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PZ Myers, the self-described Paris Hilton of atheists, on junk DNA

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Here:

The authentic Word from Da Beard, and – as he isn’t a Christian Darwinist – you don’t need to start flinging sandals to hear it. (If you own any sandals.)

Here’s the real story on junk DNA.

Paris Hilton, in case you wondered. It could be your kid who gets … well, squished … in the cause of celebrity. What does that matter?

Comments
So paul, I'm beginning to catch the hang of this evolutionary biology stuff,,, 1. insertion events only count when they quasi-support a evolutionary position and don't count the vast majority on time when they support a design position. 2. The equations of population genetics only count when they support and evolutionary position (for calculating obscene percentages of junk DNA) and don't count the vast majority of times when they support the design position., And 3. experimental evidence for knocking your beloved Junk DNA out, since you have no knock out experiments to point to (not even in the mice experiments), NEVER EVER counts against the evolutionary position. I think that pretty much sums it up. Did I miss anything Paul???bornagain77
December 12, 2011
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paulmc, Without an experiment that removes the alleged junk- I don't care how much they remove at a time- then there isn't any evidence that it is junk. You want an evidenced-based argument-> do the experiment. Short of that you don't have one.Joe
December 12, 2011
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Haphazardly, like the majority of the insertions that occur that do have a notable phenotypic effect are deleterious, e.g. implicated in disease, and are not implicated in function.paulmc
December 12, 2011
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Perhaps you could take it as an "admission" that I want to discuss the topic of junk DNA, not everything in evolutionary biology under the sun. If you have any points on the topic of this thread - great. Otherwise, see you. You can disagree with my explanation for not simply removing 90% of the genome and expecting the emergence of the same phenotypes. But perhaps it would be more civil to do so by way of a logical, evidence-based argument rather than resorting to calling me "afraid" and "whining".paulmc
December 12, 2011
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see post 17bornagain77
December 12, 2011
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'haphazardly inserted' REALLY???
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
i.e. Why is it so important for you to believe, and push, that they were 'haphazardly inserted' unless you were, contrary to your denial, pushing a unfounded atheistic interpretation that is motivated by ideology rather than science??? notes:
On Not Reading Signature in the Cell: A Response to Francisco Ayala Excerpt: Contrary to Ayala’s claim, Alu sequences (and other mammalian SINEs) are not distributed randomly but instead manifest a similar “bar-code” distribution pattern along their chromosomes (Chen and Manuelidis, 1989; Gibbs et al., 2004; Korenberg and Rykowski, 1988). Rather like the distribution of the backslashes, semi-colons and spaces involved in the formatting of software code, the “bar-code” distribution of Alu sequences (and other SINEs) reflects a clear functional logic, not sloppy editing or random mutational insertions. For example, Alu sequences are preferentially located in and around protein-coding genes as befits their role in regulating gene expression (Tsirigos and Rigoutsos, 2009). They occur mainly in promoter regions–the start sites for RNA production–and in introns, the segments that break up the protein-coding stretches. Outside of these areas, the numbers of Alu sequences sharply decline. Further, we now know that Alu sequences are directed to (or spliced into) certain preferential hotspots in the genome by the protein complexes or the “integrative machinery” of the cell’s information processing system (Levy et al., 2010). This directed distribution of Alu sequences enhances the semantic and syntactical organization of human DNA. It appears to have little to do with the occurrence of random insertional mutations, contrary to the implication of Ayala’s “sloppy editor” illustration and argument. (page down for 33 references of ALU functionality) http://www.stephencmeyer.org/news/2010/03/_this_is_part_2.html
bornagain77
December 12, 2011
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paulmc:
I understand that it suits you to believe this, but I have already answered this point. Changing the size of introns will mess with gene regulation, as intron length has the side effect of altering rates of expression.
Then those introns are NOT junk and you don't remove them. Geez all your whining about conducting an experiment exposes your anti-science agenda.Joe
December 12, 2011
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As I said until you go about removing all that you consider junk and get a functional organism to develop, you don’t have anything but speculation.
You can repeat this ‘remove all the junk’ stuff as many times as you like, and it doesn’t help make it a better answer than it was when I wrote this (see last paragraph).
Whatever Paul. Until you or someone conducts that experiment the claim of the majority of our genome is junk is total BS.
And you can talk about speculation all you want, but it should be obvious to the informed reader that there is much more than ‘speculation’ going on; there are several strong, independent lines of evidence that support the junk DNA inference.
Yet there is ONLY ONE WAY to confirm that inference and apparently people are too afraid to perform the experiment.
Can your framework explain a) why one species of onion requires 4x as much DNA as a similar and closely related species of onion within the same genus; and b) why junk accumulation is proportional to mutation rate x effective population size?
Dude, your framwork can’t even explain onions, nor functional genomes. Perhaps you should focus on that. Or actually perform the experiment I mentioned.
Back on topic,...
I will take that as an admission that your position cannot explain anything beyond broken things. BTW if the experiment I ask for cannot be done then the claim of junk DNA being the majority of the genome is total BS. And your whining is not going to change that.Joe
December 12, 2011
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REALLY??? Are we even on the same thread reading the same things??? Earth to paul,, WAKE UP!!!
I don't know. I think we're on a thread about junk DNA, you seem to think we're on a thread about anything you have a ready-made link for.paulmc
December 11, 2011
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Speaking of 'uphill battles', how's that refutation of Abel's Null Hypothesis working out???
Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, Testable hypotheses about FSC What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses: Null hypothesis #1 Stochastic ensembles of physical units cannot program algorithmic/cybernetic function. Null hypothesis #2 Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function. Null hypothesis #3 Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function. Null hypothesis #4 Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time. We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified. http://www.tbiomed.com/content/2/1/29 The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html The Law of Physicodynamic Incompleteness - David L. Abel - August 2011 Summary: “The Law of Physicodynamic Incompleteness” states that inanimate physicodynamics is completely inadequate to generate, or even explain, the mathematical nature of physical interactions (the purely formal laws of physics and chemistry). The Law further states that physicodynamic factors cannot cause formal processes and procedures leading to sophisticated function. Chance and necessity alone cannot steer, program or optimize algorithmic/computational success to provide desired non-trivial utility. http://www.scitopics.com/The_Law_of_Physicodynamic_Incompleteness.html The GS (genetic selection) Principle – David L. Abel – 2009 Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.” http://www.bioscience.org/2009/v14/af/3426/3426.pdf
bornagain77
December 11, 2011
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All you have is empty rhetoric describing my motivation as being 'atheist' and my reasoning as 'shallow excuses'. What part of the above very basic explanation do you find difficult to follow? Introns affect gene expression. We regularly identify new functional segments of DNA, something that won't slow down for a while. Both of these mean you can't simply remove 90% of the genome and expect no phenotypic effects. Neither of these things demonstrate function for a majority of the genome. Nor do they undermine the arguments for junk DNA. It simply means you can't do what you/Joe have proposed. Also, I'll ask you again, maybe you'll answer me this time: Can you explain how yet another copy of Alu haphazardly inserted in your genome would typically represent something functional? If you don’t think it would be functional, why do you believe something different for the other million copies of Alu?paulmc
December 11, 2011
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as to,,, You are making the assumption that 10-15% of the genome is not enough, but providing no reason for this, only incredulity (e.g. “undreamt level of jaw-dropping complexity”). REALLY??? Are we even on the same thread reading the same things??? Earth to paul,, WAKE UP!!! more notes for you to ignore:
Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." http://www.sciencedaily.com/releases/2009/06/090616103205.htm Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.html Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a
Also of interest is that a cell apparently seems to be successfully designed along the very stringent guidelines laid out by Landauer's principle of 'reversible computation' in order to achieve such amazing energy efficiency, something man has yet to accomplish in any meaningful way for computers:
Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf Programming of Life - Biological Computers - video http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/5/hRooe6ehrPs
further notes:
Michael Behe - Life Reeks Of Design - 2010 - video http://www.metacafe.com/watch/5066181
And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.
"There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist
The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,,
‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,,
Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,,
,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology
further note:
William Bialek - Professor Of Physics - Princeton University: Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," http://www.princeton.edu/~wbialek/wbialek.html
music:
Evanescence - Bring me to life (high quality) http://www.youtube.com/watch?v=9qlDveUeVNk
bornagain77
December 11, 2011
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so when it suits your atheistic purposes DNA is 85 to 95% junk/garbage, but when push comes to shove to actually prove your point scientifically then you have all sorts of shallow excuses as to why it is not really garbage that you can just remove! The hypocrisy in your reasoning is just oozing out of you!!!bornagain77
December 11, 2011
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Only in your imagination!
Not a blueprint: about the junk in your trunk Response to Jonathan Wells (when he wrote this). Population size, and the evolution of junk. Part I: Origins
As Joe said, if you can’t remove the 85% ‘garbage’ it ain’t junk! and It is thoroughly disingenuous of you to pretend that this basic fact does not undermine your whole contrived argument!
I understand that it suits you to believe this, but I have already answered this point. Changing the size of introns will mess with gene regulation, as intron length has the side effect of altering rates of expression. For this reason you cannot just remove them and expect no consequence. Also, there are unknown functional bits and pieces scattered through the genome - miRNAs and the like are regularly being discovered. Removing everything without known function will also remove these in the process. In other words, it is an experiment that will fail and it is not - nor has it ever been - a prediction of mine that such a thing could be soundly done. It is instead a ridiculous caricature of my position to claim that this is a sound avenue to test the junkiness of the mammalian genome.paulmc
December 11, 2011
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paul, so you don’t find declaring that 85%, upwards to 95%, of the DNA to be ‘garbage’, to use PZ’s word, to be obscene???
No, it is not obscene to present the reasoned inference that 85-90% of mammalian genomes lack current function. You are making the assumption that 10-15% of the genome is not enough, but providing no reason for this, only incredulity (e.g. "undreamt level of jaw-dropping complexity"). One of the many uphill battles on your side would be to explain how yet another copy of Alu haphazardly inserted in your genome represents an untold wonder of function, masterfully crafted by The Designer. If you don't believe it does, why do you believe something different for the other million copies?paulmc
December 11, 2011
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as to: there are several strong, independent lines of evidence that support the junk DNA inference. Only in your imagination! As Joe said, if you can't remove the 85% 'garbage' it ain't junk! and It is thoroughly disingenuous of you to pretend that this basic fact does not undermine your whole contrived argument!bornagain77
December 11, 2011
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As I said until you go about removing all that you consider junk and get a functional organism to develop, you don’t have anything but speculation.
You can repeat this 'remove all the junk' stuff as many times as you like, and it doesn't help make it a better answer than it was when I wrote this (see last paragraph). And you can talk about speculation all you want, but it should be obvious to the informed reader that there is much more than 'speculation' going on; there are several strong, independent lines of evidence that support the junk DNA inference.
Can your framework explain a) why one species of onion requires 4x as much DNA as a similar and closely related species of onion within the same genus; and b) why junk accumulation is proportional to mutation rate x effective population size?
Dude, your framwork can’t even explain onions, nor functional genomes. Perhaps you should focus on that. Or actually perform the experiment I mentioned.
Back on topic, I'll take that to mean your framework can't explain a) or b). That's fine, just checking.paulmc
December 11, 2011
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paul, so you don't find declaring that 85%, upwards to 95%, of the DNA to be 'garbage', to use PZ's word, to be obscene??? Actually from the choice of words I've could have used instead, considering the undreamt level of jaw-dropping complexity being discovered in DNA, that word was rather mild in response to your blatant materialistic delusions!!!,, Notes for you to ignore, and to pretend don't matter, once again:
Non-Local (beyong space and time) Quantum Information/Entanglement In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/ Quantum Computing in DNA – Stuart Hameroff Excerpt: Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.,,, We can then consider DNA as a chain of qubits (with helical twist). Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement. http://www.quantumconsciousness.org/views/QuantumComputingInDNA.html Falsification Of Neo-Darwinism by Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US 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 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm 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
Of 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 http://en.wikipedia.org/wiki/NP-hard
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, then it is readily apparent that this monster 'traveling salesman problem', for DNA repair, is somehow being computed by 'non-local' quantum computation within the cell and/or within DNA; Of related interest:
DNA Computer Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today's most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours. http://www.tech-faq.com/dna-computer.html
Music and Verse:
Sarah McLachlan - Answer – http://www.youtube.com/watch?v=i8B1ai25lUo 2 Thessalonians 2:3 Let no man deceive you by any means: for that day shall not come, except there come a falling away first,,
bornagain77
December 11, 2011
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junk DNA- yes if we take a 2 dimensional approach and say all DNA that does not code for some type of RNA is “junk”, then PaulMc, PZ, Larry Moran, et al., have a point.
This is not my position, nor is it PZ’s from his video, nor Larry’s from his writing.
So all DNA that doesn't code for some type of DNA is not junk?
For one, structural DNA does not fit under this description.
Can your position even explain structural DNA? Can it explain coding DNA? It sure seems good at explaining broken things.
For two, any definition should not include spurious, or junk transcripts – producing “some type of RNA” is not good enough.
That would be in addition to what I was talking about. The point being is there could be a basic need for stretches of DNA that do not code for any RNA.
There could be lots of things, but without evidence they remain idle speculation and peripheral to science.
Dude, the position the majority of our genome is junk and speculation and peripheral to science. As I said until you go about removing all that you consider junk and get a functional organism to develop, you don't have anything but speculation.
Can your framework explain a) why one species of onion requires 4x as much DNA as a similar and closely related species of onion within the same genus; and b) why junk accumulation is proportional to mutation rate x effective population size?
Dude, your framwork can't even explain onions, nor functional genomes. Perhaps you should focus on that. Or actually perform the experiment I mentioned.Joe
December 11, 2011
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junk DNA- yes if we take a 2 dimensional approach and say all DNA that does not code for some type of RNA is “junk”, then PaulMc, PZ, Larry Moran, et al., have a point.
This is not my position, nor is it PZ's from his video, nor Larry's from his writing. For one, structural DNA does not fit under this description. For two, any definition should not include spurious, or junk transcripts - producing "some type of RNA" is not good enough.
The point being is there could be a basic need for stretches of DNA that do not code for any RNA.
There could be lots of things, but without evidence they remain idle speculation and peripheral to science. Can your framework explain a) why one species of onion requires 4x as much DNA as a similar and closely related species of onion within the same genus; and b) why junk accumulation is proportional to mutation rate x effective population size?paulmc
December 11, 2011
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Obscene... interesting choice of words. If something about junk DNA offends you morally, I suspect that you are probably not in a good position to objectively evaluate the evidence! But thanks for the ironic bible quote - funny!paulmc
December 11, 2011
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paul, and yet for all your denial, you still support that obscenely huge portions of the DNA is junk! Go figure!!!
2 Peter 1:16 For we did not follow cleverly devised tales when we made known to you the power and coming of our Lord Jesus Christ, but we were eyewitnesses.
bornagain77
December 11, 2011
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junk DNA- yes if we take a 2 dimensional approach and say all DNA that does not code for some type of RNA is "junk", then PaulMc, PZ, Larry Moran, et al., have a point. HOWEVER Intelligent Design does NOT look at DNA in two dimensions as there are multiple levels of organization and information. Then there are structural constraints to be considered. The point being is there could be a basic need for stretches of DNA that do not code for any RNA.Joe
December 11, 2011
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Now paulmc, I have put up with more than my fair share of malarkey from you with your 95% junk DNA tripe,, and have put some very compelling evidence for you to consider on the table that shows you to be completely off base.
I'm sure you actually believe that, too. Yet, for some reason you continue to link to news stories about adaptation and the limits of positive selection, showing you don't understand the argument being made at all. I've already explained how positive selection is completely unrelated to the argument for putative genomic junk. In other words, what you think is compelling is at best tangential, but mostly irrelevant.
the true rule for all biological adaptations falls under the rigid principle of genetic entropy not under your ‘religion’ of neo-Darwinism.
I follow neoDarwinism as a religion? Do I need to remind you that half of your posts end with bible quotes? This is not only a mischaracterisation of my position, but comically ironic. And there you go with adaptations again. FWIW, I am fairly sceptical of the classical neoDarwinian basis of adaptation, although I don't think Austin Hughes provides a particularly compelling case against it (much of his other work is excellent, however). There are arguments for non-adaptive origins of complexity. What more can I say - read Fernandez & Lynch (2011).paulmc
December 11, 2011
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PaulMC, Thanks for responding. Is it safe to say that you and Francis Collins are not on the same page? Also, what do you think the teleological ramifications are for the junk DNA hypothesis. Do you think the science indicates that its all just a puddle of goo works very inefficiently and points to a random, purposeless history of life or is it too difficult to tell what any of it means, from a metaphysical viewpoint? Thanks in advance for your reply.wgbutler
December 9, 2011
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paulmc, the true rule for all biological adaptations falls under the rigid principle of genetic entropy not under your 'religion' of neo-Darwinism. Moreover, the following is what the empirical evidence, not your imaginary models, actually dictates for all biological adaptations,,,
A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html
Moreover paulmc, the principle of genetic entropy is in full compliance with the second law of thermodynamics and with law of conservation of information, with what we witness in the fossil record, as well as with what we witness in genetic population studies:
EXPELLED - Natural Selection And Genetic Mutations - video http://www.metacafe.com/watch/4036840 "...but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have..." Maciej Marian Giertych - Population Geneticist - member of the European Parliament - EXPELLED
The following 'should' interest you paulmc (though you will probably completely ignore it as you do with anything else that falsifies neo-Darwinism)
DNA Degeneration: Top Population Geneticists agree neo-Darwinism is not supported by the data - John Sanford http://www.youtube.com/watch?v=tYEkqwOXE5U
Now paulmc, I have put up with more than my fair share of malarkey from you with your 95% junk DNA tripe,, and have put some very compelling evidence for you to consider on the table that shows you to be completely off base. As far as I'm concerned I have made my case more than sufficiently, and will not play your stupid games anymore since you show no reasonableness to evidence.!bornagain77
December 8, 2011
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Just when I thought you were making progress... so you accept the occurrence of slightly deleterious mutations and genetic entropy, but you don't accept the accumulation of junk DNA? Sincerely, what do you think happens at a population level? Do you think that neutral and nearly neutral mutations can fix in populations? If not, why not? And if so, why is junk DNA so hard to accept?paulmc
December 8, 2011
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NO!
Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010 Excerpt:,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html Scientists Map All Mammalian Gene Interactions – August 2010 Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome. http://www.sciencedaily.com/releases/2010/08/100809142044.htm
bornagain77
December 8, 2011
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Great - so am I take it from this that you now accept the argument for junk DNA?paulmc
December 8, 2011
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paulmc, for crying out loud, if you can't prove even one instance of how complex functional information arises in genomes, with population genetics, why in blue blazes should I even give a hoot about anything else you have to say about what percentage of garbage you think is in the genomes??? You don't seem to have a very good grasp on what it takes to maintain coherent scientific integrity towards a point you are trying to make scientifically. Shoot paulmc, neo-Darwinism is SO GOOD at breaking things (Behe, 2010), I'm absolutely positive it is very easy for you, or anyone else, to, with a little slight of hand, 'mathematically' prove however much 'garbage' in the genomes they wanted to! But in the real world, using population genetics, with realistic rates of detrimental mutations compared to 'hypothetical' beneficial mutations, Dr. John Sanford, inventor of the 'gene gun, along with other top notch researchers in genetics, who have no hidden agenda, but only want to find the truth, developed a computer program that shows us exactly what will happen in a geneome in any size population you care to examine,, i.e. the answer is 'genetic entropy' in every case!
Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load: Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE http://mendelsaccount.sourceforge.net http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086
So paulmc, you problem is not for you to prove that neo-Darwinism can break things, it does that extremely well thank you very much, your problem is to prove that it can do anything, whatsoever, as to building functional complexity/information!!! (Moreover, you have that little problem of being falsified by quantum information in DNA that, if you were honest, you need to be extremely concerned about!) notes:
The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html The Law of Physicodynamic Incompleteness - David L. Abel - August 2011 Summary: “The Law of Physicodynamic Incompleteness” states that inanimate physicodynamics is completely inadequate to generate, or even explain, the mathematical nature of physical interactions (the purely formal laws of physics and chemistry). The Law further states that physicodynamic factors cannot cause formal processes and procedures leading to sophisticated function. Chance and necessity alone cannot steer, program or optimize algorithmic/computational success to provide desired non-trivial utility. http://www.scitopics.com/The_Law_of_Physicodynamic_Incompleteness.html
bornagain77
December 8, 2011
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