Does Evolutionary Theory Really Help Scientists?

_{February 3, 2014

'Junk DNA', Intelligent Design}

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

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

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

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

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

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

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

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

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

Comments

Unguided evolution cannot account for regulatory networks. It cannot account for the genetic code. Unguided evolution is a useless heuristic.Joe_{February 4, 2014
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WD400: Thanks for telling us just how sensitive the now collapsing Junk DNA claim is for Darwinists, by trying to project that citing the evidence of the claim being made and widely promoted by evolutionary biologists is a blunder. Shades of the Ministry of Truth in 1984. Sorry, WD, I was there to see the claim being used by Darwinists as a supposed definitive knockdown argument on a routine basis. Makes me wonder just what else is being revisionised beyond recognition by such. KFkairosfocus_{February 4, 2014
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A great many mainstream biologists explicitly said that non-coding DNA likely had function, right from the early days after it was discovered. Immediately after Ohno’s very first presentation at the conference proceedings where he coined the term “junk DNA” he gave an interview describing his expectation that Darwinian adaptation should remove non-functional DNA, and therefore by implication remaining DNA is likely functional, even if we don’t know what the function is. The transcript is published in Ohno, S. (1973) “Evolutional reason for having so much junk DNA” in Modern Aspects of Cytogenetics: Constitutive Heterochromatin in Man (ed. R.A. Pfeiffer), pp. 169-173. F.K. Schattauer Verlag, Stuttgart, Germany:
Ohno: “If there is any gene which is doing some good for your general well-being, you will suffer when you lose that gene. For this very reason a fraction of randomly sustained mutations of that locus would be deleterious. There is simply no way of having a useful gene without paying a certain price for the cost of natural selection. If, on the other hand, there is a gene which is totally irrelevant, you will lose that gene sooner or later, for natural selection would not police that gene.”
In fact, way back in 1971 before Ohno coined the term “junk DNA”, biologists were discovering large portions of the genome that did not code for proteins and/or was repetitive, and had no known function. Nonetheless, they were proposing numerous possible functions for such, and subsequent research has shown some of their proposals to be correct:
Ever since the initial demonstration of the existence of repetitive DNA there has been no dearth of theories on the function of this material. … Following is a list of functions that have been proposed … 1. Recognition of centromeres of common origin. 2. Recognition between homologous chromosomes during pairing. 3. Regions involved in the initiation of replication and/or transcription. 4. Sites concerned with specifying the folding patterns of chromosomes. 5. Recognition sites for the process of genetic recombination. 6. Provision of raw material for genetic divergence. 7. Reflection of similarities in the structure of different proteins. 8. DNA concerned with the regulation of gene expression (regulatory DNA). 9. Reflection of multiplicity of repeated genes, as for example, in the master and slave or multistranded chromosome hypothesis. … None of the recognition functions, i.e., recognition of centromeres, initiation sites, pairing sites, recombination sites, folding sites, or regulatory sites, that we have discussed is mutually exclusive of the others. They all relate to cellular phenomena that have been demonstrated or inferred from other data. All these phenomena probably exist within every higher organism. Therefore, DNA involved in each of these functions could contribute in varying degrees to the repeated portion of the genome. – Bostock, C. (1971) “Repetitious DNA” Advances in Cell Biology 2: 153-223.
And there are many, many more papers over subsequent decades describing the expectation that much “junk” DNA actually has function; some examples appear below. 1974 — E. Southern, “Eukaryotic DNA” in MTP International Review of Science, Biochemistry Series One, Volume 6, Biochemistry of Nucleic Acids, (1974) University Park Press, Baltimore. pp. 101 – 139:
“.. large variations in genome size could readily be accomodated if a high proportion of the DNA were used for functions other than coding for proteins. A number of such functions have been proposed and incorporated into hypothetical structures for the eukaryotic genome.”
1977 — D.M. Skinner, “Satellite DNAs” BioScience 27 (1977) pp. 790-796:
Satellites [tandemly repeating, non-coding DNA] constitute from 1% to 66% of the total DNA of numerous organisms, including that of animals, plants, and prokaryotes. Their existence has been known for about 15 years but, although it is thought that they must be biologically important … their functions are still largely in the realm of speculation.
1980 — Orgel & Crick, Nature (284: 604-607), p. 606:
Thus, some selfish DNA may acquire a useful function and confer a selective advantage on the organism.
1982 — R. Lewin, “Repeated DNA still in search of a function” Science 217 (1982) pp. 621-623:
Some repetitive DNA will undoutedly be shown to have a function, in the formal sense, some will likely be shown to exert important effects, and the remainder may well have no function or effect at all and can therefore be called selfish DNA. Repetitive DNA constitutes a substantial proportion of the genome (up to 90% in some cases), and there is considerable speculation on how it will eventually be divided between these three groups.
Clearly, mainstream biologists have claimed for decades that non-coding DNA has functions, ever since the term “junk” DNA entered the scientific literature. CheersCLAVDIVS_{February 4, 2014
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Wd400 I think the biggest problem is that while many scientists may have not thought that non-coding regions are junk just because they are not understood yet, they have been happy to let the illusion spread. This is worrying, happily let the media/public think one thing (which can been seen to be true from the many instances posted above) all the while knowing full well we don't have the complete picture yet. It gives the impression (rightly or wrongly) that they want it to be junk... why? I find it frightening.bw_{February 4, 2014
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"When you contrast this to the evolutionist position that most of the genome is junk because we don’t know what it does a" Please, try and read what I have said. Here it is, one more time: 1. Evolutoinary biologists have long thought most of the genome is junk 2. The fact most of the genome has no known function is not the main reason they no this 3. No one who knows the first thing aout molecular biology has argued all non-coding sequences are junk 4. Most of the genome is, in fact, junkwd400_{February 3, 2014
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Wd400: "Do you really think people thought all non-coding DNA was junk at the same time that detereming the basis fo gene regulation was a central topic in molecular biology? Or that peope tought all non-coding sequences where junk when functional RNAs have been known about since the 1970s?" Yes, based on what BA and I have both posted and you have completely ignored, I think we can be certain that evolutionists once believed that non coding sequences were junk. In fact it's not just an ID mistake because it's not an ID mistake at all! ID takes the pro-science, pro-progression of thought position that the non-coding sequences have function, just we don't know what they do yet, and more research is important. When you contrast this to the evolutionist position that most of the genome is junk because we don't know what it does and thus we don't need to bother investigating it because we already don't know what it does, it's clear which side is impeding scientific progress. Wd400, I don't care about whether or not you are taking the fault for others mistakes, I just think it is absolutely appalling that when an evolutionist has one of their favorite "evidences" of evolution shattered they just switch their position to the opposite and say the evidence still supports their position (Richard Dawkins). Evolutionists cannot be anything other than complete hypocrites when they constantly accuse creationists and ID advocates of moving the goal posts regarding micro vs macro evolution or information via mutations when they believe that everything is evidence for evolution, even things that directly contradict each other. That evolutionists have to employ these tactics to keep their theory alive (at least in their imaginations) should show that their beliefs are not based upon any sort of science.sixthbook_{February 3, 2014
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(and again, can you see the mistake Luskin made in the passage quoted in #14, it should be instructive...)wd400_{February 3, 2014
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I think anyone who has had a glimpse at the mind blowing complexity being dealt with in DNA, who still thinks that the vast majority of DNA is junk just because we don’t fully understand exactly what it all does, is a more than a few fries short of a happy meal,, Then I'll repeat myself, as people find it hard to get past this myth: I do not think the most important argument for the proposition that most of our genome is junk is that most of the genome has no known function.wd400_{February 3, 2014
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wd400 you state:
It’s true that most non-coding DNA is junk.
I think anyone who has had a glimpse at the mind blowing complexity being dealt with in DNA, who still thinks that the vast majority of DNA is junk just because we don’t fully understand exactly what it all does, is a more than a few fries short of a happy meal,, Notes along that line: 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm DNA Packaging: Nucleosomes and Chromatin each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth’s equator 2.5 million times! How is this possible? http://www.nature.com/scitable/topicpage/DNA-Packaging-Nucleosomes-and-Chromatin-310 DNA – Replication, Wrapping & Mitosis – video https://vimeo.com/33882804 ‘How good would each typists have to be, in order to match the DNA’s performance? The answer is almost too ludicrous to express. For what it is worth, every typists would have to have an error rate of about one in a trillion (conservatively a billion);. Richard Dawkins – The Blind Watchmaker – Page 123-124 DNA: The Ultimate Hard Drive – Science Magazine, August-16-2012 Excerpt: “When it comes to storing information, hard drives don’t hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare.” http://news.sciencemag.org/sciencenow/2012/08/written-in-dna-code.html DNA Computer Excerpt: A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours. http://www.tech-faq.com/dna-computer.html Cells Are Like Robust Computational Systems, – June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,”We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail.” http://www.sciencedaily.com/releases/2009/06/090616103205.htm “Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.” Edward N. Trifonov – 2010 Systems biology: Untangling the protein web – July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.” http://www.nature.com/nature/journal/v460/n7253/full/460415a.html “applying Darwinian principles to problems of this level of complexity is like putting a Band-Aid on a wound caused by an atomic weapon. It’s just not going to work.” - David Berlinski etc.. etc.. etc..bornagain77_{February 3, 2014
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Excerpt: (A) On the one hand, you try to rewrite history by arguing that evolutionary biologists never argued that the genome was full of junk (“Wells and Luskin have promoted the absurd falsehood that molecular biologists believed non-coding DNA was non-functional ‘junk.’”) (B) On the other hand, you then claim the genome is full of junk DNA. (“As for junk, it is between 65 to 91.3%.”) Do you not see how the Can everyone spot Luskin's mistake in A? It's the one everyone keeps making here...wd400_{February 3, 2014
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wd400, Son get caught stealing cookies. "caught you boy!" http://www.youtube.com/watch?v=zagxOqIWmHcbornagain77_{February 3, 2014
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I can't be responsible for other people's mistakes. All I can say is read Ohno, who very clearly states that non-coding sequences sould be part of the non-junk. Or even better, think for yourself. Do you really think people thought all non-coding DNA was junk at the same time that detereming the basis fo gene regulation was a central topic in molecular biology? Or that peope tought all non-coding sequences where junk when functional RNAs have been known about since the 1970s? It's true that most non-coding DNA is junk. Be informed pepole never claimed all non-coding sequences where junk, or that the absensce of known functions for sequences were the best argument for the junkiness of our genome. That myth, as your quotes show, extends far beyond the ID crowd, but it's still dead wrong.wd400_{February 3, 2014
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PZ Myers argues for well over 50% junk DNA in the following video: PZ Myers, the self-described Paris Hilton of atheists, on junk DNA - December 2011 - video https://uncommondescent.com/junk-dna/pz-myers-the-self-described-paris-hilton-of-atheists-on-junk-dna/ Casey Luskin responds to a mean-spirited attack by a neo-Darwinist on 'Junk DNA' - July 2012 Excerpt: (A) On the one hand, you try to rewrite history by arguing that evolutionary biologists never argued that the genome was full of junk ("Wells and Luskin have promoted the absurd falsehood that molecular biologists believed non-coding DNA was non-functional 'junk.'") (B) On the other hand, you then claim the genome is full of junk DNA. (“As for junk, it is between 65 to 91.3%.”) Do you not see how the fact that you’re making argument (B) makes it really hard for me to believe your argument (A)? In any case, your point (A) is an attempt to rewrite history, which is a predictable response to the overwhelming mass of evidence,,, http://www.evolutionnews.org/2012/07/what_are_the_to_1062011.html#comment-15282571 The human genome is littered with pseudogenes, gene fragments, “orphaned” genes, “junk” DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. . . . In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection. – Ken Miller Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution … we expect to find, in the genomes of many species, silenced, or ‘dead,’ genes: genes that once were useful but are no longer intact or expressed … the evolutionary prediction that we’ll find pseudogenes has been fulfilled—amply … our genome—and that of other species—are truly well populated graveyards of dead genes - Jerry Coyne We have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, gene fragments, tandem repeats, and pseudo¬genes, none of which are involved directly in the making of a human being. In fact, of the entire human genome, it appears that only a tiny percentage is actively involved in useful protein production. Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution. – Michael Shermerbornagain77_{February 3, 2014
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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/2007/06/will_darwinists_try_to_pull_a.html Another leading biologist, Sydney Brenner argued in a biology journal in 1998 that: "The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it." The Unseen Genome, Gems Among the Junk: “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.” (John S. Mattick Scientific American (November, 2003) http://www.evolutionnews.org/ Casey Luskin response to Farrel - several quotes from Jonathan Wells book - 'The Myth of Junk DNA' - May 2011 http://blogs.forbes.com/johnfarrell/2011/05/20/the-myth-of-the-myth-of-junk-dna/#comment-153 Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such - March 2011 Excerpt: Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.” This claim is easily disproved: Francis Crick and Leslie Orgel published an article in Nature in 1980 (284: 604-607) arguing that such DNA “is little better than junk,” and “it would be folly in such cases to hunt obsessively” for functions in it. Since then, Brown University biologist Kenneth R. Miller, Oxford University biologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design. National Institutes of Health director Francis Collins argued similarly in his widely read 2006 book The Language of God. It is true that some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) have long been skeptical of “junk DNA” claims, but probably a majority of biologists since 1980 have gone along with the myth. The revisionists are misinformed (or misinforming). https://uncommondescent.com/junk-dna/jonathan-wells-on-his-book-the-myth-of-junk-dna-yes-it-is-a-darwinist-myth-and-he-nails-it-as-such/#more-18154 Dawkins, 2009: on “junkDNA” “Junk DNA is just what a Darwinist would expect,” Dawkins, 2012: on non-junkDNA… “"junk DNA" isn’t junk at all but is instead "exactly what a Darwinist would hope for," http://www.evolutionnews.org/2012/09/in_debate_brita_1064521.html Richard Dawkins ENCODE 2013 “Junk DNA” - video http://www.youtube.com/watch?feature=player_detailpage&v=_bjKH43pRB0#t=94s First Holistic View of How Human Genome Actually Works: ENCODE Study Produces Massive Data Set - ScienceDaily (Sep. 5, 2012) Excerpt: "During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong," said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI), a part of the National Institutes of Health. "ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms." http://www.sciencedaily.com/releases/2012/09/120905140913.htm Amazingly, many leading evolutionists as of 2010-11 (Ayala in 2010; Francis Collins in 2010) still insist that most of the genome, which does not directly code for proteins, is useless 'Junk DNA'. Francis Collins, Darwin of the Gaps, and the Fallacy Of Junk DNA - Wells, Meyer, Sternberg - video http://www.evolutionnews.org/2010/11/francis_collins_is_one_of040361.htmlbornagain77_{February 3, 2014
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Junk DNA Predictions By Leading Evolutionists Haldane's Dilemma Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift - creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors - it surely would have killed us. Since Haldane's dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation - but has obtained identical results. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 159-160 Walter ReMine on Haldane's Dilemma - interview http://kgov.com/Walter-ReMine-on-Haldanes-Dilemma Kimura's Quandary Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most 'evolution' must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom's (neo-Darwinism's) very validity. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 161 - 162 A graph featuring 'Kimura's Distribution' being ‘properly used’ is shown in the following video: Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086 At the 2:45 minute mark of the following video, the mathematical roots of the junk DNA argument, that is still used by many Darwinists, can be traced through Haldane, Kimura, and Ohno's work in the late 1950’s, 60’s through the early 70’s: What Is The Genome? It's Not Junk! - Dr. Robert Carter - video - (Notes in video description) http://www.metacafe.com/w/8905583 Carter: Why Evolutionists Need Junk DNA - Robert W. Carter - 2009 Excerpt: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane's work. Without junk DNA, evolutionary theory cannot currently explain how everything works mathematically. Think about it; in the evolutionary model there have only been 3-6 million years since humans and chimps diverged. With average human generation times of 20-30 years, this gives them only 100,000 to 300,000 generations to fix the millions of mutations that separate humans and chimps. This includes at least 35 million single letter differences, over 90 million base pairs of non-shared DNA, nearly 700 extra genes in humans (about 6% not shared with chimpanzees), and tens of thousands of chromosomal rearrangements. Also, the chimp genome is about 13% larger than that of humans, but mostly due to the heterochromatin that caps the chromosome telomeres. All this has to happen in a very short amount of evolutionary time. They don't have enough time, even after discounting the functionality of over 95% of the genome--but their position becomes grave if junk DNA turns out to be functional. Every new function found for junk DNA makes the evolutionists' case that much more difficult. Robert W. Carter - biologist http://creation.com/junk-dna-slow-death Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional. Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, "they are the remains of nature's experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?" Sternberg traces how the junk DNA argument developed through the mid 1970’s to the early 80’s and beyond in the following article: How The Junk DNA Hypothesis Has Changed Since 1980 - Richard Sternberg - October 8, 2009 Excerpt: Two papers appeared back to back in the journal Nature in 1980: "Selfish Genes, the Phenotype Paradigm and Genome Evolution" by W. Ford Doolittle and Carmen Sapienza and "Selfish DNA: The Ultimate Parasite" by Leslie Orgel and Francis Crick. These laid the framework for thinking about nonprotein-coding regions of chromosomes, judging from how they are cited. What these authors effectively did was advance Dawkins's 1976 selfish gene idea in such a way that all the genomic DNA evidence available up to that time could be accounted for by a plausible scenario. The thesis presented in both articles is that the only specific function of the vast bulk of "nonspecific" sequences, especially repetitive elements such as transposons, is to replicate themselves -- this is the consequence of natural selection operating within genomes, beneath the radar of the cell. These junk sequences, it was postulated, can duplicate and disperse throughout chromosomes because they have little or no effect on the phenotype, save for the occasional mutation that results from their mobility. http://www.evolutionnews.org/2009/10/how_the_junk_dna_hypothesis_ha026421.html Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true “purpose” of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA. …. “creationists…might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.” Richard Dawkins - Selfish Gene (mid 1970’s) https://uncommondescent.com/books-of-interest/new-book-junk-dna-junked-in-favour-of-what/#comment-374475 Selfish DNA: the ultimate parasite. Orgel LE, Crick FH. - 1980 The DNA of higher organisms usually falls into two classes, one specific and the other comparatively nonspecific. It seems plausible that most of the latter originates by the spreading of sequences which had little or no effect on the phenotype. http://www.ncbi.nlm.nih.gov/pubmed/7366731 Dr. Wells gives some historical background as to why some neo-Darwinists are doing everything they can to discredit the recent (Sept. 2012) ENCODE findings: Why All the Fuss Over Some Junk? - Jonathan Wells - September 25, 2012 Excerpt: Some historical context might help. After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found "the secret of life," a popular formulation of which became "DNA makes RNA makes protein makes us." But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term "junk" to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional). Why didn't biologists simply call non-protein-coding sequences "DNA of unknown function" rather than "junk DNA?" For some, it was because "junk DNA" seemed more suited to the defense of Darwinism and survival of the fittest. In 1976, Richard Dawkins wrote in The Selfish Gene that "the true 'purpose' of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA." In 1980, W. Ford Doolittle and Carmen Sapienza wrote in Nature (284:601) that many organisms contain "DNAs whose only 'function' is survival within genomes," and that "the search for other explanations may prove, if not intellectually sterile, ultimately futile." In the same issue of Nature (284:604), Leslie Orgel and Francis Crick wrote that "much DNA in higher organisms is little better than junk," and its accumulation in the course of evolution "can be compared to the spread of a not-too-harmful parasite within its host." Since it is unlikely that such DNA has a function, Orgel and Crick concluded, "it would be folly in such cases to hunt obsessively for one." Two biologists then wrote to Nature (285:617,618) expressing their disagreement. Thomas Cavalier-Smith considered it "premature" to dismiss non-protein-coding DNA as junk, and Gabriel Dover wrote that "we should not abandon all hope of arriving at an understanding of the manner in which some sequences might affect the biology of organisms in completely novel and somewhat unconventional ways." Cavalier-Smith and Dover were not criticizing evolutionary theory; they were merely questioning the claim that non-protein-coding DNA is non-functional. After the rise of intelligent design (ID) in the 1990s, "junk DNA" became a favorite weapon against ID in the hands of some Darwinists, including Richard Dawkins and the four bloggers mentioned above. According to ID, it is possible to infer from evidence in nature that some features of the world, including some features of living things, are explained better by an intelligent cause than by unguided natural processes. The Darwinists' argument was that an intelligent designer would not have filled our genomes with so much junk, but that it could have accumulated as an accidental by-product of unguided evolution. In 2004, Dawkins wrote in A Devil's Chaplain that much of our genome "consists of multiple copies of junk, 'tandem repeats,' and other nonsense which may be useful for forensic detectives but which doesn't seem to be used in the body itself." Dawkins suggested that creationists (among whom he included ID advocates) "might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA." Dawkins continued to rely on junk DNA in his 2009 book The Greatest Show on Earth: The Evidence for Evolution. "It is a remarkable fact," he wrote, "that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes." In particular, pseudogenes "are genes that once did something useful but have now been sidelined and are never transcribed or translated." Dawkins concluded: "What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene... unless he was deliberately setting out to fool us." But if most of our DNA is functional, as the ENCODE results suggest, then the "junk DNA" argument against ID collapses. So the four bloggers listed above are doing everything they can to discredit the ENCODE project's estimate of functional DNA. Yet whatever the estimate may currently be, it is certain to increase with further research. In 2007, the ENCODE pilot project reported on the basis of about 200 datasets that our DNA is "pervasively transcribed," suggesting functionality. The 2012 results, based on 1,640 datasets, documented that "the vast majority (80.4%) of the human genome" is biochemically functional in at least one cell type. But ENCODE has so far sampled only a fraction of the cell types in the human body. Clearly, we have a lot more to learn about our genome -- but not if we start by assuming that most of it is junk. http://www.evolutionnews.org/2012/09/why_all_the_fus_1064721.html In 1994, the authoritative textbook, Molecular Biology of the Cell, co-authored by National Academy of Sciences president Bruce Alberts, suggested (incorrectly!) that introns are "largely genetic 'junk'": Unlike the sequence of an exon, the exact nucleotide sequence of an intron seems to be unimportant. Thus introns have accumulated mutations rapidly during evolution, and it is often possible to alter most of an intron’s nucleotide sequence without greatly affecting gene function. This has led to the suggestion that intron sequences have no function at all and are largely genetic “junk” Soon thereafter, the 1995 edition of Voet & Voet's Biochemistry textbook explained that "a possibility that must be seriously entertained is that much repetitive DNA serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that, over many generations, has disseminated itself throughout the genome..."bornagain77_{February 3, 2014
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As I have posted before when Wd400 claims that no one has ever called non coding DNA junk: "From AP Biology Textbook by Campbell and Reece, 7th Edition page 374: “The bulk of most eukaryotic genomes consists of noncoding DNA sequences, often described in the past as ‘junk DNA’” Furthermore, Querius also posted in response to Wd400: "There certainly is! Why just look at what the idiots at Medical News wrote: Junk DNA – What is Junk DNA? In genetics, “junk DNA” or noncoding DNA describes components of an organism’s DNA sequences that do not encode for protein sequences. In many eukaryotes, a large percentage of an organism’s total genome size is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding versus noncoding DNA varies greatly between species. Much of this DNA has no known biological function. However, many types of noncoding DNA sequences do have known biological functions, including the transcriptional and translational regulation of protein-coding sequences. (snip) Junk DNA Term Junk DNA, a term that was introduced in 1972 by Susumu Ohno, is a provisional label for the portions of a genome sequence of a for which no discernible function has been identified. According to a 1980 review in ”Nature” by Leslie Orgel and Francis Crick, junk DNA has “little specificity and conveys little or no selective advantage to the organism”. The term is currently, however, a somewhat outdated concept, being used mainly in popular science and in a colloquial way in scientific publications, and may have slowed research into the biological functions of noncoding DNA. Emphasis added by Querius See http://www.news-medical.net/he.....k-DNA.aspx Also, Nature magazine . . . http://www.nature.com/scitable.....k-dna-1211 Appalling, isn’t it! This kind of stuff is all over the internet and various scientific journals. Apparently, only wd400 is properly informed. " Taking both of these from the comments section here: https://uncommondescent.com/junk-dna/junk-dna-turns-out-to-influence-diabetes-risk/ Wd400, you can keep denying that evolutionists have been calling most of the genome "junk" for years, but I for one refuse to believe you and would rather take the side of the facts.sixthbook_{February 3, 2014
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OT: Podcast - Dr. Michael Egnor: Do Humans Have Free Will? http://intelligentdesign.podomatic.com/entry/2014-02-03T15_58_01-08_00 Listen in as Dr. Egnor explains why the argument against free will is self-refuting and shows how determinism as a theory in physics is dead.bornagain77_{February 3, 2014
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Moreover, 'Junk' DNA is hardly the only place where Darwinian presuppositions are useless for useful guidance. In medical diagnostics Darwinian presuppositions are useless:
Darwinian Medicine and Proximate and Evolutionary Explanations - Michael Egnor - neurosurgeon - June 2011 http://www.evolutionnews.org/2011/06/darwinian_medicine_and_proxima047701.html
and even In the development of medicine itself with animal testing, the false Darwinian presupposition that we are all related to lower animals is useless and misleading for research (besides wasting billions of dollars of research money)
The mouse is not enough - February 2011 Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.” http://www.the-scientist.com/news/display/57986/ What scientific idea is ready for retirement? – Mouse Models Excerpt: A recent scientific paper showed that all 150 drugs tested at the cost of billions of dollars in human trials of sepsis failed because the drugs had been developed using mice. Unfortunately, what looks like sepsis in mice turned out to be very different than what sepsis is in humans. Coverage of this study by Gina Kolata in the New York Times incited a heated response from within the biomedical research community. AZRA RAZA – Professor of medicine and director of the MDS Centre, Columbia University, New York http://www.theguardian.com/science/2014/jan/12/what-scientific-idea-is-ready-for-retirement-edge-org Animal Testing Is Bad Science: Point/Counterpoint Excerpt: The only reason people are under the misconception that animal experiments help humans is because the media, experimenters, universities and lobbying groups exaggerate the potential of animal experiments to lead to new cures and the role they have played in past medical advances.,,, The Food and Drug Administration (FDA) has noted that 92 percent of all drugs that are shown to be safe and effective in animal tests fail in human trials because they don’t work or are dangerous.,,, Physiological reactions to drugs vary enormously from species to species. Penicillin kills guinea pigs but is inactive in rabbits; aspirin kills cats and causes birth defects in rats, mice, guinea pigs, dogs, and monkeys; and morphine, a depressant in humans, stimulates goats, cats, and horses. http://www.peta.org/issues/animals-used-for-experimentation/animal-testing-bad-science.aspx
In fact, as to the somewhat minor extent evolutionary reasoning has influenced medical diagnostics, it has led to much ‘medical malpractice’ in the past:
Evolution's "vestigial organ" argument debunked Excerpt: "The appendix, like the once 'vestigial' tonsils and adenoids, is a lymphoid organ (part of the body's immune system) which makes antibodies against infections in the digestive system. Believing it to be a useless evolutionary 'left over,' many surgeons once removed even the healthy appendix whenever they were in the abdominal cavity. Today, removal of a healthy appendix under most circumstances would be considered medical malpractice" (David Menton, Ph.D., "The Human Tail, and Other Tales of Evolution," St. Louis MetroVoice , January 1994, Vol. 4, No. 1). "Doctors once thought tonsils were simply useless evolutionary leftovers and took them out thinking that it could do no harm. Today there is considerable evidence that there are more troubles in the upper respiratory tract after tonsil removal than before, and doctors generally agree that simple enlargement of tonsils is hardly an indication for surgery" (J.D. Ratcliff, Your Body and How it Works, 1975, p. 137). The tailbone, properly known as the coccyx, is another supposed example of a vestigial structure that has been found to have a valuable function—especially regarding the ability to sit comfortably. Many people who have had this bone removed have great difficulty sitting. http://www.ucg.org/science/god-science-and-bible-evolutions-vestigial-organ-argument-debunked/
And then of course when we get to society at large, the horror from Darwinian presuppositions is almost unimaginable:
How Darwin's Theory Changed the World - Rejection of Judeo-Christian values Excerpt: Weikart explains how accepting Darwinist dogma shifted society’s thinking on human life: “Before Darwinism burst onto the scene in the mid-nineteenth century, the idea of the sanctity of human life was dominant in European thought and law (though, as with all ethical principles, not always followed in practice). Judeo-Christian ethics proscribed the killing of innocent human life, and the Christian churches explicitly forbade murder, infanticide, abortion, and even suicide. “The sanctity of human life became enshrined in classical liberal human rights ideology as ‘the right to life,’ which according to John Locke and the United States Declaration of Independence, was one of the supreme rights of every individual” (p. 75). Only in the late nineteenth and especially the early twentieth century did significant debate erupt over issues relating to the sanctity of human life, especially infanticide, euthanasia, abortion, and suicide. It was no mere coincidence that these contentious issues emerged at the same time that Darwinism was gaining in influence. Darwinism played an important role in this debate, for it altered many people’s conceptions of the importance and value of human life, as well as the significance of death” (ibid.). http://www.gnmagazine.org/issues/gn85/darwin-theory-changed-world.htm the body count for abortion is now well over 50 million unborn babies in America since it was legalized, by judicial fiat not by public decree, in 1973 (legislation by liberal justices from the bench!): Abortion Statistics http://www.voiceofrevolution.com/2009/01/18/abortion-statistics/
And let's not forget the horror of the holocaust which, although Darwinists are in complete denial of this fact of history, Richard Weikart has done a excellent job in tying evolutionary reasoning directly to the 'scientific justification' behind the holocaust:
From Darwin To Hitler - Richard Weikart - video http://www.youtube.com/watch?v=w_5EwYpLD6A
Verse and Music:
John 10:10 The thief comes only to steal and kill and destroy; I have come that they may have life, and have it to the full. Avalon - I don't want to go - lyrics http://www.youtube.com/watch?v=QOEOX_Rxm8E
bornagain77_{February 3, 2014
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as to:
Does Evolutionary Theory Really Help Scientists?
NO!!! Materialists like to claim evolution is indispensable to experimental biology and led the way to many breakthroughs in medicine, Yet in a article entitled "Evolutionary theory contributes little to experimental biology", this expert author begs to differ.
"Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No.,,, In the peer-reviewed literature, the word "evolution" often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for "evolution" some other word – "Buddhism," "Aztec cosmology," or even "creationism." I found that the substitution never touched the paper's core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology." Philip S. Skell - (the late) Emeritus Evan Pugh Professor at Pennsylvania State University,
The Late Dr. Skell is hardly alone in this sentiment
"In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, and physiology, have not taken evolution into account at all." Marc Kirschner, Boston Globe, Oct. 23, 2005 "While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that “Nothing in biology makes sense except in the light of evolution”, most can conduct their work quite happily without particular reference to evolutionary ideas. Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superflous one.” A.S. Wilkins, editor of the journal BioEssays, Introduction to "Evolutionary Processes" - (2000). Does Biology Make Sense Without Darwin? - Dr. David Menton - video https://www.youtube.com/watch?v=K9znyGQo2QE Science Owes Nothing To Darwinian Evolution - Jonathan Wells - video http://www.metacafe.com/watch/4028096
Even the famed atheist Francis Crick, co-discoverer of the DNA helix, admitted as much:
"Biologists must constantly keep in mind that what they see was not designed, but rather evolved. It might be thought, therefore, that evolutionary arguments would play a large part in guiding biological research, but this is far from the case. It is difficult enough to study what is happening now. To figure out exactly what happened in evolution is even more difficult. Thus evolutionary achievements can be used as hints to suggest possible lines of research, but it is highly dangerous to trust them too much. It is all too easy to make mistaken inferences unless the process involved is already very well understood." Francis Crick - What Mad Pursuit (1988)
At the 7:00 minute mark of this following video, Dr. Behe gives an example of how evidence is falsely attributed to Darwinian processes by using the word 'evolution' as a sort of coda in peer-reviewed literature for how a system came about with never an actual demonstration by Darwinian processes of how the system actually came about:
Michael Behe - Life Reeks Of Design - video http://www.metacafe.com/watch/5066181/
In fact, in so far as Darwinian presuppositions have influenced scientific research they have had a overwhelming tendency to mislead researchers. Nowhere is this more evident than in the recent Junk DNA fiasco,,,
Matheson's Intron Fairy Tale - Richard Sternberg - June 2010 Excerpt: The failure to recognize the importance of introns "may well go down as one of the biggest mistakes in the history of molecular biology." --John Mattick, Molecular biologist, University of Queensland, quoted in Scientific American,,, http://www.evolutionnews.org/2010/06/mathesons_intron_fairy_tale035301.html On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. - Richard Sternberg - 2002 Excerpt: It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian “narratives” have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes. http://www.ncbi.nlm.nih.gov/pubmed/12547679 Is Panda's Thumb Suppressing the Truth about Junk DNA? Excerpt: Dr. Pellionisz sent me an e-mail regarding his recent experiences at Panda's Thumb. Pellionisz reports that Panda's Thumb is refusing to print his stories about how he has personally witnessed how the Darwinian consensus rejected suggestions that "junk" DNA had function. Dr. Pellionisz's e-mail recounts how some rogue Darwinian biologists have believed that "junk" DNA had function, but it also provides historical proof that this went against the prevailing consensus, and thus such suggestions that "junk"-DNA had function were ignored or rejected by most Darwinian scientists. http://www.evolutionnews.org/2007/07/is_pandas_thumb_supressing_the003947.html
And please bear in mind that even though the information in the DNA, that researchers have barely been able to decode thus far, is orders of magnitude more sophisticated than anything man has yet devised in his most advanced computers and computer programs,
ENCODE: Encyclopedia Of DNA Elements - video http://www.youtube.com/watch?v=Y3V2thsJ1Wc Quote from preceding video: "It's very hard to get over the density of information (in the genome),,, The data says its like a jungle of stuff out there. There are things we thought we understood and yet it is much, much, more complex. And then (there are) places of the genome we thought were completely silent and (yet) they're (now found to be) teeming with life, teeming with things going on. We still really don't understand that." Ewan Birney - senior scientist - ENCODE 2012
,,,and even with the leader of ENCODE 2012 declaring the metaphor of Junk DNA isn't that useful for research,,,
Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome" - Casey Luskin - September 5, 2012 Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well: "And what's in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project's Lead Analysis Coordinator and self-described "cat-herder-in-chief". He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. "It's likely that 80 percent will go to 100 percent," says Birney. "We don't really have any large chunks of redundant DNA. This metaphor of junk isn't that useful."" http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html
,,,in spite of all this unfathomed complexity in DNA, We still find hard core neo-Darwinists such as Coyne, Moran, Meyers, and even our own wd400 on UD, fighting tooth and nail for the concept of DNA. I would think the whole thing fiction if I had not witnessed them do it first hand!bornagain77_{February 3, 2014
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edit: Referring to observed homologies [as] evolutionary conservation is begging the question.JGuy_{February 3, 2014
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Except, of course, this myth that all non-coding DNA was once considered junk is absurd. From the very first mention of junk DNA regulatory sequences were considered functional, and functional RNAs have been known since the 1970s.
Then why the discovery lag?
On the other hand, this protein was identified in part due to it’s evolutionary conservation…
That isn't really on the other hand, because that is comparative anatomy - not evolution. Referring to observed homologies evolutionary conservation is begging the question.JGuy_{February 3, 2014
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wd400- Just how does unguided evolution explain regulatory networks? How does the blind watchmaker make sense non-coding sequences having a function? From a design standpoint that is easily explained due to our knowledge of cause and effect relationships. However if you are looking at living organisms from a materialistic PoV, then such layers of information would not be expected and impossible to explain, scientifically.Joe_{February 3, 2014
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Except, of course, this myth that all non-coding DNA was once considered junk is absurd. From the very first mention of junk DNA regulatory sequences were considered functional, and functional RNAs have been known since the 1970s. On the other hand, this protein was identified in part due to it's evolutionary conservation...wd400_{February 3, 2014
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