Yet More “Junk DNA” Not-so-Junk After All

_{Jonathan McLatchie

October 20, 2010

Intelligent Design}

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Proponents of intelligent design (ID) have long predicted that many of the features of living systems which are said to exhibit “sub-optimal” design will, in time, turn out to have a rationally engineered purpose. This is one of several areas where ID actively encourages a fruitful research agenda, in a manner in which neo-Darwinian evolution does not. One such area, and a field for which I have long held an inquisitive fascination for, is the subject of so-called “junk DNA,” and the non-coding stetches of RNA which are transcribed from them.

Skepticism of the “junk DNA” paradigm is not a phenomenon which is limited to proponents of ID. This popular view of the genome — while still resonating as the conventional view among neo-Darwinian thinkers — has also been challenged by John Mattick of the University of Queensland and Jim Shapiro of the University of Chicago.

Earlier this month, an article appeared in the journal Cell by a Spanish team. The article announced the discovery of the ability of long non-coding RNA, which are often encoded in DNA near genes known to be important to both stem cells and cancer, to serve as enhancer elements (which promote gene expression).

According to the paper’s Abstract: Read More>>>

Comments

Dr. Richard Sternberg had an interesting exchange with Dr. Falk, on what we should expect to find in DNA, at the Vibrant Dance of Faith and Science http://www.evolutionnews.org/2010/10/questions_and_answers_with_dar039791.html#morebornagain77_{October 28, 2010
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Lenoxus: 1) Why are “evolutionists” the ones finding functions for “junk” DNA? Given their deeply-entrenched, nigh-”religious” biases, how is it possible? What’s going on there? You make the usual ideologic characterization of science. Biologists are biologists. Some of them are very good, and they discover things. That has been going on, and will be going on. That does not mean that an ideological bias does not exists in the interpretation of data. Darwinism is an ideological bias. And a very detrimental one. But it cannot certainly stop research, thanks God. Its power over minds is not so absolute. But it is strong. 2) That’s the whole point IDists try to make here — that the “design paradigm” enables us to take a closer look at all aspects of life where the “chance paradigm” requires that we close our eyes and stop the science. My point is simply that the chance paradigm doesn’t seem to be doing a very good job of that! I don't agree with you. The "science stopping" theory is a darwinist theory about ID. Maybe some IDist, out of enthusiasm or spite, has retorted it against darwinism. But it's darwinists who have always tried to declare ID "non scientific", or a "science stopper". Indeed, I believe that neither darwinism nor ID can "stop" science. But a bad scientific theory, which has gained an undue support by the greater part of the scientific community, can certainly make understanding slower and more difficult. 3) I’m also still waiting for a design-minded researcher to (a) find a function and (b) show how the design model was a superior way of determining that particular function — beyond the nebulous “design says it should be mostly functional” and “If it’s designed, it’s worth looking into”. Whatever you may say, the "junk" model has had heavy consequences on research. That those consequences have not been able to stop good research does not mean they don't exist. On this same blog, eminent and good biologists like Arthur Hunt have just recently defended the junk paradigm. In a way, you yourself do the same, to some degree, in your posts here. So, it would be false to state that darwinism has not some "a priori fondness" for the junk paradigm. ID must not necessarily show better ways to "find a function". How to find a function should be well known to biology. ID is a higher level interpretation paradigm. It says that functions can well exists even if the current non design paradigm has no way to explain them. It says that functions are designed, connected, and expression of a plan. That is some difference, when you have to model data. 4) DNA is analyzed with such notions in mind as common descent and random mutations. This approach has worked very, very well. Meanwhile, ID tells us that mutations are nonrandom, yet, wait a minute, nearly all mutations are harmful, so therefore, we should see an efficient, mostly-junk-free genome that’s also littered with “deteriorating”, junky DNA. Common descent works very very well to explain what we observe. Random mutations, alone or with NS, absolutely don't. Please, don't conflate the two things. 5) ID also goes so far as to keep its mouth shut about common descent, like common descent is no big deal, when that’s a huge factor in both our understanding of genomes and our ability to increase that understanding. Behe has not "kept his mouth shut" about CD. I have defended CD many times on this blog. There is nothing in ID theory which is against CD. CD is a big deal. But the origin of biological information is certainly a bigger deal. There is some connection between the two things, but not a strict one. I know that some ID proponents do not believe in CD (maybe Debbski is one of them). But that has nothing to do with the ID theory. Many IDists do believe in CD. I am one of them. Anyway, there is no difference in basic ID theory, whatever your position on CD may be. CD does become a reason for differences, however, when, after having accepted the ID inference, we try to build models of how the designer works. I have discussed that point many times here. 6) So it is with “neo-Darwinism” and the various animal genomes. Thus far, the genomes appear to include many pseudogenes (for example), which are sort of an equivalent to planets that may have once harbored life but probably no longer do (such as Mars). The basic hypothesis that evolutionary processes produce psuedogenes has held up quite well, leaving IDists with nothing but a vague appeal to their own future vindication. The point is that we in ID are generally convinced that most of non coding DNA will be shown to be functional. That seems not the position of many darwinists, including Hunt. We will see. "Future" vindications may already be happening :) 7) Related to that astronomy example, I can think of one huge area that this very blog-site has repeatedly discouraged research into: The actual means by which life first came into existence. We are repeatedly told that it is going to be a mystery forevermore until scientists bite the bullet and accept that natural laws alone could never have caused it — a fancy way of saying that the appearance of life was a semi-miraculous event, one which, somewhere along the line, simply cannot be “broken down” into smaller steps. Non-life + “design” = life. Again I cannot agree with what you say. It's strange how you tend to put darwinist arguments in the mouth of IDists. Many darwinists (but not all of them) have repeatedly argued, even here, That OOL is beyond the understanding of science. That Darwin himself refused to consider it, and that we should do the same. That we will never be able to really explain it. That is a darwinist position, and a rather common one, anthough certainly not shared by anybody, even in the darwinist field. ID has all the reasons to believe that OOL can be explained scientifically. It will be explained exactly by the same model which can explain the evolution of species: natural laws plus an input of information from a designer. You say: "We are repeatedly told that it is going to be a mystery forevermore". But that's not true. It is not going to be a mystery at all. Who told that? And: "until scientists bite the bullet and accept that natural laws alone could never have caused it — a fancy way of saying that the appearance of life was a semi-miraculous event, one which, somewhere along the line, simply cannot be “broken down” into smaller steps. Non-life + “design” = life." What scientists have simply to acknowledge is that "natural laws alone" can never explain designed things. Including human designed things. Do you consider human design a "semi-miraculous" thing? I can be happy of either a "yes" or a "no". Your choice. 8) Well, you should know that design has nothing everything to say about the nature and means of the designer. Not sure it could be made any clearer, really. I have stated many times here that the analysis of design (after desing has been acknowledged) has a lot to say about "the nature and means of the designer". I have discussed that in some detail here many times. The point in ID is different: a previous knowledge of "the nature and means of the designer" is not necessary to make the design inference. That's absolutely true. I hope you can see the difference.gpuccio_{October 28, 2010
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Maybe its the word 'zero', after chance, you got a problem with Doomsday? Well let's kick around a few numbers besides zero: The Universal Plausibility Metric (UPM) & Principle (UPP) - Abel - Dec. 2009 Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes.",,, c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108 c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96 c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85 c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70 http://www.tbiomed.com/content/6/1/27 The probabilities against life 'spontaneously' originating are simply overwhelming: In fact Dean Kenyon, who was a leading Origin Of Life researcher as well as a college textbook author on the subject, admitted after years of extensive research: "We have not the slightest chance for the chemical evolutionary origin of even the simplest of cells". Origin Of Life? - Probability Of Protein And The Information Of DNA - Dean Kenyon - video http://www.youtube.com/watch?v=9VhR2BHhxeo Signature in the Cell - Book Review - Ken Peterson Excerpt: the “simplest extant cell, Mycoplasma genitalium — a tiny bacterium that inhabits the human urinary tract — requires ‘only’ 482 proteins to perform its necessary functions…(562,000 bases of DNA…to assemble those proteins).” ,,, amino acids have to congregate in a definite specified sequence in order to make something that “works.” First of all they have to form a “peptide” bond and this seems to only happen about half the time in experiments. Thus, the probability of building a chain of 150 amino acids containing only peptide links is about one chance in 10 to the 45th power. In addition, another requirement for living things is that the amino acids must be the “left-handed” version. But in “abiotic amino-acid production” the right- and left-handed versions are equally created. Thus, to have only left-handed, only peptide bonds between amino acids in a chain of 150 would be about one chance in 10 to the 90th. Moreover, in order to create a functioning protein the “amino acids, like letters in a meaningful sentence, must link up in functionally specified sequential arrangements.” It turns out that the probability for this is about one in 10 to the 74th. Thus, the probability of one functional protein of 150 amino acids forming by random chance is (1 in) 10 to the 164th. If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power. http://www.spectrummagazine.org/reviews/book_reviews/2009/10/06/signature_cell In fact years ago Fred Hoyle arrived at approximately the same number, one chance in 10^40,000, for life spontaneously arising. From this number, Fred Hoyle compared the random emergence of the simplest bacterium on earth to the likelihood “a tornado sweeping through a junkyard might assemble a Boeing 747 therein”. Fred Hoyle also compared the chance of obtaining just one single functioning protein molecule, by chance combination of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously. Professor Harold Morowitz shows the Origin of Life 'problem' escalates dramatically over the 1 in 10^40,000 figure when working from a thermodynamic perspective,: "The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!" (Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University) Dr. Don Johnson lays out some of the probabilities for life in this following video: Probabilities Of Life - Don Johnson PhD. - 38 minute mark of video a typical functional protein - 1 part in 10^175 the required enzymes for life - 1 part in 10^40,000 a living self replicating cell - 1 part in 10^340,000,000 http://www.vimeo.com/11706014 Dr. Morowitz did another probability calculation working from the thermodynamic perspective with a already existing cell and came up with this number: DID LIFE START BY CHANCE? Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias) http://members.tripod.com/~Black_J/chance.html The following videos give a small glimpse into how probabilities are calculated for the origin of life: The Origin of Life - Lecture On Probability - John Walton - Professor Of Chemistry - short video http://www.metacafe.com/watch/4012749 Intelligent Design: Required by Biological Life? K.D. Kalinsky - Pg. 11 Excerpt: It is estimated that the simplest life form would require at least 382 protein-coding genes. Using our estimate in Case Four of 700 bits of functional information required for the average protein, we obtain an estimate of about 267,000 bits for the simplest life form. Again, this is well above Inat and it is about 10^80,000 times more likely that ID (Intelligent Design) could produce the minimal genome than mindless natural processes. http://www.newscholars.com/papers/ID%20Web%20Article.pdf Could Chance Arrange the Code for (Just) One Gene? "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)." http://www.creationsafaris.com/epoi_c10.htm Even the low end 'hypothetical' probability estimate given by evolutionist, for life spontaneously arising, is fantastically impossible: General and Special Evidence for Intelligent Design in Biology: - The requirements for the emergence of a primitive, coupled replication-translation system, which is considered a candidate for the breakthrough stage in this paper, are much greater. At a minimum, spontaneous formation of: - two rRNAs with a total size of at least 1000 nucleotides - ~10 primitive adaptors of ~30 nucleotides each, in total, ~300 nucleotides - at least one RNA encoding a replicase, ~500 nucleotides (low bound) is required. In the above notation, n = 1800, resulting in E <10-1018. That is, the chance of life occurring by natural processes is 1 in 10 followed by 1018 zeros. (Koonin's intent was to show that short of postulating a multiverse of an infinite number of universes (Many Worlds), the chance of life occurring on earth is vanishingly small.) http://www.conservapedia.com/General_and_Special_Evidence_for_Intelligent_Design_in_Biology Evolutionist Koonin's estimate of 1 in 10 followed by 1018 zeros, for the probability of the simplest self-replicating molecule 'randomly occurring', is a fantastically large number. The number, 10^1018, if written out in its entirety, would be a 1 with one-thousand-eighteen zeros following to the right! The universe itself is estimated to have only 1 with 80 zeros following to the right particles in it. This is clearly well beyond the 10^150 universal probability bound set by William Dembski and is thus clearly a irreducibly complex condition. Why do evolutionists not heed their very own 'overly optimistic' numbers for the plausibility of the Origin Of Life? It seems more than reasonable to me that leading researchers, and scientists, should at least be honest to what their very own conclusions are telling them about the Origin Of Life. Yet rather than concede the need for Intelligent Design to explain the Origin of Life, Koonin, when faced by by the sheer magnitude of his own numbers, makes a 'desperate', though very imaginative, appeal to the never before witnessed quantum mechanism of Many Worlds. Basically Koonin, in appealing to never before observed quantum mechanisms, clearly illustrates that the materialistic argument essentially appears to be like this: Premise One: No materialistic cause of specified complex information is known. Conclusion: Therefore, it must arise from some unknown materialistic cause. On the other hand, Stephen Meyer describes the intelligent design argument as follows: “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information. “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information. “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.” There remains one and only one type of cause that has shown itself able to create functional information like we find in cells, books and software programs -- intelligent design. We know this from our uniform experience and from the design filter -- a mathematically rigorous method of detecting design. Both yield the same answer. (William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 90 (InterVarsity Press, 2010).)bornagain77_{October 24, 2010
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excuse me Doomsday here are your two highlighted passages:
'It is generally accepted that the present order reflects structures acquired during a long evolution.'
Well I'm sorry I don't 'generally' accept that present order,,, perhaps you would like to cite some evidence, any evidence, for 'vertical evolution' of a gain in functional information above what is already present in a parent species??? your other highlighted quote from the abstract does your futile atheistic position no better:
'In the first place one has systems that have evolved spontaneously to extremely organized and complex forms.'
Doomsday do please cite the peer reviewed evidence for anything whatsoever 'spontaneously evolving' :) That particular quote you highlighted Reminds me of the man who was miraculously healed of advanced cancer, and the doctor's prognosis to the man was that the advanced cancer went into 'spontaneous remission'. i.e. exactly how is his explanation for the OOL any different from the miraculous Doomsday??? The quotes you highlighted are exactly why I can clearly see that the abstract is actually laying the groundwork for hypothesizing some 'law-like' explanation for the origin of life that 'overcomes the 'chance hypothesis'!!! i.e. Perhaps doomsday you want to buck what is 'universally accepted' and reinvigorate the 'chance hypothesis'???? Look forward to your peer-review :)bornagain77_{October 24, 2010
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Sorry: your -> you're in the last sentence above.Doomsday Smith_{October 24, 2010
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Not up to me, BA: you're the one citing it as support for your position. I've already shown you that the citation was mangled and doesn't accord with the abstract. What Meyer has to say is irrelevant, because we're not talking about Meyer. We're talking about your cut-and-paste use of a dubious "quotation". I.e., your changing the subject.Doomsday Smith_{October 24, 2010
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actually doomsday, since Stephen Meyer himself goes through great detail to show how and why the 'chance hypothesis' has been abandoned in 'Signature In The Cell',,, http://www.signatureinthecell.com/ Ayala begins his review by attempting to trivialize the argument of Signature in the Cell. But he does so by misrepresenting its thesis. According to Ayala, “The keystone argument of Signature of the Cell [sic] is that chance, by itself, cannot account for the genetic information found in the genomes of organisms.” He notes—as I do in the book—that all evolutionary biologists already accept that conclusion. He asks: “Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point?” But, of course, the book does not spend hundreds of pages arguing that point. In fact, it spends only 55 pages out of 613 explaining why origin-of-life researchers have—since the 1960s—almost universally come to reject the chance hypothesis. It does so, not because the central purpose of the book is to refute the chance hypothesis per se, but for several other reasons intrinsic to the actual thesis of the book. ,,,, Doomsday, Perhaps you would care to buy the article and prove that the authors was not in fact offering devastating critique of the 'chance hypothesis'. Until then doomsday I feel quite comfortable using the quote, in context, with the duly noted correction in spelling of authors (Ilya Prigogine, Gregoire Nicolis, and Agnes Babloyantz,) Doomsday Do you now perhaps want to talk about the other failed hypothesis for origin of life (RNA world?? etc..), that also fail to recognize the primal physical entity of information, separate from matter and energy, that is absolutely crucial for any successful origin of life scenario to incorporate??? Or will you whistle in the dark drawing false satisfaction from my error in properly attributing authors?bornagain77_{October 24, 2010
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ba^77@24: Ok, first off, you don't know the quote is correct because you're not using the actual paper, are you? Second: The citation is most definitely incorrect. The actual authors are not "I. Prigogine, N. Gregair, A. Babbyabtz" but rather Ilya Prigogine, Gregoire Nicolis, and Agnes Babloyantz, which you'd know had you bothered to actually check into this for yourself more than superficially. You can find the original abstract here: Thermodynamics of Evolution It says (bolding mine):
The physicochemical basis of biological order is a puzzling problem that has occupied whole generations of biologists and physicists and has given rise, in the it, to passionate discussions. Biological systems are highly complex and ordered objects. It is generally accepted that the present order reflects structures acquired during a long evolution. Moreover, the maintenance of order in actual living systems requires a great number of metabolic and synthetic reactions as well as the existence of complex mechanisms controlling the rate and the timing of the various processes. All these features bring the scientist a wealth of new problems. In the first place one has systems that have evolved spontaneously to extremely organized and complex forms. On the other hand metabolism, synthesis and regulation imply a highly heterogeneous distribution of matter inside the cell through chemical reactions and active transport. Coherent behavior is really the characteristic feature of biological systems.
Which doesn't exactly support the use to which you and other have put that "quotation". I put that in quotes because it's highly doubtful, given the overall mangling of the citation and the content of the abstract, that the alleged "quote" from the paper proper has fared any better. Feel free to pay for and read the actual article, however, and prove it's accurate and also accurately represents the authors' views. Third: Wikiquote ain't Wikipedia. People don't pay nearly as much attention to stuff there as they do on Wikipedia proper, so it's rather easy to just paste stuff in so long as it looks properly source (which, just to remind you, this is not). So, yeah...Doomsday Smith_{October 24, 2010
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peepul, even wikipedia, no friend of ID, lists the quote as 'sourced': http://en.wikiquote.org/wiki/Western_Thought_on_Creationbornagain77_{October 24, 2010
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peepul, I think you better update your references, This quote is correct: “The statistical probability that organic structures and the most precisely harmonized reactions that typify living organisms would be generated by accident, is zero.” ~ Ilya Prigogine (Chemist-Physicist) Recipient of 1977 Nobel Prize in chemistry I. Prigogine, N. Gregair, A. Babbyabtz, Physics Today 25, pp. 23-28 http://books.google.com/books?id=wXGyV0vdDoUC&pg=PA258&lpg=PA258&dq=%E2%80%9CThe+statistical+probability+that+organic+structures+and+the+most+precisely+harmonized+reactions+that+typify+living+organisms+would+be+generated+by+accident,+is+zero.%E2%80%9D&source=bl&ots=BDC_TpV4dM&sig=RnKwtueMg5qHFXhqXTpo12y5mNI&hl=en&ei=YyXETN79I8iKnQfI74HkCQ&sa=X&oi=book_result&ct=result&resnum=7&ved=0CCoQ6AEwBg#v=onepage&q=%E2%80%9CThe%20statistical%20probability%20that%20organic%20structures%20and%20the%20most%20precisely%20harmonized%20reactions%20that%20typify%20living%20organisms%20would%20be%20generated%20by%20accident%2C%20is%20zero.%E2%80%9D&f=falsebornagain77_{October 24, 2010
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But peepul, what is really indicative of Darwinists detachment from reality is the the whole 'Junk DNA' trial and error argument is falsified since it is now shown the DNA does not even control body plan morphogenesis in the first place: Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video http://www.metacafe.com/watch/4187488 This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show 'exceedingly rare' beneficial morphological changes from mutations to the DNA code. The Origin of Biological Information and the Higher Taxonomic Categories - Stephen Meyer"Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion." http://eyedesignbook.com/ch6/eyech6-append-d.html Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 This following video is a bit more clear for explaining exactly why mutations to the DNA do not control Body Plan morphogenesis, since the mutations are the ‘bottom rung of the ladder’ as far as the 'higher levels of the layered information’ of the cell are concerned: Stephen Meyer on Craig Venter, Complexity Of The Cell & Layered Information http://www.metacafe.com/watch/4798685 It is also interesting to point out that the materialistic philosophy has an extremely difficult time assigning any proper value to humans in the first place: How much is my body worth? Excerpt: The U.S. Bureau of Chemistry and Soils invested many a hard-earned tax dollar in calculating the chemical and mineral composition of the human body,,,,Together, all of the above (chemicals and minerals) amounts to less than one dollar! http://www.coolquiz.com/trivia/explain/docs/worth.aspbornagain77_{October 24, 2010
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peepul: When we first approach life we are struck by its immense complexity, Fearfully and Wonderfully Made - Glimpses At Human Development In The Womb - video http://www.metacafe.com/watch/4249713 The Human Body - You Are Amazing - video http://www.metacafe.com/watch/5246456 ,,,thus the natural prior presupposition that we should have upon our investigation of life should be that pretty much all DNA should have some function. Yet evolution does not respect this common sense presupposition. In fact evolution demands that much of what we find in life is junk since evolution presupposes that the 'trial and error' of Darwinism created life on earth instead of God. In fact the now refuted vestigial organ argument is a classic example of this natural 'trial and error' outflow from evolutionary thinking that has poisoned science: Among the most blatant failed predictions of materialists is this one. For many years materialists predicted much of human anatomy was vestigial (useless and leftover evolutionary baggage). Yet once again, they were proven completely wrong in this prediction. “The thyroid gland, pituitary gland, thymus, pineal gland, and coccyx, … once considered useless by evolutionists, are now known to have important functions. The list of 180 “vestigial” structures is practically down to zero. Unfortunately, earlier Darwinists assumed that if they were ignorant of an organ’s function, then it had no function.” "Tornado in a Junkyard" - book - by former atheist James Perloff ,,,and just like the vestigial organ argument Junk DNA is a-priori forced upon the evidence because it is a required prediction for the evidence we should find for Darwinism to be true: 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 Yet despite this 'unnatural' presupposition of Darwinism for Junk DNA, evidence is gathering at a fairly rapid clip, for the 'high level" functionality of 'Junk DNA': All Proposed Elements Of Junk DNA Are Now Found To Show Signs Of Containing High Level Function - List Of Over 100 Studies http://docs.google.com/View?id=dc8z67wz_25gqm4zzfd Some materialists have tried to get around the failed prediction of Junk DNA by saying evolution never really predicted Junk DNA. This following site list several studies and quotes by leading evolutionists that expose their falsehood in denying the functionless Junk DNA predictions that were made by leading evolutionists: Functionless Junk DNA Predictions By Leading Evolutionists http://docs.google.com/View?id=dc8z67wz_24c5f7czgm Yet despite the belittling of life that evolutionists have a-priori forced upon the evidence prior to the thorough investigation of life, the fact is we are,,, Fearfully and Wonderfully Made - video http://www.metacafe.com/watch/5289335/ Believe it or not, I've even debated evolutionists who insist the human eye is 'poorly designed', as if they had any hope at all of designing a better eye, and despite humans can't even produce a single novel functional protein much less trillions of integrated proteins working in precise concert: Evolution Vs. The Miracle Of The Eye - Molecular Animation - video http://www.metacafe.com/watch/4189562 Evolution vs The Eye - Miracle Or Mistake? - article http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMThmd25mdjRocQbornagain77_{October 24, 2010
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Bornagain I searched for this reference you gave:- Prigogine, N. Gregair, A. Babbyabtz, Physics Today 25, pp. 23-28. This is not a valid reference.Peepul_{October 24, 2010
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Bornagain you said :- 'So lenoxus, let’s be a little more direct in our questions, “Exactly what is the scientific reason we should presuppose non-coding DNA to be junk if it is only postulated to protect the neo-Darwinian framework in the first place?”' It is not postulated for that reason. It's strange that you think it is. What evidence are you relying on in making that statement?Peepul_{October 24, 2010
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Lenoxus you then state: 'Related to that astronomy example, I can think of one huge area that this very blog-site has repeatedly discouraged research into: The actual means by which life first came into existence.' No actually Lenoxus science is in the business of removing wishful speculations and superstitions. If you want to believe that complexity in the simplest cells we can find, which far exceeds what man can produce in his most advanced machines, can just 'naturally pop out of the mud somewhere' in dramatic violation of the second law, and despite a thorough search to find any plausible mechanism that can generate information. That is a 'natural' mechanism that does not involve Intelligence, that is your prerogative. But do not call it being 'scientific' when you are in fact ignoring what the science has consistently been telling you about the generation of information! By the way, there is a one million dollar 'Origin-of-Life' prize being offered: "The Origin-of-Life Prize" ® (hereafter called "the Prize") will be awarded for proposing a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. http://www.us.net/life/index.htm Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information - David L. Abel and Jack T. Trevors - Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf Ilya Prigogine was an eminent chemist and physicist who received two Nobel Prizes in chemistry. Regarding the probability of life originating by accident, he said: “The statistical probability that organic structures and the most precisely harmonized reactions that typify living organisms would be generated by accident, is zero.” Prigogine, N. Gregair, A. Babbyabtz, Physics Today 25, pp. 23-28. http://www.miraclesormagic.com/intelligent-design-vs-evolution.html “The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information.” Origin of life theorist Bernd-Olaf Kuppers in his book "Information and the Origin of Life". "Information is information, not matter or energy. No materialism which does not admit this can survive at the present day." Norbert Weiner - MIT Mathematician - Father of Cyberneticsbornagain77_{October 23, 2010
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lenoxus, Unless God created life on other planets the 'astronomical probability is that is does not exist! Probability For Life On Earth - List of Parameters, References, and Math - Hugh Ross http://www.reasons.org/probability-life-earth-apr-2004 http://www.meaningfulscience.com/FineTuningForLifeOnEarthHughRoss.pdf Dr. Don Johnson lays out some of the probabilities for life in this following video: Probabilities Of Life - Don Johnson PhD. - 38 minute mark of video a typical functional protein - 1 part in 10^175 the required enzymes for life - 1 part in 10^40,000 a living self replicating cell - 1 part in 10^340,000,000 http://www.vimeo.com/11706014 Thus unless you add the qualifier of God possibly creating life elsewhere in the universe, there is at least one astrophysicist who does not believe life naturally arose elsewhere in the universe! Lenoxus you state: 'The basic hypothesis that evolutionary processes produce psuedogenes has held up quite well, leaving IDists with nothing but a vague appeal to their own future vindication.' yet despite your claim: How The Junk DNA Hypothesis Has Changed Since 1980 - Richard Sternberg - Oct. 2009 - Excellent Summary Excerpt: A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way. http://www.evolutionnews.org/2009/10/how_the_junk_dna_hypothesis_ha.html Excerpt Of Conclusion: When examined in detail, the full pseudogene dataset we collected does not lend itself to a reasonable neo-Darwinian interpretation. http://creation.com/images/pdfs/tj/j21_3/j21_3_118-127.pdf Another Day, Another Bad Day For Darwinism - June 2010 - Pseudogenes Excerpt: These findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs. https://uncommondescent.com/intelligent-design/another-day-another-bad-day-for-darwinism/ "Junk DNA" Takes Yet More Heavy Blows - June 2010 Excerpt: PTENP1 is (thought to be) a pseudogene: a non-synonymous mutation at the beginning of what would otherwise be the coding region of its transcript prevents its translation. But Poliseno et al. reveal that PTENP1 -- along with KRAS1P, the pseudogene of the gene KRAS, and potentially other pseudogenes -- is not a non-functional relic, but a modulator of gene expression. http://www.evolutionnews.org/2010/06/the_myth_of_junk_dna_continues036031.html Pier Paolo Pandolfi of BIDMC explained, “This means that not only have we discovered a new language for mRNA, but we have also translated the previously unknown language of up to 17,000 pseudogenes and at least 10,000 long non-coding (lnc) RNAs. Consequently, we now know the function of an estimated 30,000 new entities, offering a novel dimension by which cellular and tumor biology can be regulated, and effectively doubling the size of the functional genome.” https://uncommondescent.com/intelligent-design/another-day-another-bad-day-for-darwinism/#comment-357675 The RNA Code: Pseudogenes Functional, Help Prevent Cancer Excerpt: The old paradigm about pseudogenes appears poised for demolition. The old story was that these were relic copies of good genes that, over time, started mutating away because natural selection no longer acted on them. The new story is that they are essential players in a complex interplay with coding genes and other genetic regulators that control when, where, and how much genes get expressed into proteins. Science Daily recounted the old Central Dogma of genetics (DNA is the master controller of proteins), but said the new study “suggests there is much more to RNA than meets the eye.” Pseudogene Decoy Reveals Hidden Evidence for Design Excerpt: It looks as if pseudogenes are functional elements in the genome that have been merely impersonating junk DNA all along http://www.reasons.org/pseudogene-decoy-reveals-hidden-evidence-designbornagain77_{October 23, 2010
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lenoxus, Unless God created life on other planets the 'astronomical probability is that is does not exist! Probability For Life On Earth - List of Parameters, References, and Math - Hugh Ross http://www.reasons.org/probability-life-earth-apr-2004 http://www.meaningfulscience.com/FineTuningForLifeOnEarthHughRoss.pdf Dr. Don Johnson lays out some of the probabilities for life in this following video: Probabilities Of Life - Don Johnson PhD. - 38 minute mark of video a typical functional protein - 1 part in 10^175 the required enzymes for life - 1 part in 10^40,000 a living self replicating cell - 1 part in 10^340,000,000 http://www.vimeo.com/11706014 Thus unless you add the qualifier of God possibly creating life elsewhere in the universe, there is at least one astrophysicist who does not believe life naturally arose elsewhere in the universe! Lenoxus you state: 'The basic hypothesis that evolutionary processes produce psuedogenes has held up quite well, leaving IDists with nothing but a vague appeal to their own future vindication.' yet despite your claim: How The Junk DNA Hypothesis Has Changed Since 1980 - Richard Sternberg - Oct. 2009 - Excellent Summary Excerpt: A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way. http://www.evolutionnews.org/2009/10/how_the_junk_dna_hypothesis_ha.html Excerpt Of Conclusion: When examined in detail, the full pseudogene dataset we collected does not lend itself to a reasonable neo-Darwinian interpretation. http://creation.com/images/pdfs/tj/j21_3/j21_3_118-127.pdf Another Day, Another Bad Day For Darwinism - June 2010 - Pseudogenes Excerpt: These findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs. https://uncommondescent.com/intelligent-design/another-day-another-bad-day-for-darwinism/ "Junk DNA" Takes Yet More Heavy Blows - June 2010 Excerpt: PTENP1 is (thought to be) a pseudogene: a non-synonymous mutation at the beginning of what would otherwise be the coding region of its transcript prevents its translation. But Poliseno et al. reveal that PTENP1 -- along with KRAS1P, the pseudogene of the gene KRAS, and potentially other pseudogenes -- is not a non-functional relic, but a modulator of gene expression. http://www.evolutionnews.org/2010/06/the_myth_of_junk_dna_continues036031.html Pier Paolo Pandolfi of BIDMC explained, “This means that not only have we discovered a new language for mRNA, but we have also translated the previously unknown language of up to 17,000 pseudogenes and at least 10,000 long non-coding (lnc) RNAs. Consequently, we now know the function of an estimated 30,000 new entities, offering a novel dimension by which cellular and tumor biology can be regulated, and effectively doubling the size of the functional genome.” https://uncommondescent.com/intelligent-design/another-day-another-bad-day-for-darwinism/#comment-357675 The RNA Code: Pseudogenes Functional, Help Prevent Cancer Excerpt: The old paradigm about pseudogenes appears poised for demolition. The old story was that these were relic copies of good genes that, over time, started mutating away because natural selection no longer acted on them. The new story is that they are essential players in a complex interplay with coding genes and other genetic regulators that control when, where, and how much genes get expressed into proteins. Science Daily recounted the old Central Dogma of genetics (DNA is the master controller of proteins), but said the new study “suggests there is much more to RNA than meets the eye.” http://www.creationsafaris.com/crev201006.htm#20100624a Pseudogene Decoy Reveals Hidden Evidence for Design Excerpt: It looks as if pseudogenes are functional elements in the genome that have been merely impersonating junk DNA all along http://www.reasons.org/pseudogene-decoy-reveals-hidden-evidence-designbornagain77_{October 23, 2010
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Modern astronomy predicts that the majority of the Universe's planets are lifeless. That hasn't lead even a single astronomer to say "Ergo, all planets which we do not know to have life don't have life." The motivation to seek signs of life on another world doesn't require a prior assumption that life is there to be found, only that it might be. So it is with "neo-Darwinism" and the various animal genomes. Thus far, the genomes appear to include many pseudogenes (for example), which are sort of an equivalent to planets that may have once harbored life but probably no longer do (such as Mars). The basic hypothesis that evolutionary processes produce psuedogenes has held up quite well, leaving IDists with nothing but a vague appeal to their own future vindication. Related to that astronomy example, I can think of one huge area that this very blog-site has repeatedly discouraged research into: The actual means by which life first came into existence. We are repeatedly told that it is going to be a mystery forevermore until scientists bite the bullet and accept that natural laws alone could never have caused it — a fancy way of saying that the appearance of life was a semi-miraculous event, one which, somewhere along the line, simply cannot be "broken down" into smaller steps. Non-life + "design" = life. Peepul @ 13:
It’s not obvious to me that the existence of a designer per se allows us to conclude ANYTHING about the design artefacts it might produce.
Well, you should know that design has nothing everything to say about the nature and means of the designer. Not sure it could be made any clearer, really. ;)Lenoxus_{October 23, 2010
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I'd like to understand why ID predicts that junk has a function, and how much of it has a function. Essentially, I mean, what properties of a designer are being asserted here, and why? It's not obvious to me that the existence of a designer per se allows us to conclude ANYTHING about the design artefacts it might produce.Peepul_{October 23, 2010
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Lenoxus: Why are “evolutionists” the ones finding functions for “junk” DNA? I would like to turn it around: What role did Darwin's theory of evolution have in this discovery? What aspects of the neo-Darwinian synthesis encouraged research into this issue?Alex73_{October 22, 2010
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My main point is simply that the original ID point about scientists-dismissing-stuff-as-junk is overstated… given that "evolutionists" are, in fact, discovering functions. They simply shouldn't be doing that if they had ironclad biases that all DNA without a currently known function is ipso facto "junk". I'm also still waiting for a design-minded researcher to (a) find a function and (b) show how the design model was a superior way of determining that particular function — beyond the nebulous "design says it should be mostly functional" and "If it's designed, it's worth looking into". DNA is analyzed with such notions in mind as common descent and random mutations. This approach has worked very, very well. Meanwhile, ID tells us that mutations are nonrandom, yet, wait a minute, nearly all mutations are harmful, so therefore, we should see an efficient, mostly-junk-free genome that's also littered with "deteriorating", junky DNA. ID also goes so far as to keep its mouth shut about common descent, like common descent is no big deal, when that's a huge factor in both our understanding of genomes and our ability to increase that understanding.Lenoxus_{October 22, 2010
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Lenoxus:
Why are “evolutionists” the ones finding functions for “junk” DNA?
They are scientists first- well they should be anyway. And yes scientists should be looking very closely at genomes to try to figure out what is really going on. That is a biologists job- to figure out biology.Joseph_{October 22, 2010
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Is it junk? How do you know?
That's the term that's commonly used (and note the scare quotes I put around "junk"). It's worth remembering, BTW, that the "junk = useless" theory never any weight in the genetics community. I studied genetics in the pre-genomics era, and even then undergrads were being taught that some "junk" DNA had function - even if we didn't know what it was. It appears I'm not banned, so I'll ask the question that was deleted - what function does ID predict for "junk" (look! Scare quotes again!) DNA like Alu sequences? And what evidence does it then have for this function?Heinrich_{October 22, 2010
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Lenoxus in 8: ""Why are “evolutionists” the ones finding functions for “junk” DNA? Given their deeply-entrenched, nigh-”religious” biases, how is it possible? What’s going on there?" It has to do with probabilistic resources that evolutionists have at their disposal because of their relatively large amount of resources i.e time, people, money etc. Lets say that ID theorists chance of finding function is 10x per resource spent as she is actively looking for it. However the amount resources evolutionists have is 10000000x times the ID theorists resources thus it follows that most if not all functionality is found by the evolutionists. This should be obvious though, yes?Innerbling_{October 21, 2010
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I'll just restate my question, which had nothing to do with any assertion that "junk" does, doesn't, should, or shouldn't exist. My question is this: Why are "evolutionists" the ones finding functions for "junk" DNA? Given their deeply-entrenched, nigh-"religious" biases, how is it possible? What's going on there? As you would spin it, biologists are surprising themselves regarding DNA. If the ID line on the subject were true, they wouldn't be surprising themelves — they would be refusing to study the subject in the first place, because they Already Know It's All Useless, or so goes the ID interpretation. That's the whole point IDists try to make here — that the "design paradigm" enables us to take a closer look at all aspects of life where the "chance paradigm" requires that we close our eyes and stop the science. My point is simply that the chance paradigm doesn't seem to be doing a very good job of that!Lenoxus_{October 21, 2010
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Of interest to 'Junk DNA": Revolution Postponed: Why the Human Genome Project Has Been Disappointing Excerpt: Put simply, the very definition of a gene—not to mention a medically significant gene—is now vexed by multiple layers of complexity. What was once assumed to be a straightforward, one-way, point-to-point relation between genes and traits has now become the “genotype-phenotype problem,” where knowing the protein-coding sequence of DNA tells only part of how a trait comes to be. In animal experiments, Joseph H. Nadeau, director of scientific development at the Institute for Systems Biology in Seattle, has tracked more than 100 biochemical, physiological and behavioral traits that are affected by epigenetic changes and has seen some of these changes passed down through four generations. “It’s totally Lamarckian!” he laughs, referring to the 18th-century biologist Jean-Baptiste Lamarck’s idea that acquired traits could be inherited. As if that level of complexity were not enough, Nadeau has experimental evidence that the function of one particular gene sometimes depends on the specific constellation of genetic variants surrounding it—an ensemble effect that introduces a contextual, postmodern wrinkle to genetic explanations of disease. It suggests, Nadeau says, that some common illnesses may ultimately be traceable to a very large number of genes in a network or pathway whose effects may each vary depending on the gene variants a person has; the presence of one gene variant, say, can exacerbate or counteract the effect of another disease-related gene in the group. “My guess is that this unconventional kind of inheritance is going to be more common than we would have expected,” Nadeau says. http://www.scientificamerican.com/article.cfm?id=revolution-postponed&page=6 Entire article: http://www.scientificamerican.com/article.cfm?id=revolution-postponedbornagain77_{October 21, 2010
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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 So lenoxus, let's be a little more direct in our questions, "Exactly what is the scientific reason we should presuppose non-coding DNA to be junk if it is only postulated to protect the neo-Darwinian framework in the first place?" Amazingly, many leading evolutionists (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'. This irrational stance by them has severely hindered scientific progress: On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system: - Sternberg R. 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 Human Genome “Infinitely More Complex” Than Expected - April 2010 Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said, speaking of the gene regulation was a straightforward, linear process of gene coding for regulator protein that controls transcription. “Biology’s new glimpse at a universe of non-coding DNA – what used to be called ‘junk’ DNA – has been fascinating and befuddling.” If it’s junk, why would the human body decode 74% to 93% of it? The plethora of small RNAs produced by these non-coding regions, and how they interact with each other and with DNA, was completely unexpected when the project began.,,, In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the ‘virtual human’. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model.,,, The p53 network she spoke of is a good example of unexpected complexity. Discovered in 1979, the p53 protein was first thought to be a cancer promoter, then a cancer suppressor. “Few proteins have been studied more than p53,” she said. “...Yet the p53 story has turned out to be immensely more complex than it seemed at first.” She gave some details: "Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein–protein interactions can be tuned by the addition of chemical modifiers, such as phosphates and methyl groups. Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems willfully ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network, as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions. Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.” http://www.creationsafaris.com/crev201004.htm#20100405abornagain77_{October 21, 2010
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Whoops, I talked like a pirate there and I can't take it back! (In two cases, I removed the word "would" from "It would be…", but forgot to change the "be" to "is".) Arrrgh.Lenoxus_{October 21, 2010
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This is one of several areas where ID actively encourages a fruitful research agenda, in a manner in which neo-Darwinian evolution does not.
It be fair to say that discoveries of function in "junk" DNA tend to be made by ID-based research groups, and not by evolutionary ones, yes? It be a safe bet that the authors of the paper are ID-ists, yes? Of course, those are "gotcha" questions; the answer to both is "no". But if that conventional ID line about "junk" is true, why would this be the case? Furthermore, does ID give any more than the "incentive" to seek function? Can it provide actual clues as to how to determine a gene's purpose (independently of evolution-minded methods that focus on common descent) for example?Lenoxus_{October 21, 2010
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Heinrich:
I posted a message asking how ID explained “junk” DNA sequences, like Alu, but it seems to have disappeared.
Is it junk? How do you know?Joseph_{October 21, 2010
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