steadfast manner. So, should I believe you, or should I believe my own experiences? Just asking.

    Also, is it your position that Darwinists/evolutionists did NOT make the argument that “vestigial organs” were evidence that organisms were NOT designed, but were the result of random mutations and NS? Do you make that claim also?

  35. 35
    bornagain77 says:

    wd400, you claim that

    “Most of the genome is, in fact, junk.”

    How do you possibly know this? Are you claiming, so as to be able to declare the genome ‘mostly junk’, to know all the intricate operations of the cell in detail. Integrated operations of the cell that researchers, such as ENCODE 2012, have barely begun to scratch the surface of? Even you can’t possibly be that arrogant! Or are you? And since you can’t possibly know all the intricate workings of the cell in detail,, since even ENCODE 2012 expressed amazement at what they were seeing,,,

    Scientists go deeper into DNA (Video report) (Junk No More) – Sept. 2012
    http://bcove.me/26vjjl5a
    Quote from preceding video:
    “It’s just been an incredible surprise for me. You say, ‘I bet it’s going to be complicated’, and then you are faced with it and you are like ‘My God, that is mind blowing.’”
    Ewan Birney – senior scientist – ENCODE 2012

    How can you possibly claim, with a straight face, that the genome is ‘mostly Junk’? i.e. Your argument, whether you realize it or not, or even whether you admit it or not, boils down to this:

    “well, we don’t what this does so it must be junk”

    or more precisely, something like this

    “well, we don’t what this does, but we know it can’t possibly be designed because that is not science, so it must be junk”

  36. 36
    wd400 says:

    You call it a “myth” that evolutionists/Darwinists made the claim that the genome is filled with junk

    You haven’t understood anything I have said. So I give up.

  37. 37
    Jul3s says:

    Claiming to be misunderstood is a weak way of deflecting counter arguments. Especially since the “real” argument for junk DNA has already been talked about on this thread, not just the argument from ignorance.

  38. 38
    sixthbook says:

    Wd400:
    “I do not think the most important argument for the proposition that most of our genome is junk is that most of the genome has no known function.”

    What is the most important argument then?

    And btw: the “fact” that most of the genome has no function is a complete argument from ignorance, is anti-scientific progress and is also being shown to be false more and more every day now, starting with the findings of the ENCODE project.

  39. 39
    Jul3s says:

    ENCODE doesn’t actually prove anything. However, the fact that 70% of the genome is transcribed strongly suggests that most of the genome is functional. It makes no sense to suggest that the cell is wasting so much of its energy making junk.

  40. 40
    wd400 says:

    THe better arguments for junk DNA include the fact that you (and the rest of us) are alive, despite each having ~70 new mutatoins. If the genome was mostly functional (as creationists claim) and the biological functions require very specific sequences (as creationists claim) then those mutations should be breaking functional DNA in every generation. On top of that you have the fact that most fo the genome is not conserved, that closely realted species have quite different genome sizes, that this variance in genome size can be partly explained by variance in the power of natural selection to remove very weekly deleterious mutations (such as producing a little extra DNA and RNA in a partciular cell type at a particular time…), the predominance of repetitive sequences and variance in repeat-number among individuals, the fact many sequences diverge at the rate expected under neutral evolution….

    We could go on, but I hope you see there are many good reasons to think most of the genoem is junk, and they don’t represaent argumetns from ignorance. Moreover, the fact tha ENCODE found most sequences produce RNA at some stage doesn’t change these arguments.

    Jul3s,

    Makes sense to who? The extra metabolic cost of the odd transcript in some cell type at some time is likely vanishingly small. In creatures will small population sizes, natural selection will not be strong enough to detect such small selective differences and such abbarent expression is expected to accrue. As I say, there is a correlation between genome size and effective population size, which suggests at least part of the variance in genome size can be explained by the inability of creatures in small populations to preven junk adding up.

  41. 41
    bornagain77 says:

    wd400 claims:

    “THe better arguments for junk DNA include the fact that you (and the rest of us) are alive, despite each having ~70 new mutatoins. If the genome was mostly functional (as creationists claim) and the biological functions require very specific sequences (as creationists claim) then those mutations should be breaking functional DNA in every generation.”

    Well for goodness sakes wd400, since the overwhelming majority of mutations are detrimental then that must mean Darwinism is true in your mind (excuse me, I meant brain)??? In case you fail to realize it wd400, the fact that we have an extremely difficult time identifying ANY truly beneficial ‘random’ mutations whatsoever is a very powerful argument for the contention that intelligence was required in the past to explain the origin of the genetic information in the first place!

  42. 42
    bornagain77 says:

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
    1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
    2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
    3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
    4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
    5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
    6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
    8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
    9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
    10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
    11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    http://www.worldscientific.com.....08728_0006

  43. 43
    Joe says:

    All arguments for junk DNA are from ignorance.

  44. 44
    Jul3s says:

    Mutations don’t necessarily reveal function (or lack thereof) for many reasons but deletions can. TALENs have been really useful for studying this. Genome size is not only correlated with population size but also metabolism and nucleus size.

    If most of the genome is junk (e.g 95%) and since 70% of the genome is transcribed, then each cell would be producing many times more transcripts then it needs (depending on cell type). This is completely different to the ‘odd junk transcript every now and then’ scenario.

    This doesn’t mean that there’s no junk DNA though.

  45. 45
    wd400 says:

    The ENCODE number (70-80%) is the percentage of the genome transcribed in at least one cell-type, not in a typical cell (I’m not sure what that number is, but it’s unlikely to be 70%). More to the point, we have known for a long time that cells make more RNA than they need. Unless you think every base of every intron serves an important role.

    The point about the “odd junk transcript” is not the final result, but the mechanism by which noisy transcription is predicted to arise. Selection can only operate on what variation is present in a single generation. One extra transcript in one cell type is not going to make a noticable difference in one generation. Over many generations those dynamics can add up to a junky genome.

  46. 46
    bornagain77 says:

    wd400 whistles in the dark:

    ENCODE Reveals Incredible Genome Complexity and Function by Jeffrey Tomkins, Ph.D. – Sept. 2012
    Excerpt: Tom Gingeras, one of the senior scientists on the ENCODE project said, “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more.”4
    And what about the remaining 20 percent of the genome—is it functional too? According to Ewan Birney, ENCODE’s lead analysis coordinator, it’s probably not meaningless junk either. Birney said in an interview, “It’s likely that 80 percent will go to 100 percent” and “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”4
    Birney expects that many critics will argue about the 80 percent figure and the definition of what is “functional.” Birney added, “[That figure] best [conveys] the difference between a genome made mostly of dead wood and one that is alive with activity” and “No matter how you cut it, we’ve got to get used to the fact that there’s a lot more going on with the genome than we knew.”4
    Some people will probably try to claim that these statements made by the scientists of ENCODE are merely hype. However, there is little to criticize since the 80 percent figure comes directly from a clearly written statement in an 18-page research paper in the prestigious secular journal Nature.1 Furthermore, this statement came from the lead paper of 30 other concurrently published ENCODE papers that were authored by hundreds of leading genomic scientists in multiple international laboratories worldwide.
    http://www.icr.org/article/7064/

    What Is The Genome? It’s Certainly Not Junk! – Dr. Robert Carter – video – (Notes in video description)
    http://www.metacafe.com/w/8905583

    Comparing genomes to computer operating systems – Van – May 2010
    Excerpt: we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology,,,
    http://www.ncbi.nlm.nih.gov/pubmed/20439753

  47. 47
    PaV says:

    wd400:

    You haven’t understood anything I have said. So I give up.

    I think I understood what you said. I disagree almost entirely. When I, as a blogger, have evolutionists tell me point blank that most of the genome is “junk”, and not more than two years ago (if not less), then your claims are not believable. It’s just your opinion. And when someone as high profile as Richard Dawkins is making this claim, all I can say is that it is the height of convenience to a posteriori aver that “we never said that.”

    So, have you understood me?

  48. 48
    wd400 says:

    Read… well any of comments. Where do you think I said that no one argued most of the genome was junk?

  49. 49
    PaV says:

    wd400:

    THe better arguments for junk DNA include the fact that you (and the rest of us) are alive, despite each having ~70 new mutatoins.

    70 out of 5 billion nucleotides? That’s going to kill you? Chances aren’t high.

    What about synonymous mutations?
    What about some of those 70 being recombinations where information is just shuttled around?

    WD: If the genome was mostly functional (as creationists claim) and the biological functions require very specific sequences (as creationists claim) then those mutations should be breaking functional DNA in every generation. . . .

    On top of that you have the fact that most fo the genome is not conserved,

    But this is an argument against NS. That so much polymorphisms exist in the genome drove Kimura to the Neutral Theory—which was fought by Darwinists, before they co-opted it, standing it on its head.

    It was just like the “junkDNA” argument: before they had the answer, they were sure polymorphisms would be at a minimum. After proven wrong, then they said, “Oh, this can explain evolution.” (Kimura saw things very differently, and he was one of the finest of all populations geneticists)

    WD: . . . that closely realated species have quite different genome sizes, that this variance in genome size can be partly explained by variance in the power of natural selection to remove very weekly deleterious mutations (such as producing a little extra DNA and RNA in a partciular cell type at a particular time…), the predominance of repetitive sequences and variance in repeat-number among individuals, the fact many sequences diverge at the rate expected under neutral evolution….

    Oh, but you see, “random” mutations are like a “random” search: not productive. That’s where, per Dawkins, NS comes in, making it a “non-random” process. So, you see, here we are at UD hearing evolutionists speak out of both sides of their mouths. What are we to think?

    And, BTW, why are we “creationists” here? I’m Catholic. So are others. Why the strawman nonsense?

    WD: We could go on, but I hope you see there are many good reasons to think most of the genoem is junk, and they don’t represaent argumetns from ignorance.

    I think you’re arguing here from a point of ignorance. The LincRNAs that star in this post, have lots of repetitive Alu sections. And yet they’re shown to have function. And they’re conserved for the most part. This is no argument for “most of the genome being ‘junk’.”

    WD: Moreover, the fact tha ENCODE found most sequences produce RNA at some stage doesn’t change these arguments.

    Have you given any consideration whatsoever to the fact that over and over again, these so-called “junk” portions of the genome are being linked to embryonic function? Guess what, when you’re born, it’s been quite some time since you’ve been an embryo. And, of course, there would be no need any longer for these portions of DNA to be expressed. This is precisely what this post is about.

  50. 50
    drc466 says:

    wd400 makes the argument that, since our DNA can endure mutations fairly well, that a significant portion of the DNA must be junk. Otherwise, all those mutations would cause us problems (3-headed children, demon possession, etc.)
    The most obvious problems with this statement:
    1) It ignores the concept of redundancy. It assumes that every piece of DNA is independent, and that no self-correction capability exists. Scientifically, we have a large amount of evidence to the contrary:
    — Inbreeding: Inbreeding is a significant danger because it increases the chance that 2 parents will share the same mutation in their DNA. This indicates that each DNA mutation DOES damage FUNCTIONAL genome, and it is only the auto-correction that comes from 1 parent not having the mutation that prevents problems
    — Experiments such as fruit fly mutations. In one example, fruit flies with damaged/removed eye genes, when bred multiple generations with other eye-less flies, will regain their eyes. This indicates that other sections of DNA contain the ability to fix mutated sections of DNA. This indicates the probability that there are segments of DNA that may serve no constant purpose, but act as a regulatory or repair function that ONLY kicks in if needed. Damage to these sections will APPEAR harmless, but will cause problems in the future.
    2) The number of mutations wd400 cites are actually very small, and as stated before, somewhat self-correcting. Over time, however, they do build up (genetic load), and we are already seeing the affects on humanity (and animals as well).
    3) If we accept the evolutionists’ timeline, humanity’s DNA carries the load of a million years of mutation. Yet human DNA studies show extremely tiny variation and mutation in the DNA (for such an amount of time – the story is different if you assume thousands, not millions). If a significant portion of the genome is junk, why is such a high percentage conserved world-wide?

    The rest of wd400’s argument resolves to our genome is significantly different than other species genome in size and definition, therefore much of those differences must be junk or they would be damaging. This is a non-empirical circular reasoning argument that, because evolution requires junk in the genome, therefore most of the genome is junk.

  51. 51
    franklin says:

    70 out of 5 billion nucleotides? That’s going to kill you? Chances aren’t high.

    what would be the odds of detrimental effect(s) via deletion of DNA nucleotides equivalent to the entire protein coding region of the organism? What effects would ID predict that this would cause?

    As far as ENCODE goes when I went through my graduate course work back in the late 80’s it was well known that DNA was promiscuously transcribed. That the transcripts,were for the most part, nonsense was also recognized. For transcription all you need to have is a initiation-site or a close match of a ‘proper’ binding sequence to get things rolling. Much like P450 enzymes metabolize a suite of chemicals with different affnities.

  52. 52
    bornagain77 says:

    franklin as to:

    back in the late 80?s it was well known that DNA was promiscuously transcribed. That the transcripts, were for the most part, nonsense not understood was also recognized.,,,

    Yet,,,

    Genomic organization of human transcription initiation complexes – Sept. 18, 2013
    Excerpt: ,,,we looked for the ‘initiation machine’ that makes the RNA.,,
    Pugh, and Venters were stunned to find 160,000 of these “initiation machines,” because humans only have about 30,000 genes. “This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes.,,,
    The remaining 150,000 initiation machines—those Pugh and Venters did not find right at genes—remained somewhat mysterious. “These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists,” Pugh said. “In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins.”,,,
    “These non-coding RNAs have been called the ‘dark matter’ of the genome because, just like the dark matter of the universe, they are massive in terms of coverage—making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there,” Pugh said. “Now at least we know that they are real, and not just ‘noise’ or ‘junk.’ Of course, the next step is to answer the question, ‘what, in fact, do they do?'”

    http://phys.org/news/2013-09-genomic-dark.html

    In fact every time they look for function they find it:

    Knockout Mice Study: Long Noncoding RNAs “Play Central Roles in Mammalian Development and Physiology” – Casey Luskin January 16, 2014
    Excerpt: After ENCODE’s finding that the vast majority of our DNA is transcribed into RNA, many Darwinian biologists have comforted themselves with the belief that most of that RNA is still useless, and our cells are full of “junk RNA.” But a few independent-minded folks sought out evidence of function for that RNA. And they’ve consistently found it.
    http://www.evolutionnews.org/2.....81221.html

    Like the concept that most of the DNA was junk, that originated from Darwinian thinking, the concept that most of the RNA transcripts are ‘nonsense’ is turning out to be misleading and wrong as well. Moreover, enough about the functionality of RNA is now known that it had ENCODE researchers calling for a redefinition of the concept of what a ‘gene’ is altogether:

    Landscape of transcription in human cells – Sept. 6, 2012
    Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,,
    Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line.
    http://www.nature.com/nature/j.....11233.html

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

    Of related note to ENCODE researchers wanting to redefine the concept of a gene, RNA’s are far more difficult to align into any presupposed evolutionary relationships than Genes are/were:

    micro-RNA and Non-Falsifiable Phylogenetic Trees – (Excellently Researched) video
    http://www.youtube.com/watch?v=qv-i4pY6_MU

    Another misconception from decades ago that got debunked was this (although this mistake can probably be seen as an ‘honest mistake’ that was not entirely the fault of Darwinian thinking),,

    “We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naïve as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB — and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. Consider an enzyme, for example. If its substrate molecule is present at a concentration of 0.5mM, which is only one substrate molecule for every 105 water molecules, the enzyme’s active site will randomly collide with about 500,000 molecules of substrate per second. And a typical globular protein will be spinning to and fro, turning about various axes at rates corresponding to a million rotations per second.
    But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”
    Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell, 92 (February 6, 1998): 291-294

  53. 53
    wd400 says:

    Pav,

    I have no idea what to make of these wild and whirling words. For what it’s worth. The genome is more like 3 billion bases, but I can’t imagine what difference the denominator makes if all the genome is function-rich. If most bases are involved in a function, and randomly changing them in each generation is no great loss, then biological function can’t be very sequence specific. Most people have no synonymous mutations – since they can only fall in the ~1% of the genome that are exons and ~75% of exonic mutations will be non-synom.

    Mutations and recombinatoin are different things. In any case, the 70 mutations include only SNPs. If you mean structural variants, well they would add to the genetic load since they dont simply shuffle information but would break up information midstream.

    Then you have all this noise about neutral theory, which I don’t understand at all. Yes, the argument for junk DNA is also an argument again prevasive selection in most genomes. That’s a very good reason to calling modern evolution biology “Darwinism” especially as it relates to junk DNA. But I don’t see what point you are trying to make with this, or the (supossed) observation that some non-coding RNAs are involved in embryogenesis. Embryo-exoressed genes are subject to selecton/mutaton too, after all.

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