'Junk DNA'

Tossing Out the Junk

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Over at the ID The Future podcast, Casey Luskin has been doing a series on “the top 10 problems with biological and chemical evolution.” Some of the problems he discusses will no doubt be of more interest to certain listeners than to others. However, the segment on junk DNA is particularly worth hearing (about 13 minutes).

For those who have been following the debate closely there may not be much new in the segment, but it provides a relatively up-to-date review of some of the recent research, with multiple citations that are useful when talking with a friend or colleague who may still be stuck in the naive and outdated idea that the genome is awash in junk.  Better yet, ask your friend if they have 15 minutes and an open mind, and then let them have a listen.

It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.  Even with the proliferation of functions for non-coding DNA, we still hear regular pronouncements from the purveyors of the materialist creation myth that “yes, there may be some function for non-coding DNA, but most of it is still junk.”

The whole idea of pervasive junk in our DNA is so naive and absurd as to boggle the mind.  Thankfully, the trajectory of the evidence is clearly trending toward a more rational and complete assessment of DNA.  Yes, hindsight is 20/20, and soon enough every biologist worth her salt will claim that she “always knew” that most DNA had function.  But let us not forget that there were a few lone voices, including prominent ID proponents, long arguing for pervasive function — in the face of ridicule and the stifling, science-limiting attitude of the Darwin establishment about their beloved icon of “junk” DNA.

47 Replies to “Tossing Out the Junk

  1. 1
    Mung says:

    But surely there’s no selective advantage to all that junk. Can’t we prove that it’s junk by showing that it’s not under selection?

  2. 2
    Mapou says:

    Junk DNA is as anti-science as you can get. Intelligent design always results in a hierarchical organization: big parts are made of small parts. It follows that the design of the genome must be a hierarchy, i.e., a genetic tree. Protein coding genes are at the bottom of the hierarchy. Layered on top are the regulatory or control genes. Just recently they found the master regulator, the one way at the top: nFGFR1.

  3. 3
    wd400 says:

    It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.

    It might be, if it were true.

    EA: Meaning what? Are you claiming that the fact that large swaths of DNA do not code for proteins has not been used by evolutionary proponents to bolster the claim that such DNA is “junk”? This has been an extremely common and pervasive tactic of Darwinist proponents for decades. Embarrassingly, some are still using this tactic today in the face of contrary evidence.

    And now that even many Darwinists are reluctantly admitting that “some” non-coding DNA might have function, whence the continuing and repeated claims that most DNA is still junk? Why on earth would any rational person make such a claim? It is a classic argument from ignorance: “We don’t know what it does, therefore it must not do anything. Oh, and by the way, our theory predicts that there should be lots of junk, so evolution is true.” Evolution-of-the-gaps thinking.

  4. 4
    bornagain77 says:

    OT: Epigenetics on steroids

    Seasonal immunity: Activity of thousands of genes differs from winter to summer – May 12, 2015
    University of Cambridge
    Summary: Our immune systems vary with the seasons, according to a study that could help explain why certain conditions such as heart disease and rheumatoid arthritis are aggravated in winter while people tend to be healthier in the summer. The study shows that the activity of almost a quarter of our genes (5,136 out of 22,822 genes tested) differs according to the time of year, with some more active in winter and others more active in summer. This seasonality also affects our immune cells and the composition of our blood and adipose tissue (fat).
    http://www.sciencedaily.com/re.....112356.htm

  5. 5
    Dionisio says:

    Here’s a challenge @907:

    http://www.uncommondescent.com.....ent-564761

    (see the post @908 in that same thread).

  6. 6
    bornagain77 says:

    Podcast: A Bonus 11th Problem – “The Top 10 Problems with Darwinian Evolution”: – Casey Luskin
    In this segment, Casey discusses a bonus eleventh problem: that humans display many behavioral and cognitive ability that offer no apparent survival advantage.
    http://www.discovery.org/multi.....h-problem/

  7. 7
    REC says:

    “It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.”

    Can we get a reference of a prominent scientist stating that the only DNA worth talking about codes for proteins?

    Your statement is laughable.

  8. 8
    REC says:

    Mung@1 gets dangerously close to undermining the post. Keep thinking, and you’ll get yourself in trouble around here.

    Mapou@2: “Protein coding genes are at the bottom of the hierarchy. Layered on top are the regulatory or control genes. Just recently they found the master regulator, the one way at the top: nFGFR1”

    …..nGFR1 is a protein, FYI.

  9. 9
    wd400 says:

    I think my comment is pretty clear: the thing you claimed to be true is not. People didn’t say the only DNA worth looking at was protein coding.

    You make several more mistakes in your follow up comments, you should probably learn a little bit about junk DNA before you comment on it further.

  10. 10
    Larry Moran says:

    It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.

    No knowledgeable scientist ever said that all noncoding DNA was junk or that it was uninteresting. Back in 1968 every knowledgeable scientist was familiar with functional noncoding DNA so they would have been laughed out of the room if they ever made such a silly statement.

    Back then, we knew about centromeres, origins of replication, regulatory regions, and various genes for functional RNAs.

    We have been patiently explaining this to ID folk for two decades. If they continue to repeat this untrue statement then they are either lying or incredibly stupid … or possibly both.

  11. 11
  12. 12
    bornagain77 says:

    Dr. Sternberg was mentioned in Casey’s talk. Here is a fairly recent talk that Dr. Sternberg gave on the human genome that overturns the Darwinian claim that most of the human genome must be junk:

    Podcast: Richard Sternberg – PhD in evolutionary biology – ” On Human Origins: Is Our Genome Full of Junk DNA? part 1
    http://www.discovery.org/multi.....-junk-dna/
    Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 2 (Major Differences in higher level chromosome spatial organization)
    5:30 minute mark quote: “Basically the dolphin genome is almost wholly identical to the human genome,, yet no one would argue that bottle-nose dolphins are our sister species”
    http://www.discovery.org/multi.....-dna-pt-2/
    Podcast: Richard Sternberg PhD – ” On Human Origins: Is Our Genome Full of Junk DNA? Part 3
    http://intelligentdesign.podom.....4_33-08_00
    Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 4
    http://www.discovery.org/multi.....-dna-pt-4/
    Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 5
    (emphasis on ENCODE and the loss of the term ‘gene’ as a accurate description in biology and how that loss undermines the modern synthesis of neo-Darwinism)
    http://www.discovery.org/multi.....-dna-pt-5/

  13. 13
    bornagain77 says:

    Here is a video along the same line:

    Biological Information – Not Junk After All 11-29-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=xO-7kVBA_JM
    In the book “Biological Information: New Perspectives” the chapter entitled “Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information” discusses the various functions of DNA and finds that non-functional DNA is a small minority.

    Here is the paper:

    Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information – Jonathan Wells
    http://www.worldscientific.com.....08728_0009

    After ENCODE came out a guy named Dan Graur about had a cow. Here is an analysis of the Dan Graur incident:

    Biological Information – (The Dan Graur incident) Criticizing ENCODE 12-13-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=zhlFJO1WqVk

    Basically, the Darwinian critics of the ENCODE study, which found widespread functionality for supposed ‘junk’ DNA, said that biochemical functionality does not really determine if a sequence is actually functional, only ‘conservation of sequence’ determines what is functional.

    With that self-serving definition for functionality, a self-serving definition in which common ancestry is presupposed in the definition of functionality, they arrived at 8.2% functionality:

    DNA mostly ‘junk?’ Only 8.2 percent of human DNA is ‘functional’, study finds – July 24, 2014
    Excerpt: To reach their (8.2%) figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution — a clear indication that this DNA matters, it has some important function that needs to be retained.
    http://www.sciencedaily.com/re.....141608.htm

    So basically, only if Darwinian evolution is assumed as true from the outset will Darwinists be willing to accept that a given sequence of ‘junk’ DNA may be functional!,, That is called ‘assuming your conclusion into your premise’ and is absolutely a horrible way to practice science!

    Needless to say, science itself does not presuppose common ancestry in the answers for functionality that it gives us, and thus, as should be obvious, functionality does not follow the presupposed ‘conserved’ pattern as Darwinists imagined it would:

    Protracted Unrest Between ENCODE Researchers and Junk-DNA Advocates Goes On – November 26, 2014
    Excerpt: It’s not exactly Fergusson, Mo., but the battle between ENCODE researchers and junk-DNA holdouts goes on.,,,
    ,,,”Evolutionary conservation of primary sequence is typically considered synonymous with conserved function, but this finding suggests that this concept should be reinterpreted, because insertions of retrotransposon elements in new genomic regions are not conserved between species.”
    In short, the Mouse ENCODE group takes direct aim at the arguments of Dan Graur and the other junk-DNA faithful, who say that everything evolution did not conserve is junk.,,,
    ,,,much of what Darwinian evolutionists had dismissed as junk appears functional. Non-coding regions of the mouse genome are transcribed, and appear to function in previously unimagined ways, such as regulation of gene expression, chromosomal stability, and maintenance of species identity. Carninci offers further thoughts:
    ,,,”we should rethink the relationship between genomic function and evolutionary conservation. Regulatory regions and long non-coding RNAs (lncRNAs) are not subject to the evolutionary constraints of protein-coding genes, which may help to explain the sequence drifts reported in these papers. However, it is striking that transcription-factor networks are conserved despite low conservation of their binding positions in the genome.”
    http://www.evolutionnews.org/2.....91501.html

  14. 14
    Mung says:

    C-Value Paradox
    A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk.

    Let’s not bother with empirical findings.

    And by all means, let’s not use genome size as a marker of relatedness. Can’t you just imagine what the tree of life would look like then? Yech!

  15. 15
    harry says:

    Ever since it became apparent that the only causally adequate explanation for the contents of the protein coding regions of DNA memory was intelligent agency, it was entirely reasonable to expect that much of the rest of DNA memory would turn out to be functional. It always seemed to me to be reasonable to expect that some of the rest of it was currently unused but might have been left in a state that would reveal something about prior functionality that no longer exists, but would remain functional in the sense that it was available for use by new functionality. If that sounds like that is how a computer programmer would look at it, that is because it is, at least for this one. ;o)

    How do we, in understanding the rest of DNA memory, get to where we are in understanding the protein coding regions of DNA? As a computer programmer who has worked at the level of CPU machine instructions, having written applications in assembler language, and written applications to simulate the instruction set of a CPU for diagnostic purposes, let me explain from my perspective of the utilization of digital information, why understanding the rest of it will probably be much more difficult.

    There is a direct correspondence between the bit pattern of an executable instruction in memory and one of the machine instructions from the set of those of which the CPU is capable. Repeated observations of how the bit patterns read in from executable memory caused the CPU to respond as programs execute would soon reveal the complete instruction set of the CPU. Understanding the correspondence between the bit patterns in executable memory locations and the instruction set of the CPU is not the same as understanding that a given range of such memory locations comprise, say, a word processor. Understanding that correspondence would do nothing to help one understand that another range of memory addresses contained ASCII encoded characters, or a JPEG image, or some other kind binary data.

    My point is simply that what we understood first, unsurprisingly, was that which was most easily detected by observation. Where functionality is not revealed by a direct and observable correspondence between the contents of digital memory and some activity, such as the assembly of protein machines, does not mean that there is no functionality, but only that the functionality may be much more indirectly associated with the contents of digital memory.

  16. 16
    Querius says:

    wd400 and Larry Moran,

    Quiz – 12 points

    1. Who popularized the term “junk DNA”?

    2. What was the exact title of the paper that first proposed an evolutionary reason for junk DNA?

    3. What was the proposed reason in the paper for so much junk?

    4. Why was it considered strong evidence for evolution?

    -Q

  17. 17
    Nullifidian says:

    Querius, you’re making a potentially unjustified assumption in your last question. What makes you think that any knowledgeable biologists ever considered the mere existence of junk DNA to be evidence of evolution?

    As for your first three questions, Moran has already answered them in this article:

    http://sandwalk.blogspot.com/2.....-case.html

  18. 18
    Mapou says:

    REC:

    Mapou@2: “Protein coding genes are at the bottom of the hierarchy. Layered on top are the regulatory or control genes. Just recently they found the master regulator, the one way at the top: nFGFR1?

    …..nGFR1 is a protein, FYI.

    Well, it goes without saying that control/regulatory/noncoding genes cannot perform their tasks directly. They must be using actual proteins to do their bidding in various locations within the organism. I could be wrong but I do not think that nFGFR1 is the actual master regulatory gene. I strongly suspect that it is but a slave gene used by other non-coding master genes. I suspect that every level of the genomic hierarchy uses one or more of these slave genes/proteins. I am only basing my hypothesis on what an intelligent designer would do.

    PS. Regardless of the final understanding, there is no question that the genome is organized like a tree, which is consistent with intelligent design.

  19. 19
    Querius says:

    Nullifidian,

    My post was addressed to wd400 and Larry Moran, not you. They made their assertions here on this UD topic, not Sandwalk.

    Presumably they can speak for themselves.

    -Q

  20. 20
    SamHManning says:

    http://www.nature.com/news/200.....018-7.html

    “Mice do fine without ‘junk DNA'”

    “Mice born without large portions of their ‘junk DNA’ seem to survive normally. The result contradicts the beliefs of many scientists who have sought to uncover the function of these parts of the genome.”

    ‘Nuff said. Non-ID, non-YEC scientists were hypothesizing and finding function in ‘junk DNA’ a decade or more before the Discovery Institute existed (see, for example, Zuckerkandl, E. 1981A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins Mol. Biol. Rep. 7149–158.).
    Regarding selective advantages – well, all of evolution is not about selection. If you folks were actually as well read as you like to present yourselves, you would have known this.

  21. 21
    bornagain77 says:

    Jonathan Wells on Darwinism, Science, and Junk DNA – November 2011
    Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome(actually 1mb from a mouse genome is about .03%, not 1%.)—and that they could “see no effect in them.”
    But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued.
    In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances.
    http://www.uncommondescent.com.....-junk-dna/

    The following study highlights the inherent fallacy in gene deletion/knockout experiments that have led many scientists astray in the past as to underestimating what the minimal genome for life should actually be:

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

    Genetic Redundancy is incompatible with Darwinism:

    The Problem Of Genetic Redundancy for Darwinism
    Excerpt: the very existence of genetic buffering, and the functional redundancies required for it, presents a paradox in light of the Darwinian (or: selectionist) concept. On one hand, for genetic buffering to take place there is a necessity for redundancies of gene function, on the other hand such redundancies are clearly unstable in face of natural selection and are therefore unlikely to be found in evolved genomes. Still, over 90% of the genes studies of model organisms were observed to be redundant [Conant GC et al, 2004; Kobayashi K et al, 2003; Baba T et al, 2006].
    http://archive.is/YxXhd

  22. 22
    Eric Anderson says:

    Nullifidian @17:

    What makes you think that any knowledgeable biologists ever considered the mere existence of junk DNA to be evidence of evolution?

    Fair enough. It was only the unknowledgeable biologists, as well as the myriad pushers of the materialist creation story who claimed that the existence of junk DNA was evidence for unguided evolution. Sadly, we don’t even need to look back several decades for many examples. The “lots of DNA is junk, which shows evolution is true” is still being put forth by claimants today.

  23. 23
    Silver Asiatic says:

    @20

    Knowles cautions that the study doesn’t prove that non-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she says. “We don’t know if they have abnormalities that we don’t test for.

    … But he also believes that non-coding regions may have an effect too subtle to be picked up in the tests to far.

    “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argues. “Darwinian selection is a tougher test.”

  24. 24
    wd400 says:

    Q,

    I’m not going to play some silly game with these questions

    You are presumably referring to Ohno’s paper where he explicitly includes non-coding DNA in the non-junk portion of the genome and articulates one of the positive arguments for junk DNA.

  25. 25
    Mung says:

    …all of evolution is not about selection. If you folks were actually as well read as you like to present yourselves, you would have known this.

    LoL!

  26. 26
    Nullifidian says:

    Quierus @ #19:

    “My post was addressed to wd400 and Larry Moran, not you. They made their assertions here on this UD topic, not Sandwalk.”

    Yes, and I was pointing out that three of your questions already had readily ascertainable answers, if you were to use just a little bit of initiative. I don’t see what difference it makes if these facts are pointed out here or at another link, nor do I see that there is some sort of magic force field around your comments that prevents other people from adding their two cents.

    Eric Anderson @ #22:

    “Fair enough. It was only the unknowledgeable biologists, as well as the myriad pushers of the materialist creation story who claimed that the existence of junk DNA was evidence for unguided evolution.”

    Well, if you concede that only unknowledgeable people are making the argument, then whether the majority of most eukaryotes’ genomes are junk or not has nothing to do with the theory of evolution as it is actually formulated, does it? After all, bacteria are acknowledged to have very little if any junk DNA, but mainstream biologists don’t think that’s because they don’t evolve.

    “Sadly, we don’t even need to look back several decades for many examples. The ‘lots of DNA is junk, which shows evolution is true’ is still being put forth by claimants today.”

    Then perhaps you could provide a representative sample of cites to these “many examples” of people saying that the mere existence of junk is evidence of evolution? I’m quite curious to see what their reasoning is, and, alas, I’ve not been as fortunate as you are to see this argument mooted by any biologist I’ve ever come across in print or in person.

    And as long as we’re talking about it, you claimed above that “It is a classic argument from ignorance: ‘We don’t know what it does, therefore it must not do anything. Oh, and by the way, our theory predicts that there should be lots of junk, so evolution is true.’” Now, if it really is the case that biologists use an argument from ignorance to conclude that the majority of, to take a specific example, the human genome is junk, then it must follow that the majority of the human genome is unidentified. So, do you think that the majority of the human genome consists of unidentified genetic elements?

  27. 27
    Larry Moran says:

    1. Who popularized the term “junk DNA”?

    I can’t read your mind, but I assume you’re referring to the 1972 paper by Susumu Ohno.

    2. What was the exact title of the paper that first proposed an evolutionary reason for junk DNA?

    The title of Ohno’s paper was “So much ‘junk’ in our genome.” His main argument was based on genetic load. Does that count in your mind as a “evolutionary reason”? I can’t read the minds of IDiots so I have no idea what you mean by “evolutionary reason.”

    Or are you referring to the King & Jukes paper of 1968?

    3. What was the proposed reason in the paper for so much junk?

    Humans could not tolerate the number of deleterious mutations that would arise if most of our genome were functional.

    4. Why was it considered strong evidence for evolution?

    It wasn’t.

    HTH HAND

  28. 28
    Mapou says:

    Moran:

    3. What was the proposed reason in the paper for so much junk?

    Humans could not tolerate the number of deleterious mutations that would arise if most of our genome were functional.

    4. Why was it considered strong evidence for evolution?

    It wasn’t.

    Of course it was and you gave us the answer yourself while feigning that it wasn’t. The author (Ohno) assumed that a high number of mutations are needed to drive man’s evolution. He assumed that, given the required mutation rate, if most of our genes were functional, we would become extinct because the number of deleterious mutations would be too high. This is typical evolutionist crappy reasoning. Why deny it? Buy yourselves some huevos and admit that you people predicted something that turned out to be 100% wrong.

  29. 29
    wd400 says:

    The author (Ohno) assumed that a high number of mutations are needed to drive man’s evolution…

    Nope. You guys should really read some of these papers…

  30. 30
    Silver Asiatic says:

    “Our view is that [Junk DNA sequences] 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?”
    — Susumu Ohno: So much ‘junk’ DNA in our Genome”

    Evolution is trial and error. There are ‘experiments that fail’. Just look at fossil remains of extinct species. They’re Junk Species – evolution’s failed experiments.

    Since evolution experiments and sometimes succeeds and sometimes fails, is it any wonder that our genome too is filled with remains of extinct genes?

    … no argument here that Junk DNA is evidence supporting evolution?

  31. 31
    bornagain77 says:

    A Short History Of The Junk DNA Argument Of Darwinists

    Here is a good overview of the Junk DNA Argument (nice presentation)
    http://notascientist.d512.com/...../junk-dna/

    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 response 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
    https://vimeo.com/91162565

    The following video provides a detailed refutation of Fisher’s work, from the 1930’s, in population genetics:

    Biological Information – Overlapping Codes 10-25-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=OytcYD5791k&index=4&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ

    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?”

    “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]

    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)

    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

  32. 32
    bornagain77 says:

    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…”

    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 (after ENCODE)…
    “”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

    In 2011, 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/

  33. 33
    bornagain77 says:

    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

    The reason why many Darwinists are now trying to distance themselves from the fact that leading Darwinists use to claim up to 90% of the DNA was junk is nicely summed up in the following excerpt:

    Don’t Miss These Two Articles Relevant to Recent Discussions on Junk DNA History and Chromosome Fusion – Jonathan M. – August 2012
    Excerpt from a Sternberg citation: A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way. Most of the RNAs produced are various nonprotein-coding transcripts that are copied from both strands in a cell type-, tissue type-, or developmental stage-specific manner. These RNAs belong to a number of different functional classes and new categories are being discovered all the time. Further, these nonprotein-coding transcriptional units extend into and arise from protein-coding segments. Many also map to the regions between protein-coding loci. The RNA map of the mammalian genome has moreover been demonstrated to be hierarchical and far from random. ,,,
    Instead of 90% of the human or fly genome being junk, it seems that 90% or more of chromosomal DNA has some kind of specific developmental function, given the available data. Indeed, the emerging picture is that the species-specific nonprotein-coding regions encode numerous RNAs that help to shape the phenotype in ways that we are only beginning to understand. This is especially true for the transposable element fraction of human chromosomes — about 50% of our DNA — much of which is arranged and expressed in a taxon-specific manner. Part of the reason for why a human is not a chimp is not a cow is not a whale, then, is that each species has its own set of sui generis “genes” — genomic texts specifying unique RNAs or even proteins that are used in embryogenesis.
    http://www.evolutionnews.org/2.....63121.html

    Inferring Widespread Functionality for Virtually 100% of the Genome
    http://www.uncommondescent.com.....ent-503441

    Optimal Metabolism and Quantum DNA repair Implicate 100% functionality in Genome
    http://www.uncommondescent.com.....ent-503451

  34. 34
    Dr JDD says:

    Let’s face it, if we have literally only just discovered and started to understand clever and sophisticated parts of prokaryotic genomes such as palindromic sequences and related sequences due to CRISPR/Cas systems, how arrogant are we to then say we can happily and confidently label 90% of the human genome as “junk”?

    Just shows the faith-led system of materialism.

  35. 35
    bornagain77 says:

    Darwinists might have a lot better chance convincing ordinary people that DNA was not designed if DNA did not overwhelmingly appear to be designed:

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

    Unwinding the Double Helix: Meet DNA Helicase – Jonathan M. February 20, 2013 – article with video
    Excerpt: With a rotational speed of up to 10,000 rotations per minute, the helicase rivals the rotational speed of jet engine turbines.
    http://www.evolutionnews.org/2.....69371.html

    Dr. Jerry Bergman, “Divine Engineering: Unraveling DNA’s Design”:
    The DNA packing process is both complex and elegant and is so efficient that it achieves a reduction in length of DNA by a factor of 1 million.
    http://www.harunyahya.com/book.....php#dipnot

    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

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009
    Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

    Scientists’ 3-D View of Genes-at-Work Is Paradigm Shift in Genetics – Dec. 2009
    Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these ‘hot spots’. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.
    http://www.sciencedaily.com/re.....160649.htm

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

  36. 36
    bornagain77 says:

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

    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

    Genetics Is Too Complex for Evolutionists to Fake It Anymore – April 30, 2013
    Excerpt: Using the same amount of space, DNA can store 140,000 times more data than iron (III) oxide molecules, which stores information on computer hard drives.
    http://www.evolutionnews.org/2.....71621.html

    Biochemical Turing Machines “Reboot” the Watchmaker Argument – Fazale Rana – July 2012
    Excerpt: Researchers recognize several advantages to DNA computers.(7) One is the ability to perform a massive number of operations at the same time (in parallel) as opposed to one at a time (serially) as demanded by silicon-based computers. Secondly, DNA has the capacity to store an enormous quantity of information. One gram of DNA can house as much information as nearly 1 trillion CDs. And a third benefit is that DNA computing operates near the theoretical capacity with regard to energy efficiency.
    http://stevebrownetc.com/2012/.....-argument/

    Information Storage in DNA by Wyss Institute – video
    https://vimeo.com/47615970
    Quote from preceding video:
    “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.”
    Sriram Kosuri PhD. – Wyss Institute

    “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

    Thirty Years of Multiple Sequence Codes – Edward N. Trifonov – 2011
    How Many “Second Genetic Codes”?
    Excerpt: According to the media sympathetic to science and enthusiastic about sensational discoveries, the “Second Genetic Code” as it was called by New York Times (8) was discovered by Ya-Ming Hou and Paul Schimmel and published in Nature in 1988 (9). It was about recognition of tRNAs by respective aminoa- cyl-tRNA synthetases. Thirteen years later New Scientist announced the second Second Genetic Code (13), discovered by Jenuwein and Allis (14) and published in Science. This time it was about histone modifications. Five years later, New York Times, again, reported about “a second code in DNA in addition to the genetic code” (15). This was already the third Second Genetic Code, discovered by Segal et al (16), sug- gesting now nucleosome positioning rules. One, surely, would raise eyebrows having learned that there is also the fourth Second Genetic Code (17)—on in- teraction specificities between proteins and DNA, and the fifth Second Genetic Code, the name given by Nature magazine (18) to the set of rules governing gene splicing(19). Bewildered reader, naturally, would say “I’m done with seconds, can I have a third?” (20)
    The conclusion from the above is obvious: one has to admit that the genetic sequences carry many different codes. If we are to know what the sequences are about, we have to detect and decipher these codes. The times of surrender to “junk” and “selfish DNA” are over, and “non-coding” becomes a misnomer.,,,
    http://www.sciencedirect.com/s.....2911600016

    At the 10:30 minute mark of the following video, Dr. Trifonov states that the idea of the selfish gene ‘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

    In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, “Reading only one message, one gets three more, practically GRATIS!”. And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read.

    Concluding powerpoint of the lecture (at the 1 hour mark):

    “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

    Multiple genetic codes
    Excerpt: Trifonov,, was also the first one to demonstrate[20] that there are multiple codes present in the DNA. He points out that even so called non-coding DNA has a function, i.e. contains codes, although different from the triplet code.
    Trifonov recognizes[19]:5–10 specific codes in the DNA, RNA and proteins:,,

    chromatin code (Trifonov 1980)
    RNA-to-protein translation code (triplet code)
    framing code (Trifonov 1987)
    translation pausing code (Makhoul & Trifonov 2002) protein folding code (Berezovsky, Grosberg & Trifonov 2000)
    fast adaptation codes (Trifonov 1989)
    binary code (Trifonov 2006)
    genome segmentation code (Kolker & Trifonov 1995)

    The codes can overlap[19]:10 each other so that up to 4 different codes can be identified in one DNA sequence (specifically a sequence involved in a nucleosome). According to Trifonov, other codes are yet to be discovered.
    http://en.wikipedia.org/wiki/E.....etic_codes

    DNA as Poetry: Multiple Messages in a Single Sequence – James Shapiro – 2012
    Excerpt: Another question is harder to answer: How do multiple messages come to be inscribed in a single sequence in the course of evolution? This is an evolutionary mystery, especially when the second message has a complex structure. My own particular intellectual headache comes from structures called “shufflons” found in some bacteria that use them to diversify extracellular protein structures. Variability in surface proteins is advantageous in extending the range of specific cell-cell attachments for transfer of DNA and other macromolecules.
    In a shufflon, the coding sequence contains two or more copies of the intricate signals required for a DNA rearrangement process known as “site-specific recombination.” When a coding region carrying two or more recombination sites undergoes an inversion, the protein sequence changes because there is now a new string of triplet codons between the recombining sites. Some shufflons have up to seven different recombination sites embedded in the coding sequence. These structures are theoretically capable of generating over 100 different protein-coding DNA sequences (33 of which have actually been isolated from one shufflon).
    Such remarkable protein diversifying systems in bacterial genomes pose a mystery. How do the recombination sites evolve within sequences encoding functional proteins? It does not make sense to argue that each one evolved by selection operating a few nucleotides at a time; there is no benefit until at least two complete recombination signals are present. Moreover, known mechanisms for duplicating and inserting copies of a complex DNA signal at multiple locations generally disrupt coding capacity. Further, as in mammalian dual-coding regions, we do not understand how both strands evolve simultaneously to encode functional protein segments.
    At a time when we pride ourselves for being able to read DNA sequences with increasing speed, it is salutary to keep in mind that we are still far from knowing how to interpret the complex overlapping meanings contained in the genomic texts we store in our databases. DNA, like poetry, often has to be read in several ways.
    http://www.huffingtonpost.com/.....29190.html

    Verse:

    John 1:1
    In the beginning was the Word, and the Word was with God, and the Word was God.

  37. 37
    bornagain77 says:

    here is a neat quote to go with Shapiro’s ‘poem’ metaphor for DNA:

    “In Science we have been reading only the notes to a poem; in Christianity we find the poem itself.”
    So wrote C. S. Lewis in his 1947 book Miracles,

  38. 38
    Querius says:

    Larry Moran @ 27 replied,

    Q: 1. Who popularized the term “junk DNA”?
    LM: I can’t read your mind, but I assume you’re referring to the 1972 paper by Susumu Ohno.

    First of all, thank you for being straightforward and answering my “quiz.” I will respond in kind. The reason that I posed the questions was to try to bring the discussion into a historical context with the assumption that this would facilitate an intelligent exchange.
    Yes, I was referring to Ohno’s paper, which I read repeatedly as a result of previous arguments here.

    Q: 2. What was the exact title of the paper that first proposed an evolutionary reason for junk DNA?
    LM: The title of Ohno’s paper was “So much ‘junk’ in our genome.” His main argument was based on genetic load. Does that count in your mind as a “evolutionary reason”? I can’t read the minds of IDiots so I have no idea what you mean by “evolutionary reason.”
    Or are you referring to the King & Jukes paper of 1968?

    Yes, that’s the title and no, I’m unaware of a 1968 King & Jukes paper. Are you thinking of Kimura? What I appreciated near the end of Dr. Ohno’s paper were his creative proposals including the idea that “junk DNA” was the genetic remnants of evolution. If I remember correctly, he thought it might be analogous to the fossil record, and suggested that investigating it as such might provide valuable insights into the evolutionary history of humans.

    Q: 3. What was the proposed reason in the paper for so much junk?
    LM: Humans could not tolerate the number of deleterious mutations that would arise if most of our genome were functional.

    That was the other evolutionary reason he proposed (maybe I should have termed it a “rationale”). It seemed to me that both of these possibilities were very insightful, reasonable, and testable.

    Q: 4. Why was it considered strong evidence for evolution?
    LM: It wasn’t.
    HTH HAND

    That surprises me to hear from you for the reasons mentioned in 2 and 3. Were Ohno’s proposed reasons for so much junk DNA not widely accepted at the time, or is there another reason why you believe it was not strong evidence for evolution?

    Thanks,

    -Q

  39. 39
    Mung says:

    The Response to Kimura (1968) and King and Jukes (1969)

    King and Jukes chose the provocative title of “Non-Darwinian Evolution” for their paper, and the name stuck to the hypothesis until the early 1970’s when it was redubbed the neutral theory of molecular evolution. Kimura was not fond of the “non-Darwinian” label and asked King and Jukes to change it to emphasize molecular evolution, instead of evolution in general. King and Jukes had choosen their title with the intention of provoking the evolutionary establishment. Although both reviewers rejected their article, it was published upon appeal and the blasphemous title remained unchanged.

  40. 40
    Eric Anderson says:

    Thanks to everyone for the comments.

    There seem to be several individuals who are all caught up by my statement in the third paragraph that many evolutionists in past years have displayed an attitude that: “. . . the only DNA worth talking about was DNA that coded for proteins.”

    To be sure, this is a generalization about the attitude that has been pervasive. I did not intend to say that no-one ever thought otherwise. Indeed, in my fourth paragraph I specifically stated: “But let us not forget that there were a few lone voices . . . long arguing for pervasive function . . .”

    I certainly acknowledge that there have been some careful individuals who have long argued for broader function in DNA beyond protein-coding sequences. But the existence of those careful voices does not change, indeed it underscores, the fact that the popular representation, the oft-made assertion, is that most DNA is junk. And why would anyone think that? Well, first of all because it doesn’t code for proteins. And second, because we haven’t yet found any other function either. That is the attitude that has long characterized the debate over junk DNA as it relates to evolution. This is hardly controversial. Nearly all of the major proponents of evolutionary theory in recent decades have trotted out some form of the junk DNA argument as evidence for the materialistic evolution story. Worse yet, that argument is still being made by some evolutionary proponents.

    It will not do, it does not refute the broader issue, to point out that some biologists here and there were aware of other functions for some small percentage of DNA and were valiantly toiling away to tease out those functions. In the context of the evolution debate, which, it hardly bears reminding, is the context of this discussion, junk DNA has absolutely been touted as evidence for evolution, with the fact that most DNA does not code for proteins being a key piece of “evidence” for such a position.

    All that said, yes, I could have limited my sentence in paragraph 3 up front, rather than making the poor reader wait until the following paragraph. So I acknowledge the error of my ways and hereby rephrase the offending sentence as follows: “. . . almost the only DNA worth talking about was DNA that coded for proteins.”

    There. That addresses the majority of the objections to what I wrote.

    —–

    The great irony in so many of the discussions about junk DNA is that so often the very individuals who take great umbrage to anyone pointing out that evolutionists have long argued that most DNA is junk — claiming with indignation that such an observation is a perversion of history — in the same breath turn around and continue to argue that most DNA is junk. A remarkable example of cognitive dissonance.

  41. 41
    Querius says:

    Mung @ 39 noted

    . . . it was published upon appeal and the blasphemous title remained unchanged.

    LOL. Thanks for the historical context. I’m glad that King and Jukes stuck to their guns on the title because their theory is indeed a significant departure from the RV+NS dogma.

    Eric Anderson @ 40 noted

    . . . in the same breath turn around and continue to argue that most DNA is junk. A remarkable example of cognitive dissonance.

    Realize that these are not easy times for Darwinists. It’s stressful to maintain the appearance of an immutable orthodoxy while evolving to a new immutable orthodoxy. Then, with all us IDiots running around making noise, it’s little wonder that alcoholism, domestic strife, and road rage are increasing at an alarming rate among these parts of academia!

    -Q

  42. 42
    wd400 says:

    You still don’t seem to understand anything about this topic, EA.

    The folks arguing that there were functions in non-coding DNA were not “lone voices”. Everyone who knew the first thing about biology, including Ohno and other proponents of junk DNA, knew about functional RNAs and regulatory sequences. In Ohno’s paper (linked about) he specifically includes some classes on non-coding DNA in the non-junk portion of the genome.

    The twin myths that the idea of junk DNA led people to simply dismiss non-coding DNA and that the arguments for junk DNA amount to “We don’t know what it does, therefore it must not do anything.” are both based on ignorance. As I have said, if you want to talk meaninfully about junk DNA you should learn about the topic.

    That people as so happy to parade their ignorance about this topic, while blathering about how “naive and absurd” evolution biology is no less, tells you a lot about the ID movement’s connection of reality.

  43. 43
    wd400 says:

    The great irony in so many of the discussions about junk DNA is that so often the very individuals who take great umbrage to anyone pointing out that evolutionists have long argued that most DNA is junk — claiming with indignation that such an observation is a perversion of history — in the same breath turn around and continue to argue that most DNA is junk. A remarkable example of cognitive dissonance.

    What? Where have I or any other evolutionary biologists taken objection to the claim evolutionary biologists have argued most DNA is junk?

    The best evidence still supports the idea that most of the DNA in the human genome is junk. Evolutionary biologists have long held this to be the case, and indeed that’s why evoltutionary biologists did a much better job than did most molecular biologists when they estimated the number of genes in the human genome.

    As I’ve said above — what you have wrong is the nature of the argument for junk DNA. If you undestood that you might see how wrong your posts on this topic are.

  44. 44
    goodusername says:

    Eric Anderson,

    To be sure, this is a generalization about the attitude that has been pervasive. I did not intend to say that no-one ever thought otherwise.

    Umm, is there anyone who ever thought otherwise? I haven’t seen that sentiment.

    But the existence of those careful voices does not change, indeed it underscores, the fact that the popular representation, the oft-made assertion, is that most DNA is junk.

    Yes, that is a common assertion.

    And why would anyone think that? Well, first of all because it doesn’t code for proteins. And second, because we haven’t yet found any other function either.

    That’s part of it, but there’s more to it than that.

    It will not do, it does not refute the broader issue, to point out that some biologists here and there were aware of other functions for some small percentage of DNA and were valiantly toiling away to tease out those functions.

    I would say that all biologists were/are aware of functions for some non-coding dna.

    The great irony in so many of the discussions about junk DNA is that so often the very individuals who take great umbrage to anyone pointing out that evolutionists have long argued that most DNA is junk — claiming with indignation that such an observation is a perversion of history — in the same breath turn around and continue to argue that most DNA is junk. A remarkable example of cognitive dissonance.

    There’s no irony or dissonance in saying that most dna is junk, and saying that many evolutionists have argued against that position.

  45. 45
    Mung says:

    How do we measure the “junkiness” of DNA?

    Is the DNA of unicellular organisms mostly junk?

    The genomes of many bacteria consist of a single, circular chromosome. Human and other animal cells have linear chromosomes. An important feature of animal genomes is that much of the DNA does not code for genes. The non-coding DNA, also known as junk DNA

    http://universe-review.ca/F11-monocell13.htm

    Noncoding DNA is not ‘junk’ but a necessity for origin and evolution of biological complexity

  46. 46
    Querius says:

    Mung asks

    How do we measure the “junkiness” of DNA?

    You have to understand that “junk” now has a very specific technical meaning among evolutionary biologists.

    It essentially means “highly valuable with unknown function worthy of further study.” Of course some of us stupidly assumed that junk meant something without function and of little value.

    Shame on us!

    -Q

  47. 47
    bornagain77 says:

    One way to infer widespread functionality in the genome, despite not having knowledge of the precise function the entire genome, is to note that the entire genome, contrary to Darwinian presuppositions, is subject to multiple layers of DNA repair:

    Repair mechanisms in DNA include:
    A proofreading system that catches almost all errors
    A mismatch repair system to back up the proofreading system
    Photoreactivation (light repair)
    Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
    Base excision repair
    Nucleotide excision repair
    Double-strand DNA break repair
    Recombination repair
    Error-prone bypass
    http://www.newgeology.us/presentation32.html

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

    In fact, multiple overlapping methods of DNA repair is contradictory to Darwinian presuppositions:

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

    Contradiction in evolutionary theory – video – (The contradiction between extensive DNA repair mechanisms and the necessity of ‘random mutations/errors’ for Darwinian evolution)
    http://www.youtube.com/watch?v=dzh6Ct5cg1o

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    per UD News

    Another way to infer widespread functionality across the entire genome, despite not having knowledge of precise function, is empirically:

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

    Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009
    Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse.
    http://www.evolutionnews.org/2.....ellig.html

    Another way to infer widespread functionality across the entire genome, despite lacking knowledge of precise function, is to note the trend in evidence. Every element that Darwinists have insisted to be junk in the past has now been shown to have function of one kind or the other. In other words, there has only been an increase in the amount of the genomic elements known to functional, not a decrease!

    Biological Information – Not Junk After All 11-29-2014 by Paul Giem – video
    https://www.youtube.com/watch?v=xO-7kVBA_JM
    In the book “Biological Information: New Perspectives” the chapter entitled “Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information” discusses the various functions of DNA and finds that non-functional DNA is a small minority.

    Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information – Jonathan Wells
    http://www.worldscientific.com.....08728_0009

    Moreover, if the DNA were mostly dead weight, i.e. ‘neutral junk’, as many Darwinists hold, then we certainly should not be seeing the optimal energy efficiency in the metabolic pathways that we see!

    Optimal Design of Metabolism – Dr. Fazale Rana – July 2012
    Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition.
    http://www.reasons.org/article.....metabolism

    I showed the following biochemical pathway (metabolic) chart to a Darwinist once, when he had asked me for ANY evidence of intelligent design in biology.

    ExPASy – Biochemical Pathways – interactive schematic
    http://biochemical-pathways.com/#/map/1

    His response upon seeing the chart was something along the lines of, ‘Just because it is horrendously complex does not prove it was designed.’. ,,, Well maybe so it does not ‘prove’ in the 100%, absolutely impossible, sense, but such ‘horrendous complexity’ certainly does not give any comfort whatsoever to the notion that such ‘horrendous complexity’ can be the accumulation of random genetic accidents either!

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