'Junk DNA' News

What? Darwin’s followers did not use junk DNA as an argument for their position?

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That Uncommon Descent post on a biotechnology magazine (GEN) saying there wasn’t much junk DNA really sparked a discussion at the Intelligent design facebook home page.

For whatever reason, I had written

(Soon we will be hearing from all quarters that Darwin’s followers never really said it was junk. If this blog disappeared, would you know any different?)

Curiously, it attracted someone (Gassaway) who absolutely insists, in the face of evidence, that Darwin’s followers did not use alleged junk DNA in the genome as an argument for their position. One of the mods began to refer to the scene as the Troll Hour. There are currently nearly 250 comments.

Guess it was people who looked, acted, and sounded just like well-known defenders of Darwin, held the same positions, and published under their names then.

By all means, check out the ID Facebook page, especially now that Telic Thoughts has teeled into the Wayback Machine.

Question for readers here: Is it a sign of weakness in the Darwinians’ position that they can’t acknowledge that they made mistakes? They seem to have to defend, then deny.

Albert Einstein is said according to one reckoning to have made 23 significant mistakes but he is still Einstein. By contrast, lesser and less secure figures err, their followers are often expected to cover up for them.

Does it come down to: Do we find evidence, or do we impose dogma and then select or announce the evidence for it?

In the first case finding out that one was wrong about a few things isn’t as big an issue because one is still on the right track just by knowing what is correct.

In the second case, unco-operative facts must be tamed or made to disappear. All the better if they are historical facts that can just drop down the memory hole. People who obstruct that process are enemies.

Thoughts? – O’Leary for News

30 Replies to “What? Darwin’s followers did not use junk DNA as an argument for their position?

  1. 1
    bornagain77 says:

    A short History of Junk DNA Predictions By Leading neo-Darwinists

    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

    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.
    – John Sanford PhD Plant Genetics

    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?”
    – Sanford

    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 now 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

  2. 2
    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)

    Casey Luskin response to Farrel – several quotes by leading Darwinists claiming junk DNA 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 in 2009 on “junkDNA”
    “Junk DNA is just what a Darwinist would expect,”

    Dawkins in 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

  3. 3
    bornagain77 says:

    PZ Myers argues for well over 50% junk DNA in the following video in 2011:

    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

    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

    This nicely sums up what is making neo-Darwinists turn tail and run from their (necessary) junk DNA prediction:

    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

    Verse and Music:

    Psalm 139:13–16
    For you created my inmost being;
    you knit me together in my mother’s womb.
    I praise you because I am fearfully and wonderfully made;
    your works are wonderful,
    I know that full well.
    My frame was not hidden from you
    when I was made in the secret place,
    when I was woven together in the depths of the earth.
    Your eyes saw my unformed body;
    all the days ordained for me were written in your book
    before one of them came to be.

    Beautiful You – Trent Monk
    http://myktis.com/songs/beautiful-you/

  4. 4
    bornagain77 says:

    of related note: as far as I know, our friendly ad hominem neighbor Larry Moran is still to this day arguing for a large percentages of junk DNA.

  5. 5
    Mapou says:

    News:

    Question for readers here: Is it a sign of weakness in the Darwinians’ position that they can’t acknowledge that they made mistakes?

    It’s a sign of the pathology of elitism in general. Elitists never admit that they are wrong. Self-appointed authority can never be wrong. They either knew it all along, or they were misunderstood, or they were popularizing for the dumb masses, or they were just kidding, or they were testing to see if you were awake, or they were just hypothesizing. They always have a legitimate excuse.

    But the rest of us mortals know better. They are all a bunch of asteroid orifices. 😀

  6. 6
    wd400 says:

    I keep asking this simple question and getting no response. What about the ENCODE results shows us that most DNA is not junk? I’m one of these hide-bound ideologues who thinks it’s like >80% of the human genome is probably junk. If I’m a fool for believing this please explain why (and why you are at it, you can try explaining how you are a live if most of your genome is not junk and you have so many new mutations…)

  7. 7
    scordova says:

    (and why you are at it, you can try explaining how you are a live if most of your genome is not junk and you have so many new mutations…)

    For the same reason a fault tolerant system like the Space Shuttle’s navigation suite can tolerate loss of 80% of its navigation components and still navigate. It has 5 levels of redundancy, and if 4 out of the 5 (80%) fail, the system can still work.

    The problem with evolutionism is it places too high a value on component knockout to determine if there is function.

    That, said, ENCODE’s assumption that something is selected for therefore it is conserved is flawed. ID proponents generally think “conserved” sequences are functional, but not because they have immediate selection value. Cornelius Hunter posted recently on the knockout experiments of deeply conserved regions.

    By the way, we would be able to have any degree of self-healing if there were not deep levels of redundancy, and it appears we’ve lost a lot of ability to heal over time. We’ve devolved….

    It might be fair to say, if there is a lot of junk in the human genome, it was functional. The Darwinian view is that it was never functional. There is a difference.

  8. 8
    Mung says:

    Salvador Cardoza:

    The Darwinian view is that it was never functional. There is a difference.

    Nonsense.

  9. 9
    scordova says:

    Nonsense.

    I was referring to the neutral regions, not supposedly vestigial ones.

  10. 10
    wd400 says:

    The Darwinian view is that it was never functional. There is a difference

    There is nothing very Darwinian about junk DNA. But it is not the mainstream evolutionary view that junk DNA was never functional. Indeed pseudogenes are a major class of junk DNA. Any of the anti-junkers want to propose a function for our vitamin C gene?

    I’ver never heard about this 5x redundancy build into our genetics before. Sufferers of Huntington’s, Phenylketonuria, Tay Sachs, Haemophilia and Duchenne muscular dystrophy might be similarly surprised…

  11. 11
    scordova says:

    Indeed pseudogenes are a major class of junk DNA.

    Are you saying most pseudogenes were functional? I thought they were functionless copies of functioning genes.

    What proportion of pseudogenes were functioning copies of the original gene.

    I’ver never heard about this 5x redundancy build into our genetics before.

    I didn’t say there was, but you asked how it could be possible some regions could be knocked out without immediate effect.

    That said:
    http://en.wikipedia.org/wiki/Genetic_redundancy

    Which says exactly what I’ve observed here at UD:

    A Darwinian Paradox Genetic redundancy has aroused significant debate in the context of evolutionary biology (Nowak et al., 1997; Kafri, Springer & Pilpel . 2009). This is because the redundant character of the genes (which are not associated with genetic duplication and which do not mutate faster) seems to defy natural selection. Usually, biologist try to fit their observations into a selection-framework, but here it does not fit.

  12. 12
    Mung says:

    Salvador:

    It might be fair to say, if there is a lot of junk in the human genome, it was functional. The Darwinian view is that it was never functional. There is a difference.

    Nonsense. Are you a Young Earth Creationist, Sal?

    Salvador:

    The Darwinian view is that it was never functional.

    Nonsense.

    Sal:

    I was referring to the neutral regions, not supposedly vestigial ones.

    Well, why didn’t you say so?

    How do you tell the difference?

    There is a difference.

    Such as?

  13. 13
    bornagain77 says:

    Thanks for the redundancy link scordova.

    Of related note:

    plasticity-relaxation-mutation (PRM)
    http://www.evolutionnews.org/2.....52941.html

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

    Dollo’s law and the death and resurrection of genes
    ABSTRACT: Dollo’s law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or “lost” developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints;
    http://www.pnas.org/content/91.....l.pdf+html

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

  14. 14
    bornagain77 says:

    Dollo’s law and the death and resurrection of genes:
    Excerpt: “As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo’s law, after its propounder, and is taken as a general statement that evolution is irreversible.”
    http://www.pnas.org/content/91.....l.pdf+html

  15. 15
    scordova says:

    WD400,

    Thanks for you comments and criticisms. Regarding genetic redundancy, I started a new discussion here:

    http://www.uncommondescent.com.....edundancy/

    Sal

  16. 16
    bornagain77 says:

    Vitamin C Pseudogene Refutation by Jonathan Wells
    https://docs.google.com/document/d/18LV9Xp1RJv4k2KRQDOpN3_cjSCwBC_XXb8WGVNP4L8M/edit

    Along that line:

    Alleged Human Chromosome 2 “Fusion Site” Encodes an Active DNA Binding Domain Inside a Complex and Highly Expressed Gene—Negating Fusion – by Jeffrey P. Tomkins – October 16, 2013
    http://www.answersingenesis.or.....ome-fusion

    Human Chromosome Fusion Debunked – Jeffrey P. Tomkins – Oct. 26, 2013
    http://designed-dna.org/blog/f.....c29-86.php

    One thing that has always struck me as particularly absurd, in the claim of neo-Darwinists that most of our DNA is junk, is that the cell expends a tremendous amount of energy and resources repairing that supposedly useless junk DNA.

    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

    Scientists Decipher Missing Piece Of First-responder DNA Repair Machine – Oct. 2009
    Excerpt: The first-responder machine, a protein complex called Mre11-Rad50-Nbs1 (or MRN for short), homes in on the gravest kind of breaks in which both strands of a DNA double helix are cut. It then stops the cell from dividing and launches an error-free DNA repair process called homologous recombination, which replaces defective genes.
    http://www.sciencedaily.com/re.....164106.htm

    A Look at the Quality Control System in the Protein Factory – JonathanM – March 2012
    Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed.
    http://www.evolutionnews.org/2.....57791.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

    Of note: DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.

  17. 17
    bornagain77 says:

    Moreover besides being contrary to the notion of Junk DNA in general, sophisticated repair mechanisms are incompatible with Darwinism in principle:

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

    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.
    http://www.uncommondescent.com.....r-systems/

    What ever happened to science in America where a theory in science is impervious to falsification from evidence such as this (of which many, many, more examples of contradictions to Darwinian predictions could be cited)

  18. 18
    THEMAYAN says:

    In my opinion one of the biggest offenders of this false revisionist paradigm, is T. Ryan Gregory at GENOMICRON, who tries to down play the fact that for decades the general public, as well as students, were told that junk DNA was exactly what you would expect to find if the theory/Darwinism were true. Of course this was not completely true, but this is what we were spoon fed.

    He claims that we knew about functionality all along, and that these new discoveries should not be surprising. And while he cites the work of others who seemed to have questioned this paradigm as far back as 30 years or so. What Gregory fails to realize, is that for the most part, their work was largely ignored by the status quo. And very little substantial research money was going towards the potential discovery of functionality of this so called junk. Instead, this same junk DNA paradigm was being milked as a poster child for bad design.

    And unfortunately even today, this kind of “don’t touch this” mindset seems to still prevail, at least among a few (such as PZ Myers, who in his talk entitled Rummaging About in the Genetic Junkyard Skepticon 4 PZ Myers) makes the claim that biologist who search for functional elements in junk DNA, are only interested in job security. I guess the message here is, lets just give up on research because we already know it’s only useless junk. Now talk about a science stopper.

    https://www.youtube.com/watch?v=DRsN7w7iW08

  19. 19
    JGuy says:

    Regarding ENCODE, coding regions of DNA, so-called “junk DNA” and the protesting Darwinists… Something occurred to me today.

    “Junk DNA” was applied to non-coding regions that supposedly didn’t do anything, such as code for proteins.

    ENCODE found that at least 80% (or 85%?) of the non-coding portion of DNA was copied & expressed as RNA molecules. Darwinists protest this does not mean it is useful, from some of the protests I hear.

    But what occurred to me today is, why do they think the coded for proteins are useful for life? Is it because every conceivable protein is useful? or Is it because the code is expressed?

    It seems there may be some inconsistency going on here.

    🙂

  20. 20
    wd400 says:

    There are good reasons to think proteins, and ORFS with homology to other known proteins, are functional beyond the fact they are expressed. Most obviously, non-functional proteins rot. The non-sense and frame-shift mutations that break are always occuring in protein coding sequences aren’t selected against and pretty quickly you end up with pseudogenes. There may well be a few “junk proteins”.

    On the other hand, it would be absurd to imagine every transcribed sequence is functional. After all, that definition would include every nucleotide of every intron!

  21. 21
    wd400 says:

    re ““Junk DNA” was applied to non-coding regions that supposedly didn’t do anything, such as code for proteins.”

    I should add: the best arguments for the junkiness of most eukaryote genomes has never been about the fact we don’t know what certain sequences might do. The load argument, the c-value paradox, intra-specific variation and lack of conservation are all good arguments for junk that don’t related to our ignorance of particular sequences function.

  22. 22
    JGuy says:

    wd400

    There are good reasons to think proteins, and ORFS with homology to other known proteins, are functional beyond the fact they are expressed. Most obviously, non-functional proteins rot. The non-sense and frame-shift mutations that break are always occuring in protein coding sequences aren’t selected against and pretty quickly you end up with pseudogenes. There may well be a few “junk proteins”.

    Seems more an argument for the existence of a few “junk-proteins” than for why ‘coding’ regions should be considered by-and-large functional. Analogous ideas that are similar enough as this kind of argument can be found within the ‘non-coding’ regions from where RNA is expressed.

    On the other hand, it would be absurd to imagine every transcribed sequence is functional. After all, that definition would include every nucleotide of every intron!

    Excluding any slightly harmful mutations in the code. It’s not necessarily any more absurd than thinking every bit of a compiled program is useful.

    I guess the position one see’s likier here depends a lot on presuppositions.

    I should add: the best arguments for the junkiness of most eukaryote genomes has never been about the fact we don’t know what certain sequences might do. The load argument, the c-value paradox, intra-specific variation and lack of conservation are all good arguments for junk that don’t related to our ignorance of particular sequences function.

    Ignorance is no excuse for calling something junk. For example, I’d leave open all kinds of possibilities. For example, regions that might not ‘conserve’, might be useful depending on the environment…or they may simply serve as a structural function relevant to other portions of non-coding region in the DNA. Of course, I’d do so assuming there was a greater chance for there to be a purpose, based on my presupposed ideas.

  23. 23
    scordova says:

    I said it might be fair to say

    if there is a lot of junk in the human genome, it was functional

    to which Mung replied,

    nonsense

    The opposing position to what I said then would be

    if there is a lot of junk in the human genome, it was never functional

    Thus if Mung asserts what I said is nonsense, this implies his “sensible” view is that

    if there is a lot of junk in the human genome, it was never functional

  24. 24
    wd400 says:

    Jguy,

    You haven’t understood my comment at all. The point is, proteins are likely to be functional because non-functional proteins rot once they are freed from stabalising selection. If there are analogous arguments for non-coding sequences I’m not aware of them – please let me know.

    It’s not necessarily any more absurd than thinking every bit of a compiled program is useful.

    Yes it absolutely is necessarily more absurd to imagine that every nucleotide of every intron is useful than it is to think every bit of a compiled program is.

    For example, regions that might not ‘conserve’, might be useful depending on the environment

    But if they are allowing mutations to fix while they are in the “wrong” environment they will lose their function.

    r they may simply serve as a structural function relevant to other portions of non-coding region in the DNA

    There are certainly DNA elements that play a structural role . Indeed the change that most DNA is “spacer” for the rest was one of the first proposals put to Ohno after his junk DNA talk. But the idea that most of our DNA is spacer is nto consistant with, for instance, intra-specific variation in junk DNA or the so called c-value paradox

  25. 25
    bornagain77 says:

    “If there are analogous arguments for non-coding sequences I’m not aware of them – please let me know.”

    well, besides the fact that it was previously mentioned at 16, I can think of a analogous argument right off the bat:

    “Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle.”
    – John Sanford – Genetic Entropy and The Mystery of The Genome – pg. 21 – Inventor of the ‘Gene Gun’

    Experimental evolution of gene duplicates in a bacterial plasmid model.- 2007
    The fate of gene duplicates subjected to diversifying selection was tested experimentally in a bacterial system.,,,
    In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow.,,,
    http://www.ncbi.nlm.nih.gov/pubmed/17211548

    Of course such important considerations are just so much more ‘junk’ for you to ignore since you know Darwinism is true no matter what the evidence says? Right wd???

  26. 26
    wd400 says:

    Unless, of course, you know the first thing about population genetics BA. Very small fitness effects are effectively neutral, and the degree to which populations can “feel” such small effects is determined by there (effective) size. Selection is a stronger force in large population, while drift dominates in small populations.

    If the addition of more junk-ish DNA is indeed a case of nearly-neutral variants accruing then we might predict that organisms with large effective population sizes have smaller genomes (as selection is stronger, and thus the genome can be purged). Indeed, just this paterrn has been shown in many organisms. It’s not the whole story of why genomes are junky – but it does show how evolutionary biology allows us to make and test predictions…

  27. 27
    THEMAYAN says:

    Ewan Birney claimed that we may not completely understand what all of this 80% is doing. But we believe it is doing something important’

    And keep in mind, we are still not finished yet and not by a long shot. And more an more function is being discovered all the time. Including by many other independent studies.

    One of the major criticisms of Encode, was it’s broad use of the term functionality, but is it really reasonable to expect anything less when the findings themselves are so broad? This is not simple yes or no stuff we’re dealing with. I believe this whole (I don’t understand it, so therefore it must be, or still is junk) paradigm has not only, not been a very useful, but It has already held us back for much to long.

    Jguy, I think you are still concentrating on the trunk of the Elephant, while many have gone well beyond that stage. It seems to me the genome is far more complex and greater than just the some of its individual parts. And I think this kind of reductionist view has not been very fruitful. And It seems there is now little doubt, that the genome is very much akin to an extremely sophisticated computer program. The question is. Is it more like a PC with all those potentially useless and junkie files? Or is it more like a Mac? In any case, we know that both were intelligently designed.

  28. 28
    bornagain77 says:

    wd400 you state:

    “Unless, of course, you know the first thing about population genetics BA.”

    Well I admit I’m a empirical evidence kind of guy and that I kind of look down on Darwinists who continually cite mathematical models of population genetics as to proving their theory instead of citing real world evidence (i.e. I ain’t got no real evidence but look at this nifty mathematical model I got on paper!). But, it has come to my attention over the past few years, from others who know population genetics quite well, that Darwinists have no real mathematical foundation within science as to make real predictions for science in the first place:

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

    Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe
    Excerpt: Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. …
    http://biologicinstitute.org/2.....emagician/

    Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008
    Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue.
    Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person.
    http://www.icr.org/i/pdf/techn.....Theory.pdf

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

    With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory – November 2011
    Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,,
    http://www.evolutionnews.org/2.....52821.html

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003)

    Macroevolution, microevolution and chemistry: the devil is in the details – Dr. V. J. Torley – February 27, 2013
    Excerpt: After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated?
    http://www.uncommondescent.com.....e-details/

    While they (Darwinian Biologists) pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’” Wolfgang Pauli

  29. 29
    bornagain77 says:

    In fact, when one tries predict something in evolution happening accurately with the nascent probability math of population genetics, the math blows up in the faces of neo-Darwinists:

    Waiting Longer for Two Mutations – Michael J. Behe
    Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.
    http://www.discovery.org/a/9461

    Don’t Mess With ID (Overview of Behe’s ‘Edge’ and Durrett and Schmidt’s paper at the 20:00 minute mark) – Paul Giem – video
    http://www.youtube.com/watch?v=5JeYJ29-I7o

    Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008
    Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue.
    Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person.
    http://www.icr.org/i/pdf/techn.....Theory.pdf

    Whereas nobody can seem to come up with a rigid demarcation criteria for Darwinism, Intelligent Design (ID) does not suffer from such a lack of mathematical rigor:

    Evolutionary Informatics Lab – Main Publications
    http://evoinfo.org/publications/

    ,, the empirical falsification criteria of ID is much easier to understand than the math is, and is as such:

    “Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.”
    – Dr Behe in 1997

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

  30. 30
    Dimitri44 says:

    Charles Darwin wrote 500 pages on adaptation evidence, and 1 page on evolution speculation; and he stated that adaptation can only happen at the lowest level of the biological table (by Carl Linnaeus), the species level. The higher levels, from the top, are kingdom, phylum, class, order, family, and genus. That’s why he essentially titled his book, Origin of the Species, and not Origin of the Phylum. Darwin based his one page of speculation on the Geological Column proposed by his contemporary, Charles Lyell; which, however, now faces increasingly apparent scientific contradictions.

    The evolution people have since seized upon the one page of speculation by Darwin, coupled with the Geological Column of Lyell, the name of which has since been changed to the Geological Time Scale. They have then used these two threads to develop what can be identified as a Pseudo-Adaptation Hypothesis. Before considering this, let us summarize the correct Theory of Adaptation that was scientifically proven by Darwin. This is something that only takes a few or so, at most, generations to work, and it relies upon the fact that there will be individual differences among the newborn from one generation to the next; so that those characteristics that are better able to cope with life are the characteristics that are going to prevail. Also bear in mind that this is something that can only happen at the species level, the lowest level from the biological table. This also means that when some evolution people say that Darwin proved evolution, they are not telling the truth.

    The key to establishing the validity of Adaptation (Natural Selection) was the different islands among the Galapagos off the coast of Ecuador having similar species which could not cross from one island to the next, nor by human assistance; but similar preferred characteristics of the species nevertheless developed to a greater or lesser extent on each island – a novel way of repeating the experiment, as it were.

    Now let us consider the Pseudo-Adaptation Hypothesis. The Geological Time Scale now allows for an estimate of the age of the earth to be in the millions, or even billions of years; rather than the few thousand years allowed by the Old Testament. The idea is then proposed that purely fortuitous, happenstance changes (mutations) might take place from time to time over a period of zillions of years, even at higher levels from the biological table, so that life forms can become more complicated that way. This means any number of major new changes, each of which is individually useless, somehow then combining up, and then useful, only then leading, for example, to an actual new genus. All of this would also had to have happened, time and again, independently, defining each genus member of the genera.

    There are also two schools of thought as to the Geological Time Scale. One school relies on catastrophic events, such as a huge asteroid hitting the planet earth, something much too infrequent for the above combining up possibility. The other school of thought relies upon ordinary events, described above, taking place over the zillions of years. All of this also means that the Pseudo-Adaptation Hypothesis is something that can never be scientifically proven, or at least it certainly hasn’t been yet. Thus, to conclude, the only thing that the evolution people have to offer us is a hypothesis that can never be proven, and nothing any better than that.

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