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Fights back.

Well, that seems to be what’s happening. Further to: New York Times science writer defends junk DNA (Old concepts die hard, especially when they are value-laden as “junk DNA” has been—it has been a key argument for Darwinism), one of the conundrums on which the junk DNA folk rely heavily is the “onion test” (why does the onion have such a large genome?). Without waiting to answer the question, the junk DNA folk assume that that’s because most of it is junk.

But let’s face it, when even Francis Collins, the original Christian Nobelist for Darwin, is abandoning ship, they really need to double down on that junk.

From Evolution News & Views:

What’s so striking about Zimmer’s current piece is his explicit worry that — should “junk” DNA turn out to be functional — the “creationists” (as he calls the baddies) would be vindicated. At least twice in this long article, Zimmer raises the alarm that genomes had BETTER be junky, OR…the bad guys will win. It’s the same anxiety driving Dan Graur and Lawrence Moran into their fits of rage about ENCODE.

Hence in a not-so-subtle way, project ENCODE researchers are put on notice that, should they continue looking for function in non-coding DNA, they will be traitors to evolution and science.

Doubtless, the ENCODE guys have already begun to stammer and splutter. That’s what tends to happen when Darwin’s boys arrive (except here). For ENCODE, when they could afford to be open, see, for example:

Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire

Junk DNA’s defender doesn’t “do” politeness (No, we bet not.)

and

At least Forbes.com’s John Farrell, while trashing Jonathan Wells’ The Myth of Junk DNA, doesn’t threaten to actually read the book, the way some do.

For free highlights of the junk DNA uproar, see:

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

Hey, by the time you can’t tell the difference between Darwin’s elite followers and his trolls, you know something is happening.

Plus, pass the chocs, will you?

File:A small cup of coffee.JPG Anyone else for the myth of junk DNA? Richard Dawkins, for one (Reliable Source Central 😉 )

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Comments
harry: RNA is an unreliable storage device, used for transient, not permanent memory. It lacks error correction and detection in the copying process. That is why DNA is necessary. Apparently not. See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: “Amplification of 10^100-fold was achieved over a period of 37.5 hr”.Zachriel
March 14, 2015
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An inexplicable fit of intellectual honesty from the abiogenesis crowd:
A pile of bricks does not make a cathedral, and a collection of organic molecules does not make a living cell. There is presently no such thing as a "primitive" cell. There is no experiment that produces anything resembling living things. Imagine a junk yard with bits and pieces of metal of various shapes. Then think of a modern automobile with GPS and onboard computer, and a voice telling you to fasten your seat belt. That is roughly the distance between the organic matter seen in experiments simulating early-Earth conditions and the life forms now extant. -- http://earthguide.ucsd.edu/virtualmuseum/virtualmuseum/PrebioticSoup.shtml
UCSD isn't exactly known for being a bastion of Young Earth Creationism. Zachriel, RNA is an unreliable storage device, used for transient, not permanent memory. It lacks error correction and detection in the copying process. That is why DNA is necessary. You don't get life until the contents of DNA memory contains the assembly instructions for the protein machines required for cellular metabolism and reproduction.harry
March 14, 2015
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"Junk DNA" is the genetic code at universal level when it is called Matrix which contains the biological code called DNA. What is called "junk DNA" is the memory of 10 billions years of universal evolutionary history before life's origins. The long repetitions of same letters means that evolution at astronomical level is too much slow in relation to time of biological level and every Matrix's evolutionary jump needs to register the changes occurring at the whole space and time. And the DNA is being observed by humans and their scientific instruments only at its horizontal material visible by visible light, but the DNA is built vertically by seven dimensions encompassing all seven differents vibrational states of natural light. So, the evolution of DNA at one dimension is dependable from the evolution at others dimensions, ans all evolutionary dimensions need be registered, that why sometimes the DNA is fulfilled with long repetitions of letters waiting the events at other dimensions. By the same motive that a human body can not exist without its bone skeleton and the code inherited from ancestors, the active regions of human DNA can not be supported without the skeleton's DNA, mistakenly called "junk". Disease like cancers when a cell is repetitive ad infinitum without control is also a problem about faults of dimension's connections. That's the nowaday state of investigation by Matrix/DNA Theory method. There is no "Darwinist evolution", but a long universal process of genetic reproduction of the unknown natural system that triggered the Big Bang ( if you want call it God or Nothing, no problem, fell free) , which is accomplished by several steps of micro-evolution and that contains the mechanisms pointed out by Darwin a lot more. There is previous design for the universal natural system being developed here, but it is a natural process without the needs of a intelligent designer, like mother giraffe is able to produce a new baby giraffe without applying intelligence.Louis C. Morelli
March 13, 2015
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harry: The probabilistic resources of the entire universe are inadequate to produce even one 150 amino acid protein by chance. Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001. These proteins are only 80 in length, but they can be made as long as you like. harry: Given that, there is still a huge gap that must be mindlessly and accidentally crossed over between replicating units of chemical activity and the arrival of a digital-information storage device.</i. RNA is a digital storage device. An RNA replicator contains the information necessary to replicate itself, and can certainly include the ability to forge peptides that might aid in that replication.Zachriel
March 13, 2015
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Zachriel @116 Let me try to convey to you the big picture. The probabilistic resources of the entire universe are inadequate to produce even one 150 amino acid protein by chance. What will make life possible is a digital-information storage device that contains the assembly instructions for the protein machines required for metabolism and reproduction. Life just isn't going to happen without such information being readily available. How do we arrive at that by chance when all matter can do is work its way towards a more probable state, which is definitely not that of a digital-information storage device? What needs to happen is that a mechanism to constructively harness the sun's energy must spontaneously arise so our project can begin. So let's assume that miraculously happens in the form of an environment that allows for, and continues to sustain, self-replicating units of chemical activity. Given that, there is still a huge gap that must be mindlessly and accidentally crossed over between replicating units of chemical activity and the arrival of a digital-information storage device. There is another huge gap between a digital-information storage device containing gibberish and one the contents of which are functional information. That functional information isn't going to evolve without machinery to utilize the contents of the storage device's memory. That machinery isn't going to evolve along with the evolution of the storage device, or afterwards, because such machinery can provide no selectable advantage while the contents of memory are gibberish. We don't have a selectable advantage until the contents of memory contain functional information and the machinery exists to constructively utilize it. That isn't ever going to happen mindlessly because you can't get the functional information without the machinery and the machinery can't evolve unless it provides some selectable advantage, which it can't because accessing/copying gibberish only wastes energy.harry
March 13, 2015
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Let's look at your original question. harry: what would have been the selectable advantage of some sort of digital-information storage device, a precursor of the DNA molecule, unless it actually contained functional information that was accessible? The functional information is the function of replication. harry: It doesn’t matter at all if the storage device and the replicator are one device. The problem remains: How did the replicator portion of the device evolve? Those replicators that are best able to make use of the available raw materials and energy would tend to predominate in a population. harry: There is no selectable advantage in reading and copying what is as yet still gibberish, not functional information; that only wastes energy. It's not gibberish. It's a functional self-replicator. harry: “there was as yet no selectable advantage” should have been “there was no selectable advantage”. Once there is replication, there is selectable advantage.Zachriel
March 12, 2015
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harry @114 Oops. "there was as yet no selectable advantage" should have been "there was no selectable advantage". There was never going to be a selectable advantage in accessing/copying gibberish. ;o)harry
March 12, 2015
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Zachriel @109,
RNA and kin can act as both information storage and replicator. That answers harry's objection.
It doesn't matter at all if the storage device and the replicator are one device. The problem remains: How did the replicator portion of the device evolve? There is no selectable advantage in reading and copying what is as yet still gibberish, not functional information; that only wastes energy. And how did the contents of the digital-information-storage component of the single device evolve into functional information without a mechanism to access/alter it (whether that mechanism was physically a component of same device or not), since there was as yet no selectable advantage in accessing/copying gibberish, so no such mechanism would evolve? Again: Mindless evolutionary processes can arrive at neither the functional information nor the mechanism to utilize it in the absence of the other. Why would matter assemble itself into digital-information storage functionality at all, regardless of whether that was a separate device or a component of another? There is a chasm that cannot crossed over mindlessly between the beginning of a natural evolutionary process lacking foresight, and the point where having such a digital-information storage device becomes a selectable advantage.harry
March 12, 2015
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Piotr, It remains that your position cannot account for any genomes. Perhaps you chumps should focus on that.Joe
March 12, 2015
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#104 PaV, Hey! You, in the hole -- stop digging! There are some polyploids (including allopolyploids) among the 750 or so species of Allium, but the common onion, A. cepa, the species featured in the Onion Test, is not one of them. What made you think it was an allopolyploid? T. Ryan Gregory wanted to compare like with like, so he chose the diploid common onion for comparison with diploid Homo sapiens. While we are at it, polyploid plants can have really huge genomes. The current record-holder is the Japanese canopy plant, Paris japonica (almost 150 billion base pairs, 50 times more than in humans). It is an octaploid, but even if you correct for the ploidy effect, each of its sets of chromosomes is still 12 times bigger than the human set.Piotr
March 12, 2015
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Cross: His referee disagrees. Referee 1: Eugene Koonin Sure, though Koonin tends to be an outlier. Koonin (2012): To wit, no one has achieved bona fide self-replication of RNA which is the cornerstone of the RNA World. Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: "Amplification of 10^100-fold was achieved over a period of 37.5 hr" However, that doesn't necessarily mean RNA was the original replicator. The experiment was highly contrived. The original replicator may have been a related polymer. However, the fact that RNA can act as both enzyme and genetic memory is proof of principle, answering a common objection (Koonin, harry). Cross: Something had to start replication to kick of evolution, RNA world is full of holes RNA World is certainly wrong, or at least incomplete.Zachriel
March 12, 2015
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Zachriel @ 109 His referee disagrees "Referee 1: Eugene Koonin I basically agree with Bernhardt. The RNA World scenario is bad as a scientific hypothesis: it is hardly falsifiable and is extremely difficult to verify due to a great number of holes in the most important parts. To wit, no one has achieved bona fide self-replication of RNA which is the cornerstone of the RNA World." I read this as a bad hypothesis that is full of holes. Then the materialist manifesto rears its head. "the RNA World appears to be an outright logical inevitability. ‘Something’ had to start efficiently replicating to kick off evolution, and proteins do not have this ability" Something had to start replication to kick of evolution, RNA world is full of holes but it must be right because the answer must be material, can't let a divine foot in the door. Just so. CheersCross
March 12, 2015
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Cross: Hopeful just so story, and evidence? RNA and kin can act as both information storage and replicator. That answers harry's objection. Cross: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/ We agree that proteins may have coevolved with RNA or kin. We disagree that the hypothesis is "probably unprovable".Zachriel
March 12, 2015
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Zachriel @ 103 "The self-replicating units, possibly RNA or kin, are posited to be both the “digital-information storage device” and the replicator." Hopeful just so story, and evidence? "The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/ CheersCross
March 11, 2015
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So, BA, biological function at the cellular level are generally carried out by complexes of proteins...this adds nothing to the conversation. Repair enzymes are still diffusing around the cell, they bind damaged DNA and recruit a complex of proteins to the site that actually carry out the repair function. Congratulations on another completely pointless post that lacks any intelligence on your part.Curly Howard
March 11, 2015
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PaV: Angiosperms, flowering plants/trees, generally have much smaller genome sizes. Onions are angiosperms. http://th00.deviantart.net/fs70/PRE/i/2012/267/1/9/honey_bee_on_flowering_onion_2_by_greyrowan-d5fs0oy.jpgZachriel
March 11, 2015
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What I'm saying is that onions are diploid (2n=16). I have no earthly idea what you are saying.wd400
March 11, 2015
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Pedantry has nothing to do with it.
Oh, but it does. You're trying to say that an onion is allopolyploid, and not polyploid, without actually coming out and saying so. You're playing games. Where are we in all of this? Well, the Darwinist's point in all of this is to announce that there is an excessive amount of DNA in the onion---as compared to humans, e.g.---thus demonstrating the truth that huge amounts of ncDNA in the genome "proves" that ID is wrong and that neo-Darwinism is right. Well, this Darwinian perspective is completely unfounded. First, it's not a lot of ncDNA; it is copied chromosomes, which have regulatory regions and coding regions throughout. So, it demonstrates nothing of the kind when it comes to the fundamental point neo-Darwinists want to make. IOW, why should the fact that chromosomes can, and are, duplicated, have anything to do with the Mendelian inheritance of traits,per se? There is no correlation between the two. That is, chromosomes are not producing or eliminating 'traits,' they're simply being duplicated. There's more of them---but it's the same "them." So, this means that some other explanation must be found for this polyploidy (allopolyploidy) since were dealing with things that are happening not at the nucleotide level, but at the chromosomal level. Accordingly, I supplied several ways of understanding what is at play here. I've mentioned that plants, unlike most animals, are sessile. When it comes to food and hydration, this can be a problem that plants have that many animals don't have. So, maybe there is a need to be able to ramp up protein production quickly when conditions are favorable for the plant. You might disagree, but at least this makes some sense. Additionally, over at ENV, Jonathan Wells writes:"There is a strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus -- which affects the rate of cell growth and division. ". Angiosperms, flowering plants/trees, generally have much smaller genome sizes. Putting this all together, and especially following what Wells has written, when it comes to plants that produce "seeds" that have lots of water, it might be necessary to have cells that are filled with larger amounts of water--hence, larger sized---and so to maintain their metabolism, they duplicate their choromosomes so as to compensate for their smaller concentration in a more hydrated cell environment. Now, what I've written is plausible, and possibly correct. I'm sure you're ready to dismiss all of this. But before you do, let me quote this from Wikipedia from their thread on 'polyploidy':
The mechanisms leading to novel variation in newly formed allopolyploids may include gene dosage effects (resulting from more numerous copies of genome content), the reunion of divergent gene regulatory hierarchies, chromosomal rearrangements, and epigenetic remodeling, all of which affect gene content and/or expression levels.[28][29][30][31] Many of these rapid changes may contribute to reproductive isolation and speciation. However seed generated from interploidy crosses, such as between polyploids and their parent species, usually suffer from aberrant endosperm development which impairs their viability,[32][33] thus contributing to polyploid speciation.
This is my last statement on all of this. I don't care to respond any further to your nitpicking senselessness.PaV
March 11, 2015
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harry: When lifeless, yet self-replicating units of some kind of chemical activity were supposedly mindlessly and accidentally evolving into that first single-celled, reproducing life form, what would have been the selectable advantage of some sort of digital-information storage device, a precursor of the DNA molecule, unless it actually contained functional information that was accessible? The self-replicating units, possibly RNA or kin, are posited to be both the "digital-information storage device" and the replicator.Zachriel
March 11, 2015
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as to: "The repair enzymes diffuse around the cell and recognize DNA errors." actually:
No, Scientists in Darwin's Day Did Not Grasp the Complexity of the Cell; Not Even Close - Casey Luskin - June 6, 2013 Excerpt: 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) http://www.evolutionnews.org/2013/06/did_scientists_072871.html
and:
Protein Researchers Unravel the Molecular Dance of DNA Repair - March 2012 Excerpt: Using state-of-the-art technology, scientists at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen and their international collaborators have successfully obtained molecular snapshots of tens of thousands processes involved in DNA damage repair.,,, "We first damaged the DNA of cells using radiation or chemical drugs and then used a technique called mass spectrometry, which is a way of precisely determining the identity of proteins and their chemical modifications," Petra Beli says. "This allowed us to follow thousands of protein modifications that happened in the process of DNA repair, shedding new light on how the networks of biochemical signals are regulated and how the infrastructure of alerts works." The data from the experiments is so extensive that it will require much further work by researchers to fully understand the significance and impact of these newly identified signaling pathways. http://www.sciencedaily.com/releases/2012/03/120315123022.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
bornagain77
March 11, 2015
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I can assure you, PaV, that I'm very genuine in my ability to extract anything of meaning from that sentence. Pedantry has nothing to do with it. All I can do is encourage you to remove yourself from your armchair and learn a little about what biologists have done on the evolution of genome size.wd400
March 10, 2015
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Congratulations BA, you can copy/paste from Wikipedia. The problem with your analogy is that in the DNA repair system there are multiple salesmen. There's no need for any of your quantum computation crap. The repair enzymes diffuse around the cell and recognize DNA errors. You are off your rocker. I don't even know why I bother. Banging my head against a wall would be more productive than talking to you, Joe, Mapou, etc. Enjoy your time on cloud nine!Curly Howard
March 10, 2015
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The reason why finding the final form of a folded protein is so hard for supercomputers is that it is like the ‘traveling salesman’ problem, which are ‘Just about the meanest problems you can set a computer (on) ‘.
DNA computer helps traveling salesman - Philip Ball - 2000 Excerpt: Just about the meanest problems you can set a computer belong to the class called 'NP-complete'. The number of possible answers to these conundrums, and so the time required to find the correct solution, increases exponentially as the problem is scaled up in size. A famous example is the 'travelling salesman' puzzle, which involves finding the shortest route connecting all of a certain number of cities.,,, Solving the traveling-salesman problem is a little like finding the most stable folded shape of a protein's chain-like molecular structure -- in which the number of 'cities' can run to hundreds or even thousands. http://www.nature.com/news/2000/000113/full/news000113-10.html
And protein folding is found to be 'NP-complete'
Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results – 2009 Excerpt: Protein Folding: Computational Complexity 4.1 NP-completeness: from 10^300 to 2 Amino Acid Types 4.2 NP-completeness: Protein Folding in Ad-Hoc Models 4.3 NP-completeness: Protein Folding in the HP-Model http://www.cs.brown.edu/~sorin/pdfs/pfoldingsurvey.pdf
Thus we have very good circumstantial evidence that proteins are very likely finding their final folded form by some method of quantum computation. ,,,, If so, as seems very reasonable to believe at this point, then this far exceeds anything man has yet accomplished in regards to quantum computation, although billions of dollars have been spent trying to build better quantum computers! Of related note: Here is the paper that proved that protein folding belongs to the physics of the quantum world and that protein folding does not belong to the physics of the classical world:
Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/
Moreover, the fact that ‘non-local’ quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints (Bell, Aspect, Leggett, Zeilinger, etc..), should be found in molecular biology on such a massive scale, in every DNA and protein molecule, is a direct empirical falsification of Darwinian claims, for how can the ‘non-local’ quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) cause when the quantum entanglement effect falsified material particles as its own causation in the first place? Appealing to the probability of various 'random' configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply!
Looking beyond space and time to cope with quantum theory – 29 October 2012 Excerpt: “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,” http://www.quantumlah.org/highlight/121029_hidden_influences.php etc.. etc..
In other words, to give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, one cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! And although Naturalists have proposed various, far fetched, naturalistic scenarios to try to get around the Theistic implications of quantum non-locality, none of the ‘far fetched’ naturalistic solutions, in themselves, are compatible with the reductive materialism that undergirds neo-Darwinian thought.
"[while a number of philosophical ideas] may be logically consistent with present quantum mechanics, ...materialism is not." Eugene Wigner Quantum Physics Debunks Materialism - video playlist https://www.youtube.com/watch?list=PL1mr9ZTZb3TViAqtowpvZy5PZpn-MoSK_&v=4C5pq7W5yRM Why Quantum Theory Does Not Support Materialism By Bruce L Gordon, Ph.D Excerpt: The underlying problem is this: there are correlations in nature that require a causal explanation but for which no physical explanation is in principle possible. Furthermore, the nonlocalizability of field quanta entails that these entities, whatever they are, fail the criterion of material individuality. So, paradoxically and ironically, the most fundamental constituents and relations of the material world cannot, in principle, be understood in terms of material substances. Since there must be some explanation for these things, the correct explanation will have to be one which is non-physical – and this is plainly incompatible with any and all varieties of materialism. http://www.4truth.net/fourtruthpbscience.aspx?pageid=8589952939
Thus, as far as empirical science itself is concerned, Neo-Darwinism is falsified in its claim that information is ‘emergent’ from a material basis. Verse and Music:
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through Him, and without Him nothing was made that was made. In Him was life, and the life was the light of men. Michael W. Smith - You Won't Let Go (Lyric Video) https://www.youtube.com/watch?v=MRb_NIQTzyA
bornagain77
March 10, 2015
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Curly Howard, the reason why quantum computation is implicated in this particular DNA repair process,,,
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
,,, is not because of quantum dots, but is because of the traveling salesman problem. First off, to show how quantum computation is possible in DNA, lets back up a bit and learn that DNA has now been shown to have quantum entanglement within it:
Quantum Information/Entanglement In DNA - short video https://vimeo.com/92405752
Moreover, it is important to also learn that ‘non-local’, beyond space and time, quantum entanglement (A. Aspect, A. Zeilinger, etc..) can be used as a ‘quantum information channel’,,,
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/
Thus it is possible, since DNA has quantum entanglement lengthwise along its entire axis, that entire DNA molecule is performing quantum computation of some sort. But how do we verify if it is? Well, back to our example. 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 Excerpt: Another example of an NP-hard problem is the optimization problem of finding the least-cost cyclic route through all nodes of a weighted graph. This is commonly known as the traveling salesman problem. - per wikipedia
Yet it is exactly this type of ‘traveling salesman problem’ that quantum computers excel at:
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
Since it is obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely ‘material’ fashion, by crunching bits, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, must somehow be solved by ‘non-local’ quantum computation within the cell and/or within DNA itself; Moreover, we also have evidence of quantum computation solving the 'travelling salesman problem' within protein folding: It is known that proteins do not find their final folded form by random processes:
The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications - Paul Nelson - October 23, 2012 Excerpt: Anyone who has studied the protein folding problem will have met the famous Levinthal paradox, formulated in 1969 by the molecular biologist Cyrus Levinthal. Put simply, the Levinthal paradox states that when one calculates the number of possible topological (rotational) configurations for the amino acids in even a small (say, 100 residue) unfolded protein, random search could never find the final folded conformation of that same protein during the lifetime of the physical universe. Therefore, concluded Levinthal, given that proteins obviously do fold, they are doing so, not by random search, but by following favored pathways. The challenge of the protein folding problem is to learn what those pathways are. http://www.evolutionnews.org/2012/10/a_revolutionary065521.html Confronting Science’s Logical Limits – John L. Casti – 1996 Excerpt: It has been estimated that a supercomputer applying plausible rules for protein folding would need 10^127 years to find the final folded form for even a very short sequence consisting of just 100 amino acids. (The universe is 13.7 x 10^9 years old). In fact, in 1993 Aviezri S. Fraenkel of the University of Pennsylvania showed that the mathematical formulation of the protein-folding problem is computationally “hard” in the same way that the traveling-salesman problem is hard. http://www.cs.virginia.edu/~robins/Confronting_Sciences_Logical_Limits.pdf
That no one really has a firm clue how proteins are finding their final folded form is made clear by the immense time (a few weeks) it takes for a few hundred thousand computers, which are linked together, to find the final folded form of a single protein:
A Few Hundred Thousand Computers vs. (The Folding Of) A Single Protein Molecule – video https://www.youtube.com/watch?v=lHqi3ih0GrI
bornagain77
March 10, 2015
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Have you figured out why you think "quantum computation is somehow involved in the repair process," BA? It's not just because you saw "quantum dots" is it? How are things over at the funny-farm anyways?Curly Howard
March 10, 2015
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For those who want to do some reading on genetic load... how accurate the calculations are...and how lucky we really are to have junk DNA or else we'd have been extinct millions of years ago... agrawal.eeb.utoronto.ca/files/2013/06/afa_mcw_2012.pdfQuest
March 10, 2015
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Curly at 89 asks: "Molecules can’t think, can you?" I wish you, and other Darwinists, would honestly ask yourself that question Curly:
Why Evolutionary Theory Cannot Survive Itself - Nancy Pearcey - March 8, 2015 Excerpt: Steven Pinker writes, "Our brains were shaped for fitness, not for truth. Sometimes the truth is adaptive, but sometimes it is not." The upshot is that survival is no guarantee of truth. If survival is the only standard, we can never know which ideas are true and which are adaptive but false. To make the dilemma even more puzzling, evolutionists tell us that natural selection has produced all sorts of false concepts in the human mind. Many evolutionary materialists maintain that free will is an illusion, consciousness is an illusion, even our sense of self is an illusion -- and that all these false ideas were selected for their survival value. So how can we know whether the theory of evolution itself is one of those false ideas? The theory undercuts itself.,,, Of course, the atheist pursuing his research has no choice but to rely on rationality, just as everyone else does. The point is that he has no philosophical basis for doing so. Only those who affirm a rational Creator have a basis for trusting human rationality. The reason so few atheists and materialists seem to recognize the problem is that, like Darwin, they apply their skepticism selectively. They apply it to undercut only ideas they reject, especially ideas about God. They make a tacit exception for their own worldview commitments. http://www.evolutionnews.org/2015/03/why_evolutionar094171.html
bornagain77
March 10, 2015
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harry @ 63 "When lifeless, yet self-replicating units of some kind of chemical activity were supposedly mindlessly and accidentally evolving into that first single-celled, reproducing life form, what would have been the selectable advantage of some sort of digital-information storage device, a precursor of the DNA molecule, unless it actually contained functional information that was accessible? Yet how would its contents evolve into such functional information without machinery exterior to it that could read and write the memory? And why would such machinery evolve while the contents of the storage device’s memory were still gibberish, and reading and writing it was just a waste of energy? Mindless evolutionary processes can arrive at neither the functional information nor the machinery to access it in the absence of the other. In other words, life just isn’t going to happen mindlessly and accidentally." Exactly, but you note that the materialists posting here will ignore the hard bits they can't explain. CheersCross
March 10, 2015
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It looks like Dan Graur finally removed his embarrassing rhetoric on Junk DNA: If @ENCODE_NIH is right, each of us should have 7 x 10^45 children... http://judgestarling.tumblr.com/post/106833397831/if-encode-nih-is-right-each-of-us-should-have I guess he finally updated his total lack of knowledge on genetic load....Quest
March 10, 2015
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Right. I'm not getting it, I'm just sitting here explaining things to you, Box.Curly Howard
March 10, 2015
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