Why doesn’t junk DNA behave like junk?

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August 1, 2014

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From Jonathan Wells at Evolution News & Views

According to a recent Science Daily news item, Oxford University researchers say that only 8.2% of our DNA is likely to be functional. The rest is “junk.”

The 8.2% figure contradicts the conclusions of the ENCODE Project (for “Encyclopedia of DNA Elements”), which was established after the Human Genome Project to make sense of our newly sequenced DNA. In September 2012, the results from over a thousand experiments — involving dozens of laboratories and hundreds of scientists on three continents, published almost simultaneously in dozens of articles in five different journals — provided evidence that 80% or more of our DNA is functional.

It might have to do with who the DNA works for:

A clue might be found in a presentation given by Dan Graur at the 2013 meeting of the Society for Molecular Biology and Evolution in Chicago. As Graur — a vocal, even nasty, opponent of ENCODE — reasoned in his presentation:

If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then Evolution is wrong.

So while the definition of “function” is close to the heart of the controversy, adherence to Darwinian evolution is even closer.

So DNA doesn’t behave like junk because it isn’t working for the Darwin lobby?

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Comments

Dr. JDD,
why don’t you go over and correct them as well eh?
Perhaps the moral paralysis is due to severe ideological contamination. Or perhaps there's differential application of intellectual indulgences based on what the other person believes in. BTW, nicely articulated, bornagain77. -QQuerius_{August 2, 2014
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http://sandwalk.blogspot.co.uk/2013/07/what-did-dan-graur-say-in-chicago.html?m=1 A_B so LA Moran can use that quote but Wells cannot? See July 15 comment half way down in above link. It would seem Graur agreed with its use. why don't you go over and correct them as well eh?Dr JDD_{August 2, 2014
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A few notes that contradict the notion that junk DNA will accumulate over time: Experimental Evolution of Gene Duplicates in a Bacterial Plasmid Model Excerpt: In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. This study highlights the importance of the cost of duplicate genes and the quantitative nature of the tradeoff in the evolution of gene duplication through functional divergence. http://www.springerlink.com/content/vp471464014664w8/ Michael Behe finds Loss of Function Mutations Challenge the Darwinian Model - Casey Luskin - August 24, 2013 Excerpt: "Because of the many ways in which a gene can be altered to lose function, the LOF mutation would have a rate several orders of magnitude greater than that of the GOF mutation for the duplicated gene." http://www.evolutionnews.org/2013/08/in_biological_i_1075591.html Douglas Axe and Ann Gauger Argue that Design Best Explains New Biological Information - Casey Luskin August 26, 2013 Excerpt: Axe and Gauger observe that “The most widely accepted explanation for the origin of new enzymes is gene duplication and recruitment.” However, they cite experimental work showing that a duplicate gene is much more likely to be silenced (because of the costly resources expended in transcribing and translating it) than it is to acquire a new function. http://www.evolutionnews.org/2013/08/douglas_axe_and075601.html The regulatory utilization of genetic redundancy through responsive backup circuits - 2006 Excerpt: many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. … We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation. http://www.pnas.org/content/103/31/11653.full The regulatory utilization of genetic redundancy through responsive backup circuits - 2006 Excerpt: Duplicate genes and paralogous gene families long have been perceived as genomic sources of genetics robustness (1–5). The assumption is that a functional overlap of these genes acts to compensate against mutations. Yet, this very fact also renders redundancy evolutionarily instable (5, 6), and functional overlaps, typically, are rapidly lost because of divergence (7). Nevertheless, numerous examples of paralogs retaining their functional overlap for extended evolutionary periods (for examples, see refs. 6 and 8–12) suggest that, at least for a fraction of gene pairs, redundancies are conserved throughout evolution despite their predicted instability.,,, In fact, although retention of redundancy is much less frequent than its loss, its widespread existence is nontrivial and cannot (6) be dismissed as leftovers of recent duplication events.,,, the paradigm that has emerged is that genes that are functionally redundant are not often independently controlled but rather they are regulated by a system that both monitors and responds to their intactness. http://www.pnas.org/content/103/31/11653.fullbornagain77_{August 2, 2014
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Acartia_bogart, if the genome is as useless as Darwinists insist it is, (since, of course, God would never design junky genomes! :) ), why in blue blazes is so much effort extended by the rest of the cell towards repairing these vast, useless, stretches of junk DNA instead of the cell allowing natural selection to do its job and get rid of all that excess baggage? Excess baggage that would be, apparently, slowing down successful reproduction???
Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm A Look at the Quality Control System in the Protein Factory - JonathanM - March 2012 Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed. http://www.evolutionnews.org/2012/03/a_look_at_the_q057791.html The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective - February 2011 Excerpt: "Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation." http://www.arn.org/blogs/index.php/literature/2011/04/26/dna_repair_mechanisms_reveal_a_contradic Contradiction in evolutionary theory - video - (The contradiction between extensive DNA repair mechanisms and the necessity of 'random mutations/errors' for Darwinian evolution) http://www.youtube.com/watch?v=dzh6Ct5cg1o The Darwinism contradiction of repair systems Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma. https://uncommondescent.com/intelligent-design/the-darwinism-contradiction-of-repair-systems/
Of note:
Richard Dawkins interview with a 'Darwinian' physician goes off track - video Excerpt: "I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly -- a few hours sometimes, they can reproduce themselves -- that they can evolve very, very quickly. And we're stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?" http://www.evolutionnews.org/2012/07/video_to_dawkin062031.html
i.e. Since successful reproduction is all that really matters on a neo-Darwinian view of things, how can anything but successful reproduction be realistically 'selected' for? Any other function besides reproduction, such as sight, hearing, thinking, (DNA REPAIR) etc.., would be highly superfluous to the primary criteria of successfully reproducing, and should, on a Darwinian view, be discarded as so much excess baggage since it would, eventually, be seen to slow down successful reproduction???
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
bornagain77_{August 2, 2014
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Why don’t you be honest and provide details on what Dan Graur said before and after the couple sentences that you present here?
Why don't you just bring in the details and call his bluff? SebestyenSebestyen_{August 2, 2014
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JW isn't like to be lurking here. If you can point me to the source of the quote I'd be happy to provide the full context.Mung_{August 1, 2014
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JW, this is one of the most blatant examples of taking a statement out of context. Why don't you be honest and provide details on what Dan Graur said before and after the couple sentences that you present here?Acartia_bogart_{August 1, 2014
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Supplemental videos
Human Anatomy - Impressive Transparent Visualization - Fearfully and Wonderfully Made - video http://vimeo.com/26011909 Introduction to Cells - Anatomy - video http://www.youtube.com/watch?v=gFuEo2ccTPA
bornagain77_{August 1, 2014
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As soon as I read the study I saw their severe bias.
DNA mostly 'junk?' Only 8.2 percent of human DNA is 'functional', study finds - July 24, 2014 Excerpt: To reach their (8.2%) figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution -- a clear indication that this DNA matters, it has some important function that needs to be retained. http://www.sciencedaily.com/releases/2014/07/140724141608.htm
i.e. So according to these Darwinian critics of the ENCODE study which found widespread functionality for 'junk' DNA, in their scheme of things functionality does not determine if a sequence is actually functional, only 'conservation of sequence' determines what is functional in their scheme???, So basically, only if Darwinian evolution is assumed as true will Darwinists accept that a given sequence of 'junk' DNA may be functional!,, That is called 'assuming your conclusion into you premise' and is horrible science! It should also be noted that these two following studies came out at about the same time as the severely biased 8.2% study from Darwinists. Studies that had drastically different conclusions as to the functionality of the supposed 'junk' DNA.
Junk DNA not as worthless as once thought - 07/24/2014 Excerpt: As early as 2007,, Hackermüller, together with a number of colleagues, was able to demonstrate,, practically the entire genome (is transcribed into RNA—a template which normally serves the production of proteins), even those areas which are completely neglected when looking at blueprints for proteins. Hackermüller: "This finding gave rise to a lively discussion as to whether this could be caused by chance events or mistakes in the regulation of cellular processes. However, I doubt that nature is so wasteful with resources that it would produce such masses of RNA for no specific reason.” In their latest study,, Hackermüller and his team,, were able to bridge yet another knowledge gap. The transcription of non-coding regions in the genome is precisely regulated by cellular signaling pathways—and on a grand scale: up to 80% of the RNA copies were non-coding. "We did not expect such a magnitude," says Hackermüller. "This is not indicative of a chance product—it is highly likely that the non-coding RNAs perform a similarly important functions to that of protein-coding RNA." http://www.rdmag.com/news/2014/07/junk-dna-not-worthless-once-thought?et_cid=4064233&et_rid=653535995&location=top Illuminating the dark side of the genome - July 29, 2014 Excerpt: "Almost 50 percent of our genome is made up of highly repetitive DNA, which makes it very difficult to be analysed. In fact, repeats are discarded in most genome-wide studies and thus, insights into this part of the genome remained limited. Scientists from the Max Planck Institute of Immunobiology and Epigenetics (MPI-IE) in Freiburg now succeeded in examining this dark side of the genome. Their analyses revealed that repeat-associated heterochromatin is essential to repress retrotransposons and thereby protects the genomic integrity of stem cells. This work opens the way for future genome-wide analyses of repetitive regions in the genome and is in line with newly emerging functions for heterochromatin." http://phys.org/news/2014-07-illuminating-dark-side-genome.html
In pointing out how far off base Darwinists are in their insistence that most of the sequences in DNA are junk, it is good to reflect on just how little we know.,,,
One Body - animation - video http://www.youtube.com/watch?v=pDMLq6eqEM4
As to how a single cell of a billion protein molecules turns into a human of trillions of cells, at roughly a billion trillion molecules total, nobody, and I repeat NOBODY, has a solid clue as to how this 'miracle', (and I don't use that word lightly), is pulled off.
HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,, Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling... and so on without end. Yet the coherence of the whole is maintained. The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary. Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way: "The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)",,, And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,, http://www.netfuture.org/2012/May1012_184.html#2
Talbott is certainly not alone in his assessment;
Alexander Tsiaras: Conception to birth — visualized – video http://www.youtube.com/watch?v=fKyljukBE70 Mathematician Alexander Tsiaras on Human Development: "It's a Mystery, It's Magic, It's Divinity" - March 2012 Excerpt: 'The magic of the mechanisms inside each genetic structure saying exactly where that nerve cell should go, the complexity of these, the mathematical models on how these things are indeed done, are beyond human comprehension. Even though I am a mathematician, I look at this with the marvel of how do these instruction sets not make these mistakes as they build what is us. It's a mystery, it's magic, it's divinity.' http://www.evolutionnews.org/2012/03/mathematician_a057741.html
Alexander Tsiaras is not exaggerating in the least:
“Complexity Brake” Defies Evolution – August 2012 Excerpt: “This is bad news. Consider a neuronal synapse — the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse — about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years…, even though it is assumed that the underlying technology speeds up by an order of magnitude each year.”,,, Even with shortcuts like averaging, “any possible technological advance is overwhelmed by the relentless growth of interactions among all components of the system,” Koch said. “It is not feasible to understand evolved organisms by exhaustively cataloging all interactions in a comprehensive, bottom-up manner.” He described the concept of the Complexity Brake:,,, “Allen and Greaves recently introduced the metaphor of a “complexity brake” for the observation that fields as diverse as neuroscience and cancer biology have proven resistant to facile predictions about imminent practical applications. Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge.”,,, to read more go here: http://www.evolutionnews.org/2012/08/complexity_brak062961.html
Thus, despite the sheer hubris of Darwinists to declare the vast majority of our DNA junk before we have even had a chance to study it in any meaningful way, the fact of the matter is that the complexity being dealt with in molecular biology is far, far, beyond anything man has ever encountered before, and certainly far from being understood,,,, much less are Darwinists anywhere close to giving a rational explanation as to how that unfathomable complexity, of how a single cell turns into trillions of cells functioning as a whole, came about. Despite what Darwinists dogmatically claim to the contrary, the plain truth of the matter is that everyone of you are fearfully and wonderfully made: Verse and Music:
Psalms 139:14) I praise you because I am fearfully and wonderfully made. MercyMe - Beautiful http://www.youtube.com/watch?v=1vh7-RSPuAA
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