Uncommon Descent Serving The Intelligent Design Community

Dan Graur Gave a Great Talk This Week


Evolution has always had a love-hate relationship with biological junk. When scientists discover something new in biology but don’t understand it, evolutionists—who believe everything in the universe just happened to form by chance—decide it is a useless evolutionary leftover. Such a useless design is pressed into service as an evolution apologetic. Is not our useless and dangerous appendix yet another proof text of Darwinism? Later, when the function is eventually uncovered, evolutionists begrudgingly admit to it while maintaining that its clumsiness still proves evolution. As Richard Dawkins explained, in response to the growing knowledge of how well our “backward” retina works, “it is the principle of the thing that would offend any tidy-minded engineer!” Just because it works doesn’t mean it isn’t junk. And whatever function it is lucky to have is claimed as an evolutionary achievement—an obvious example of the power of natural selection.  Read more

Here is evidence for 'top down' control of the genome that neo-Darwinists will ignore because of their a-priori philosophical commitment to reductive materialism (i.e. their commitment to atheism): Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information - Jonathan Wells - published online May 2013 Conclusion:,, Recent discoveries of multiple overlapping functions in non-protein-coding DNA show that the biological information in the genome far exceeds that in the protein-coding regions alone. Yet biological information is not limited to the genome. Even at the level of gene expression - transcription and translation — the cell must access information that is not encoded in DNA. Many different RNAs can be generated from a single piece of DNA by alternative splicing, and although some splicing codes occur in intronic DNA there is no empirical justification for assuming that all of the information for tissue- and developmental-stage-specific alternative splicing resides in DNA.,, even after RNA has specified the amino acid sequence of a protein, additional information is needed: Protein function depends on three-dimensional shape, and the same sequence of amino acids can be folded differently to produce proteins with different three-dimensional shapes [144–147]. Conversely, proteins with different amino acid sequences can be folded to produce similar shapes and functions [148,149]. Many scientists have pointed out that the relationship between the genome and the organism - the genotype-phenotype mapping = cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. So non-protein-coding regions of DNA that some previously regarded as “junk” turn out to encode biological information that greatly increases the known information-carrying capacity of DNA. At the same time, DNA as a whole turns out to encode only part of the biological information needed for life. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0009 Multidimensional Genome – Dr. Robert Carter – video (Notes in video description) http://www.metacafe.com/w/8905048 Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm bornagain77
corrected link: Proof reading of DNA polymerase (Reduces error rate to 1 in 100 million) - video http://www.youtube.com/watch?v=YcNhuYh34P4 bornagain77
Since it is readily apparent that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers (crunching bits) to this monster logistic problem, in a purely ‘material’ fashion, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by the ‘non-local’ quantum information/entanglement inherent within the cell; And indeed we have evidence that quantum information can accomplish exactly this type of extremely difficult computational problem:
Speed Test of Quantum Versus Conventional Computing: Quantum Computer Wins – May 8, 2013 Excerpt: quantum computing is, “in some cases, really, really fast.” McGeoch says the calculations the D-Wave excels at involve a specific combinatorial optimization problem, comparable in difficulty to the more famous “travelling salesperson” problem that’s been a foundation of theoretical computing for decades.,,, “This type of computer is not intended for surfing the internet, but it does solve this narrow but important type of problem really, really fast,” McGeoch says. “There are degrees of what it can do. If you want it to solve the exact problem it’s built to solve, at the problem sizes I tested, it’s thousands of times faster than anything I’m aware of. If you want it to solve more general problems of that size, I would say it competes — it does as well as some of the best things I’ve looked at. At this point it’s merely above average but shows a promising scaling trajectory.” http://www.sciencedaily.com/releases/2013/05/130508122828.htm
For those who think Quantum computation is not possible within the cell, I remind them that 'non-local', beyond space and time, quantum entanglement/information has now been found within molecular biology on a massive scale.:
Quantum Information/Entanglement In DNA - Elisabeth Rieper - short video http://www.metacafe.com/watch/5936605/ Quantum entanglement between the electron clouds of nucleic acids in DNA - Elisabeth Rieper, Janet Anders and Vlatko Vedral - February 2011 http://arxiv.org/PS_cache/arxiv/pdf/1006/1006.4053v2.pdf
Supplemental notes:
Quantum Entanglement and Information Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory. http://plato.stanford.edu/entries/qt-entangle/ Looking Beyond Space and Time to Cope With Quantum Theory - (Oct. 28, 2012) Excerpt: To derive their inequality, which sets up a measurement of entanglement between four particles, the researchers considered what behaviours are possible for four particles that are connected by influences that stay hidden and that travel at some arbitrary finite speed. Mathematically (and mind-bogglingly), these constraints define an 80-dimensional object. The testable hidden influence inequality is the boundary of the shadow this 80-dimensional shape casts in 44 dimensions. The researchers showed that quantum predictions can lie outside this boundary, which means they are going against one of the assumptions. Outside the boundary, either the influences can't stay hidden, or they must have infinite speed.,,, The remaining option is to accept that (quantum) influences must be infinitely fast,,, "Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them," says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,, http://www.sciencedaily.com/releases/2012/10/121028142217.htm
Celtic Woman - The last Rose of Summer http://www.youtube.com/watch?v=h-P15xujxoI
Among many problems with the Junk DNA scenario, if the genome was mostly junk as Darwinists contend, then it seems rather strange that there would be multiple overlapping DNA repair mechanism dedicated to preventing any 'random' changes from happening to this supposedly 'junk' DNA:
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 Proof reading of DNA polymerase (Reduces error rate to 1 in 100 million) - video http://www.youtube.com/watch?v=tOi88novQV0
The multiple overlapping repair mechanisms in DNA include:
A proofreading system that catches almost all errors A mismatch repair system to back up the proofreading system Photoreactivation (light repair) Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase Base excision repair Nucleotide excision repair Double-strand DNA break repair Recombination repair Error-prone bypass http://www.newgeology.us/presentation32.html 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 More DNA Repair Wonders Found - October 2010 Excerpt: This specialized enzyme may attract other repair enzymes to the site, and “speeds up the process by about 100 times.” The enzyme “uses several rod-like helical structures... to grab hold of DNA.”,,, On another DNA-repair front, today’s Nature described a “protein giant” named BRCA2 that is critically involved in DNA repair, specifically targeting the dangerous double-stranded breaks that can lead to serious health consequences http://www.creationsafaris.com/crev201010.htm#20101007a Extreme Genome Repair - 20 March 2009 Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal. http://www.sciencedirect.com/science/article/pii/S0092867409002657
The most spectacular example for DNA repair I have seen thus far is this:
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
Please note, DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.
NP-hard problem – Examples http://en.wikipedia.org/wiki/NP-hard#Examples

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