Non-Coding RNA-Activators Regulate Genes Via a “Mediator”

_{Cornelius Hunter

March 4, 2013

Intelligent Design}

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Remember when it was discovered that most of our DNA does not code for proteins and evolutionists said it was probably junk? And remember when it was discovered that most of that non coding DNA is nonetheless transcribed and evolutionists said it was probably erroneous transcription? Well it turns out that this non coding DNA continues to surprise, as not only is it transcribed, but it reveals all kinds of function. For instance, as one recent reportexplained, thousands of long segments of non coding DNA have, err, “a crucial role in turning genes on and off.” Read more

Comments

lolingatallofyou:
HOW is this a victory for ID believers? HOW is it a loss for Darwinists?
By attracting people like you to our blog here so we can laugh at you as you make a fool of yourself.Mung_{March 5, 2013
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lolingatallofyou @9: Well, I'm sad to see that my fears were well founded. You are not here with a desire to actually learn, but to parade around trying to score cheap points. That, unfortunately, is not worth my time. Before leaving you, however, I will just point out that virtually everything you said in you response #9 is wrong or misleading. Briefly: - Much was made of junk DNA as evidence for blind undirected evolution and against design. It is perfectly reasonable to make much of the evidence in the opposite direction. And, contrary to your ridiculous implication, the fall of junk DNA is hardly the only thing going for ID. - Sure a few evolutionary biologists quietly mused that some portion of junk DNA might have function. But those were the exceptions that proved the rule. Junk DNA was though to be pervasive, was thought to prove evolution, was thought to disprove design, and was loudly proclaimed as such (indeed, is still recently being proclaimed as such). - Contrary to your baseless assertion, I have no religious or philosophical need for ID. I did not come to ID in support of any such belief, but because of the scientific evidence. Ironically, however, your attitude demonstrates that you are dismissive of ID to support your philosophical position. Break out the mirror sometime and be willing to take a hard look. - ENCODE is interesting, but is hardly the only evidence. And keep this in mind: By definition, essentially every new function discovered for DNA will reduce the amount of junk and increase the amount of functional DNA. You are playing the wrong side of the trend of evidence. But then, the materialist creation myth never really was about the evidence, was it? ----- If you are willing to take time to actually engage the issues, you will find that there are some very interesting issues relating to design. At that point I'm sure we would be willing to discuss in detail. But as long as you are here just to 'laugh out loud at all of us,' your presence is not particularly meaningful and will not be rewarded accordingly.Eric Anderson_{March 5, 2013
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supplemental note to post #11 Accounting for Variations – Dr. David Berlinski: – video http://www.youtube.com/watch?v=aW2GkDkimkEbornagain77_{March 5, 2013
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To the newest sock puppet- The article is a plus for ID and a minus for Darwinism because we actually observe agencies producing regulatory newtworks and have never observed blind and undirected chemical processes doing such a thing.Joe_{March 5, 2013
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newest sock puppet:
Bornagain77 states that 25 mutations must occur per year that confer a reproductive advantage.
No, he did NOT say that. Obvioulsy you have reading comprehension issues. The author said that 25 mutations must become fixed each year to account for the genetic differences observed between chimps and humans. However no one knows if any amount of genetic change can account for all of the physical differences that are observed.
In fact, there is one fusion that ALONE counts for an extra 150,000 nucleotides in the human genome.
You fuse two genes and gain 150,000 nucleotides? Reference please.Joe_{March 5, 2013
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lolingatallofyou, you seem to think as if the failed prediction of junk DNA by Darwinists was not much of a big deal, but as I pointed out in post #1:
It is good to remember that not only is the junk DNA argument from Darwinists a ‘religious argument’ as to how Darwinists think God should or should not act in this world, but also that the junk DNA argument from Darwinists was actually required in neo-Darwinism by the mathematics of population genetics https://uncommondescent.com/intelligent-design/non-coding-rna-activators-regulate-genes-via-a-mediator/#comment-448521
Thus, so what if some Darwinists had enough common sense not to buy the junk DNA argument? It was the math itself that predicted/required junk DNA for Darwinism not the personal opinion of any particular Darwinist. Moreover, rather than admitting that the mathematics of population genetics is correct, and that Darwinism is woefully inadequate as a scientific theory, this embarrassing turn of events has further highlighted the fact that Darwinism doesn't have any firm mathematical basis. i.e. Darwinists have no real mathematical basis within science to support Darwinism!
Oxford University Admits Darwinism's Shaky Math Foundation - May 2011 Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years. http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation.. http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf Macroevolution, microevolution and chemistry: the devil is in the details - Dr. V. J. Torley - February 27, 2013 Excerpt: Evolutionary biology has certainly been the subject of extensive mathematical theorizing. The overall name for this field is population genetics, or the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. Population genetics attempts to explain speciation within this framework. However, at the present time, there is no mathematical model – not even a “toy model” – showing that Darwin’s theory of macroevolution can even work, much less work within the time available. Darwinist mathematicians themselves have admitted as much.,,, We have seen that there’s currently no good theory that can serve as an adequate model for Darwinian macroevolution – even at a “holistic” level. As we saw, Professor Gregory Chaitin’s toy models don’t go down to the chemical level requested by Professor James Tour, but these models have failed to validate Darwin’s theory of evolution, or even show that it could work. At this point, there is an alternative line that (Nick) Matzke might want to take. He could claim that macroevolution is ultimately explicable in terms of bottom-level laws and physical processes, but that unfortunately, scientists haven’t discovered what they are yet. From a theoretical perspective, reductionism would then be true after all, and the chemical explanation of macroevolution demanded by Professor Tour could be given. From a practical standpoint, however, it would be impossible for scientists to provide such an explanation within the foreseeable future. If Matzke wishes to take this road, then he is tacitly admitting that scientists don’t yet know either the scientific laws (which are written in the language of mathematics) or the physical processes that ultimately explain and drive macroevolution. But if they don’t know either of these, then I would ask him: why should we believe that it actually occurs? After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated? https://uncommondescent.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/
Indeed lolingatallofyou, why does macroevolution belong in the province of science at all, if its scientific basis cannot be (Mathematically) demonstrated? Supplemental notes:
Dr. David Berlinski: Head Scratching Mathematicians - video http://www.youtube.com/watch?v=hEDYr_fgcP8 quote from preceding video: “John Von Neumann, one of the great mathematicians of the twentieth century, just laughed at Darwinian theory, he hooted at it!” Dr. David Berlinski The Unreasonable Effectiveness of Mathematics in the Natural Sciences - Eugene Wigner - 1960 Excerpt: ,,certainly it is hard to believe that our reasoning power was brought, by Darwin's process of natural selection, to the perfection which it seems to possess.,,, http://www.dartmouth.edu/~matc/MathDrama/reading/Wigner.html “Darwin’s theory is easily the dumbest idea ever taken seriously by science." Granville Sewell - Professor Of Mathematics - University Of Texas - El Paso Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory - 2008 Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue. Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person. http://www.icr.org/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdf
bornagain77_{March 5, 2013
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loling at #3, The "mistake" as you call it regarding junk DNA is not really a victory for ID, as much as it is a defeat of science and reason in the face of abundant evidence to the contrary. The significance of non-coding DNA was ludicrously under-assessed and then improperly sold to both peers and public. The fact, as you clearly state, that there were always a few who did not buy into the sales pitch, only serves to reinforce the point you are trying to dismiss. In your desire to be insulting, perhaps this failed to occur to you. And as for the small satisfaction that ID proponents sometimes display during the inevitable unraveling, you might want to remember that your "underestimation" was only the tip of the iceberg. You still need a mechanism, outside of Darwinian evolution, to establish the semiotic state that Darwinian evolution requires in order to exist. And you'll need that mechanism prior to information-based organization. We await your next round of concessions. :)Upright BiPed_{March 5, 2013
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Eric, The fact that you need to rally on little victories like "junk DNA isn't 100% junk! woo! we got one right!" speaks to the ridiculousness of ID in volumes. Further, there are plenty of evolutionists who never bought that junk DNA was 100% junk, it wasn't only ID people claiming that. I appreciate you giving me that answer because it does enlighten me somewhat on why someone thought it was okay to post this article here. While I respect that you all are trying to incorporate science into your belief in a higher power, you are clearly grasping at straws. I would also like to mention that the ENCODE project states that it is still unclear if up to 60% of this noncoding DNA has any function. I will not say that this DNA is junk DNA or that it is evidence for natural selection, but given that grossly large figure (more than half, anyone?) I still find it hard to believe that Designists can truly tout this as anything close to a victory...lolingatallofyou_{March 4, 2013
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lolingatallofyou: I don't know what your background is, but from your posts above it seems you may have jumped on here with a bit of a chip on your shoulder (your handle doesn't help the impression, incidentally). It may be worthwhile checking out a couple of the prior threads in which junk DNA was discussed in some detail before jumping to any conclusions. Nevertheless, on the assumption that your initial question was sincere and that you are actually interested in understanding the design perspective, I will provide a summary response. Briefly, both naturalistic evolution and design paradigms can accommodate some amount of true junk DNA. However, the alleged existence of pervasive amounts of junk DNA has been regularly touted by evolutionists as powerful evidence for blind undirected evolution and against design. In contrast, many in the design community have contested these claims for many years and have suggested that a much larger portion of DNA would be found to have function than was typically proclaimed. As new evidence rolls in it is therefore quite natural for design proponents to: (i) feel somewhat vindicated that the evidence for function is growing, and (ii) more importantly, call the bluff of those who have been loudly proclaiming junk DNA as evidence for blind evolution and against design.Eric Anderson_{March 4, 2013
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Box, Bornagain77 states that 25 mutations must occur per year that confer a reproductive advantage. While you are right that he never says they must occur in coding sequence, the statement that they must confer an advantage is false. As studied in the Chimpanzee Genome project (look it up) about 30% of all human genes are identical in sequence to those of chimpanzees. The rest differ on average by TWO amino acids. This = roughly 2, maybe 3 or 4 nucleotide differences per gene for 70% of genes. Like I said, not that much mutation in coding sequence. Also stated in the Chimpanzee Genome Project is the fact that most of the sequence difference between humans and chimps comes from gene deletions and duplications as I mentioned above. In fact, there is one fusion that ALONE counts for an extra 150,000 nucleotides in the human genome. Do your research, guys. I'm not sure who this P.J. Levi guy is, but if he is listened to by any significant amount of people, that is pretty bad. Did I say people? I meant Sheeple.lolingatallofyou_{March 4, 2013
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lolingatallofyou: Bornagain77, What you say is actually false. Not every mutation needs to occur within a gene sequence. Many, MANY mutations occur in the so called junk DNA.
These are strong words. Can you show me where Bornagain77 states that every mutation needs to occur in the gene sequence?
lolingatallofyou: You are making the assumption (likely due to your lack of education in genetics) that every mutation that makes up the difference between human and chimp genomes occurred in coding sequence.
YOU are the one making assumptions. Bornagain77 is quoting P.J.Levi.Box_{March 4, 2013
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Bornagain77, What you say is actually false. Not every mutation needs to occur within a gene sequence. Many, MANY mutations occur in the so called junk DNA. In fact, the mutation rate is highly accelerated in non-coding sequence. SO, it is incredibly possible that this amount of change could occur over this time period. You are making the assumption (likely due to your lack of education in genetics) that every mutation that makes up the difference between human and chimp genomes occurred in coding sequence. Further, there are other types of deletions than point mutations (or single base mutations). There are whole section deletions, substitutions, gene fusions and duplications. These likely account for why the difference seems to not work out perfectly and seemingly comes out to 25 mutations per year. So yeah, basically you are uneducated on the subject and quoting random papers doesn't make you or intelligent design correct.lolingatallofyou_{March 4, 2013
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OT: Why Evolution Is Misunderstood - P.J. Levi - March 4, 2013 Excerpt: Consider the evolution of humans and chimps from a common ancestor, to which Coyne in his talk referred several times. Rather than offering evidence for such common ancestry, Coyne simply took it as a fact and then used it to support Darwinian selection. Yet the ubiquity of selection in creating these species makes little sense at the level of DNA -- the very level at which heritable change (evolution) occurs. By current estimates, the genomes of these two species differ by at least 300 million nucleotides. Given the premise that humans and chimps shared a common ancestor 6 million years ago, such a degree of divergence can only be accounted for by an average of 25 nucleotide changes per year in each line of descent. For Coyne's gradual version of the Darwinian mechanism to account for these differences, 25 new mutations would have to appear, conferring a reproductive advantage, and spread through each population every year. Yet even 25 advantageous substitutions per generation is unfathomable. http://www.evolutionnews.org/2013/03/why_evolution_i069771.htmlbornagain77_{March 4, 2013
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I would like to address the community at large and ask why it is a triumph for Intelligent Design believers that scientists made a mistake in assigning the role of junk DNA? It was underestimated at the time it was discovered, like many things. I do not see how it has anything to do with Darwinism being incorrect or God creating anything. It is simply one more scientific oversight along the road to discovery. These happen every day, with almost every pathway or concept discovered in science. If it was easy to figure these things it out there wouldn't be millions of scientists dedicating their lives to uncovering the mysteries of biology, chemistry and physics. I will reiterate my question for those who can not process information well enough to recall it at this point: HOW is this a victory for ID believers? HOW is it a loss for Darwinists? No scientist ever has been afraid to say they don't know the full story.......lolingatallofyou_{March 4, 2013
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OT: Cell Positioning Uses "Good Design" - March 2, 2013 Excerpt: All in all, we see a complex answer to a simple question: how does a cell know where it is? Here we have seen multiple interacting mechanisms for gathering information from a noisy environment, refining it, and making decisions reliably. This is a form of irreducible complexity -- not so much of physical parts interacting, but strategies interacting, much like a software engineer would use multiple strategies to provide robustness for high-reliability software. Cells are so good at it, they gain "exceedingly reliable" information even from noisy, unreliable inputs. ,, "In biology, simple questions rarely have simple answers, and "how do cells know where they are?" is no exception.",,, Lander says nothing about how these sensory strategies might have evolved by a Darwinian process. Indeed, Darwinian theory is essentially useless to the entire discussion.,,, http://www.evolutionnews.org/2013/03/cell_positionin069471.htmlbornagain77_{March 4, 2013
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It is good to remember that not only is the junk DNA argument from Darwinists a 'religious argument' as to how Darwinists think God should or should not act in this world, but also that the junk DNA argument from Darwinists was actually required in neo-Darwinism by the mathematics of population genetics: Carter: Why Evolutionists Need Junk DNA - December 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://indicium.us/2009/12/carter-why-evolutionists-need-junk-dna.html Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional. 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 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/8905583bornagain77_{March 4, 2013
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