Home » 'Junk DNA', Darwinism, Intelligent Design » Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives

Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives

Jonathan Wells

In a recent interview for Salvo magazine, I was asked what advice on junk DNA I would give to Francis Collins or Richard Dawkins.

On November 3, UD posted my response. According to the first comment following that post,

Jonathan Wells is the last person from whom Richard Dawkins and Francis Collins would solicit advice.

I agree. But the commenter, “Single Malt,” went on to question whether I’m qualified to give advice to anybody about anything in biology:

For those not familiar here is a quote…?“Father’s [Sun Myung Moon's] words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism.” That’s incredibly damning if true. It basically tells us that before Wells had even studied the subject he had been instructed to devote his life to destroying it! ?Does this not color completely anything Wells publishes concerning the biological sciences?

Now, I don’t know who “Single Malt” is. To the best of my knowledge he (or she) has never met me, spoken with me on the telephone, or corresponded with me by letter or email. Since I like single malt scotch, however, if he or she had contacted me I would have been happy to explain over a friendly drink why I wrote the sentence quoted above.

Here’s what I would have said:

As an undergraduate at Princeton and Berkeley in the 1960s I studied mathematics, geology, physics and biology (with minors in philosophy and German). Along the way—despite my upbringing as a nominal Presbyterian—I became an agnostic and a Darwinist.(Note: By “Darwinism,” I mean the claim that all living things are descended from one or a few common ancestors, modified solely by unguided natural processes such as variation and selection. For the sake of brevity, I use the term here also to include Neo-Darwinism, which attributes new variations to genetic mutations.)

In 1963, I dropped out of Princeton and drove a New York City taxicab until I was drafted into the U.S. Army in 1964. While spending two years in Germany as a medical laboratory technologist, I became opposed to the Vietnam War, and after I was separated from active duty in 1966 I transferred to Berkeley and joined the antiwar movement.

The Army called me back as a reservist in 1967, but I refused and spent a year and a half in prison. After being released from Leavenworth in 1969, I completed my bachelor’s degree at Berkeley. By 1970, however, I was repulsed by the increasingly violent and hypocritical Berkeley Left, and I soon headed for the hills. Living in a cabin I built in the mountains of Mendocino County, I was transformed by the beauty, peace and evident design around me. I ceased being an agnostic and a Darwinist.

In 1974 I joined Reverend Sun Myung Moon’s Unification Church. In 1976 I entered Unification Theological Seminary in New York, where I studied the Pentateuch under a Romanian Orthodox Jewish rabbi; the New Testament under a Reformed Church of America minister; the Early Church Fathers under a Greek Orthodox priest; philosophy under a Polish Roman Catholic priest with three earned doctorates; medieval theology under a Church of Christ missionary with a doctorate from the University of Tübingen; and Reformation and modern theology under a Presbyterian with a doctorate from Harvard.

I read—and was repelled by—modern theologians who took Darwinism for granted and tried to re-fashion Christian doctrine in the light of it. I also took advantage of a weekly seminary shuttle to New York City to do research at the Columbia University biology library, where I became convinced that the Darwinian mechanism of accidental mutations and natural selection is incapable of producing the changes required by evolution.

As I researched more I concluded that the Achilles’ heel of Darwinism is its assumption that genetic programs control embryo development, with DNA mutations supplying raw materials for evolution. At the time, however, I did not question Darwin’s claim that all living things are descended from a common ancestor.

Reverend Moon occasionally criticized Darwinism in his speeches, because it conflicted with reason and denied design. He often visited the seminary during my two years there, and we students would walk with him in the nearby fields and woods. He urged us (among other things) to pray in order to find out what God wanted us to do with our lives. I followed his advice, and my prayers strengthened the conviction I had arrived at through my studies that Darwinism (like Marxism and Freudianism) is materialistic philosophy masquerading as empirical science—and that I should set out to destroy its dominance in our culture.

In 1978, I was one of a score of seminary graduates awarded church scholarships to pursue doctorates in religious studies at other schools. I went to Yale, where I did research on the nineteenth-century Darwinian controversies and received a Ph.D. in theology in 1985. After that, I was appointed Director of the Unification Church’s inter-religious outreach organization in New York City.

I still felt called to devote myself to toppling Darwinism, however, so in 1988 I resigned from my position to return to graduate school—this time in biology. I applied to several schools in California and moved there with my family, only to learn that I had not been admitted anywhere. I took a job as a medical laboratory technologist (the Army had taught me a trade!) and sometime afterwards went back to New York to attend a meeting between Unification Church leaders and Reverend Moon. When he learned that I was planning to go back to graduate school he admonished me not to do it, saying that I was too old (I was 45 at the time). After the meeting, however, I prayed for a long time and decided that I had to continue on my course.

I returned to California and applied again to various graduate schools. In 1989 I was granted interviews at Cal Tech, Stanford, U.C. Berkeley, and U.C. Davis. I chose Berkeley, where I completed a Ph.D. in molecular and cell biology in 1994. By then—having been exposed to the actual evidence—I was skeptical of Darwin’s claim that all living things share a common ancestor.

A senior Unification Church leader then asked me to write something for other church members explaining why I went for a second Ph.D. even after Reverend Moon had admonished me against doing so. I wrote an essay that I thought would be for in-house use only, but it was subsequently posted on the Internet without my knowledge or permission.

I first learned that my essay was available online in 2001, when Jerry Coyne made it the alpha and omega of his review in Nature of my book Icons of Evolution.

Since then, many of my critics have quoted the now-infamous line, “Father’s words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism.” (For a sampling, just do a Google search on the words.) Remarkably, Darwinists never quote much else from my essay, even though the 18 words in this one line represent only 1% of it, while a subsequent passage dealing with my scientific reasons for rejecting Darwinism represents 37%. Talk about quote mining…

Nor (as far as I know) have any Darwinists bothered to learn anything about the context in which I wrote the essay. If they had, they would know that Reverend Moon did not instruct or command me to destroy Darwinism (though years later he commended me on publishing Icons of Evolution.)

So, can I be trusted to say anything concerning the biological sciences? I freely admit that I was motivated to pursue a biology Ph.D., in part, because of my religious views. On the other hand, Francis Crick freely admitted (to historian Horace Freeland Judson) that he went into biology, in part, because of his atheistic views. What ultimately mattered in Crick’s case was not his motivation, but whether his biological claims were consistent with the evidence. The same is true in my case. That’s why I cite abundant scientific references in my publications—such as Icons of Evolution, The Politically Incorrect Guide to Darwinism and Intelligent Design, The Myth of Junk DNA, and “Why Darwinism Is False”, a detailed critique of Jerry Coyne’s book, Why Evolution Is True.

I encourage readers not simply to take my word for anything, but to go the scientific literature and check for themselves. After all, nothing in biology makes sense except in the light of evidence.

Now, wouldn’t it have been more enjoyable listening to that over a glass of Glenlivet or Macallan?

Follow UD News at Twitter!

  • Delicious
  • Facebook
  • Reddit
  • StumbleUpon
  • Twitter
  • RSS Feed

145 Responses to Here’s Jonathan Wells on destroying Darwinism – and responding to attacks on his character and motives

  1. Although I’m fairly certain Single Malt will not pay much attention to the context of what you wrote, I want to thank you, Dr. Wells, for clearing that ad hominem from Single Malt up.

  2. What are the odds any of those schools would grant Dr Wells an interview today- say for another PhD in some other biological/ biochemical science?

  3. Thanks for your post Jonathan. It made for interesting reading.

    I’ll restrict myself to a couple of brief comments and let the resident denizens evicerate me at their leisure.

    Since then, many of my critics have quoted the now-infamous line, “Father’s words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism.” (For a sampling, just do a Google search on the words.) Remarkably, Darwinists never quote much else from my essay, even though the 18 words in this one line represent only 1% of it, while a subsequent passage dealing with my scientific reasons for rejecting Darwinism represents 37%.

    You can’t really complain, though.

    Imagine a collection of like-minded folk got together to “overthrow the stifling dominance of particle physics” and “replace it with a science consonant with Hindu principles”.

    Further imagine that one of the most prominent members of this group wrote up an essay on why they sought further qualifications in QED. This essay amongst other information contained the exclamation;

    “Pandit, my prayers and my studies convinced me to devote my life to destroying the Standard Model”.

    Now, is there realistically any world in which that line wouldn’t have become an albatross around the authors neck?

    Talk about quote mining…

    Quote-mining, Jonathan? You really want to go there?

    You really ought to waited a little longer before posting, though. My last screed against you was pretty ‘out there’; given a few more days I’m fairly certain I could have placed you at Dealey Plaza.

    Next time….next time.

  4. Dealey Plaza? You mean from where Kennedy was assassinated?

    Some of us remember that. Goodbye.

  5. Well if particle physics was as easy a target as Darwinism, people would be in favor of the Hindus.

    As for:

    Now, is there realistically any world in which that line wouldn’t have become an albatross around the authors neck?

    Yes- a world interested in reality, as opposed to your position’s imagination-based science dominated by unpayable promissory notes.

  6. Imagine a collection of like-minded folk got together to “overthrow the stifling dominance of particle physics”

    So your first comment is an invalid caricature.

    Now, is there realistically any world in which that line wouldn’t have become an albatross around the authors neck?

    And you second comment applauds the defenders of materialism for foresaking the science to do a good job at obfuscation.

    You really ought to waited a little longer before posting, though. My last screed against you was pretty ‘out there’; given a few more days I’m fairly certain I could have placed you at Dealey Plaza. Next time…next time.

    And your final comment is adolescent narccicism on display.

    Good job.

  7. Methinks he ain’t an upright biped… :)

  8. If Darwinism were actually science, then dedicating your life to overthrowing it WOULD be on a par with dedicating your life to overthrowing the standard model. But it isn’t. It isn’t science. What it is is metaphysics masquerading as science. It is, as people like Dawkins and others make clear, apologetics for a materialist/atheist worldview. (Theistic evolutionists notwithstanding. They have their own theological/philosophical reasons for wanting Darwinism to be true that also have very little to do with science.)

    This debate is and has been from the very beginning a contest between materialism and a belief in the existence of a Creator. This is why it generates so much more heat than any other scientific debate with which I am familiar. Since my own metaphysics includes the existence of and a very large role for God, I am quite happy that the actual science overwhelmingly shows that Darwinism fails as an explanation for macro-evolutionary change, and the more science discovers about the exquisitely complex engineering of living systems, the stronger this refutation of Darwinism becomes.

    I predict that within the next 20 to 30 years, not only will Darwinism be relegated to the dustbin of history, along with Ptolemaic cosmology, phlogiston, and the ether, it will take atheism along with it.

  9. Thank you Dr Wells, your work stands on it’s own, but it’s always fascinating to learn more about the man behind the science.

    Well I really think Single_Malt has exposed himself for what he truly is; a Darwinian zealot interested in nothing but ad hominem attacks. His response to a cordial response from Dr Wells, nothing more than dismissive arrogance.

    Just a little ironic the news following was Frank Turek asks: Why do atheists so often seem to be angry?

  10. Bruce David

    This debate is and has been from the very beginning a contest between materialism and a belief in the existence of a Creator. This is why it generates so much more heat than any other scientific debate with which I am familiar. Since my own metaphysics includes the existence of and a very large role for God, I am quite happy that the actual science overwhelmingly shows that Darwinism fails as an explanation for macro-evolutionary change, and the more science discovers about the exquisitely complex engineering of living systems, the stronger this refutation of Darwinism becomes.

    But ID is not supposed to be about supporting any religious views. KariosFocus has been ranting at me all week for suggesting the same thing you just wrote. Maybe you two should talk and get the story straight.

  11. This is my own personal opinion. I have no connection whatsoever with anyone else who posts to this site other than a commonality of interest and in some cases similar views.

    That said, let me clarify a little. The following is my view of the history of Darwinism:

    When Darwin published Origin, there was gong on in European intellectual culture a war, you might say, between atheist materialism and Christianity. Origin of Species gave the materialists a powerful new weapon in that war, and people like Huxley used it to full advantage. When Darwinism was finally consolidated with genetics into the neo-Darwinian synthesis, and became the established scientific explanation, theists (Christians and others) were forced to accommodate it into their own views. But as scientific advances in the last 40 years began to reveal the staggering complexity and exquisite engineering of living systems, and as other scientific problems with Darwinism began to emerge, scientists who were not atheists and thus had neither an emotional nor an intellectual stake in the truth of the theory began to realize that the only viable explanation for the existence of life was that it is designed. This then gave those theists like Jonathan Wells (and myself) who see atheism as an idea that has severe negative consequences for society a new weapon to counter the advantage Darwinism has given to the atheists for the last 150 years.

    However, this does not negate the fact that the original and ongoing impetus for ID is at bottom scientific. The science shows clearly to anyone with an open mind that Darwinism as an explanation for macro-evolutionary change is false, and the only viable alternative explanation is ID. And there are scientists, such as Michael Behe, who are proponents of ID that seem to have no particular religious agenda at all. (He is a catholic, and the Vatican has officially taken the position that there is no conflict between Darwinism and faith.) There are even people like David Berlinski who see that Darwinism has failed but who take a stance of agnosticism, both with respect to the existence of God and with respect to what is the explanation for the existence of life.

    On the other hand, the Darwinists, particularly those like Dawkins and Coyn who are highly visible and vocal in their defense of Darwinism, clearly see in ID a threat to their cherished philosophy of atheism, and in defending Darwinism they are defending their metaphysical position, and they do so with far more intensity than is normally brought to scientific disputes.

  12. How about we end this conversation on a happy note?
    Dear Mr. Wells, thank you for responding to your critics here at Uncommon Descent. I must say through the years I had lost my faith… in science.

    I cannot think of a higher goal for a Scientist/Author than inspiring the reader. Because of your books, you rekindled my love of science. I have now read most of the pro ID books (The Design of Life being my favorite) as well as many pro-evolution books.

    It must be hard for you because the critics are always the loudest, but a lot of people really appreciate and respect the work your doing. Thank you again Mr. Wells, Julian.

  13. Single_Malt
    You fail to realize that Jonathan Wells has embarked on a noble mission of restoring science to its foundations of objective truth from the anti-religious stance of Darwinism.

    I expect you think you uphold science based on truth. However, I think that you probably fail to realize that you have probably a priori restricted science to purely physical stochastic processes and have excluded any possibility of objectively examining and testing for possibility of the existence or involvement of intelligent agents. e.g., forensics assumes that intelligent agents may be involved, and explicitly examines whether evidence points to natural or intelligent causes.

    Until you recognize and correct that foundational fallacy in Darwinian “science”, you are unlikely to recognize that the amoral principles of Darwinism lead to the immoral “might makes right” and all the consequent evils of individuals and regimes acting on that principle instead of “love your neighbor as yourself”. e.g. See The Black Book of Communism.

  14. By “Goodbye”, do you mean you are banning sigle_malt?

  15. I second that. Dr. Wells, I have always particularly admired the calm clarity with which you express your views. Of the many cogent things you have said in interviews I have seen, one I particularly like and have used myself (shamelessly plagiarizing, I admit) is, speaking of the many mutagenesis experiments on fruit flies, that there have been only three results, a normal fruit fly, a defective fruit fly, and a dead fruit fly.

    I also admire the honesty you display in the current post. I expect it will be quote mined, but what can you do?

  16. Over at Sandwalk, Larry Moran has a chapter-by-chapter review of The Myth of Junk DNA. All links are listed in the final part here.

    Would like to see Wells – or any other interested party – respond to this detailed criticism. If a response exists, I’d appreciate a link as it has slipped under my radar.

  17. Well Paul, if simply denying that neo-Darwinists predicted junk DNA constitutes a rebuttal for you, I don’t know if you are really wanting to see this issue fairly:

    notes:

    Junk DNA Predictions By Evolutionists

    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

    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

    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

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

    The slow, painful death of junk DNA:
    Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function; it is something that is required by evolution. 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….Junk DNA is a necessary mathematical extrapolation…Without Junk DNA, evolution runs into insurmountable mathematical difficulties.
    http://creation.com/junk-dna-slow-death

    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?”

    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

    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
    http://www.uncommondescent.com.....ent-374475

    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/

    “To the skeptic, the proposition that the genetic programmes of higher organisms, consisting of something close to a thousand million bits of information, equivalent to the sequence of letters in a small library of 1,000 volumes, containing in encoded form countless thousands of intricate algorithms controlling, specifying, and ordering the growth and development of billions and billions of cells into the form of a complex organism, were composed by a purely random process is simply an affront to reason. But to the Darwinist, the idea is accepted without a ripple of doubt – the paradigm takes precedence!”
    Michael Denton

    verse and music:

    Psalm 139: 14-15
    “I praise you because I am fearfully and wonderfully made;,,, When I was woven together in the depths of the earth, your eyes saw my unformed body.”

    Amy Grant – Better Than A Hallelujah
    http://www.youtube.com/watch?v=Rm5kx3xqmg0

  18. BA77, such silliness. Larry Moran did not write a 14-part review in which he was “simply denying that neo-Darwinists predicted junk DNA”. Go have a read.

    There are a number of strong lines of evidence that suggest junk DNA comprises a majority of the human genome. If you have a worthwhile response here, it should comprise a quantitative reanalysis of what proportion of the genome is functional, and – if this proportion is much larger than currently predicted – how this is maintained under purifying selection considering the mutational load.

  19. paulmc, despite your protestations of ‘such silliness’, I find the neo-Darwinian position to be completely absurd:,,, Tell you what why don’t you tell me how neo-Darwinism accounts for quantum information in DNA in the first place!

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

    Falsification Of Neo-Darwinism by Quantum Entanglement/Information
    https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US

    A few comments on ‘non-local’ epigenetic information implicated in 3-D spatial organization of Body Plans:
    https://docs.google.com/document/pub?id=1iNy78O6ZpU8wpFIgkILi85TvhC9mSqzUSE_jzbksoHY

    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

    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

    The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford – Genetic Entropy

    The multiple codes of nucleotide sequences. Trifonov EN. – 1989
    Excerpt: Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code).
    http://www.ncbi.nlm.nih.gov/pubmed/2673451

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

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

    Perhaps a single protein fold?

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

    Seeing as atheists are the ones trying to call such complexity junk, or whatever, I think the burden is clearly on you to actually produce evidence instead of bluster!!!

  20. It’s almost as if you didn’t read a word I wrote. ‘Such silliness’ referred to your wild misrepresentation of Larry Moran’s extensive review.

    Also, let’s not have another thread derailed by your irrelevant linkfest.

  21. I’m curious if ‘junk’ ‘excess’ ‘useless’ or whatever DNA was predicted, before it was found??

  22. further notes:

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

    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

    DNA Computer
    Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today’s most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours.
    http://www.tech-faq.com/dna-computer.html

    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

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

    Astonishing DNA complexity update
    Excerpt: The untranslated regions (now called UTRs, rather than ‘junk’) are far more important than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes.
    http://creation.com/astonishin.....ity-update

    etc.. etc.. etc..

    verse and music:

    Isaiah 40:28
    Have you never heard? Have you never understood? The LORD is the everlasting God, the Creator of all the earth. He never grows weak or weary. No one can measure the depths of his understanding.

    Michael W. Smith – Agnus Dei
    http://www.youtube.com/watch?v=HPBmFwBSGb0

  23. Hi paulmc-

    When Moran spews nonsense like:

    Most of the IDiots at the Discovery Institute feel threatened by the existence of large amounts of junk DNA in some eukaryotic genomes, including our own.

    It is obvious that he is just a bloviating coward who should be ignored.

  24. No- there wasn’t any such prediction.

    What happened was that scientists observed large amounts of non-protein coding DNA and couldn’t figure out what was up.

    Then they starting finding functions for some of this non-coding DNA.

    But the “prediction” was AFTER- as in once “junk” DNA was assumed then evis said “well our position predicted that because it is an imperfect processes but no designer worth its salt would ever design junk into the genome”

  25. Biologists found that only 2% of the genome consisted of code for proteins. The other 98% was (wrongly) assumed to be evolutionary junk. Dr. John Mattick, professor of molecular biology at University of Queensland, Brisbane, Australia, noted that the ‘junk DNA’ theory was an example of scientific tradition derailing objective analysis of the facts.

    Much of what used to be considered ‘junk’ is now noted to contain a recipe, if you will, for regulatory RNA, which plays a key role in how the cell develops, matures, and functions.

  26. Hi Jonathan,

    Unlike Single Malt, we have met before, on more than one occasion. In fact, you singled me out after a lecture by Dembski, to discuss (and compliment, thank you) a point I raised, with which you agreed.

    Unfortunately, I missed the talk you gave at that event and would have liked to have heard it in person, though this written summary is welcome also.

    If you don’t mind, I’d be glad for some clarification on two things regarding what you wrote above.

    “I was transformed by the beauty, peace and evident design around me.” – Dr. Wells

    Would you be willing to substitute ‘order’ for ‘design’ in the above sentence? Iow, you were transformed by finding ‘meaning’ of some kind (presumably) ‘in’ or ‘beyond’ nature, a new (transcendental) recognition of sorts that you hadn’t discerned before, is that right?

    I’m quite sure you wouldn’t call it a ‘scientific’ discovery that you made “in the mountains of Mendocino County”, but rather something else entirely. You didn’t do any ‘scientific’ experiments after all, to reach your new conclusion or awareness, if I understand your words.

    By the way, the hills are a great place for discoveries, I most certainly agree!

    My second question is a sociological one about these ‘Darwinists,’ as you call them, i.e. meaning people who hold a particular ideology while they do biological science. I notice you did not identify Teilhard de Chardinists, Bertalanffyians, Dobzhanskyists, Laszloists, Gouldians or Margulisians, of course, as that would distinguish their ‘scientific contribution’ from Darwin’s.

    The question then is: What percentage of living biologists (practising) today in the USA do you consider to be ‘Darwinists’? Or, if you’d like to go further than that, what percentage of US citizens today do you consider to be ‘Darwinists’?

    What I’m trying to understand is exactly how big or widespread you believe this ‘ideology’ actually is ‘in biology’ – i.e. “materialistic philosophy masquerading as empirical [biological] science” – which you attribute solely to the name ‘Charles Robert Darwin’ of Down, England, that you felt and still feel it needs to be ‘destroyed’.

    Nietzscheans and Derrideans aside, I’m just curious how many Darwinists you think are ‘out there’ as of November 2011.

    Thanks,
    Gregory

    p.s. as a midget in biology, I would have no hesitation to discuss this subject with you over a malt (but let’s make it a double in this unfortunate culture war environment, please! ; )

  27. Evolutionary theory does not make specific predictions about the amount of DNA expected in any particular group of organisms, nor its distribution between coding/noncoding and functional/nonfunctional. I’m not aware of any “evi/evo/evotard” claiming the kind of retrospective prediction you suggest.

    The mouse has 10% more DNA than a human – who’d have thought it? Certainly not an evolutionary theorist. In the 1970′s, the expectation was that DNA would be mostly functional. In this context, the huge excess of apparently nonfunctional sequence discovered in the 1980′s came as something of a surprise.

    We now find that some apparently nonfunctional sequence is functional after all – ie, as was thought in the 1970′s. Both the 1970′s and the 1980′s positions have been refined – quelle surprise.

    Nonetheless, this discovered function covers a fraction of the genome – the rest remains, provisionally, junk. That may be proved wrong in the fullness of time, but it is a bit early to be invoking the 1-2% of discovered function as strong evidence for the remaining 90-odd percent – “we don’t know it isn’t functional, so it must be functional”. We will have to see. Undoubtedly, you will be after some POSITIVE EVIDENCE that it isn’t functional … Either way, evolutionary theory will be untroubled by the eventual percentage, since it does not depend upon it in any way.

  28. Single Malt: As if “qualifications” meant anything. Ad hominem attacks are irrelevant to the merits of what is being discussed. What do they teach kids these days, anyway?

  29. Biologists found that only 2% of the genome consisted of code for proteins. The other 98% was (wrongly) assumed to be evolutionary junk. Dr. John Mattick, professor of molecular biology at University of Queensland, Brisbane, Australia, noted that the ‘junk DNA’ theory was an example of scientific tradition derailing objective analysis of the facts.

    Not exactly a long tradition – junk has only been around as a concept for about 40 years. And it’s not really a theory. If you find 98% of the genome to have no discernible function, then that is an objective fact. If function is discovered for it, then your percentage goes down from 98% – turns out your provisional estimate was wrong, and your new one could be too.

    Much of what used to be considered ‘junk’ is now noted to contain a recipe, if you will, for regulatory RNA, which plays a key role in how the cell develops, matures, and functions.

    And an awful lot of the rest remains without an apparent function – including, for example, 11% of the genome devoted to 1.1 million inactive copies of the 300-base repetitive sequence Alu, and 17% devoted to about 500,000 copies of the longer LINE1. While some of these have become inserted into functional positions, the bulk remain in intergenic space, without even being transcribed to support a hypothetical “regulatory RNA” role. Unless a role is found, which also takes account of their substantial numbers, they remain in the wishful thinking pile, if one is wedded to the idea that every base is sacred (or the ‘junk’ pile, if not).

  30. The mouse has 10% more DNA than a human

    Wrong way round! … but approx the same no. of genes.

  31. Substantial amount of non-coding DNA have been deleted from mice and engineered yeast chromosomes have been built without it, without apparent ill effect.

  32. Junk was not a prediction of neoDarwinian evolutionary biologists per se, but the story is not so simple as it is sometimes made out to be. In fact, Ohno’s (1972) paper where the term, in scarequotes, was introduced placed a limit on the number of genes that could occur in the mammalian genome with the rate of mutation as it was (i.e. a limit on the amount of purifying selection that a population can tolerate before being doomed to extinction as deleterious mutations become too numerous to escape).

    From this reasoning, Ohno predicted that 30,000 genes was the upper limit for humans (rather accurate in hindsight) and that because of the typical size of genes, 90% of the genome would have to be without a sequence-specific function. This was a bold claim as the composition of the genome was unknown. It was an argument from logic because of the necessary consequence of mutation.

    This genetic load argument for ‘junk’ – or at least for DNA sequences that are not subject to purifying natural selection – is one that is difficult to sidestep. The theoretical prediction is closely matched by what we know quantitatively about function in the genome today.

  33. As with redundant systems you can take 1/2 of the stuff out and it still works.

  34. I’m quite sure you wouldn’t call it a ‘scientific’ discovery that you made “in the mountains of Mendocino County”, but rather something else entirely.

    Fortunately science is not the only way to make discoveries nor advance knowldge.

    As for how many Darwinists are “out there”- all of them! :)

  35. Let’s assume that Wells’s motives are terrible. Perhaps he wants to overthrow Darwinism for some totally evil purpose. Are his arguments therefore wrong? Put a different way, if a bad man tells you that 2 plus 2 equals 4 are you going to say that 2 plus 2 actually equals 5 because you don’t want to agree with a bad man?

    Now, I’m NOT saying Wells has bad motives. I actually think it is a good thing for him to be out to destroy Darwinism if that is indeed his goal. But his arguments should be taken at face value no matter what his motives.

  36. Chas D – so, if there is no apparent function, should biologists and scientists stop looking for one?

    Interestingly, some of the malfunctions in noncoding RNA are associated with diseases including cancer, psoriasis, and Alzheimer’s. It’s possible that further study might lead to improved treatments and diagnoses for these diseases.

  37. As far as Dr. Wells is concerned, true science stands or falls on the evidence and not the worldview of the scientist. To suggest that his views on ID should be rejected because of his association with Moon’s Unification Church is to commit a genetic fallacy, which states that something should be rejected because of its source.

    For example, the alternating current motor is accepted as scientific even though Tesla got the idea from a vision he had while reading the German poet Goethe. This theory withstood the test of scientific investigation and had scientific justification. It wasn’t rejected because of its source.

  38. I didn’t know that about Tesla. Thanks.

  39. Dr. Wells, if you’re still reading this thread, I have a couple of questions:

    1) If all DNA was one day discovered to have a function, what would that mean for the theory of Intelligent Design?

    2) Why?

  40. Collin:

    I don’t know about this case, but the report I have had was that Tesla could build a motor etc in his head, run it there for two weeks or whatever, then disassemble it mentally and inspect the wear.

    That speaks of someone with a huge base of shop experience to intuitively know the wear patterns etc, and a visualising capacity that is extraordinarily powerful. (Unfortunately, much of what is on the web about him is just a tad fringe-ish. )

    So, to hit on the idea of a motor that works by letting a rotating magnetic field pull a conductor free to carry an induced current through a vision while reading a poet would be par for the course for that man.

    Of course, there is the famous story of Kekule in Chemistry and how he finally solved the Benzine structure problem: the dream of the snake swallowing its tail.

    Einstein took an imaginary ride on a beam of light, too.

    Thought experiments and thought exercises can be very powerful.

    Today, computer simulations with 3-D animations do some of the same things, but we have to be very wary of GIGO.

    Rule of thumb: a computer simulation is a thought world exercise, not an observation of a real world event.

    (Those who fell for Dawkins’ Weasel and kin should have remembered that.)

    GEM of TKI

  41. F/N: The secret to the classic squirrel cage induction motor is that the cage is a circuit free to carry an induced current. The induction is occasioned by a slip between the rotating B-field in the AC-fired stator coils and the rotating cage, typically a few percent. This also implies capacity for a short spike in power if some resistance is momentarily encountered as the slip will spike, leading to a brief power surge. A subtle and beautiful design.

    _________

    (BTW, the induced current is best explained, in my view, by using the Lorentz force relationship, F = q * v x B. I used to use a sacrificial CRO set to x-y mode and a bar magnet to show the deflection of the electron-beam dot on the screen, and how it would be pulled by rotation of the bar magnet. Once you have SEEN this, all else follows at once, bang, bang, bang. Maybe, someone with an old analogue CRO and a bar magnet of moderate intensity would care to do a YouTube video and let us all have a link? A great trick would be to mount the bar magnet on a plexiglass rod and spin it with a crank.

    That would be a gift to global education.

    And, of course the Lorentz force approach unifies motors, generators, induction, transformers, televisions and particle physics. I used to teach the hand rules, together, as shorthand. To tell the difference, you crank the generator right handed . . . . )

  42. LYO: The inference to design is independent of whether the percentage of DNA found to be specifically functional is or is close to 100%, as the issue is, once you have enough to pass th4e FSCI threshold, we are already in territory only plausibly accounted for on design. In addition, the presence of codes, implementing machines to put codes to work algorithmically, etc and the associated von Neumann self replicator facility all point to irreducible complexity and systems that are inherently informational, symbol based and linguistic, so reflective of mind. But that most DNA is functional in some way is something that design would tend to point to; needs not be true, but it is unlikely that most of the DNA is non-functional, if the system is designed. (We must remember, too, that if you go to a junkyard and find some working machinery amidst the piles of non-functional junk, the presence of junk does not negate the design of the working machinery, or even of what has now deteriorated into junk.) KF

  43. F/n 2: Oddly, the difficult case is the single phase AC motor [not the polyphase one!], which depends on engineering tricks to get relative rotation, especially to start. The capacitor start motor is a classic, depending on phase relationships in ac components.

  44. F/n 3: Resemblance to the ion driven motors found in the cell — cf the flagellum top this and every UD page — are NOT coincidental.

  45. Despite this, all the evidence suggests that most human DNA (~90%) must be non-functional, or functional in some currently unknown way that requires neither sequence specificity nor conservation. Mutational load alone makes this argument, but it is also evidenced by the observed lack of sequence conservation in that 90%.

  46. You hit the nail on the head Bruce. It is nothing more than a worldview battle or belief system battle as you mentioned.

    Aldous Huxley was a British novelist who wrote Brave New World (1932), and was a grandson of ‘Darwin’s Bulldog’, T.H. Huxley. He was also the brother of the leading atheistic evolutionist Sir Julian Huxley. Aldous Huxley made this frank admission about his anti-theistic motivation:

    ‘I had motive for not wanting the world to have a meaning; consequently assumed that it had none, and was able without any difficulty to find satisfying reasons for this assumption. The philosopher who finds no meaning in the world is not concerned exclusively with a problem in pure metaphysics, he is also concerned to prove that there is no valid reason why he personally should not do as he wants to do, or why his friends should not seize political power and govern in the way that they find most advantageous to themselves. … For myself, the philosophy of meaninglessness was essentially an instrument of liberation, sexual and political.’ Huxley, A., Ends and Means, pp. 270 ff.

    I suspect this is the reason why so many atheists are so passionate about their anti-god beliefs. We are all bias when it comes to what we believe and I bet that what we want to believe has a much stronger influence on us than we realize.

  47. Please see just above. A fairer view is that we do not know the function of a lot of DNA, though it should be clear (on inference) that much of it fulfills body-plan specific regulatory function, which obviously would vary with the organism.

  48. letztes Jahr:

    1) “If all DNA was one day discovered to have a function, what would that mean for the theory of Intelligent Design?”
    ====

    Off hand I’d say the theory would end. I.D.’s faith and hope that DNA would all have purpose and function would cease to exist as the fact would prove the reality of what they have been saying and believing in all along.
    —-

    letztes Jahr:

    2) “Why?”
    ====

    I think the why would be obvious!
    —-

    kairosfocus:

    “We must remember, too, that if you go to a junkyard and find some working machinery amidst the piles of non-functional junk, the presence of junk does not negate the design of the working machinery, or even of what has now deteriorated into junk.”
    ====

    Hey – Junk is in the eye of the beholder – *smile*

    I’d say you could compare it to say, ‘Windows 7′ and setting up your raw brand new PC. Once the various setups are in place and all functional, those instructions for setup are dormant, but still functional if need be called on again to reboot or delete and set up again. In perfect human beings where all switches and control mechanisms would be functional for renewal, then repairing and rebuilding could be turned on again as in the case of injury. Though not always functional all the time, such systems could be retreived at any time in a perfectly running biological human machine. Unforunately, as a result of improper behavior of one man, epigenetics took over and switched off some of the original functional programming for renewal.

    Genesis 2:16-17 , Eodus 20:5 , Jeremiah 31:29 , Lamenations 5:7 , Romans 5:12 , Romans 7:23

  49. Well, I’m glad that you and Dr. Moran are clearly on the record stating that your faith is in the junk DNA position. As you know, more and more functions are being found for “junk” DNA so the trend is clearly not in your favor. I guess we will have to revisit the issue in 5 years and see who is right. It is interesting that you are taking a stand here on something that has not been proven and may never be able to be completely proven. It is just something that you currently “believe” or place your faith in based on your interpretation of the facts/observations.

    It is similar to IDer’s placing their faith in some kind of Intelligence to explain the seemingly chance-defying design of the cell, etc. Are they right? We’ll have to wait and see. The evidence for this position is increasing more each year. Can it be 100% proven? No, but I think there is enough evidence to make faith in an Intelligent Designer seem quite reasonable. Faith is involved on both sides here.

  50. tjguy:

    “Well, I’m glad that you and Dr. Moran are clearly on the record stating that your faith is in the junk DNA position.”
    ====

    And ultimately that is what all of this JUNK subject is all about, their FAITH. It’s also about their inability to admit they don’t know something and therefore the intellectual need to invent a terminology to prop up a Dogma.

    The biggest difference between Evolutionists and IDers when it comes to the term FAITH is not that one has it and the other doesn’t. They clearly both have it. It’s that IDers are the only ones who admit it.

  51. “If you find 98% of the genome to have no discernible function, then that is an objective fact. If function is discovered for it, then your percentage goes down from 98% – turns out your provisional estimate was wrong, and your new one could be too.”

    How can it be an observable fact if it is later overturned. It was something that was thought to be true – assumed to be true. Why? Because the function was not immediately apparent and was therefore assumed to be without function. This assumption was easy to make. I think scientists were actually eager to make that assumption because it fit so well with their ideas of evolution. This is an example of how worldview often colors our interpretation of what we observe. Scientists are NOT as objective as they want us to believe. Worldview/belief system plays a huge role in their interpretations.

    I don’t know, but I don’t think finding a little real junk(however, I doubt that can ever be really proven)would be a problem for ID science. Over time, as mutations build up in the genome, this certainly could happen, although not to a really large extent.

    Anyway, all the evolutionists can say now is that as of yet, a function hasn’t been found for a large portion of the genome. That does not mean that there is none. It simply means that one has not been found yet. No one really knows whether one will ever be found or not. A person’s particular belief regarding that will largely depend upon his worldview.

    Many evolutionists would be happy if we quit looking for functions in this non-coding section of “junk” because the continued ignorance of function serves their purposes well. This is how evolution can also be a science stopper!

  52. So would you be comfortable to be a guinea pig and volunteer to have that 90% of your genome deleted from your cells to see if it will have any kind of an effect on you?

  53. I must be emphatic: it is not fairer to say that we simply do not know its function. It is also certainly far from clear that “much” of the DNA fulfills a regulatory function. All of the known coding, regulatory, and structural DNA in the human genome – from microRNAs to cistrons – fits into about 9%. If you have evidence of more regulatory DNA than this, it is new to science to the best of my knowledge.

    If the remaining DNA were to to be functional, then its sequence should be important. If its sequence is important then it should show signs of evolutionary constraint. About 90% of the human genome does not fit this bill. About half of the genome is made of highly repetitive transposable elements. While a tiny, known number of these are functional (i.e. active) almost all contain disabling mutations and have no known or suspected function. They are typically repetitive sequences that only vary because when they experience mutation, there is no constraint from purifying natural selection acting upon them.

    In a separate line of argument, if more than about 10% of the genome were subject to purifying selection, the mutation rate would be excessively high. See Ohno 1972, and subsequent work. Note the 9% above and Ohno’s 10% are entirely independent predictions, but happen to closely agree.

    Again, if there is a function somehow it is not dependent on sequence specificity. Please address how that is likely to be the case.

  54. F/N: We should all do the exercise of opening a Word Document, and typing in just one short sentence. Save, close and re-open in something that will inspect the underlying content, like Notebook; using Open With. Let us know what you see. say:

    ÐÏࡱá >  þÿ   !  #  þÿÿÿ ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ . . .  þÿÿÿÿÿÿÿÿÿ

    That is, MOST of the document looks like junk.

    Next, snip out some of the seeming junk at-random more or less. Say:

    þÿÿÿ ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ

    Effect on returning to Word: Word Cannot open the document.

    But, that was just one odd character and a lot of useless looking repeats of the y-like character?

    Live experiment over.

    Take home lesson: if we do not know yet, it would be unwise to pretend to dismissal of what LOOKS like junk to us, even evidently endless repeats of a silly looking pattern.

    GEM of TKI

  55. tjguy:

    “So would you be comfortable to be a guinea pig and volunteer to have that 90% of your genome deleted from your cells to see if it will have any kind of an effect on you?”
    ====

    Careful, don’t give them any new ideas. Some of young generation in these modern times actually like body mutilation. I can just see some future clinics advertising the latest iconic rage of becomming a new kind of generation Freak. Move over tatoos, piercings, black death makeup, Junk DNA removal is the new kid in town.

  56. Um, I would rather a guinea pig be the guinea pig. Or a mouse. But rather than dealing in hypotheticals, there is literature on this topic.

    Notably, some putative junk sequences, such as pseudogenes, might still be transcribed and regulate the expression of functional genes, despite not being otherwise functional themselves. So removing them would have an effect, even though it is an odd way of regulating gene expression by design, when there are more direct mechanisms for achieving the same outcome. Note that pseudogenes themselves only comprise 1 or 2 % of the genome though.

  57. You’re proving my point.

    The reality is that the putative junk does accumulate mutations much faster than do functional sequences. This is why it is hard to imagine how they might be functionally important.

  58. As far as I know, Mendeleyev saw his periodic system of chemical elements in a dream. Without a slightest intent to diminish the significance of Divine Revelation in science, I hazard a guess that on this particular occasion it might be because he had been thinking about it hard enough.

  59. Geez Paul, Wells goes over that in his book- that is he discusses non-sequence specific functionality.

    Did YOU read the book, Paul?

  60. 1- Alleged pseudo-genes may not be

    2- Genes that are at the present time functionless good be “in waiting”- that is waiting for activation-

    The GULO gene is a prime example- it isn’t that we lost the ability to synythesize vitamin C- we NEVER had it. The “broken” GULO gene is for possible FUTURE use.

    The same goes for other alleged pseudo genes.

    Then we have other sequences of DNA not currently being used- again for future possible use- think recombination.

    Then there are spacers for timing of expression- Wells’ non-sequence specific functionality.

    The bottom line is only IGNORANCE says that 50% or more of our DNA is junk.

  61. Chas D – so, if there is no apparent function, should biologists and scientists stop looking for one?

    Not at all. No one is more delighted than the scientist when something new is discovered! The tone around here is to view scientists as searching for sufficient information to support some mythical atheist-materialist worldview, then stop when they find it. That is simply untrue. Everybody wants to discover something no-one else has discovered. That’s how reputations are made, and that’s the fundamental driver – simple curiosity.

    If I could discover a better reason for the 28% of the genome devoted to simple repetition of 2 transposable sequences, Alu and LINE1, than the simple fact that they contain the means to propagate around genomes ‘selfishly’ and increase their own copy number, then I would grab it two-fisted, and a paper to Nature would be hot on the heels of this discovery. But from where we stand, such a discovery seems hugely unlikely. And the same goes for much else in the genome. Find a function if you can, but all ‘junk DNA’ says is that there is a proportion of the genome that does not need to be there. How big that proportion, and what it contains, are matters for debate and ongoing investigation. But ‘Junk/non-Junk’ is simply a classification, a recognition of an apparent biologial reality.

  62. Chas D,

    Wells discusses a function for ALU and LINE1.

    You didn’t read the book did you?

  63. tjguy

    This assumption was easy to make. I think scientists were actually eager to make that assumption because it fit so well with their ideas of evolution.

    Simply untrue. Evolutionists like Dawkins are pretty quiet about junk because, like ID-ers, he is inclined to see a kind of ‘perfectionism’ in organismal form. Unlike ID-ers, he has a strong positive opinion on the power of Natural Selection. Others, like Moran, set more store by the ‘accidental’ nature of much change at the molecular level – it is largely invisible to selection, but still subject to the inescapable process of Genetic Drift. No-one really cares if junk is large or small; they simply argue for the most sensible interpretation of the available data. Even then, it is important to be clear what kind of organism you are arguing about. The constraints on Prokaryotic, Single-celled Eukaryotic and Multicellular Eukaryotic genome sizes are very different.

    Many evolutionists would be happy if we quit looking for functions in this non-coding section of “junk” because the continued ignorance of function serves their purposes well. This is how evolution can also be a science stopper!

    No, no, no, no, NO!!! As I said in the response to Barb above, scientists are hungry for discovery. It is a bizarre caricature perpetuated solely in ID/Creationist mythology that scientists are looking only for the information that bolsters their worldview. Goddidit is the science stopper.

  64. Chas D,

    Wells discusses a function for ALU and LINE1.

    You didn’t read the book did you?

    I am well aware of the existence of Alu and LINE1 in functional positions. You didn’t read the whole post did you? There are 1.1 million Alus and 500,000 LINE1′s. Most of them are NOT in functional positions. Most of them are not even transcribed. You need to explain away 28% of the genome, which you can’t do by invoking some other part – even if it happens to have a related sequence. Each functional element is only functional in context.

  65. This talk of 10% and 90% reminded me of the Pareto principle as it is applied to software optimisation.

    In short “90% of the execution time of a computer program is spent executing 10% of the code”.

    If someone was to try and work out what a piece of software actually did based on it’s execution (i.e. trace output), it seems reasonable to assume that the 10% that was used most often would be the easiest to determine. The remaining 90% would require a great deal more time.

  66. The 90/10 rule is irrelevant unless you explain why random changes to the 90 percent don’t have any functional effect.

    Even removing the code has no effect.

  67. Again redundancy and future functions- you guys really need to get out of your little box.

  68. The 90/10 rule is irrelevant unless you explain why random changes to the 90 percent don’t have any functional effect.

    The 90/10 rule would predict that determining what, if anything, the 90% does, is much more difficult.

    Before you acccept the above as “relevant” we first need to explain what the 90% does? Have I understood you correctly?

    Even removing the code has no effect.

    Given my very limited understanding of biology I can only assume this must be true (although perhaps you can provide a reference?). However, even if true, if we still use the 90/10 rule as a guide, the 90% of code is only needed in 10% of cases. After removing the 90% of code, it would have to be shown that 100% of possible cases has been executed to prove that the code does nothing.

  69. And, how did you OBSERVE these wonderful fast mutations across deep time, again? [Or, is this a case of inferring on the assumption you were meant to prove?]

  70. And, assuming what was to be shown.

  71. Well Paul, if simply denying that neo-Darwinists predicted junk DNA constitutes a rebuttal for you, I don’t know if you are really wanting to see this issue fairly:

    I can see that reading and reading comprehension aren’t your strong points. Here’s what I actually said in the last posting of my review of The Myth of Junk DNA.”

    Wells never defines “junk DNA” correctly. The correct definition of “junk” is DNA that has no known function. Wells pretends that the original definition of junk DNA was “noncoding” DNA. Thus, all those bits of noncoding DNA that have a function are evidence that refutes the notion of junk DNA.

    The truth is that no knowledgeable scientist ever suggested that regulatory regions, origins of replication, centromeres, telomeres, genes that produce functional RNA molecules, and chromatin organizing regions were ever classified as junk DNA. They all knew that there was lots of noncoding DNA that had a well-defined function. Right from the beginning of his book, Wells is attacking a strawman and misleading his readers.

    That’s not the only example of deception. Wells also claims that the existence of large amounts of junk DNA was a prediction of Darwinism and is promoted as proof of Darwinian evolution. This is a lie. Junk DNA actually represents a serious problem for Darwinism (evolution by natural selection) and it certainly was never “predicted” by adaptationists.

  72. Eocene says,

    And ultimately that is what all of this JUNK subject is all about, their FAITH. It’s also about their inability to admit they don’t know something and therefore the intellectual need to invent a terminology to prop up a Dogma.

    Do you know why I refer to Intelligent Design Creationists as IDiots? It’s because of statements like that.

    You’re not the least bit interested in learning about the evidence for junk DNA, are you? I spent months understanding and reviewing The Myth of Junk DNA. Surely the least you could have done is read my reviews before exposing your stupidity for all the world to see?

  73. Joseph says,

    Genes that are at the present time functionless good be “in waiting”- that is waiting for activation-

    The GULO gene is a prime example- it isn’t that we lost the ability to synythesize vitamin C- we NEVER had it. The “broken” GULO gene is for possible FUTURE use.

    The same goes for other alleged pseudo genes.

    LOL

    I appreciate the satire. You’ve done a really good job of imitating an IDiot.

    But you have to be careful. There are some people posting here who might think you are serious.

  74. Well Larry you state:

    ‘The truth is that no knowledgeable scientist ever suggested that regulatory regions, origins of replication, centromeres, telomeres, genes that produce functional RNA molecules, and chromatin organizing regions were ever classified as junk DNA.’

    That’s pretty much a after the fact rationalization after function was discovered (As I listed several articles that do indeed show many ‘knowlegeable scientist’ predicted it:. But I guess you get to cherry pick who is a knowledgeable scientist and who is not???. ,,,

    you then state:

    Wells also claims that the existence of large amounts of junk DNA was a prediction of Darwinism and is promoted as proof of Darwinian evolution. This is a lie.

    Apparently you have never promoted the supposed Vitamin C pseudogene as powerful evidence of neo-Darwinism???

    Larry Moran: Vitamin C Pseudogene is Powerful Evidence
    http://darwins-god.blogspot.co.....ne-is.html

    But then that can’t be true Larry for then that would make you a liar for denying that you even have promoted junk DNA as proof of neo-Darwinism!?! :)

    Notes as to wide scale functionality:

    http://www.uncommondescent.com.....ent-408027

  75. Yes Larry, I understand that you are far too stupid to understand oft-used design techniques-> ie planning for future needs.

    The issue is, as I see it, that blind, undirected chemical processes cannot account for the genes and regulatory networks involved in synthesizing vitamin C in the first place.

    That said I also understand that blind, undirected chemical processes are good at breaking things.

    So at first glance it may appear that is what happened.

    However given our knowledge of design techniques it is also possible that these are just “genes in waiting” for some enivironmental cue.

    Not that your devolved sense of awareness could grasp any of that.

  76. “The junk concept can be confronted with a series of inferred or presumptive features of molecular evolution that collectively seem capable of pushing the junk DNA paradigm out of the central position that in many quarters it is still considered to occupy.

    Who said that? Emile Zuckerkandl

    What year? 1991

    There are roughly 33,000 references to “junk DNA” in googlescholar alone, published in every professional venue without exception. Take a look at the number of “revisiting” “reformulating” “rethinking” junk DNA papers that exist in the record. To suggest that junk DNA was not a marketing term among ideological biologists is to be a flat out dumbass.

  77. Well, these unconstrained changes – including both the accumulation of mutations and new insertions of retrotransposons – can be observed between people. It doesn’t require assumptions of deep time, and it cannot be explained by functional differences between species.

    It does rely on mutation being responsible for the changes. But then, we have also observed mutation as close to directly as possible – happening between generations of people. Presumably, you wouldn’t be rejecting that mutation is responsible for genetic differences observed between people.

    You didn’t answer my question before: you stated “it should be clear (on inference) that much of [an organism's DNA] fulfills body-plan specific regulatory function” to which I ask: all regulatory, coding and other known functional DNA accounts for 9% of the genome. What evidence do you have for widespread regulatory function beyond that? And how would this operate, given the lack of sequence constraint?

  78. Note to Larry Moran-

    On your blog you said:

    Any amount of junk DNA is a threat to the basic concept of intelligent design.

    That is just plain ignorant. Intelligent Design does not say the design is perfect. Intelligent Design does not say that even if the design started out perfect that it had to remain that way (entropy and all).

    But thanks for the laughs…

  79. Wells discusses that exact sequences are not necessary for function. Does he suggest anywhere that for most functions, any old sequence will do? I don’t think so. A majority of the genome accumulates changes at a much faster rate than functional genes, showing no evidence of sequence evolution being constrained by natural selection. That is like saying any old sequence will do.

    Also, stating that Wells mentioned something in his book, is not quite the same as making an actual argument, is it? If you’d like to make a case for enormous, functional tracts of the genome that require no sequence specificity, then why not make it yourself?

  80. Nonetheless, a large amount of junk DNA would be a threat to ID, as functionality for junk DNA is a prediction of ID.

    While function is being found regularly in the genome in places it wasn’t previous known, it’s a matter of a microRNA there, a pseudogene that regulates gene expression there. You could literally discover 1 million microRNAs and you’d be accounting for 1% of the genome. There’d still be 90% unexplained.

  81. My principal observation is that we were not there to see the deep-time variants that are suggested (noting as well that variations among people have many possible sources, not just mutations), and I noted that we should be very restrained in our dismissals of the genome that we only very partly understand [hence, my comparison to something as simple as a Word Doc . . . . notice the great number of apparently useless repeats that do something, as snip and the doc dies].

  82. And an additional note – there is still the problem of the mutational load. You simply cannot have a majority of the genome with functional specificity in any mammal, given a typical mammalian mutation rate. 10% of the genome is the approximate limit (based on typical genome size). This applies generally – i.e to humans, to mice and to other mammals. The more functional bases, the more function that is degraded by mutation in each generation. This was the origin of the junk DNA concept (i.e. Ohno, 1972).

  83. Notice, all of this is rather red herring-y. The piles of junk in a junkyard do not detract from the evidence of a bit of working machinery that points to design. In addition, the onward inferences and dismissals seem to be driven more by what we do not know but assume than what we do know. Cf again the above Word snip seemingly endless and meaningless repeat example.

  84. So, you’re actually going to fall back on the “we weren’t there” argument? The ultimate source of variation amongst the DNA of different people is indeed mutation. When observations can be made of the the differences that exist between parents and offspring, the de novo differences are indeed the result of mutation.

    We don’t understand everything about the genome – sure. But we understand enough to make some inferences. I have given you several lines of evidence that supports a most-likely picture of a majority of the genome being junk, and you have not answered any of them directly yet.

  85. I don’t see it as a red-herring. An analogy about a junkyard does not detract from the fact that ID has made the prediction that function will be found for junk DNA.

    Once again the Word snip example proves my point. Sure, you could have something that seems endless and meaningless but was functional, like a Word document opened in Notepad, but then its functionality is highly contingent on that seemingly meaningless sequence being maintained. This doesn’t happen in the case of putative DNA junk.

  86. F/N: Let me draw this out a tad.

    1: We know, long since, that the only observed source of FSCI, and of coded, symbolic information, especially of algorithmic coded information is design.

    2: For cell based, dna driven life forms to exist, we are looking at creation of a von Neuman self replication facility that has to code for the key components of the entity, not just autocatalyse itself or something like that.

    3: So, the cell is credibly — save to those locked into a priori materialism wearing a lab coat — designed.

    4: Similarly, to get to major body plans up to our own but including dozens along the way, the only credible explanation is again design, just off the need to account for jumps in information that greatly exceed the capacity of blind chance and necessity on the gamut of our observed cosmos.

    5: So, we have good grounds for inferring de4sign in teh first place, even if the genome is like odds and ends of working machinery amidst a junkyard.

    6: But, we also know that there is a LOT about the cell that we do not know, and we do not know how to explain.

    7: Common sense is to reason from what we can credibly know per good warrant, to what we do not yet know, leaving unresolved puzzles as we find them.

    8: So, it makes good sense to see that we do not know enough to dismiss ever so much as “junk.” Especially in a context where we know that designers generally have a purpose for the main features of the systems they have.

    9: As a crude comparison, would you infer that, say, the Voynich manuscript is meaningless, simply because we have not as yet deciphered it?

    10: Or that the endless repeats etc in a Word document are junk?

    Let’s use a little common sense here.

    GEM of TKI

  87. PS, O/T: And I see the AntiEvo folks are off again barking out yet another mantra, this time falsely accusing me of lying.

    I note for record since clearly they monitor.

    It should be clear to any responsible person:

    (i) that there are NO, ZIP, ZILCH responsible Bible believing Christians who support genocide, INCLUDING Dr Craig — that should not even be a question,

    (ii) the spreading of a false accusation against any significant number of such will lead to the spreading of a much broader false accusation (one that by the way ALSO implies that Jews who take the scriptures seriously support genocide — see how poisonous this is . . . ) against Christians in general

    (iii) Such poisonous slander can also be spread by making invidious associations and asking loaded questions, and it seems

    (iv) will easily be believed by a fringe of people who seem to harbour a lot of bigoted hostility against Christians — “ignorant, stupid, insane or wicked” — as we have seen here at UD in recent days [cf here and here, note onward links]

    . . . so, it is high time that responsible people stop this nonsense before someone innocent gets seriously hurt as the unhinged fringe of the fringe goes off the deep end.

    Blood libel is how pogroms get started.

    If the lot at Anti Evo continue in this vein in the teeth of such warnings, that tells us that we are up against a very destructive and irresponsible, angry and in some cases evidently outright hateful movement.

    Of which, due notice will be taken.

    GEM of TKI

  88. Again redundancy and future functions- you guys really need to get out of your little box.

    You are permanently out of your little box.
    That sounds awfully like a substitution of more sciencey-sounding words for “junk”.

    Redundancy
    Noun:

    1) The state of being no longer needed or useful: “the redundancy of 19th-century heavy plant machinery”.
    2) The use of words or data that could be omitted without loss of meaning or function; repetition or superfluity of information.

    Of course, there is the redundancy of informatics/electronics too – keeping a backup in case of failure. But what on earth are these 1.5 million Alu/LINE1s backing up? Each other?

    So – in the absence of input from the man himself – are you saying that the big deal about The Myth of Junk DNA – what motivated Dr Wells to stick his neck out and write such a book – is the vital fact that junk is not junk but is, in fact, redundant? Hold the front page, we wuz such idiots not to see it.

    Future function
    – even if I were to agree that 1.5 million repeats of these two elements Alu/LINE1 could be beneficial as a source of future mutation, junk is about current function. Till you make your hovercraft on Junkyard Wars, it’s a pile of junk.

    Some poor individuals may well think that keeping bottles of piss and old newspapers and every piece of food wrapping they ever bought means that there is no such thing as junk – “lookee – future function!” – but I don’t think most would.

    You would chop your bollocks off rather than admit it, but “redundancy and future functions” = present JUNK!

  89. Yup one person’s “junk” is another person’s treasure.

    But anyway you didn’t read the book so you have no idea what Wells said.

  90. paulmc:

    Nonetheless, a large amount of junk DNA would be a threat to ID, as functionality for junk DNA is a prediction of ID.

    Maybe a prediction of some IDists but not of ID. We don’t understand the design well enough to say that.

    It should be noted that blind, undirected chemical processes cannot account for regulatory networks.

    That is what ID predicts- that non-coding DNA will be found to have a function- a function that blind, undirected processes cannot account for.

    If we observed one gene, one protein just being hammered out as a matter of course, ie just in turn down the DNA sequence, then I wouldn’t infer design.

    But when we observe the coordinated gene regulation, overlapping genes and alternative gene splicing, it is obvious we have left the blind watchmaker behind.

    But anyway how can we test the claim that 90% of the human genome is useless?

  91. Hear ye, hear ye-

    I have a solution that enables both ID and the blind watchmaker to coexist in this junk DNA thingy-

    (assuming a 10/90 split)

    ID accounts for the 10% functional part and the blind watchmaker can take credit for the 90% junk

    :)

  92. A question or two first: what do you think that 90% says about the designer? And what does it say about ID in general, when ID predicts that DNA should largely be functional?

  93. Joseph:

    It should be noted that blind, undirected chemical processes cannot account for regulatory networks.

    This is a meaningless claim. Where is your proof? Whatever evidence you’d like to present to support this definitive claim should address this paper by Mike Lynch.

    But anyway how can we test the claim that 90% of the human genome is useless?

    We need a starting point to understand why the claim of junk is made in the first place. Ohno (1972) demonstrates that selection cannot maintain the integrity of more than about 30,000 genes under a mammalian mutation rate. This gives us a good reason to suspect that a majority of the genome is not experiencing purifying selection. This theoretical population genetics argument is supported by observations that these large tracts of apparently functionless DNA do in fact accumulate mutations much faster than functional sequences.

    Next we have tests in mice where putative junk has been removed with no observable effects on the mice. I have already cited this above.

    So there are arguments from theory and observation that supports the inference that mammalian genomes, including the human genome, contains large tracts of junk.

  94. well, I personally have some faith in ID. It seems to me that the trend is to find more and more function in junk DNA. By the way, the Nature study showing that “large” portions of DNA being removed… well apparently the large portion was “3%” of the genome. I was thinking maybe 40 to 80%.

  95. The Lynch paper is a nice story but the way you promoted it I thought there was going to be some actual experimental evidence- like with Lenski and citrate. I could use it to put my daughter to sleep but that is about it.

    30,000 genes? Yet with alternative gene splicing and overlapping genes human genomes really have more than 30,000 genes.

    I worked for a company in which 1/2 of the operating equipment could be removed and the system wouldn’t even notice- removed while the system was running even. Does that mean that 1/2 was junk? No, it was a redundant system with fallback capabilities.

    Also we had designed in features that would allow for future growth- add-ons, plug-ins, things that could be removed without affecting the performance of the system today. Again that does not mean those features are junk.

  96. Before you start claiming 3% is somehow trivial, you should recognise that it is more than all of the protein-coding genes in the genome.

    The ‘trend’ towards finding function in putative junk has to be put into perspective. I’m not sure what part of the quantitative argument are you not getting here. A microRNA here, a pseudogene there: these findings are not reducing in any meaningful way the 91% of the genome that lacks a known function. You guys seem so fond of analogies, so I’ll give you one: just because occasionally the world record for the 100m sprint is broken, it doesn’t mean that eventually humans will be able to run 100m in 1 second. The reality, it is, the record breakers are making incremental improvements. A great achievement – sure – but it must be kept in perspective.

  97. But anyway you didn’t read the book so you have no idea what Wells said.

    What a feeble argument! I’m talking to you, not Wells.

    How does Wells explain why there are 1.1 million Alu’s? Or 500,000 LINE1′s? Lemme guess – the fact that some are found in functional sequence. They’re ex-transposons; of course they are.

    And that functional role explains all of ‘em – about 12 chromosomes’ worth out of our 46? And that’s just two particular elements; there are loads of less populous ones. There really is no methodological need to see junk in the genome, but – unless someone comes up with a better explanation than transpositional accumulation of copy number – there ain’t much else we can call it. I’m betting you won’t enlighten me and save me reading Wells’s book to give me a functional explanation for this huge chunk of the genome without looking hopefully at something that happens in the other 72%. If I found 28% of a program consisting of unexecutable repeats of “LET A = 10,000″, the existence of this line in executed parts of the code would not make that 28% any more functional.

    So, if “you haven’t read it so you don’t know The Answer” is your best shot, I will depart. Toodles!

  98. Joseph @ 17.1.1.1.1

    The tale you spin is a pure fantasy, at odds with everything that is known about genomes. Redundancies with fallback capabilities? What – located in Alu repeats, perhaps? Could I trouble you for the evidence?

    Yes, of course with alternative splicing we might add some extra genes to the total (let’s keep that in perspective too: the current known human total is 20,500 or thereabouts). That misses the point. The argument from Ohno is that with more than about 30,000 functional loci, deleterious mutations begin to unavoidably accumulate. Alternative splicing might concentrate function in the already-functional part of the genome, but it doesn’t even begin to touch on why 91% of the genome appears to have no function at all.

  99. paulmc:

    A question or two first: what do you think that 90% says about the designer?

    It says the designer did a heck of a job seeing it can withstand such an onslaught.

    And what does it say about ID in general, when ID predicts that DNA should largely be functional?

    ID doesn’t make such a prediction.

  100. paulmc:

    The tale you spin is a pure fantasy, at odds with everything that is known about genomes.

    The theory of evolution is a pure fantasy, at odds with everything we know about genomes.

    But anyway when someone removes that alleged 90% from a human embryo and a human develops- without any difficulties and grows and reproduces, let me know.

  101. I think I can safely say that nobody wants to remove 90% of the human genome from an embryo just to see what happens. You are flip-flopping here between the POV that the genome is filled to the brim with function (despite the lack of evidence), and the alternative POV that a lack of function in 90% of the genome is completely fine and unimportant to your theory’s predictions. That doesn’t match up with all your talk of frontloading. You really think ID has no prediction about how much DNA should be functional? Wells wrote an entire book espousing junk DNA as a ‘myth’! A claim about function in putative junk is the sole example on this website’s FAQ about ID making scientific predictions.

    If all ID says is that some, unquantified amount of function will eventually be found in what is putatively junk, then it is not making a fruitful scientific claim – it could be talking about 0.1% of the remaining genome or 90%. Where does that get us? If – as Demski says – intelligent design advocates “expect DNA, as much as possible, to exhibit function” then 90% can’t be a comfortable number.

  102. 102

    paulmc,

    A prediction of materialism is that the transfer of information from the genome is a purely physical transfer and is only analogous to the transfer of information in other forms. The rise of true symbol systems (displaying the physicality of true symbols systems) would not have happened in the advancement of organisms for billions of years into the future.

    On the other hand, ID predicts the transfer is (not only physical like any other transfer of information, but also) semiotic, and therefore not merely analogous to other transfer of information.

    The physical entailments of recorded information transfer are observable, and have been observed. They provide positive evidence of a semiotic state in protein synthesis, and therefore validate the ID prediction.

  103. Upright BiPed, this appears to be heading off topic. ID’s usefulness for explaining the mostly functional 9% of the genome is a separate issue. This is where I would see your information transfer question sitting. I would not be averse to discussing this in another thread, but really would like to discuss here the evidence or otherwise for function in 91% of the genome, which I have referred to here as putative junk.

  104. 104

    Thanks paulmc, it is your right on this board to decide what you will and will not respond to.

    cheers

  105. Like I say – most happy to talk about that at some point. Just don’t want to bury and/or derail the conversation at hand :)

  106. Larry ‘The Closet IDiot’ Moran:

    “Do you know why I refer to Intelligent Design Creationists as IDiots?”
    ====

    Yes I do. You have accountability issues and hardcore resentment of definitions of what contitutes morality and immorality. Your pseudo-science smokescreen of a blog is dedicated to pimping just such a degenerate worldview.
    —-

    Larry ‘The Closet IDiot’ Moran:

    “You’re not the least bit interested in learning about the evidence for junk DNA, are you?”
    ====

    Larry, I’d rather have Science pursue a more mature honest approach to finding out just what ALL DNA’s purpose and function is if they’re not sure. No matter how long it takes. Making up a bogus term to mask and smoke screen one’s inability at explaining something is nothing more than desparate ideological worldview promotion, not science.

    Back in October 2004, evolutionary biologist John S Mattick(who you and your girlfriend PZ Meyers figuratively spat and urinated on) gave his responsible take on the overbloated cowards egoistic term JUNK DNA:

    “The Hidden Genetic Program of Complex Organisms”(Scientific American)

    “Assumptions can be dangerous, especially in science. They usually start as the most plausible or comfortable interpretation of the available facts. But when their truth cannot be immediately tested and their flaws are not obvious, assumptions often graduate to articles of faith, and new observations are forced to fit them. Eventually, if the volume of troublesome information becomes unsustainable, the orthodoxy must collapse.”

    It’s nobody’s fault for being ignorant. But it is your fault if you choose to stay there.
    —-

    Larry ‘The Closet IDiot’ Moran:

    “I spent months understanding and reviewing The Myth of Junk DNA. Surely the least you could have done is read my reviews before exposing your stupidity for all the world to see?”
    ====

    Sorry, but I’ve seen the filth, vulgar insults, foul language and character assination fluff you call a scientific blog and the degenerates who are encouraged to comment over there. I’ll pass.

  107. paukmc:

    You really think ID has no prediction about how much DNA should be functional?

    It doesn’t and you cannot produce such a prediction.

    wrote an entire book espousing junk DNA as a ‘myth’!

    You didn’t read the book, did you.

  108. So you are too lazy to do the work for yourself and you need me to spoon feed you. And if you want to make this personal then let’s get together and take care of it- “I’m talking to you”- bully nonsense.

    The data exists whether or not it comes from me- moron.

    Alu elements contain functional binding sites for transcription factors. RNAs derived from alu sequences repress transcription during cellular response to elevated temperatures. Alus are also involved in the editing and alternative splicing of RNAs and in the translation of RNAs into proteins.- page 62

  109. In the preface Wells states:

    [T]he idea that most of our DNA is junk became the dominant view among biologists. That view has turned out to be spectacularly wrong … Far from consisting mainly of junk … our genome is increasingly revealing itself to be a multidimensional, integrated system

    Here, Wells is making a direct claim that a majority of the genome is not junk. So in what way have I misrepresented his view?

    And to answer your question – no. I might have picked up a copy before reading the preface, but I wouldn’t pay money for it after. I might still read it if I happen across a free copy. Does it matter? I have only made a minor reference to it, and only to its title. You are welcome to present any arguments you or Wells have against the several lines of evidence that I have already presented above. But the science at the moment really does fall on one side of this: large amounts of putative junk exist in the human genome.

  110. bornagain77 says,

    That’s pretty much a after the fact rationalization after function was discovered (As I listed several articles that do indeed show many ‘knowlegeable scientist’ predicted it:. But I guess you get to cherry pick who is a knowledgeable scientist and who is not???. ,,,

    Long before the concept of junk DNA ever became popular, we knew about genes for functional RNA molecules (e.g. non-coding DNA), regulatory regions (noncoding DNA), origins of replication (noncoding DNA), and centromeres (noncoding DNA).

    Back in the early 1970s, no respectable scientist could possibly defend the position that all noncoding DNA was junk. They would be laughed off the stage.

    Apparently you have never promoted the supposed Vitamin C pseudogene as powerful evidence of neo-Darwinism???

    That’s partially correct. I never claimed that pseudogenes were evidence of Darwinian evolution (e.g. evolution by natural selection). That would have been an incredibly stupid thing to have said. It would put me in the same category as most IDiots.

    But in addition to misreading what I said, you are making the same fundamental error that Wells made in his book. Just because scientists raise the problem of pseudogenes does not mean that they “predicted” the existence of junk DNA. And it certainly doesn’t mean they “predicted” junk DNA based on evolution by natural selection. It also doesn’t mean they “predicted” the presence of massive amounts of junk DNA in the human genome.

    Let me remind you of the quote I was responding to, since reading comprehension seems to one of your weak points. I was challenging Wells’ claim that the presence of large amounts of junk DNA was a “prediction” of Darwinism.

    But then that can’t be true Larry for then that would make you a liar for denying that you even have promoted junk DNA as proof of neo-Darwinism!?!

    Those goalposts are moving so fast I can’t keep up. Now you’re referring to “neo-Darwinism” and you’ve forgotten about “prediction.”

    Now do you know why you are called IDiots?

  111. Eocene says,

    It’s nobody’s fault for being ignorant. But it is your fault if you choose to stay there.

    A few lines later, in response to my suggestion that he read my review, he says …

    Sorry, but I’ve seen the filth, vulgar insults, foul language and character assination fluff you call a scientific blog and the degenerates who are encouraged to comment over there. I’ll pass.

  112. Insults, rationalizations, and cherry picking, pretty much the trifecta for a neo-Darwinist.

    notes on wide scale ‘non-local quantum’ functionality (entanglement/information) across entire DNA structure:

    http://www.uncommondescent.com.....ent-408027

    further notes that Moran will rationalize away:

    Larry Moran: Vitamin C Pseudogene is Powerful Evidence – Cornelius Hunter
    Excerpt: In his on-going criticism of Jonathan Wells’ new book, The Myth of Junk DNA, evolutionist Larry Moran now asserts that the much discussed vitamin C pseudogene is powerful evidence for evolution and common descent:

    The main argument of scientists like Ken Miller and Jerry Coyne is not that the GULOP pseudogene exists. It’s that the GULOP gene and its pseudogene are at the same location in the genomes of all mammals. In the primate lineage this gene is non-functional due to a number of mutations that make it impossible to produce a functional protein. Some of the same deactivating mutations are found in related species such as humans and chimpanzees. This suggests strongly that the non-functional pseudogene was inherited from a common ancestor.

    How did Moran arrive at such a conclusion? Why is the vitamin C pseudogene such strong evidence for inheritance via common descent? Unfortunately, Moran fails to explain his reasoning. He simply asserts this amazing claim.

    Evolution and common descent have failed to explain how the original vitamin C gene could have arisen. In fact they fail to explain how any protein could have arisen. They have also failed to explain how all of biology could have arisen.

    This is not a good start. So far this evidential claim of Moran’s seems unlikely. But let’s look at the pseudogene in particular. Perhaps there is something about this pseudogene that will make the evidence more obvious. For example, perhaps evolution made a strong, heroic prediction about this pseudogene.

    In fact, evolution and common descent made no such prediction.

    Well is there, at least, a powerful retrodiction? Again, no. Well perhaps evolution and common descent would absolutely be falsified if there were no such vitamin C pseudogene. Again, the answer is no.

    No prediction, no retrodiction, and no falsification. Evolution and common descent do not predict the vitamin C pseudogene, and they are not harmed if there was no such thing. This in addition to the fact that evolution and common descent do not explain how the original gene could have arisen in the first place.

    Moran’s assertion that the vitamin C pseudogene is powerful evidence for his unlikely idea appears to be just that, an empty assertion.
    http://darwins-god.blogspot.co.....ne-is.html

  113. Further notes that will be ignored:
    http://www.uncommondescent.com.....ent-408046

  114. Joseph says,

    That is just plain ignorant. Intelligent Design does not say the design is perfect. Intelligent Design does not say that even if the design started out perfect that it had to remain that way (entropy and all).

    You may be correct. You seem to be promoting a new extended version of the the scientific theory of intelligent design. This new version seems to be compatible with any amount of junk DNA in the genome. According to the new scientific theory of intelligent design, junk DNA can be explained in three different way.

    1. The intelligent designer made a mistake.

    2. The original intelligently designed genes could have degenerated.
    3. Junk DNA could have been put in the genome by the intelligent designer as preparation for future creations.

    This new scientific version of ID isn’t widely known among my colleagues. I’d like to post it on my blog, giving full credit to whoever invented it (Joseph?). But first, let me hear from the other IDiots posting here. Do you agree that Joseph’s version of intelligent design is correct?

    Does it mean that the IDiots no longer predict that most of our genome will have a function?

    I’d also like to run Joseph’s claim past the leaders of the Intelligent Design Creationist movement but the best way to do that is to post on my blog and let them respond to those revisions.

    I’ll wait 24 hours to see what others have to say on this thread. If nobody objects to Joseph’s new version of ID, I’ll assume that it’s acceptable to the group here.

  115. Mr. Moran, since you subscribe to and preach the atheistic/materialistic form of neo-Darwinism, let’s go, step by step, through the scientific evidence that falsifies your atheistic/materialistic position:

    Falsification Of Neo-Darwinism by Quantum Entanglement/Information

    Neo-Darwinian evolution purports to explain all the wondrously amazing complexity of life on earth by reference solely to chance and necessity processes acting on energy and matter (i.e. purely material processes). In fact neo-Darwinian evolution makes the grand materialistic claim that the staggering levels of unmatched complex functional information we find in life, and even the ‘essence of life’ itself, simply ‘emerged’ from purely material processes. And even though this basic scientific point, of the ability of purely material processes to generate even trivial levels of complex functional information, has spectacularly failed to be established, we now have a much greater proof, than this stunning failure for validation, that ‘put the lie’ to the grand claims of neo-Darwinian evolution. This proof comes from the fact that it is now shown from quantum mechanics that ‘information’ is its own unique ‘physical’ entity. A physical entity that is shown to be completely independent of any energy-matter space-time constraints, i.e. it does not ‘emerge’ from a material basis. Moreover this ‘transcendent information’ is shown to be dominant of energy-matter in that this ‘transcendent information’ is shown to be the entity that is in fact constraining the energy-matter processes of the cell to be so far out of thermodynamic equilibrium.

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

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

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

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

    ‘Quantum Magic’ Without Any ‘Spooky Action at a Distance’ – June 2011
    Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically.
    http://www.sciencedaily.com/re.....111942.htm

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

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

    of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light. This following video illustrates just how ‘spooky’, to use Einstein’s infamous word, this instantaneous quantum action truly is:

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182/

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

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

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

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

    Quantum Entanglement/Information is confirmed in DNA by direct observation here;

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

  116. The necessity of ‘transcendent’ information, to ‘constrain’ a cell, against thermodynamic effects is noted here:

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

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

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

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

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

    And to dovetail into Dembski and Marks’s previous work on Conservation of Information;,,,

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

    ,,,Encoded ‘classical’ information such as what Dembski and Marks demonstrated the conservation of, and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of ‘transcendent’ (beyond space and time) quantum entanglement/information by the following method:,,,

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

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

    ,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,

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

    Further note:

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC (Functional Sequence Complexity). FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,
    Testable hypotheses about FSC
    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    The following describes how quantum entanglement is related to functional information:

    Quantum Entanglement and Information
    Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems.
    http://plato.stanford.edu/entries/qt-entangle/

    Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;

    Quantum Entanglement and Teleportation – Anton Zeilinger – video
    http://www.metacafe.com/watch/5705317/

    A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:

    Quantum Teleportation
    Excerpt: To perform the teleportation, Alice and Bob must have a classical communication channel and must also share quantum entanglement — in the protocol we employ*, each possesses one half of a two-particle entangled state.
    http://www.cco.caltech.edu/~qoptics/teleport.html

    And quantum teleporation has now shown that atoms, which are suppose to be the basis from which ALL functional information ‘emerges’ in the atheistic neo-Darwinian view of life, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of in the first place!

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    http://www.freerepublic.com/fo.....1769/posts

    Thus the burning question, that is usually completely ignored by the neo-Darwinists that I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA, or any other atoms, when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments??? i.e. It is simply COMPLETELY IMPOSSIBLE for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ‘emerge’ from, any material basis of particles!!! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a trivial matter in the least as far as developments in science have gone!!

  117. Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video (notes in description)
    http://vimeo.com/29895068

    non-local ‘epigenetic’ information is implicated in controlling the 3-D spatial organization of body plans;
    https://docs.google.com/document/d/1iNy78O6ZpU8wpFIgkILi85TvhC9mSqzUSE_jzbksoHY/edit?hl=en_US

    verses and music:

    John 1:1-3
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made.

    1 Corinthians 2:14
    The natural person does not accept the things of the Spirit of God, for they are folly to him, and he is not able to understand them because they are spiritually discerned.

    Third Day – I can feel it – with Lyrics
    http://www.youtube.com/watch?v=gdhAdz6wHWc

  118. To reiterate, there are several lines of evidence that support the inference that a majority of the human genome is putatively junk, a claim in direct opposition to the writing of Jonathan Wells as quoted above.

    The lack of known function is not the main argument here, instead the problems of genetic load and lack of sequence conservation are central. That much of the genome is repeats of broken transposible elements is also of interest, but perhaps a secondary interest, for those making a case for the majority of the human genome being functional.

    So far, the ideas have variously been put forward by ID advocates that a majority of the genome is used to regulate body plan in development, albeit without evidence. It has also been suggested that some type of redundancy in the genome could be pertinent design to allow for future contingencies. Again, evidence for this line of thought has not been presented. Supporters for such cases have not explained how such roles would be performed without a degree of sequence specificity similar to known coding and regulatory sequences (i.e. without a similar degree of purifying selection on these genomic regions).

    As this is a thread is about Jonathan Wells, the OP is written by Wells, the topic at hand is the topic of his recent book, and the writer of the most thorough review of his book is commenting in this thread, it would be great to see Wells intercede to make his case here.

  119. Larry,

    Intelligent Design Creationist only exists in the minds of the willfully ignorant so don’t hold your breath waiting for the “leadership” to respond to you.

    1. The intelligent designer made a mistake.

    1- Physical constraints and design compromises prevented a perfect design

    2. The original intelligently designed genes could have degenerated

    2- Due to genetic entropy the originally designed genomes have degenerated

    3. Junk DNA could have been put in the genome by the intelligent designer as preparation for future creations.

    3- Currently unused portions of our genomes are for possible future use

    That is what you can post.

    But anyway, according to what Wells said in the book there are functions for more than 50% of our genome, yet you say it is only 10%…

  120. That preface doesn’t support your claim.

  121. Strange that you didn’t present something from Wells’ book.

    But I do see that Dembski and Meyer say the functional part should dwarf the non-functional part.

    So how can we tell what % of the genome is functional, what part is for redundancy, what part is for future functionality, and what part is just for data storage, like RAM?

    IOW how can YOU support YOUR claim?

  122. What are those alleged lines of evidence that you say support YOUR claim?

    And we directly observe redundancy and future functions in existing designs.

    Also supporters of 90% junk still cannot explain the 10% that they say does function.

  123. Well, I’ll oblige you, but I’ll note you have responded to serveral of my comments where they are laid out above.

    Firstly, there are parts of the genome that show constrained evolution, and parts that do not. By contraint, I mean that their rates of molecular evolution are reduced – they change less over time. This constraint is produced by purifying natural selection – the removal of the less fit. While some of this evidence comes from phylogenetic inferences that at least some here will reject because of cross-species comparisons, we can also observe the same patterns occurring within humans – e.g. between subpopulations. As we all accept common ancestry for humans at some point in the past, this shoud be fairly uncontroversial.

    The parts of the genome that show evolutionary constraint are quite small – e.g. the coding and regulatory genes that we all agree are functional. Many changes that can happen to these sequences reduce function – sometimes catestrophically so. Large sections of the genome evolve without evidence of this constraint. This implies that changes to these sequences do not affect fitness.

    This is why, when Kairosfocus suggested above that most of the genome is used to regulate body plan, I disagreed. While we undoubtedly don’t know all of the regulatory sequences in the genome, we expect that for them to be functional they need a degree of evolutionary constraint – i.e. they need a degree of specificity.

    So, whatever function might be posited, it doesn’t appear to rely on sequence specificity. This points to it not being function – or putatively being junk.

    Secondly, when mutations happen the result is one of three things. It might fall somewhere non-functional (or change something in a relatively unimportant way – i.e. a synonymous codon change) and have little or no affect on fitness. Or it might fall somewhere functional and have a positive effect. This is of course relatively rare – we can ignore these occurrences for this discussion. Lastly, it might fall somewhere functional and have a negative effect.

    When the last option happens it comes at a ‘cost’ to the population. Natural selection might remove the individual, or the individual might survive with lower fitness. Were the new allele to spread through the population, the population fitness would have been lowered. Ohno points out that genes in an individual have a 1×10^-5 chance of a de novo deleterious mutation. So, if we had 100,000 (10^5) genes every individual would carry new deleterious mutations and the population fitness would inescapably decrease with time. This led to an estimate of an upper limit of about 30,000 functional loci in humans. This is quite admirable work for the era – the current estimate is a few shy of 21,000.

    On a nucleotide basis, Ohno estimated that there would be upwards of 90% ‘degeneracy’ in the genome. Larry Moran’s most recent estimate is that the known functional component is 8.7%.

    The point here is that the more that is essential in the genome, the more that you have for stuff to go wrong with. The current mutation rate would literally be the death of us if most of the genome required maintenance on the scale that functional genes do.

    These lines of evidence point to the same thing. Most of the genome doesn’t have the hallmark of function – sequence conservation. Our mutation rate is too high for sequence conservation to be plausible via natural selection. Hence, either the rest of the genome has functions that don’t require sequence specificity – which precludes the two explanations proposed above by ID advocates – or we conclude that we have putatively junky genomes.

    These are far from the only lines of evidence. Mike Lynch’s work on the ability of populations of different effective sizes to purge slightly deleterious mutations like the duplication of non-functional DNA gives us a useful paradigm to understand the accumulation of junk in the genome. Some of the junk may eventually become functional. But this is unlikely to be the future story of the majority of our genome.

  124. “Fortunately science is not the only way to make discoveries nor advance knowldge.” – Joseph

    Yes, this is obvious & not really worth repeating. The point is that, without ‘doing science,’ Jonathan Wells personally concluded ‘evident design’ in “the mountains of Mendocino county.” Thus, the argument that “intelligent design is a purely scientific pursuit” is obviously untrue. Iow, it appears that a non-scientific ‘design hunch’ played a role in Jonathan’s ‘destroy Darwinism’ approach.

    I’d still welcome Dr. Wells’ guestimate of how many biologists are ‘Darwinists’ these days. My view, having worked in close proximity with biologists, is that most do not call themselves ‘Darwinists’ anymore, but rather use the ideas of Darwin that are still valid and relevant and discard those that are erroneous and outdated. Isn’t this continual updating what ‘scientists’ are supposed to do?

    Repeatedly citing a few ‘media active’ scholars who call themselves ‘Darwinists’ does not mean that a majority or even a minority of biologists active today are ‘Darwinists,’ according to their own labels, not Dr. Wells’.

    “Darwinism (like Marxism and Freudianism) is materialistic philosophy masquerading as empirical science—and that I should set out to destroy its dominance in our culture.” – Dr. Wells

    Leaving aside Freudianism, on the ideological front it would seem that the IDM should spend more time on Marxism, in addition to Darwinism. The current international association president of a major academic field is a neo-Marxist. In the USA, it is as easy to consider Marxism ‘dead’ or ‘destroyed’ as it is to believe that the Cold War was won and socialism forever defeated (capitalism’s great victory, freedom, democracy, etc!). Once one steps outside of the US context, however, things change signifiantly and Marxism is still alive and well in global scholarship, including its on-going reevaluation in China and Latin America. The ‘material-empirical’ base for natural sciences is still a common feature of ‘doing science’ that Dr. Wells is apparently seeking to change (the definition of) from within.

    Mind, Intelligence, Order, codewords for capital-D ‘Design’ = isn’t this Wells’ extra-scientific epiphany in the mountains?

    In this case, it seems clear that ‘design philosophy’ or ‘design religion’ has overlapped with ‘design science’ and thus undermines IDs claims to ‘scientific purity.’ From the point I made to Dembski, and how Wells reacted positively and personally to me, it would seem that Wells is content to rebuke the ‘ID is a purely scientific pursuit’ wing of the IDM. Wells’ mountain revelation and ‘destroy ideology’ approach shows aptly that ID isn’t ‘pure science.’

  125. paulmc:

    So, whatever function might be posited, it doesn’t appear to rely on sequence specificity. This points to it not being function – or putatively being junk.

    OK so your ignorance sez it’s junk. Got it.

    But anyway with all your talk about degeneration it appears that you evos are shooting yourselves in the foot as it appears there isn’t anything that can cause the changes your position requires.

    But keep up the good work as soon your position won’t have any evidence at all except for this alleged junk.

  126. Gregory:

    Wells’ mountain revelation and ‘destroy ideology’ approach shows aptly that ID isn’t ‘pure science.’

    No, it would mean that Wells has an agenda- Wells, not ID.

    Also if Darwinism is ruining science, and I say it is, then it should be welcome to have someone destroy it.

    But anyway perhaps it was the evidence that Wells was considering on that mountain. Reading Gothe gave Tesla inspiration for the AC generator.

  127. Joseph:

    OK so your ignorance sez it’s junk. Got it.

    Ignorance? What a bizarre answer.

    If that is actually what you took from everything I’ve written above, then you have not understood it. The irony that you would accuse me of ignorance in this exchange is staggering.

  128. Well paulmc, on one hand we have the team from ENCODE saying the humans genome is “pervasively transcribed” and on the other there is you, Larry and perhaps some others.

    True that was over 3 years ago but has someone found out otherwise?

    When the day comes tat someone goes into a lab and removes 90%- the junk- and gets a human to develop, let me know.

    Heck use mice- they have already seen that removong small amounts of DNA don’t have any effect- go for the full 90% and get back to us.

  129. BTW I- we- say Larry, et al.- you included- are wrong about introns- obviously they are functional as they allow for alternative gene splicing- some are even used. And that is just for starters.

    Right there is 30% that goes to the non-junk side of the scale.

  130. Joseph @ 21.1.1.1.2/3

    True that was over 3 years ago but has someone found out otherwise?

    If the debate about genomic “dark matter” and pervasive transcription was something you had a genuine scientific interest in, you would be well aware that there is an active other side to the debate.

    Here are a few things: a synopsis, a Nature News piece, and a peer-reviewed paper.

    Larry Moran has written a few times about the topic.

  131. One would think that to be active would mean removing the portion (90%) deemed junk and see if something develops.

    Also DNA does not need to be transcribed in order to have a function.

    Introns, for example, function as spacers for exons to facilitate alternative gene splicing.

  132. So you are too lazy to do the work for yourself and you need me to spoon feed you.

    If you are attempting to advance an argument, it is sheer laziness on your part not to back it up with direct answers. “It’s in a book, somewhere; go read it. ”

    And if you want to make this personal then let’s get together and take care of it- “I’m talking to you”- bully nonsense.

    I was ‘making it personal’ by a simple statement of the individual with whom I was attempting to communicate? You find that to be bullying, and offer to meet up for a rumble? For goodness’ sake! I would suggest that calling someone ‘moron’, ‘stupid’, ‘ignorant’ and so on is a much better example of ‘making it personal’. To be personal, you can’t go three posts without descending to such a level.

    Anyhoo… all you have quoted is the presence of Alus in functional positions, which I have already noted. There are 1.1 million of them. What fraction is functional?

  133. Introns, for example, function as spacers for exons to facilitate alternative gene splicing.

    In principle, all you actually need to facilitate alternative splicing is a splice site. You don’t need the intronic regions to be 10+ times as big as the exonic regions to achieve this, so the alternative splice theory needs to find an answer for intron size – as well as a much clearer view on which intron-containing genes are actually alternatively spliced, and what proportion of those alternative transcripts make the Function cut, pardon the pun.

  134. Oh, and introns are transcribed, just not translated.

  135. Joseph, All major leaders of the IDM display an agenda. E.g. Stephen Meyer says he wants to change the rules of science. He simply doesn’t wish to accept the ‘rules of the game’ as they are currently written. Would you then also say “Meyer, not ID?”

    Darwin’s legitimate contribution(s) to ‘science’ have not ruined ‘science.’ However, “Darwin’s errors” should be more widely understood and overcome. I’m not casting a stone at Darwin by saying this. Are you and Wells doing so by seeking to ‘destroy’ Darwin’s major contribution(s) to natural science, e.g. ‘species are mutable’?

    “Destroy Darwinism” is just rhetoric and posturing, when the ‘bad ideology’ is not fairly and clearly distinguished from the ‘good science.’ Darwin himself (defensively armed with T.H. Huxley’s ‘agnosticism’) did not ‘ruin science’ any more than the Orthodox Christian I. Pavlov did. Now if you want to speak about B.F. Skinner’s ‘behaviorism’…

    Yeah, Joseph, you’re correct that Wells might have been considering ‘the evidence’ on that mountain. I’m assumiing there were obviously ‘designed’ things there, i.e. for Wells’ basic living needs, like a human-made house or cabin, kitchen table, knives, forks & spoons, hot plate, etc. Since Wells has not ‘specified’ what he was referring to that was ‘evident design,’ we are left without any ‘evidence’ to consider, just Wells’ personal revelation.

  136. Gregory,

    Back ways around, I am afraid.

    A better warranted description is that we have recently had a coup in science and education institutions that thought the backdoor of so-called methodological naturalism (and aided by false revisionism of the history of science), has sought to impose a priori materialism on science and education. In some cases thinly vieled threats have been made.

    For the long term good of science and of society, they have to be corrected.

    (The links have more details.)

    GEM of TKI

  137. F/N: In addition, you need to correct some serious polarising caricatures and distortions in your understanding of design theory that are propagated far and wide by objectors who should know better but do not seem to care about truthfulness or fairness. Cf NWE — not the Wikipedia hatchet job — here and look also at the weak argument correctives under the resources tab top this and every UD page. KF

  138. Some are translated- that is in the book you didn’t read.

  139. Chas:

    In principle, all you actually need to facilitate alternative splicing is a splice site.

    And introns provide that.

    You don’t need the intronic regions to be 10+ times as big as the exonic regions to achieve this,

    How do YOU know what is needed?

    as well as a much clearer view on which intron-containing genes are actually alternatively spliced

    For more protein products- IOW for getting more proteins from the same number of “genes”.

    But anyway your position doesn’t have any explanation for alternative gene splicing.

  140. Intron size is also used as a timing mechanism.

  141. Joseph says,

    Well paulmc, on one hand we have the team from ENCODE saying the humans genome is “pervasively transcribed” and on the other there is you, Larry and perhaps some others.

    The consensus view among molecular biologists is that most of that transcription is either artifact or nonfunctional junk RNA. This particular controversy is so obvious that Wells couldn’t ignore it, as he ignores all other contrary views. He had to devote a few pages to explaining why he disagrees with most scientists.

    When you use disputed results to bolster your argument it’s only fair that you mention when they aren’t facts. It is not a fact that most of the genome is transcribed and it is not a fact that most transcripts are functional.

    But you read my review so you already knew that didn’t you?

  142. Joseph says,

    BTW I- we- say Larry, et al.- you included- are wrong about introns- obviously they are functional as they allow for alternative gene splicing- some are even used. And that is just for starters.

    Right there is 30% that goes to the non-junk side of the scale.

    We don’t know whether alternative transcripts are common or rare. The consensus view among molecular biologists is that most splice variants are artifacts or splicing errors. We don’t know what percentage actually represent functional alternative transcripts.

    My own view is that less the 5% of our genes have functional alternative transcripts. Other scientists think that number could be higher&maybe even 50%.

    See Alternative Splicing and Why IDiots Don’t Understand How Science Works
    Splicing Error Rate May Be Close to 1%

    Even if you accept the higher number, that only means that one intron per gene could be required for alternative transcription. It does not mean that ALL introns are needed for alternative transcripts.

    See IDiots Do Arithmetic a Second Time – Same Result

    Let’s assume that all introns are necessary. They aren”t junk. Does this mean that all intron sequences are functional and 30% of the genome can be eliminated as junk? Not at all. You only need 80 bp of DNA to have a functional intron. Almost all of the rest is junk. A considerable percentage of intron sequences consists of defective transposon pseudogenes that are junk by any definition. I estimate that about 0.4% of the genome consists of functional intron sequences.

    See What’s in Your Genome?
    Junk in Your Genome: Protein-Encoding Genes
    Junk in Your Genome: Intron Size and Distribution

    Joseph, you are passing yourself off as an expert on this subject so I presume you knew all this, right? In that case, why are you misleading the readers of Uncommon Descent?

    (Is it possible that you didn’t know any of this important information?)

  143. Intron length contributes to the timing of the transcript product. Also unused splices- that is unused alternative splicing is definitely a future function.

    As I said obviously you don’t have any experience with designing complex technology. And in that case why are YOU misleading readers everywhere?

    But anyway Larry, I agree that you could be right and over 90% of our genome is junk.

    How the heck can you go out and scientifically demonstrate such a claim?

    Could some of the alleged junk be to maintain the gamete? Could some of it be for gamete recognition?

    The point being Larry is only ignorance sez 90%+ of our genome is junk, which means you are misleading readers.

  144. Larry Moran:

    My own view is that less the 5% of our genes have functional alternative transcripts. Other scientists think that number could be higher&maybe even 50%.

    How many genes vs how many proteins- that is how we can figure out how much alternative gene splicing is going on.

Leave a Reply