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

_{Denyse O'Leary

December 7, 2011

'Junk DNA', News}

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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

paul, you ain't even in the right ballpark to play the game. You are operating off a antiquated foundation of genetic reductionism, yet epigenetics has rendered that entire position null and void of any true explanatory power within science:
https://uncommondescent.com/junk-dna/pz-myers-the-self-described-paris-hilton-of-atheists-on-junk-dna/comment-page-1/#comment-411208
moreover:
The next evolutionary synthesis: Jonathan BL Bard Excerpt: We now know that there are at least 50 possible functions that DNA sequences can fulfill [8], that the networks for traits require many proteins and that they allow for considerable redundancy [9]. The reality is that the evolutionary synthesis says nothing about any of this; for all its claim of being grounded in DNA and mutation, it is actually a theory based on phenotypic traits. This is not to say that the evolutionary synthesis is wrong, but that it is inadequate – it is really only half a theory! http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf Astonishing DNA complexity update Excerpt: The untranslated regions (now called UTRs, rather than ‘junk’) are far more important than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes. http://creation.com/astonishing-dna-complexity-update 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 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 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 "Today there is an explosion of knowledge going on in the study of gene regulatory networks. But it is not led, assisted, or even inspired by the theory of evolution. "We have little empirical knowledge on the evolutionary history of such networks."-- Dean, Antony M., Joseph W. Thornton. September 2007. Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics, Vol. 8, pp. 675-688. http://www.newgeology.us/presentation32.html
The paradox between having elegant DNA repair mechanisms and the need for random mutations to 'drive evolution' is discussed here;
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
etc.. etc.. etc..bornagain77_{December 7, 2011
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paulmc: Presumably you've also looked at this discussion: https://uncommondescent.com/junk-dna/vidthe-debate-that-never-was-craig-vs-dawkins-junk-dna-does-show-up-though/ Arguing for pervasive amounts of junk DNA is a fool's errand.Eric Anderson_{December 7, 2011
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paulmc, so you are 100% certain, bet your life on it, that the DNA is mostly useless junk
What? Why should I be betting my life on it or be 100% certain? I am not 100% certain about any scientific inference. What I am certain about is this: the best, current, evidence-based explanation for the structure of the human genome and other eukaryotic genomes is genetic drift fixing slightly deleterious mutations, including duplicate retrotransposons. Large populations with more efficient purifying selection experience these fixations at much lower rates than small populations with weaker purifying selection. By small, we mean things like mammals, compared to things like bacteria. Look at what happens to genome content as genomes expands across the array of life's diversity. Coding sequences reach a maximum, which is never exceeded. Introns and retrotransposons continue to accumulate, dominating large genomes. Look at the types of organisms and think about what their relative population sizes are. It might indeed be wrong - of course it might - however it is the best answer with the current knowledge that we have and it is supported by a plethora of independent lines of evidence.paulmc_{December 7, 2011
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paulmc, so you are 100% certain, bet your life on it, that the DNA is mostly useless junk, i.e 'garbage', just as PZ claimed??? Frankly paulmc, not to be rude, but considering the multiple levels of functionality revealed thus far (in the 'linkfest' you refuse to consider), that is a fool's bet that I have never seen the likes of before!!!,,, No matter how much smarter you tyhink yourself to be over other people, that is the most foolish, ignorant, stupid, proclamation I've ever seen from neo-Darwinists!!!!!!bornagain77_{December 7, 2011
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I wonder why you've only addressed that comment to me and not to Joe, whose first comment to me was to dismiss me as being ignorant? Perhaps you are being selective in your criticism? I doubt I am the one being selective with the evidence, here. Where is the evidence for function that I have missed? Have you got a counterargument to any of this for example?paulmc_{December 7, 2011
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BA77, I have no interest in addressing your irrelevant linkfest. The argument for junk DNA is not intellectually related to claims of vestigial organs. There is positive evidence that the bulk of retrotransposon duplications that fix in populations happen through the escape from purifying natural selection, not from positive selection for function. Again, why not read a little Lynch before talking about arguments from ignorance.paulmc_{December 7, 2011
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Actually paulmc, I consider it you who is being very selective with the evidence you will consider, moreover I consider it extremely biased on your part to call others ignorant who don't subscribe to your extremely narrow and cheery picked view of the evidence.bornagain77_{December 7, 2011
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Actually, no Joe, claims about your ignorance are testable. For example, I have provided several lines of evidence that demonstrate the best interpretation of defective retrotransposons and long introns is that they are junk. I have emphasised that these arguments are entirely independent of simply not knowing of function for those sequences. I have argued that there is an upper limit imposed by purifying selection on the number of bases that can be specified. This is in line with what we know about genome-wide sequence conservation. Importantly, the accumulation of junk across the diversity of life is extremely variable, but closely and predicatably linked to a) the effective population size and b) the mutation rate. Please read some Lynch. When you choose to *ignore* these lines of evidence, rather than address them and say things like "It could be that the argument for junk DNA- that is for junk DNA being the majority- is based on ignorance and is not testable. Other than that, good job." I interpret that as ignorance.paulmc_{December 7, 2011
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Moreover, aside from neo-Darwinists rushing to judgement to declare everything they don't understand to be junk, just so as to make their theologically based 'bad design' argument, the fact of the matter is that there are now some very strong lines of evidence that strongly indicate that the programming in DNA is far, far, more advanced than anything man has ever even dreamt of, much less anything he has actually implemented into a 'intelligently designed' code.
Human DNA is like a computer program but far, far more advanced than any software we've ever created. Bill Gates, The Road Ahead, 1996, p. 188
Bill Gates, in recognizing the superiority found in Genetic Coding compared to the best computer coding we now have, has now funded research into this area:
Welcome to CoSBi - (Computational and Systems Biology) Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas. Do you believe Richard Dawkins exists? Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives. http://creation.com/does-dawkins-exist 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 The multiple codes of nucleotide sequences. Trifonov EN. - 1989 Excerpt: Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code). http://www.ncbi.nlm.nih.gov/pubmed/2673451 "In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Donald E. Johnson – Programming of Life – pg.51 - 2010 DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011 Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code, http://www.sciencedaily.com/releases/2011/01/110128104244.htm Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011 Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer." http://www.evolutionnews.org/2011/09/ends_and_means050391.html Histone Inspectors: Codes and More Codes - Cornelius Hunter - March 2010 Excerpt: By now most people know about the DNA code. A DNA strand consists of a sequence of molecules, or letters, that encodes for proteins. Many people do not realize, however, that there are additional, more nuanced, codes associated with the DNA. http://darwins-god.blogspot.com/2010/03/histone-inspectors-codes-and-more-codes.html Four More DNA Bases? - August 2011 Excerpt: As technology allows us to delve ever deeper into the inner workings of the cell, we continue to find layer-upon-layer of complexity. DNA, in particular, is an incredibly complex information-bearing molecule that bears the hallmarks of design. http://www.evolutionnews.org/2011/08/four_more_dna_bases049091.html "There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). Dr. John Sanford; Genetic Entropy 2005
Besides multiple layers of 'classical information' embedded in overlapping layers throughout the DNA, there has now been discovered another layer of 'quantum information' embedded throughout the DNA:
Quantum Information In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/
And, as pointed out previously, quantum information is not even within the materialistic framework of neo-Darwinism to consider in the first place! Thus clearly, for those who refuse to concede the falsification, neo-Darwinism is now overwhelmingly shown to be a position of dogmatic atheistic/materialistic religion instead of anything resembling honest inquiry! etc.. etc.. etc.. music and verse:
Grown Up Christmas List by Amy Grant http://www.godtube.com/watch/?v=JFC9MFNU Genesis 1:26-27 Then God said, "Let us make man in Our image, according to Our image, according to Our likeness; let them have dominion ..." So God created man in His own image; in the image of God He created him; male and female He created them.
bornagain77_{December 7, 2011
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Yeah, it's EASY for YOU to claim I am ignorant but more importantly it is yet another one of your untestable claims.Joe_{December 7, 2011
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Yet paulmc, the junk DNA argument is precisely a argument from ignorance. Just as with the now discredited vestigial organ argument,,, i.e. if neo-Darwinists were ignorant of a organs function they declared is useless, leftover, evolutionary garbage if you will,,, a false viewpoint that took a very, very, long time to overturn,
“The thyroid gland, pituitary gland, thymus, pineal gland, and coccyx, … once considered useless by evolutionists, are now known to have important functions. The list of 180 “vestigial” structures is practically down to zero. Unfortunately, earlier Darwinists assumed that if they were ignorant of an organ’s function, then it had no function.” "Tornado in a Junkyard" - book - by former atheist James Perloff
For a prime example of evolution's failed predictions of vestigial organs, recently in October 2007, the appendix has been found to have essential purpose in the human body:
Appendix has purpose: Excerpt: "The appendix acts as a good safe house for bacteria," said Duke surgery professor Bill Parker. http://en.wikinews.org/wiki/Scientists:_appendix_has_purpose Surgical removal of the tonsils and appendix associated with risk of early heart attack - June 2011 Excerpt: The surgical removal of the appendix and tonsils before the age of 20 was associated with an increased risk of premature heart attack in a large population study performed in Sweden. Tonsillectomy increased the risk by 44% (hazard ratio 1.44) and appendectomy by 33% (HR 1.33). The risk increases were just statistically significant, and were even higher when the tonsils and appendix were both removed. http://medicalxpress.com/news/2011-06-surgical-tonsils-appendix-early-heart.html#share
as well, to top matters off on this point, the junk DNA argument is in fact a Theologically based 'bad design' argument which has absolutely no business in science,,, i.e. Darwinists, arguing adamantly for 'junk' from such a position of ignorance, declare that God would not have done it that way therefore it must be a accidental product of blind evolution,,,
Refuting The Myth Of 'Bad Design' vs. Intelligent Design - William Lane Craig - video http://www.youtube.com/watch?v=uIzdieauxZg
In fact Darwin's entire theory turns out to be, at its core, a theological argument,,
Charles Darwin, Theologian: Major New Article on Darwin's Use of Theology in the Origin of Species - May 2011 Excerpt: I have argued that, in the first edition of the Origin, Darwin drew upon at least the following positiva theological claims in his case for descent with modification (and against special creation): 1. Human begins are not justfied in believing that God creates in ways analogous to the intellectual powers of the human mind. 2. A God who is free to create as He wishes would create new biological limbs de novo rather than from a common pattern. 3. A respectable deity would create biological structures in accord with a human conception of the 'simplest mode' to accomplish the functions of these structures. 4. God would only create the minimum structure required for a given part's function. 5. God does not provide false empirical information about the origins of organisms. 6. God impressed the laws of nature on matter. 7. God directly created the first 'primordial' life. 8. God did not perform miracles within organic history subsequent to the creation of the first life. 9. A 'distant' God is not morally culpable for natural pain and suffering. 10. The God of special creation, who allegedly performed miracles in organic history, is not plausible given the presence of natural pain and suffering. http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html From Philosopher to Science Writer: The Dissemination of Evolutionary Thought - May 2011 Excerpt: The powerful theory of evolution hangs on this framework of thought that mandates naturalism. The science is weak but the metaphysics are strong. This is the key to understanding evolutionary thought. The weak arguments are scientific and the strong arguments, though filled with empirical observation and scientific jargon, are metaphysical. The stronger the argument, the more theological or philosophical. http://darwins-god.blogspot.com/2011/05/from-philosopher-to-science-writer.html Peacefulness, in a Grown Man, That is Not a Good Sign - Cornelius Hunter - August 2011 Excerpt: Evolution cannot even explain how a single protein first evolved, let alone the massive biological world that ensued. From biosonar to redwood trees, evolution is left with only just-so stories motivated by the dogma that evolution must be true. That dogma comes from metaphysics, http://darwins-god.blogspot.com/2011/08/peacefulness-in-grown-man-that-is-not.html On the Vastness of the Universe Excerpt: Darwin’s objection to design inferences were theological. And in addition, Darwin overlooked many theological considerations in order to focus on the one. His one consideration was his assumption about what a god would or wouldn’t do. The considerations he overlooked are too numerous to mention here, but here’s a few:,,, - C.Yankee https://uncommondescent.com/intelligent-design/on-the-vastness-of-the-universe/comment-page-2/#comment-362918
And the theological 'bad design' argument, which Darwinists unwittingly continually use to try to make their case, is actually its own independent discipline of study within Theology itself called Theodicy:
Is Your Bod Flawed by God? - Feb. 2010 Excerpt: Theodicy (the discipline in Theism of reconciling natural evil with a good God) might be a problem for 19th-century deism and simplistic natural theology, but not for Biblical theology. It was not a problem for Jesus Christ, who was certainly not oblivious to the blind, the deaf, the lepers and the lame around him. It was not a problem for Paul, who spoke of the whole creation groaning and travailing in pain till the coming redemption of all things (Romans 8). http://www.creationsafaris.com/crev201002.htm#20100214a Did God Create Evil? (William Dembski) – video http://www.youtube.com/watch?v=cCVYqg6TFmA
Little do most atheists realize that the existence of evil itself necessitates the existence of Good. i.e. you cannot disprove God by pointing to evil. All a atheist does when he points to evil in this world is to point out the fact that this world is not perfectly good, Yet Christianity never claimed we were in heaven in the first place. i.e. by pointing to evil (the absence of good), the atheist actually affirms the Christian belief that we are in a fallen world.bornagain77_{December 7, 2011
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And your reply is ignorance battered in sarcasm.paulmc_{December 7, 2011
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It could be that the argument for junk DNA- that is for junk DNA being the majority- is based on ignorance and is not testable. Other than that, good job.Joe_{December 7, 2011
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Is there anything of substance in particular about the argument for junk DNA that PZ Myers makes that you find objectionable, or is it simply his style? I have attempted serious discussions about junk DNA on UD before, and have raised several independent lines of argument - including directly addressing claims made by Jonathan Wells - but have not had the points raised adequately addressed. I have also written about this elsewhere a couple of times.paulmc_{December 7, 2011
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A fundamentalist if I've ever seen one :) As Philip Johnson said, atheism truly has morphed into the monster that is secular religion.Stu7_{December 7, 2011
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Paris Hilton is a known air-head. PZ is admiting that he is an air-head of atheism. heh-heh Also what is up with these allged "skeptics"? They should apply their skepticism towards their position- that is why those alleged skeptics get a load of stuff on the internet.Joe_{December 7, 2011
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bornagain77, thanks for watching and taking notes. There is no way I could have watched that thing -- weak stomach and all that, you know . . . PZ Myers needs some serious help. In addition to being a ranting, unstable guy, he doesn't know that much about biology. Pretty sad. Oh well, this video will give us something to point to in coming years as his assessment (already way off) continues to be more and more laughable. By the way, I'm going to proclaim myself the Anti-Myers. He claims 5% is not junk? I've stated openly on this blog that, at most, 5-10% of DNA will turn out to be junk.Eric Anderson_{December 7, 2011
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The following describes how quantum entanglement is related to functional information:
Quantum Entanglement and Information Excerpt: 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. http://plato.stanford.edu/entries/qt-entangle/
Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;
Quantum Entanglement and Teleportation – Anton Zeilinger – video http://www.metacafe.com/watch/5705317/
A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:
Quantum Teleportation Excerpt: To perform the teleportation, Alice and Bob must have a classical communication channel and must also share quantum entanglement — in the protocol we employ*, each possesses one half of a two-particle entangled state. http://www.cco.caltech.edu/~qoptics/teleport.html
And quantum teleporation has now shown that atoms, which are suppose to be the basis from which ALL functional information ‘emerges’ in the atheistic neo-Darwinian view of life, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of in the first place!
Ions have been teleported successfully for the first time by two independent research groups Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,, http://www.rsc.org/chemistryworld/Issues/2004/October/beammeup.asp Atom takes a quantum leap – 2009 Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,, “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second. http://www.freerepublic.com/focus/news/2171769/posts
Thus the burning question, that is usually completely ignored by the neo-Darwinists that I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA, or any other atoms, when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments? i.e. It is simply 'COMPLETELY IMPOSSIBLE' for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ‘emerge’ from, any material basis of particles! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a trivial matter in the least as far as developments in science have gone!
Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff - video (notes in description) http://vimeo.com/29895068 non-local ‘epigenetic’ information is implicated in controlling the 3-D spatial organization of body plans; https://docs.google.com/document/d/1iNy78O6ZpU8wpFIgkILi85TvhC9mSqzUSE_jzbksoHY/edit?hl=en_US
verses and music:
John 1:1-3 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. 1 Corinthians 2:14 The natural person does not accept the things of the Spirit of God, for they are folly to him, and he is not able to understand them because they are spiritually discerned. Brooke Fraser – Lord of Lords(Legendado Português) - http://www.youtube.com/watch?v=rkF3iVjOZ1I
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Quantum Entanglement/Information is confirmed in DNA by direct observation here;
DNA Can Discern Between Two Quantum States, Research Shows – June 2011 Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property. http://www.sciencedaily.com/releases/2011/03/110331104014.htm Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/ Quantum states in proteins and protein assemblies: The essence of life? - STUART HAMEROFF, JACK TUSZYNSKI Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign. http://www.tony5m17h.net/SHJTQprotein.pdf Myosin Coherence Excerpt: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. Living systems have mastered the making and breaking of chemical bonds, which are quantum mechanical phenomena. Absorbance of frequency specific radiation (e.g. photosynthesis and vision), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects. http://www.energetic-medicine.net/bioenergetic-articles/articles/63/1/Myosin-Coherence/Page1.html
The necessity of 'transcendent' information, to ‘constrain’ a cell, against thermodynamic effects is noted here:
Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. http://journals.witpress.com/paperinfo.asp?pid=420
i.e. It is very interesting to note, to put it mildly, that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! 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, you 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 ‘specified’ 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! ,,,To refute this falsification of neo-Darwinism, one must overturn Alain Aspect, and company’s, falsification of local realism (reductive materialism) ! ================= Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007 ================= And to dovetail into Dembski and Marks’s previous work on Conservation of Information;,,,
LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information William A. Dembski and Robert J. Marks II http://evoinfo.org/publications/lifes-conservation-law/
,,,Encoded ‘classical’ information such as what Dembski and Marks demonstrated the conservation of, and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of ‘transcendent’ (beyond space and time) quantum entanglement/information by the following method:,,,
,,,This following research provides solid falsification for the late Rolf Landauer’s decades old contention that the information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it; Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm
,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,
Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html
Further note:
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 (Functional Sequence Complexity). 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
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Actually Joe, to be fair, PZ just declared Dembski's prediction that most of the DNA would exhibit functionality 'FALSIFIED', and did not declare the entire ID framework falsified. But even in that modest claim for falsification, PZ has greatly overstated his case and has come no where near the rigor required for genuine 'falsification' of that particular prediction;, Indeed there is much evidence that argues forcefully against each point he brought up!!!,, Whereas, on the other hand, the fact that the genetic reductionism model, which PZ is working from in the first place, is 'falsified', is coming into general acceptance with the gradual realization of just how pervasive, and foundational, epigenetics is. (as briefly noted),, Moreover, the fact that non-local, beyond space and time, quantum entanglement/information is now found in molecular biology, on a massive scale,,, far from the superficial falsification PZ thought he had achieved, goes all the way down to the foundation of reality itself to rigorously FALSIFY the materialistic foundation upon which the entire neo-Darwinian framework is built!!! notes: Falsification Of Neo-Darwinism by Quantum Entanglement/Information Neo-Darwinian evolution purports to explain all the wondrously amazing complexity of life on earth by reference solely to chance and necessity processes acting on energy and matter (i.e. purely material processes). In fact neo-Darwinian evolution makes the grand materialistic claim that the staggering levels of unmatched complex functional information we find in life, and even the ‘essence of life’ itself, simply ‘emerged’ from purely material processes. And even though this basic scientific point, of the ability of purely material processes to generate even trivial levels of complex functional information, has spectacularly failed to be established, we now have a much greater proof, than this stunning failure for validation, that ‘put the lie’ to the grand claims of neo-Darwinian evolution. This proof comes from the fact that it is now shown from quantum mechanics that ‘information’ is its own unique ‘physical’ entity. A physical entity that is shown to be completely independent of any energy-matter space-time constraints, i.e. it does not ‘emerge’ from a material basis. Moreover this ‘transcendent information’ is shown to be dominant of energy-matter in that this ‘information’ is shown to be the entity that is in fact constraining the energy-matter processes of the cell to be so far out of thermodynamic equilibrium. First, Here is the falsification of local realism (reductive materialism). Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:
The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video http://www.metacafe.com/w/4744145
The falsification for local realism (reductive materialism) was recently greatly strengthened:
'Quantum Magic' Without Any 'Spooky Action at a Distance' - June 2011 Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically. http://www.sciencedaily.com/releases/2011/06/110624111942.htm Physicists close two loopholes while violating local realism – November 2010 Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview. http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009 Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/releases/2009/07/090722142824.htm
of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light. This following video illustrates just how 'spooky', to use Einstein’s infamous word, this quantum action truly is:
Light and Quantum Entanglement Reflect Some Characteristics Of God – video http://www.metacafe.com/watch/4102182/
And yet, this ‘spooky’ quantum entanglement, which rigorously falsified local realism (reductive materialism) as the ‘true’ description of reality, is now found in molecular biology on a massive scale!
Quantum Information/Entanglement In DNA & Protein Folding – short video http://www.metacafe.com/watch/5936605/ Quantum entanglement holds together life’s blueprint – 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/ The relevance of continuous variable entanglement in DNA – July 2010 Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix. http://arxiv.org/abs/1006.4053v1
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notes:
Human Genome “Infinitely More Complex” Than Expected - April 2010 Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said,,,, Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.” http://www.creationsafaris.com/crev201004.htm#20100405a Deep Genomics: In the Case of DNA, the Package Can Be as Important as Its Contents, New Work With Fruit Flies Reveals - January 2011 http://www.sciencedaily.com/releases/2011/01/110113102158.htm The Origin at 150: is a new evolutionary synthesis in sight? - Koonin - Nov. 2009 Excerpt: The edifice of the modern synthesis has crumbled, apparently, beyond repair. http://www.arn.org/blogs/index.php/literature/2009/11/18/not_to_mince_words_the_modern_synthesis With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory - November 2011 Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,, http://www.evolutionnews.org/2011/11/with_a_startling_candor_oxford052821.html What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: But it’s obvious enough that a section of a DNA molecule does not “sculpt” anything. In fact, the research emphasis today is in the reverse direction: how proteins and the overall activity of the cell sculpt the genes and chromosomes. ,,, The activity of individual genes reflects the choreography of chromosomes, which reflects the larger choreography of the nucleus, which reflects the choreography of the cell and organism as a whole. Who, then, is sculpting whom?,,, http://www.thenewatlantis.com/publications/what-do-organisms-mean 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
etc.. etc.. etc..bornagain77_{December 7, 2011
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Yes BA77, they have indeed falsified their strawman version of ID. They hung it out, beat the crap out of it and now they say they are laying it to rest. My bet is they will resurrect it again and again just so they can falsify it some more....Joe_{December 7, 2011
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notes:
26:00 minute mark PZ states '5% of the genome is not junk'; 29:00 minute mark, 'fire the guy' for 'bad design', 'stupid function' for repeat 10%; 31:00 minute mark: LINE segments, 21%, PZ staes they 'do nothing for the cell', states LINEs are 'viral relics', 'useless',,, SINE's and ERV's both declared useless waste,,, PZ's final pronouncement at 35:30 mark is,,, 45% known, parasitic junk DNA 10% structural DNA 5% functional DNA paraphrase,,, We 'know' half of DNA is garbage,,, 36:15, PZ 'predicts' most of the remaining 'unknown' DNA will be found to be 'garbage', although he concedes 'some surprises'; ,,,mentions 'Onion test' Declares ID 'FALSIFIED' at 41:00 minute mark.
The reports of my death have been greatly exaggerated - Mark Twainbornagain77_{December 7, 2011
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