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Does Evolutionary Theory Really Help Scientists?

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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
Pav, I have no idea what to make of these wild and whirling words. For what it's worth. The genome is more like 3 billion bases, but I can't imagine what difference the denominator makes if all the genome is function-rich. If most bases are involved in a function, and randomly changing them in each generation is no great loss, then biological function can't be very sequence specific. Most people have no synonymous mutations - since they can only fall in the ~1% of the genome that are exons and ~75% of exonic mutations will be non-synom. Mutations and recombinatoin are different things. In any case, the 70 mutations include only SNPs. If you mean structural variants, well they would add to the genetic load since they dont simply shuffle information but would break up information midstream. Then you have all this noise about neutral theory, which I don't understand at all. Yes, the argument for junk DNA is also an argument again prevasive selection in most genomes. That's a very good reason to calling modern evolution biology "Darwinism" especially as it relates to junk DNA. But I don't see what point you are trying to make with this, or the (supossed) observation that some non-coding RNAs are involved in embryogenesis. Embryo-exoressed genes are subject to selecton/mutaton too, after all.wd400
February 8, 2014
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franklin as to:
back in the late 80?s it was well known that DNA was promiscuously transcribed. That the transcripts, were for the most part, nonsense not understood was also recognized.,,,
Yet,,,
Genomic organization of human transcription initiation complexes - Sept. 18, 2013 Excerpt: ,,,we looked for the 'initiation machine' that makes the RNA.,, Pugh, and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes.,,, The remaining 150,000 initiation machines—those Pugh and Venters did not find right at genes—remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins.",,, "These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage—making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'" http://phys.org/news/2013-09-genomic-dark.html
In fact every time they look for function they find it:
Knockout Mice Study: Long Noncoding RNAs “Play Central Roles in Mammalian Development and Physiology” – Casey Luskin January 16, 2014 Excerpt: After ENCODE’s finding that the vast majority of our DNA is transcribed into RNA, many Darwinian biologists have comforted themselves with the belief that most of that RNA is still useless, and our cells are full of “junk RNA.” But a few independent-minded folks sought out evidence of function for that RNA. And they’ve consistently found it. http://www.evolutionnews.org/2014/01/knockout_mice_s081221.html
Like the concept that most of the DNA was junk, that originated from Darwinian thinking, the concept that most of the RNA transcripts are 'nonsense' is turning out to be misleading and wrong as well. Moreover, enough about the functionality of RNA is now known that it had ENCODE researchers calling for a redefinition of the concept of what a 'gene' is altogether: Landscape of transcription in human cells – Sept. 6, 2012 Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,, Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line. http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Time to Redefine the Concept of a Gene? - Sept. 10, 2012 Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins! While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25. Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance. http://networkedblogs.com/BYdo8 Of related note to ENCODE researchers wanting to redefine the concept of a gene, RNA’s are far more difficult to align into any presupposed evolutionary relationships than Genes are/were:
micro-RNA and Non-Falsifiable Phylogenetic Trees - (Excellently Researched) video http://www.youtube.com/watch?v=qv-i4pY6_MU
Another misconception from decades ago that got debunked was this (although this mistake can probably be seen as an 'honest mistake' that was not entirely the fault of Darwinian thinking),,
"We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naïve as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB -- and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. Consider an enzyme, for example. If its substrate molecule is present at a concentration of 0.5mM, which is only one substrate molecule for every 105 water molecules, the enzyme's active site will randomly collide with about 500,000 molecules of substrate per second. And a typical globular protein will be spinning to and fro, turning about various axes at rates corresponding to a million rotations per second. But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines." Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92 (February 6, 1998): 291-294
bornagain77
February 7, 2014
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70 out of 5 billion nucleotides? That’s going to kill you? Chances aren’t high.
what would be the odds of detrimental effect(s) via deletion of DNA nucleotides equivalent to the entire protein coding region of the organism? What effects would ID predict that this would cause? As far as ENCODE goes when I went through my graduate course work back in the late 80's it was well known that DNA was promiscuously transcribed. That the transcripts,were for the most part, nonsense was also recognized. For transcription all you need to have is a initiation-site or a close match of a 'proper' binding sequence to get things rolling. Much like P450 enzymes metabolize a suite of chemicals with different affnities.franklin
February 7, 2014
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wd400 makes the argument that, since our DNA can endure mutations fairly well, that a significant portion of the DNA must be junk. Otherwise, all those mutations would cause us problems (3-headed children, demon possession, etc.) The most obvious problems with this statement: 1) It ignores the concept of redundancy. It assumes that every piece of DNA is independent, and that no self-correction capability exists. Scientifically, we have a large amount of evidence to the contrary: -- Inbreeding: Inbreeding is a significant danger because it increases the chance that 2 parents will share the same mutation in their DNA. This indicates that each DNA mutation DOES damage FUNCTIONAL genome, and it is only the auto-correction that comes from 1 parent not having the mutation that prevents problems -- Experiments such as fruit fly mutations. In one example, fruit flies with damaged/removed eye genes, when bred multiple generations with other eye-less flies, will regain their eyes. This indicates that other sections of DNA contain the ability to fix mutated sections of DNA. This indicates the probability that there are segments of DNA that may serve no constant purpose, but act as a regulatory or repair function that ONLY kicks in if needed. Damage to these sections will APPEAR harmless, but will cause problems in the future. 2) The number of mutations wd400 cites are actually very small, and as stated before, somewhat self-correcting. Over time, however, they do build up (genetic load), and we are already seeing the affects on humanity (and animals as well). 3) If we accept the evolutionists' timeline, humanity's DNA carries the load of a million years of mutation. Yet human DNA studies show extremely tiny variation and mutation in the DNA (for such an amount of time - the story is different if you assume thousands, not millions). If a significant portion of the genome is junk, why is such a high percentage conserved world-wide? The rest of wd400's argument resolves to our genome is significantly different than other species genome in size and definition, therefore much of those differences must be junk or they would be damaging. This is a non-empirical circular reasoning argument that, because evolution requires junk in the genome, therefore most of the genome is junk.drc466
February 7, 2014
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wd400: THe better arguments for junk DNA include the fact that you (and the rest of us) are alive, despite each having ~70 new mutatoins. 70 out of 5 billion nucleotides? That's going to kill you? Chances aren't high. What about synonymous mutations? What about some of those 70 being recombinations where information is just shuttled around? WD: If the genome was mostly functional (as creationists claim) and the biological functions require very specific sequences (as creationists claim) then those mutations should be breaking functional DNA in every generation. . . . On top of that you have the fact that most fo the genome is not conserved, But this is an argument against NS. That so much polymorphisms exist in the genome drove Kimura to the Neutral Theory---which was fought by Darwinists, before they co-opted it, standing it on its head. It was just like the "junkDNA" argument: before they had the answer, they were sure polymorphisms would be at a minimum. After proven wrong, then they said, "Oh, this can explain evolution." (Kimura saw things very differently, and he was one of the finest of all populations geneticists) WD: . . . that closely realated species have quite different genome sizes, that this variance in genome size can be partly explained by variance in the power of natural selection to remove very weekly deleterious mutations (such as producing a little extra DNA and RNA in a partciular cell type at a particular time…), the predominance of repetitive sequences and variance in repeat-number among individuals, the fact many sequences diverge at the rate expected under neutral evolution…. Oh, but you see, "random" mutations are like a "random" search: not productive. That's where, per Dawkins, NS comes in, making it a "non-random" process. So, you see, here we are at UD hearing evolutionists speak out of both sides of their mouths. What are we to think? And, BTW, why are we "creationists" here? I'm Catholic. So are others. Why the strawman nonsense? WD: We could go on, but I hope you see there are many good reasons to think most of the genoem is junk, and they don’t represaent argumetns from ignorance. I think you're arguing here from a point of ignorance. The LincRNAs that star in this post, have lots of repetitive Alu sections. And yet they're shown to have function. And they're conserved for the most part. This is no argument for "most of the genome being 'junk'." WD: Moreover, the fact tha ENCODE found most sequences produce RNA at some stage doesn’t change these arguments. Have you given any consideration whatsoever to the fact that over and over again, these so-called "junk" portions of the genome are being linked to embryonic function? Guess what, when you're born, it's been quite some time since you've been an embryo. And, of course, there would be no need any longer for these portions of DNA to be expressed. This is precisely what this post is about.PaV
February 7, 2014
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Read... well any of comments. Where do you think I said that no one argued most of the genome was junk?wd400
February 7, 2014
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wd400: You haven’t understood anything I have said. So I give up. I think I understood what you said. I disagree almost entirely. When I, as a blogger, have evolutionists tell me point blank that most of the genome is "junk", and not more than two years ago (if not less), then your claims are not believable. It's just your opinion. And when someone as high profile as Richard Dawkins is making this claim, all I can say is that it is the height of convenience to a posteriori aver that "we never said that." So, have you understood me?PaV
February 7, 2014
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wd400 whistles in the dark: ENCODE Reveals Incredible Genome Complexity and Function by Jeffrey Tomkins, Ph.D. - Sept. 2012 Excerpt: Tom Gingeras, one of the senior scientists on the ENCODE project said, “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more.”4 And what about the remaining 20 percent of the genome—is it functional too? According to Ewan Birney, ENCODE’s lead analysis coordinator, it’s probably not meaningless junk either. Birney said in an interview, “It’s likely that 80 percent will go to 100 percent” and “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”4 Birney expects that many critics will argue about the 80 percent figure and the definition of what is “functional.” Birney added, “[That figure] best [conveys] the difference between a genome made mostly of dead wood and one that is alive with activity” and “No matter how you cut it, we’ve got to get used to the fact that there’s a lot more going on with the genome than we knew.”4 Some people will probably try to claim that these statements made by the scientists of ENCODE are merely hype. However, there is little to criticize since the 80 percent figure comes directly from a clearly written statement in an 18-page research paper in the prestigious secular journal Nature.1 Furthermore, this statement came from the lead paper of 30 other concurrently published ENCODE papers that were authored by hundreds of leading genomic scientists in multiple international laboratories worldwide. http://www.icr.org/article/7064/ What Is The Genome? It's Certainly Not Junk! - Dr. Robert Carter - video - (Notes in video description) http://www.metacafe.com/w/8905583 Comparing genomes to computer operating systems - Van - May 2010 Excerpt: we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology,,, http://www.ncbi.nlm.nih.gov/pubmed/20439753bornagain77
February 6, 2014
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The ENCODE number (70-80%) is the percentage of the genome transcribed in at least one cell-type, not in a typical cell (I'm not sure what that number is, but it's unlikely to be 70%). More to the point, we have known for a long time that cells make more RNA than they need. Unless you think every base of every intron serves an important role. The point about the "odd junk transcript" is not the final result, but the mechanism by which noisy transcription is predicted to arise. Selection can only operate on what variation is present in a single generation. One extra transcript in one cell type is not going to make a noticable difference in one generation. Over many generations those dynamics can add up to a junky genome.wd400
February 6, 2014
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Mutations don't necessarily reveal function (or lack thereof) for many reasons but deletions can. TALENs have been really useful for studying this. Genome size is not only correlated with population size but also metabolism and nucleus size. If most of the genome is junk (e.g 95%) and since 70% of the genome is transcribed, then each cell would be producing many times more transcripts then it needs (depending on cell type). This is completely different to the 'odd junk transcript every now and then' scenario. This doesn't mean that there's no junk DNA though.Jul3s
February 5, 2014
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All arguments for junk DNA are from ignorance.Joe
February 5, 2014
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Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006bornagain77
February 5, 2014
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wd400 claims: "THe better arguments for junk DNA include the fact that you (and the rest of us) are alive, despite each having ~70 new mutatoins. If the genome was mostly functional (as creationists claim) and the biological functions require very specific sequences (as creationists claim) then those mutations should be breaking functional DNA in every generation." Well for goodness sakes wd400, since the overwhelming majority of mutations are detrimental then that must mean Darwinism is true in your mind (excuse me, I meant brain)??? In case you fail to realize it wd400, the fact that we have an extremely difficult time identifying ANY truly beneficial 'random' mutations whatsoever is a very powerful argument for the contention that intelligence was required in the past to explain the origin of the genetic information in the first place!bornagain77
February 5, 2014
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THe better arguments for junk DNA include the fact that you (and the rest of us) are alive, despite each having ~70 new mutatoins. If the genome was mostly functional (as creationists claim) and the biological functions require very specific sequences (as creationists claim) then those mutations should be breaking functional DNA in every generation. On top of that you have the fact that most fo the genome is not conserved, that closely realted species have quite different genome sizes, that this variance in genome size can be partly explained by variance in the power of natural selection to remove very weekly deleterious mutations (such as producing a little extra DNA and RNA in a partciular cell type at a particular time...), the predominance of repetitive sequences and variance in repeat-number among individuals, the fact many sequences diverge at the rate expected under neutral evolution.... We could go on, but I hope you see there are many good reasons to think most of the genoem is junk, and they don't represaent argumetns from ignorance. Moreover, the fact tha ENCODE found most sequences produce RNA at some stage doesn't change these arguments. Jul3s, Makes sense to who? The extra metabolic cost of the odd transcript in some cell type at some time is likely vanishingly small. In creatures will small population sizes, natural selection will not be strong enough to detect such small selective differences and such abbarent expression is expected to accrue. As I say, there is a correlation between genome size and effective population size, which suggests at least part of the variance in genome size can be explained by the inability of creatures in small populations to preven junk adding up.wd400
February 5, 2014
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ENCODE doesn't actually prove anything. However, the fact that 70% of the genome is transcribed strongly suggests that most of the genome is functional. It makes no sense to suggest that the cell is wasting so much of its energy making junk.Jul3s
February 4, 2014
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Wd400: "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." What is the most important argument then? And btw: the "fact" that most of the genome has no function is a complete argument from ignorance, is anti-scientific progress and is also being shown to be false more and more every day now, starting with the findings of the ENCODE project.sixthbook
February 4, 2014
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Claiming to be misunderstood is a weak way of deflecting counter arguments. Especially since the "real" argument for junk DNA has already been talked about on this thread, not just the argument from ignorance.Jul3s
February 4, 2014
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You call it a “myth” that evolutionists/Darwinists made the claim that the genome is filled with junk You haven't understood anything I have said. So I give up.wd400
February 4, 2014
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wd400, you claim that
"Most of the genome is, in fact, junk.”
How do you possibly know this? Are you claiming, so as to be able to declare the genome 'mostly junk', to know all the intricate operations of the cell in detail. Integrated operations of the cell that researchers, such as ENCODE 2012, have barely begun to scratch the surface of? Even you can't possibly be that arrogant! Or are you? And since you can't possibly know all the intricate workings of the cell in detail,, since even ENCODE 2012 expressed amazement at what they were seeing,,,
Scientists go deeper into DNA (Video report) (Junk No More) - Sept. 2012 http://bcove.me/26vjjl5a Quote from preceding video: “It's just been an incredible surprise for me. You say, ‘I bet it's going to be complicated', and then you are faced with it and you are like 'My God, that is mind blowing.'” Ewan Birney - senior scientist - ENCODE 2012
How can you possibly claim, with a straight face, that the genome is 'mostly Junk'? i.e. Your argument, whether you realize it or not, or even whether you admit it or not, boils down to this:
“well, we don’t what this does so it must be junk”
or more precisely, something like this
“well, we don’t what this does, but we know it can't possibly be designed because that is not science, so it must be junk”
bornagain77
February 4, 2014
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wd400: You make no mention whatsoever of Susumu Ohno's remark that the genome is filled with evolution's "failures" as well as "successes." You call it a "myth" that evolutionists/Darwinists made the claim that the genome is filled with junk, and this shows that it is the residue of random chance and NS. And, yet, I've had arguments online with scientists taking that very position, and in a steadfast manner. So, should I believe you, or should I believe my own experiences? Just asking. Also, is it your position that Darwinists/evolutionists did NOT make the argument that "vestigial organs" were evidence that organisms were NOT designed, but were the result of random mutations and NS? Do you make that claim also?PaV
February 4, 2014
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Pab I’m sure, from the very beginning, that there was some form of ncRNA that had function. Yes, all the tRNAs and the rRNAs for a start. Much more non-coding DNA that doesn't amke RNA has also been kown to serve a function for a long time. As Ohno made clear when he started talking about junk DNA. . But the argument was made, up until but a year or so ago, that the genome was littered with non-functional DNA, hence “junk”, Yes. This argument remains strong. The myth is that the best argument for junk DNA went something like "well, we don't what this does so it must be junk". That's never been the case, so hauling out that story every time another fraction of a percent of genome is shown to have a function is silly. Not that this thread gives me any hope that this myth will diewd400
February 4, 2014
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Semi OT: Excellent article up on ENV:
(Dual Coding) RNA Shows Design, Too - February 4, 2014 Excerpt: A paper in Nature describes how information is stored not only in RNA's base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures," the authors begin (emphasis added). In their conclusion, they say, "We identify hundreds of specific mRNA regions that are highly structured in vivo, and we show for three examples that these structures affect protein expression." In other words, the structure, not just the sequence, carries functional information. "Our studies provide an excellent set of candidate regions, among the truly enormous number of structured regions seen in vitro, for exploring the regulatory role of structured mRNAs.",,, If RNAs show design, why not design them ourselves? In an experimental twist, researchers at Carnegie Mellon invited the public to be their design lab. In a "crowdsourcing" experiment, they found that volunteers could create new RNA designs better than computers could. The starting pool of 37,000 citizen scientists has grown to 130,000 members exercising their intelligent design skills. "An enthusiastic group of non-experts, working through an online interface and receiving feedback from lab experiments, has produced designs for RNA molecules that are consistently more successful than those generated by the best computerized design algorithms, researchers at Carnegie Mellon University and Stanford University report." http://www.evolutionnews.org/2014/02/rna_shows_desig081841.html
Of related note: This following peer-reviewed paper holds that there is 'irreducible organizational complexity' between the genetic (digital) information and the epigenetic (analog/structural) information:
Refereed scientific article on DNA argues for irreducible complexity - October 2, 2013 Excerpt: This paper published online this summer is a true mind-blower showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc.,, ,,,First, the digital information of individual genes (semantics) is dependent on the the intergenic regions (as we know) which is like analog information (syntax). Both types of information are co-dependent and self-referential but you can’t get syntax from semantics. As the authors state, “thus the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell”. In short, the linear DNA sequence contains both types of information. Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. This implies that the position and organization of genes on the chromosome is not arbitrary,,, http://www.christianscientific.org/refereed-scientific-article-on-dna-argues-for-irreducibly-complexity/
To state what should be needless to say, these findings are not conducive to Darwinian presuppositions but are conducive to Intelligent Design presuppositions!bornagain77
February 4, 2014
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And only Intelligent Design would tell us to look for functionality in non-coding DNA, as opposed to stumbling across it. Just sayin'Joe
February 4, 2014
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Neither Darwinism, neo-darwinism nor Intelligent Design predict a high % of junk DNA.Joe
February 4, 2014
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CLAVDIVS: 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.
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.”
At the end, CLAVDIVS adds: Clearly, mainstream biologists have claimed for decades that non-coding DNA has functions, ever since the term “junk” DNA entered the scientific literature. So, for forty years "mainstream biologists have claimed . . . that non-coding DNA has functions." OK. And they've known for some time, now, that ncDNA is quite often "highly conserved." Let's, then, put this all together: (1) Since Ohno, "mainstream biologists" have reasoned if it's there in the genome then there must be some function to it. (2) Not only that, since introns are so highly conserved, this gives every indication that it has a vital role to play. (3) And, yet, up until WGA (whole genome analysis) Darwinists have eschewed prying into this apparently vital DNA, and, instead, chose to continue to focus on coding DNA for almost forty years. You see, CLAVDIVS, what scientists may have said, and what they did, are two completely different things. And, BTW, here's what Ohno also wrote:
The chance of acquiring a new function by unrestricted accumulation of mutations, however, should be as small as that of an isolated population emerging triumphant as a new species. Degeneracy is the more likely fate. The creation of every new gene must have been accompanied by many other redundant copies joining the ranks of silent DNA base sequences, and these silent DNA base sequence may now be serving the useful but negative function of spacing those which have succeeded. Triumphs as well as failures of nature’s past experiments appear to be contained in our genome.” [From, “So much ‘junk’ DNA in our Genome”, Susumu Ohno, 1972]
Notice the title of the paper: So much "junk" DNA in our Genome. This is 1984, and Newspeak: i.e., those in power attempting to re-write the past when their predictions prove wrong.PaV
February 4, 2014
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wd400 Except, of course, this myth that all non-coding DNA was once considered junk is absurd. Really. Why? Because you say so? BTW, when you throw in the modifier "all", that does change the statement. I'm sure, from the very beginning, that there was some form of ncRNA that had function. But the argument was made, up until but a year or so ago, that the genome was littered with non-functional DNA, hence "junk", and that this was a severe argument against ID. And it was made by Ph'Ds who worked with genetics. It's not a myth. The only myth that now exists is the "myth" that Darwinists never made this kind of argument. Now that is a myth.PaV
February 4, 2014
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wd400, You declare "4. Most of the genome is, in fact, junk." How do you know that is a "fact"? What is your definition of "junk' as pertains to the genome? How do you determine which parts are "junk" and which parts are not "junk"? What properties of a given section of DNA identify it as not "junk" as opposed to "junk"? Please elucidate. StephenSteRusJon
February 4, 2014
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wd400, you accuse others of 'persisting in a convenient myth', when it is in fact the neo-Darwinists who refuse to concede even one inch of their 'convenient myth' that they believe in! Go figure! Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video http://www.metacafe.com/w/10395212 ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”. Professor Denis Noble is President of the International Union of Physiological Sciences. Physiology is rocking the foundations of evolutionary biology - Denis Noble - 17 MAY 2013 Excerpt: The ‘Modern Synthesis’ (Neo-Darwinism) is a mid-20th century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection.,,, We now know that genetic change is far from random and often not gradual.,,, http://onlinelibrary.wiley.com/doi/10.1113/expphysiol.2012.071134/abstract At the 10:30 minute mark of the following video, Dr. Trifonov states that the concept of the selfish gene has 'inflicted an immense damage to biological sciences', for over 30 years: Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637 Of note: Though the evidence against neo-Darwinian evolution is overwhelming, anyone who dares question the sufficiency of neo-Darwinism to explain all life on earth in the public school classroom, or academia in general, is persecuted, as the following clearly points out: EXPELLED - Starring Ben Stein - video http://www.youtube.com/watch?v=P-BDc3wu81U Slaughter of Dissidents - Book "If folks liked Ben Stein's movie "Expelled: No Intelligence Allowed," they will be blown away by "Slaughter of the Dissidents." - Russ Miller http://www.amazon.com/Slaughter-Dissidents-Dr-Jerry-Bergman/dp/0981873405 “In the last few years I have seen a saddening progression at several institutions. I have witnessed unfair treatment upon scientists that do not accept macroevolutionary arguments and for their having signed the above-referenced statement regarding the examination of Darwinism. (Dissent from Darwinism list)(I will comment no further regarding the specifics of the actions taken upon the skeptics; I love and honor my colleagues too much for that.) I never thought that science would have evolved like this. I deeply value the academy; teaching, professing and research in the university are my privileges and joys… ” Professor James M. Tour – one of the ten most cited chemists in the world Top Ten Most Cited Chemist in the World Knows That Evolution Doesn’t Work – James Tour, Phd. – video http://www.youtube.com/watch?v=JB7t2_Ph-ck Even atheists themselves, who break ranks with the ‘consensus’ party line, are severely castigated by Darwinian atheists: The Heretic – Who is Thomas Nagel and why are so many of his fellow academics condemning him? – March 25, 2013 http://www.weeklystandard.com/articles/heretic_707692.html The Altenberg 16: An Exposé of the Evolution Industry – book Excerpt: In the other camp are those challengers who want to steer evolutionary science in a more honest, scientifically accurate direction. However, the Darwinian theory has become a political powerhouse brand that is hard to unseat because of the money and power associated with it. The Altenberg 16 is about a group of evolution scientists who met in 2008 in Austria to discuss and attempt to tell the truth about this “brand.”,,, http://books.google.com/books/about/The_Altenberg_16.html?id=wk2FfQQ_DmsCbornagain77
February 4, 2014
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The inability of people in this thread to actaully read what I'm saying, rather than persist in a convenient myth, is astounding. I'm not arguing that evolutionary biologists never said most of the genome was junk, or even that the junkiness of our genome. I'm saying people who conflat non-coding DNA for junk DNA are making a mistake. And, more importantly, that this is not a mistake that the peope who developed the argument for junk DNA made, and the fact most of genome has no known function is not the best evidence for the fact our genome is junk. It's a shame that the myth of the myth of junk DNA is so widespread, but if IDists want to do better than the popular press an engaging in science they ought to learn a bit about the actual arguments for the presence of junk DNA.wd400
February 4, 2014
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wd400 and CLAVDIVS, it is not that some evolutionary biologists, which did not have their brains completely scrambled by Darwinian thinking yet and still had a bit of common sense, predicted that some of the non-protein coding DNA might have function, it is the fact that Darwin's theory itself predicts most of the DNA to be of little or no function i.e. junk! Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle - "Haldane's Ratchet" - Christopher L. Rupe and John C. Sanford - 2013 Excerpt: We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as "Haldane's Dilemma" is very real. Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon "Haldane's Ratchet". http://media.wix.com/ugd/a704d4_47bcf08eda0e4926a44a8ac9cbfa9c20.pdfbornagain77
February 4, 2014
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