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Junk DNA back “with a vengeance”

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human RNA-RNA interactions detected by LIGR-Seq./U Toronto

From ScienceDaily:

What used to be dismissed by many as “junk DNA” is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) — genome’s messages that do not code for proteins — in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions.

Yes, that’s what they said.

ncRNAs come in multiple flavours: there’s rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA’s place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe’s group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings.Paper. (paywall) – Eesha Sharma, Tim Sterne-Weiler, Dave O’Hanlon, Benjamin J. Blencowe. Global Mapping of Human RNA-RNA Interactions. Molecular Cell, 2016; DOI: 10.1016/j.molcel.2016.04.030 More.

It’s curious how blunt media releases are becoming, in dismissing the idea of “junk DNA.” But then Darwin didn’t predict junk DNA. Or junk RNA. Or that his stalwart followers would develop and promote the concept. So, leaving their interests aside, there isn’t a big investment in protecting the idea.

One result is that it’s probably not a great time to be Dan Graur. A better time, actually, to be Jonathan Wells

See also: “Inactive” gene helps prevent strokes A gene that “scientific dogma insists” is inactive in adults actually plays a vital role in preventing the underlying cause of most heart attacks and strokes, researchers have determined.


Jonathan Wells’s The Myth of Junk DNA

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gpuccio: You wrote above:
IOWs, transposons are important actors increasingly mentioned as a cause of functional and regulatory diversity. IOWs, tools of design. Does that sound familiar? :)
Indeed, it does sound familiar. Here's a thread from 2007 on this very subject. If you look at my comments at #4,5, and 7, you'll see that "design principles" lead you very quickly to proper conclusions; unlike evolutionists. PaV
of related note, the disconnect between mutations to DNA and the 'form', i.e. the spatial organization, of an organism is fairly profound:
The Insurmountable Problem of “Form” for Darwinian Explanations – video (2016) https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1138468566166075/?type=2&theater
also of related note:
On Human Origins: Is Our Genome Full of Junk DNA? Pt 2. – Richard Sternberg PhD. Evolutionary Biology - podcast Excerpt: “Here’s the interesting thing, when you look at the protein coding sequences that you have in your cell what you find is that they are nearly identical to the protein coding sequences of a dog, of a carp, of a fruit fly, of a nematode. They are virtually the same and they are interchangeable. You can knock out a gene that encodes a protein for an inner ear bone in say a mouse. This has been done. And then you can take a protein that is similar to it but from a fruit fly. And fruit flies aren’t vertebrates and they certainly are not mammals., so they don’t have inner ear bones. And you can plug that gene in and guess what happens? The offspring of the mouse will have a perfectly normal inner ear bone. So you can swap out all these files. I mentioning this to you because when you hear about we are 99% similar (to chimps) it is almost all referring to those protein coding regions. When you start looking, and you start comparing different mammals. Dolphins, aardvarks, elephants, manatees, humans, chimpanzees,, it doesn’t really matter. What you find is that the protein coding sequences are very well conserved, and there is also a lot of the DNA that is not protein coding that is also highly conserved. But when you look at the chromosomes and those banding patterns, those bar codes, (mentioned at the beginning of the talk), its akin to going into the grocery store. You see a bunch of black and white lines right? You’ve seen one bar code you’ve seen them all. But those bar codes are not the same.,, Here’s an example, aardvark and human chromosomes. They look very similar at the DNA level when you take small snippets of them. (Yet) When you look at how they are arranged in a linear pattern along the chromosome they turn out to be very distinct (from one another). So when you get to the folder and the super-folder and the higher order level, that’s when you find these striking differences. And here is another example. They are now sequencing the nuclear DNA of the Atlantic bottle-nose dolphin. And when they started initially sequencing the DNA, the first thing they realized is that basically the Dolphin genome is almost wholly identical to the human genome. That is, there are a few chromosome rearrangements here and there, you line the sequences up and they fit very well. Yet no one would argue, based on a statement like that, that bottle-nose dolphins are closely related to us. Our sister species if you will. No one would presume to do that. So you would have to layer in some other presumption. But here is the point. You will see these statements throughout the literature of how common things are.,,, (Parts lists are very similar, but how the parts are used is where you will find tremendous differences) http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-2/ Kangaroo and Human Genomes (are unexpectedly similar genetically) 1-30-2016 by Paul Giem - video https://www.youtube.com/watch?v=QtmG2QzqJEA Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 First Decoded Marsupial Genome Reveals "Junk DNA" Surprise - 2007 Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,, The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off. http://news.nationalgeographic.com/news/2007/05/070510-opossum-dna.html A Closer Look At Human and Chimp Similarities and Differences – video (2016) https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1134643976548534/?type=2&theater
BA: "Extensive, large INDEL (Insertion, Deletion) variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them." QED! :) gpuccio
Of related interest to species specific alternative splicing in tissues is the fact that there is also tissue-specific spatial organization of chromosomes :
Tissue-specific spatial organization of genomes - 2004 Excerpt: Using two-dimensional and three-dimensional fluorescence in situ hybridization we have carried out a systematic analysis of the spatial positioning of a subset of mouse chromosomes in several tissues. We show that chromosomes exhibit tissue-specific organization. Chromosomes are distributed tissue-specifically with respect to their position relative to the center of the nucleus and also relative to each other. Subsets of chromosomes form distinct types of spatial clusters in different tissues and the relative distance between chromosome pairs varies among tissues. Consistent with the notion that nonrandom spatial proximity is functionally relevant in determining the outcome of chromosome translocation events, we find a correlation between tissue-specific spatial proximity and tissue-specific translocation prevalence. Conclusion: Our results demonstrate that the spatial organization of genomes is tissue-specific and point to a role for tissue-specific spatial genome organization in the formation of recurrent chromosome arrangements among tissues. http://genomebiology.com/content/5/7/R44
As well, as Dr. Wells has pointed out, the 3-D spatial arrangement of parts in the cell is not reducible to DNA sequences:
Not in the Genes: Embryonic Electric Fields – Jonathan Wells – December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels — which determines the form of the endogenous electric field — constitutes an independent source of information in the developing embryo. http://www.evolutionnews.org/2011/12/not_in_the_gene054071.html Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms - Casey Luskin - June 2, 2014 Excerpt: Jonathan Wells has published a new peer-reviewed scientific paper in the journal BIO-Complexity, "Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA." With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA. This ontogenetic information guides the development of an organism, but because it is derived from sources outside of the DNA, it cannot be produced by mutations in DNA. Wells concludes that because the neo-Darwinian model of evolution claims that variation is produced by DNA mutations, neo-Darwinism cannot account for the origin of epigenetic and ontogenetic information that exists outside of DNA. (Read more here:) http://www.evolutionnews.org/2014/06/peer-reviewed_p_2086201.html
Of related note to regulatory RNAs:
Characterization and potential functional significance of human-chimpanzee large INDEL variation - October 2011 Excerpt:,,, we categorized human-chimpanzee INDEL (Insertion, Deletion) variation mapping in or around genes and determined whether this variation is significantly correlated with previously determined differences in gene expression. Results: Extensive, large INDEL (Insertion, Deletion) variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them. http://www.mobilednajournal.com/content/pdf/1759-8753-2-13.pdf
Jonathan Wells comments on the fallacious 'Darwinian Logic', within the preceding paper, that falsely tried to attribute the major differences that were found in INDEL variation to unguided Darwinian processes:
Darwinian Logic: The Latest on Chimp and Human DNA – Jonathan Wells - October 2011 Excerpt: Protein-coding regions of DNA in chimps and humans are remarkably similar -- 98%, by many estimates -- and this similarity has been used as evidence that the two species are descended from a common ancestor. Yet chimps and humans are very different anatomically and behaviorally, and even thirty years ago some biologists were speculating that those differences might be due to non-protein-coding regions, which make up about 98% of chimp and human DNA. (In other words, the 98% similarity refers to only 2% of the genome.) Now a research team headed by John F. McDonald at Georgia Tech has published evidence that large segments of non-protein-coding DNA differ significantly between chimps and humans,,,, If the striking similarities in protein-coding DNA point to the common ancestry of chimps and humans, why don’t dissimilarities in the much more abundant non-protein-coding DNA point to their separate origins? http://www.evolutionnews.org/2011/10/the_latest_on_chimp_and_human052291.html
These following, more recent, papers also found that Alternative Splicing patterns are 'species specific':
Evolution by Splicing - Comparing gene transcripts from different species reveals surprising splicing diversity. - Ruth Williams - December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F The Evolutionary Landscape of Alternative Splicing in Vertebrate Species - 2012 Excerpt: How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type.,,, http://science.sciencemag.org/content/338/6114/1587 ,,,Alternative splicing,,, may contribute to species differences - December 21, 2012 Excerpt: After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns—which determine the segments of those genes included or excluded—vary from species to species.,,, The results from the alternative splicing pattern comparison were very different. Instead of clustering by tissue, the patterns clustered mostly by species. "Different tissues from the cow look more like the other cow tissues, in terms of splicing, than they do like the corresponding tissue in mouse or rat or rhesus," Burge says. Because splicing patterns are more specific to each species, it appears that splicing may contribute preferentially to differences between those species, Burge says,,, Excerpt of Abstract: To assess tissue-specific transcriptome variation across mammals, we sequenced complementary DNA from nine tissues from four mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of previously unknown, lineage-specific, and conserved alternative exons were identified; http://phys.org/news/2012-12-evolution-alternative-splicing-rna-rewires.html Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013 Excerpt: Although humans and chimpanzees share,, similar genomes, previous studies have shown that the species evolved major differences in mRNA (messenger RNA) expression levels.,,, http://www.sciencedaily.com/releases/2013/10/131017144632.htm
Of related interest: The position and organization of elements on the chromosome is not arbitrary but is the "irreducible organizational complexity of the genetic regulation system of any cell"
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/
So, the scenario becomes increasingly clearer: 1) Non coding RNAs are mostly functional 2) They have mainly regulatory roles 3) Non coding DNA is much less conserved than coding DNA 4) The main reason for that is not that it is not functional, but that it has regulatory functions which differ from species to species. IOWs, non coding DNA is an important part of what makes species different. We can expect that a significant part of the procedures which control cellular differentiation are written there. IOWs, itr is an importanty example of "function which changes" 5) Those procedures in non coding DNA are obviously designed and, guess what? "insertions of retrotransposon elements in new genomic regions are not conserved between species" IOWs, transposons are important actors increasingly mentioned as a cause of functional and regulatory diversity. IOWs, tools of design. Does that sound familiar? :) gpuccio
goodusername, Well, if you look at statements from the ENCODE researchers even they all but admit that. All I know is that the main guys of the ENCODE are sticking to their guns even if they are regularly threatened by Darwinist or they had spoken conservatively about their findings. They know that eventually they are going to be exonerated and Darwinists will pretend that they knew it all and predicted it all along... I have seen the denial first hand when Darwinists moved from 98% junk to 90% because they couldn't deny it anymore. Larry Moran and the gang blamed the "not so knowledgeable Darwinists for making such claims". Who is going to stop the new generation of Darwinists blaming Larry and the gang for not being so knowledgeable? They are not going to be alive or available to admit that they were wrong.... J-Mac
Junk or functional DNA? ENCODE and the function controversy Pierre-Luc Germain, Emanuele Ratti, Federico Boem - 21 Mar 2014 Abstract: In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk. http://link.springer.com/article/10.1007%2Fs10539-014-9441-3 Protracted Unrest Between ENCODE Researchers and Junk-DNA Advocates Goes On - November 26, 2014 Excerpt: It's not exactly Fergusson, Mo., but the battle between ENCODE researchers and junk-DNA holdouts goes on.,,, ,,,"Evolutionary conservation of primary sequence is typically considered synonymous with conserved function, but this finding suggests that this concept should be reinterpreted, because insertions of retrotransposon elements in new genomic regions are not conserved between species." In short, the Mouse ENCODE group takes direct aim at the arguments of Dan Graur and the other junk-DNA faithful, who say that everything evolution did not conserve is junk.,,, ,,,much of what Darwinian evolutionists had dismissed as junk appears functional. Non-coding regions of the mouse genome are transcribed, and appear to function in previously unimagined ways, such as regulation of gene expression, chromosomal stability, and maintenance of species identity. Carninci offers further thoughts: ,,,"we should rethink the relationship between genomic function and evolutionary conservation. Regulatory regions and long non-coding RNAs (lncRNAs) are not subject to the evolutionary constraints of protein-coding genes, which may help to explain the sequence drifts reported in these papers. However, it is striking that transcription-factor networks are conserved despite low conservation of their binding positions in the genome." http://www.evolutionnews.org/2014/11/protracted_unre091501.html The ENCODE Embroilment, - part 3 - Summer 2015 Excerpt: Very Little DNA Is "Conserved" After raising the C-value paradox, ENCODE critics often follow with a logical argument. "Only about 10 percent of our DNA is 'conserved,' or has a similar sequence, compared to the genomes of other mammals," they point out. "This means that only about 10 percent of our genome is under selection to preserve the DNA sequence." They then reason: "Since natural selection is the only force that creates and preserves functional elements in our genome, it's impossible that more than about 10 percent of our genome is functional." This argument was on display in a 2014 paper claiming that only 8.2 percent of human DNA is functional because only that percentage of our genome is "conserved" between humans and other mammals like mice and pandas.7 But there's a glaring problem with this thinking: it assumes that all DNA sequences are the result of undirected mutation and selection to begin with, and that biological function only comes from natural selection. Throw out the assumption of an evolutionary origin of species and there's no reason to believe that only conserved DNA can be functional. After all, an intelligent agent could independently design functional genetic elements with widely divergent DNA sequences in the genomes of different species—no "conservation" required. Only if we assume that strictly unguided evolutionary mechanisms produced our genome can we infer that such a small fraction of our genome is functional. Under this logic, when evolutionists cite the preponderance of junk DNA as evidence for evolution, they engage in circular reasoning. Junk proponents seem blind to these flaws. A co-author of the 8.2-percent paper boasted, "our approach is largely free from assumptions or hypotheses."8 Apparently he was forgetting about assumptions and hypotheses like evolution. Even worse, ENCODE critic Dan Graur called it "'idiotic' to suggest that a part of the genome could be functional if it didn't respond to pressure from natural selection."9 He further charges that "what ENCODE researchers did not take into account . . . is that everything is shaped by evolution."10 In Graur's Darwinian world, the possibility that some important functional genetic element arose from a cause other than natural selection is simply inconceivable.... In any case, ENCODE provides a nice empirical test of the evolutionary assumption that only conserved DNA can be functional: It finds evidence of mass functionality in "non-conserved" (i.e., unique) DNA sequences. As one lead ENCODE researcher explains: "Most elements defined by biochemical signatures lacked strong evolutionary conservation."12 Other ENCODE defenders argue that the research shows that "absence of conservation cannot be interpreted as evidence for the lack of function."13 - They conclude that ENCODE's empirical evidence for functionality is the ultimate test: "differential expression (including extensive alternative splicing) of RNAs is a far more accurate guide to the functional content of the human genome than logically circular assessments of sequence conservation."21 Bottom line: good evidence trumps bad theory.,,, A Great Divorce Critics like Dan Graur charge that ENCODE is guilty of "divorcing genomic analysis from its evolutionary context"22—and that's exactly right. ENCODE's empirically based finding that the vast majority of our genome is functional has withstood theoretical, evolution-based objections from critics. Maybe a divorce from evolutionary thinking is exactly what we need to liberate biology from bad evolutionary assumptions and explain what's happening inside our cells.,,, http://www.salvomag.com/new/articles/salvo33/the-encode-embroilment-part-III.php Why Are Biologists Lashing Out Against Empirically Verified Research Results? - Casey Luskin July 13, 2015 Excerpt: no publication shook this (ID vs Darwin) debate so much as a 2012 Nature paper that finally put junk DNA to rest--or so it seemed. This bombshell paper presented the results of the ENCODE (Encyclopedia of DNA Elements) Project, a years-long research consortium involving over 400 international scientists studying noncoding DNA in the human genome. Along with 30 other groundbreaking papers, the lead ENCODE article found that the "vast majority" of the human genome shows biochemical function: "These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions."3 Ewan Birney, ENCODE's lead analyst, explained in Discover Magazine that since ENCODE studied 147 types of cells, and the human body has a few thousand cell types, "it's likely that 80 percent will go to 100 percent."4 Another senior ENCODE researcher noted that "almost every nucleotide is associated with a function."5 A headline in Science declared, "ENCODE project writes eulogy for junk DNA."6,,, Evolutionists Strike Back Darwin defenders weren't going to take ENCODE's data sitting down.,,, How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm--and by personally attacking, (i.e. ad hominem), those who challenge their position.,,, http://www.evolutionnews.org/2015/07/the_encode_embr097561.html bornagain77
IN IT, he is going to prove again that ENCODE deceived the public about their findings about “junk DNA”
Well, if you look at statements from the ENCODE researchers even they all but admit that. goodusername
Larry Moran is writing a book on "junk DNA". http://sandwalk.blogspot.ca/2016/05/research-for-book.html IN IT, he is going to prove again that ENCODE deceived the public about their findings about "junk DNA" and despite ALL of the new evidence against "junk DNA", Larry is going to continue to claim that human genome is still 90% junk. You gotta love "true scientists" like Larry who hasn't published one paper or performed one experiment to prove his point on "junk DNA" or other... J-Mac
It would appear that RNA is an informational molecule. But what conditions must obtain for that to even be the case? Was the entire idea of "junk DNA" predicated on the belief that these areas of DNA were not being transcribed into RNA? Would things have been different if the "junk DNA" advocates had been operating under an informational paradigm? If so, how so? What do people think? Mung
source of study: University of Toronto Isn't Larry 'neutral' Moran, who teaches at the University of Toronto, also a big junk DNA proponent? Ouch! Right in his own backyard! This certainly ain't going to sit well with him. Maybe we ought to send him a box of Kleenex? Moran even went so far as to argue with a ENCODE researcher on a science blog to try to change the ENCODE researcher's mind back in 2012 when ENCODE research had found widespread functionality in the genome.
"Moran further lamented that "the creationists are going to love this," and he feared that ENCODE's results were "going to make my life very complicated,"15 since "it's going to take a lot of effort to undo the damage caused by [ENCODE]."16" - Luskin http://www.evolutionnews.org/2015/07/the_encode_embr097561.html
Supplemental note:
Haldane's Dilemma Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift - creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors - it surely would have killed us. Since Haldane's dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation - but has obtained identical results. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 159-160 Walter ReMine on Haldane's Dilemma - interview http://kgov.com/Walter-ReMine-on-Haldanes-Dilemma Kimura's Quandary Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in response 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 Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional. – Sanford
i.e. Neutral theory, and junk DNA, was not developed because of any empirical observation, but was developed primarily because it was forced upon Darwinism by the mathematics. In other words, neutral theory is actually the result of a theoretical failure of Darwinism within mathematics!
Carter: Why Evolutionists Need Junk DNA - Robert W. Carter - 2009 Excerpt: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane's work. Without junk DNA, (neutral theory), evolutionary theory cannot currently explain how everything works mathematically. Robert W. Carter - biologist http://creation.com/junk-dna-slow-death
Here a cool video by Dr Carter that goes over some of the mind blowing complexity of the genome
The Multi-dimensional Genome--impossible for Darwinism to account for-- by Dr Robert Carter - video (talk begins at 11:30 minute mark) https://youtu.be/K3faN5fU6_Y?t=690

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