Comb jelly files: Complex features do not each emerge once

_{Denyse O'Leary

May 24, 2014

Evolution, Information, Intelligent Design, News}

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Further to the comb jellies having a separate course of evolution from other animals, here’s Amy Maxmen at Nautilus:

In an essay for Nautilus called “Evolution, You’re Drunk,” I described how hypotheses entrenched in the notion that evolution leads toward increasing complexity have recently begun to teeter. Now Moroz’s study adds another shove. It seconds the finding that simple sponges, long placed at the base of the evolutionary tree, actually evolved after the sophisticated comb jelly group arose. The story of how complexity evolves is more complex than scientists realized.

Furthermore, the brain—the epitome of complexity—seems to have sprouted up at least twice over evolutionary time. This clashes with the traditional notion that complex, multifaceted features come about in a very specific way, and each emerges just one time. “What everyone has said about complexity is wrong,” Moroz says. “It can happen more than once.”

If traditional evolution theory is this wrong, a theory of information in life forms is more needed than ever.

Comments

Thank you for the reference, bornagain77. -QQuerius_{May 26, 2014
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Dr JDD @ 27, It sounds like a career-versus-career challenge . . . the old experienced male lion is challenged by a young male lion for his pride. The young lion usually loses. Just thinking about it, the parallels to the Serengeti are chilling. I like to keep an open mind. So what if it does turn out to be 2) negative? Here's a proposed explanation using an evolutionary paradigm why this is actually a good thing: A. Let's assume that E.coli or whatever has genetically adapted extremely well to a range of environments over billions of years, but contrary to Lenski's claim, there is an upper limit to adaptation. A loss of function will pull E.coli down the evolutionary tree to a much simpler, earlier version so that it can evolve in new directions. Yay. Then propose that evolution should be able to repair or compensate for that damage. B. Let's assume that E.coli has lost most of its evolutionary plasticity over billions of years of fixation. Would there be a way to strip down or "zero out" its genetic and epigenetic information? Of course, it might just be that E.coli can't climb up much further, nor can it climb down much further on its evolutionary branch. Incidentally, I have no problem with the Creator designing various kinds of archetypes and letting them radiate into ecological niches. Finally, I'd say that what clever people have done over the centuries to challenge monolithic political, social, and now perhaps scientific institutions is to rely on satire, taunting, and other creative alternatives---using a pseudonym, of course. What fun one could have! - The Effects of Global Warming on Evolution - The Evolutionary Benefits of Extinction - Recalibrating the Age of the Earth Using E.coli -QQuerius_{May 26, 2014
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Hi Born Again, While that is excellent work that highlights important Issues that saturation mutagenesis fails to address, the advantage of E coli and other bacterial models is they can simulate huge numbers of generations due to doubling times so short therefore the "time" issue that cannot be addressed with Drosophila mutagenesis is somewhat overcome and cannot be as easily used as an argument why macroevolution is not observed.Dr JDD_{May 26, 2014
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Querius, this may interest you: Response to John Wise - October 2010 Excerpt: A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.htmlbornagain77_{May 26, 2014
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Querius, I'm with you on that - I have always wanted to see those sets of experiments. Consider 3 outcomes though: 1) it has no effect mutation-wise (neutral) 2) it has a net-loss effect and is evolution-reductive (negative) 3) novel beneficial mutations are observed (positive) Now how many people do you think would publish results #1 or #2? Not only is it often difficult to publish negative results, if some negative results were to question a well accepted theory would you risk your career? I applaud those who publish these things that challenge central dogma because I can guarantee for everyone that does publish such work, there are more people who have done similar experiments yet chosen not to publish as the results "don't make sense" I.e. go against the status quo. you can also guarantee that if an experiment is straightforward and relatively easy to perform in the lab, someone will have done it. Thus the lack of publication speaks volumes about the likely result of such an experiment... JDDr JDD_{May 26, 2014
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bornagain77@15,
Querius, that was your fascinating example I cited, I just added a bit of background. Of related interest to deep time studies,
Heh. Yeah, I'm still curious. The experiment you found bacteria that were remarkably resistant to radiation by zapping 99% of them. According to evolutionary theory, this means that (a) the genetic trait had been selected for sometime in the past and was never fixed, even after what might have been billions of years, or (b) the resistance evolved in loco. What I'm interested in is the genetic changes in bacteria subjected to variety of stressful environments with elevated, not extreme, levels of ionizing radiation. The idea is to simulate hundreds of millions of years of evolution under laboratory conditions. -QQuerius_{May 25, 2014
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Piotr@17 rationalized,
Franklin has already pointed out that blind cave fish can do very well with the sort of lateral-line orientation that they already have. There is little competition in cave waters, food is easy to find, so there’s no pressure to develop anything more sophisticated.
But we can't actually observe what you're claiming musta happened. Were conditions always this easy? You would say they musta been which takes us around the circle again. But that's not even my point. Can you provide some examples of evolution adding complexity by evolving something entirely NEW that we can observe right now? Surely evolution hasn't stopped. As bogart said there are lots of examples where evolution can reduce complexity. And this can be observed today. Many species can be observed evolving to the brink of extinction. Are there any that you can cite are evolving back again? -QQuerius_{May 25, 2014
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Not sure if this is OT? http://www.cell.com/trends/cell-biology/abstract/S0962-8924(13)00224-9?elsca1=etoc&elsca2=email&elsca3=0962-8924_201406_24_6_&elsca4=Cell%20PressDionisio_{May 25, 2014
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,,,And here is evidence 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 Quantum no-deleting theorem Excerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist. http://en.wikipedia.org/wiki/Quantum_no-deleting_theorem#Consequence
Besides providing direct empirical falsification of a primary neo-Darwinian claim, as to the materialistic generation of information, the implication of finding 'non-local', and ‘conserved’, quantum information in molecular biology on a massive scale is fairly, and pleasantly, obvious:
Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff - video (notes in description) http://vimeo.com/29895068
Verse and Music:
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through Him, and without Him nothing was made that was made. In Him was life, and the life was the light of men. Redeemed – Big Daddy Weave http://myktis.com/songs/redeemed/
bornagain77_{May 25, 2014
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Quantum Information/Entanglement In DNA - short video https://vimeo.com/92405752 Coherent Intrachain energy migration at room temperature – Elisabetta Collini and 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/ Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/
That quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints (Bell Aspect, Leggett, Zeilinger), should be found in molecular biology on such a massive scale is a direct empirical falsification of Darwinian claims, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own causation in the first place? Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply!
Looking beyond space and time to cope with quantum theory – 29 October 2012 Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” http://www.quantumlah.org/highlight/121029_hidden_influences.php Closing the last Bell-test loophole for photons - Jun 11, 2013 Excerpt:– requiring no assumptions or correction of count rates – that confirmed quantum entanglement to nearly 70 standard deviations.,,, http://phys.org/news/2013-06-bell-test-loophole-photons.html
In other words, to give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, 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 ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! Or related note, encoded ‘classical’ digital information, such as what William Dembski and Robert Marks demonstrated the conservation of,
Conservation of Information in Search: Measuring the Cost of Success William A. Dembski and Robert J. Marks II http://www.evoinfo.org/index/
,,i.e. classical 'digital' information, such as what we find encoded in computer programs, and yes, as we find encoded in DNA,
Every Bit Digital: DNA’s Programming Really Bugs Some ID Critics - Casey Luskin Excerpt: "There’s a very recognizable digital code of the kind that electrical engineers rediscovered in the 1950s that maps the codes for sequences of DNA onto expressions of proteins." http://www.salvomag.com/new/articles/salvo12/12luskin2.php
,,classical 'digital' information is found to be a subset of ‘non-local' (i.e. beyond space and time) quantum entanglement/information by the following method:
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
bornagain77_{May 25, 2014
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to clean up post 19 a bit for clarity: The empirical falsification of Darwinism is as such,,, Darwinian presuppositions hold that information, (and even consciousness), is merely an ‘emergent’ property of a material basis, but it is now found that material reduces to an information basis: First, in explaining the empirical falsification of Darwinism, it is important to learn that ‘non-local’, beyond space and time, quantum entanglement (A. Aspect, A. Zeilinger) can be used as a ‘quantum information channel’,,,
Quantum Entanglement and Information Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory. http://plato.stanford.edu/entries/qt-entangle/
And by using this ‘non-local’, beyond space and time, ‘quantum information channel’ of entanglement, physicists have reduced both matter and energy to quantum information.
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 How Teleportation Will Work - Excerpt: In 1993, the idea of teleportation moved out of the realm of science fiction and into the world of theoretical possibility. It was then that physicist Charles Bennett and a team of researchers at IBM confirmed that quantum teleportation was possible, but only if the original object being teleported was destroyed. — As predicted, the original photon no longer existed once the replica was made. http://science.howstuffworks.com/science-vs-myth/everyday-myths/teleportation1.htm Quantum Teleportation – IBM Research Page Excerpt: “it would destroy the original (photon) in the process,,” http://researcher.ibm.com/view_project.php?id=2862
In fact an entire human can, theoretically, be reduced to quantum information and teleported to another location in the universe:
Quantum Teleportation Of A Human? – video https://vimeo.com/75163272
Thus not only is information not reducible to a energy-matter basis, as is presupposed in Darwinism, but in actuality both energy and matter reduce to a information basis as is presupposed in Christian Theism (John1:1). Moreover, this ‘spooky’ non-local quantum information, though at first thought to be impossible to maintain in ‘hot and noisy’ cells, is now found in molecular biology on a massive scale, in every DNA and protein molecule:
Quantum entanglement in hot systems – 2011 Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement.,,, In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules. http://quantum-mind.co.uk/quantum-entanglement-hot-systems/ 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. “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/ Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009 Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible. per daily galaxy 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
bornagain77_{May 25, 2014
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Piotr:
As you may guess, I don’t buy Axe’s calculations (or his responses to criticism).
No one cares what you buy, Piotr. What matters is what you can demonstrate scientifically. And unguided/blind watchmaker evolution has nothing.Joe_{May 25, 2014
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Of related note: Neo-Darwinian presuppositions hold that information is merely an 'emergent' property of a material basis, but it is now found that material reduces to an information basis: ,,, First, it is important to note that ‘non-local’, beyond space and time, quantum entanglement (Aspect, Zeilinger) can be used as a ‘quantum information channel’,,,
Quantum Entanglement and Information Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory. http://plato.stanford.edu/entries/qt-entangle/
And by using this ‘non-local’, beyond space and time, ‘quantum information channel’ of entanglement, both matter and energy are found to reduce to quantum information. In fact an entire human can, theoretically, be reduced to quantum information and teleported to another location in the universe:
Quantum Teleportation Of A Human? – video https://vimeo.com/75163272
Thus not only is information not reducible to a 3-Dimensional energy-matter basis, as is presupposed in Darwinism, but in actuality both energy and matter reduce to a information basis as is presupposed in Christian Theism: Moreover, this ‘spooky’ non-local quantum information, though at first thought to be impossible to maintain in ‘hot and noisy’ cells, is now found in molecular biology on a massive scale, in every DNA and protein molecule
Quantum entanglement in hot systems – 2011 Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement.,,, In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules. http://quantum-mind.co.uk/quantum-entanglement-hot-systems/ 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. “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/ Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009 Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible. per daily galaxy 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 Quantum entanglement between the electron clouds of nucleic acids in DNA – Elisabeth Rieper, Janet Anders and Vlatko Vedral – February 2011 http://arxiv.org/PS_cache/arxiv/pdf/1006/1006.4053v2.pdf Coherent Intrachain energy migration at room temperature – Elisabetta Collini and 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/
It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure 'quantum form' is completely transcendent of any time and space constraints (Bell Aspect, Leggett, Zeilinger), 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) 'cause' when the quantum entanglement 'effect' falsified material particles as its own 'causation' in the first place? Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply!
Looking beyond space and time to cope with quantum theory - 29 October 2012 Excerpt: "Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them," http://www.quantumlah.org/highlight/121029_hidden_influences.php
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 'special' configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! Verse and Music:
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through Him, and without Him nothing was made that was made. In Him was life, and the life was the light of men. Redeemed – Big Daddy Weave http://myktis.com/songs/redeemed/
bornagain77_{May 25, 2014
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Gpuccio: I'll write more later. It's a family week-end for me (not to mention the Euro elections), so I'm a bit pressed for time. As you may guess, I don't buy Axe's calculations (or his responses to criticism).Piotr_{May 25, 2014
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My point was regarding the evolution of complexity, something entirely NEW. That’s why I picked sonar.
In order to have a good sonar you need ears that pick up high-frequency sounds. Mammals evolved a complex inner ear during their early evolution (which took them some 100 million years), so some of them have been able to evolve sonars as well. You could say that they are pre-adapted for high-frequency echolocation There are echolocating birds (oilbirds, swiftlets) as well, but since their hearing range is mush lower than in bats, their sonar works at 2-10 kHz (as compared with 20-200 kHz in bats) and doesn't allow them to "see" in fine detail. The structure of the avian ear constrains their ability to echolocate. Franklin has already pointed out that blind cave fish can do very well with the sort of lateral-line orientation that they already have. There is little competition in cave waters, food is easy to find, so there's no pressure to develop anything more sophisticated.Piotr_{May 25, 2014
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Piotr: Some of Hunt's criticisms to Axe's work can be considered, but they do not falsify his results. As usual, ID tries to address the problem of protein space, while the only purpose of the other side seems to be to keep it in a convenient obscurity, because only in that obscurity can their theory appear credible. First of all, Axe has detailed his thoughts about protein space with more general approaches in later papers. Second, Behe's arguments in TEOE are in full accord with those results. Third, as I have discussed with you recently, another important paper, the one about rugged landscape, fully supports those quantitative orders of magnitude. The only paper which tries to propose a completely different order of magnitude is the Szostak paper, on which I have already expressed, many times, my ideas.gpuccio_{May 25, 2014
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Querius, that was your fascinating example I cited, I just added a bit of background. Of related interest to deep time studies, The irreversible process of ‘Genetic Deterioration’ over deep time is indicated in ‘realistic’ computer simulations over deep time: Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013 Excerpt: We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as “Haldane’s Dilemma” is very real. Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon “Haldane’s Ratchet”. http://media.wix.com/ugd/a704d4_47bcf08eda0e4926a44a8ac9cbfa9c20.pdfbornagain77_{May 24, 2014
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bornagain77@13, Yes, exactly. I liked the example of microbes that you used. In fact, wouldn't exposing microbes to a higher level of ionizing radiation be an interesting laboratory of evolution? One could more quickly simulate many millions of years of evolution. -QQuerius_{May 24, 2014
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Of note to Piotr not paying attention, here is a post from a week ago: https://uncommondescent.com/intelligent-design/evolution-professor-orphans-not-a-problem-for-evolution/#comment-500554bornagain77_{May 24, 2014
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Piotr and Franklin, My point was regarding the evolution of complexity, something entirely NEW. That's why I picked sonar. Surely, you're not claiming that the lateral line system is new in cave fish and not present in other fish, are you? http://www.mapoflife.org/topics/topic_443_Lateral-line-system-in-fish-and-other-animals/ The other stuff is learned behavior, just like non-sighted people compensate with their other senses. I would also expect changes driven by epigenetics, as is the case with the beaks of Darwin's finches. What I'm talking about is observed evolution of complexity. As bogart said, there are a lot of examples of evolution reducing complexity. -QQuerius_{May 24, 2014
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actually it is far worse than you woulf prefer to believe Piotr: Minimal Complexity Relegates Life Origin Models To Fanciful Speculation - Nov. 2009 Excerpt: Based on the structural requirements of enzyme activity Axe emphatically argued against a global-ascent model of the function landscape in which incremental improvements of an arbitrary starting sequence "lead to a globally optimal final sequence with reasonably high probability". For a protein made from scratch in a prebiotic soup, the odds of finding such globally optimal solutions are infinitesimally small- somewhere between 1 in 10exp140 and 1 in 10exp164 for a 150 amino acid long sequence if we factor in the probabilities of forming peptide bonds and of incorporating only left handed amino acids. http://www.arn.org/blogs/index.php/2/2009/11/10/minimal_complexity_relegates_life_origin The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe, Jay Richards - audio http://intelligentdesign.podomatic.com/player/web/2010-05-03T11_09_03-07_00 The following site offers a short summary of the 'Darwinian shortcuts' that failed to overcome Axe's finding for the rarity of protein folds: Shortcuts to new protein folds? - October 2010 Excerpt: Axe concludes that all of these putative shortcuts are dead ends. The Darwinian search mechanism is not capable of finding new protein folds by random sampling and all the shortcuts to new folds are dead ends. http://idintheuk.blogspot.com/2010/10/shortcuts-to-new-protein-folds.html Moreover, Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator - Fazale Rana Excerpt of Review: ‘Another interesting section of Creating Life in the Lab is one on artificial enzymes. Biological enzymes catalyze chemical reactions, often increasing the spontaneous reaction rate by a billion times or more. Scientists have set out to produce artificial enzymes that catalyze chemical reactions not used in biological organisms. Comparing the structure of biological enzymes, scientists used super-computers to calculate the sequences of amino acids in their enzymes that might catalyze the reaction they were interested in. After testing dozens of candidates,, the best ones were chosen and subjected to “in vitro evolution,” which increased the reaction rate up to 200-fold. Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?” http://www.amazon.com/gp/product/0801072093 Dr. Fuz Rana, at the 41:30 minute mark of the following video, speaks on the tremendous effort that went into building the preceding protein: Science - Fuz Rana - Unbelievable? Conference 2013 - video http://www.youtube.com/watch?v=-u34VJ8J5_c&list=PLS5E_VeVNzAstcmbIlygiEFir3tQtlWxx&index=8bornagain77_{May 24, 2014
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Piotr, There isn't any evidence at that link that shows unguided evolution can do anything, let alone create novel proteins.Joe_{May 24, 2014
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Natural selection can't explain jellies. It has nothing to say about metazoans. It has proven to be a totally useless heuristicJoe_{May 24, 2014
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bornagain77 Boom! Boom! As for Axe's calculations, see link.Piotr_{May 24, 2014
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further notes on sight:
The reason evolutionary biologists believe in "40 known independent eye evolutions" isn't because they've reconstructed those evolutionary pathways, but because eyes don't assume a treelike pattern on the famous Darwinian "tree of life." Darwinists are accordingly forced, again and again, to invoke convergent "independent" evolution of eyes to explain why eyes are distributed in such a non-tree-like fashion. This is hardly evidence against ID. In fact the appearance of eyes within widely disparate groups speaks eloquently of common design. Eyes are a problem, all right -- for Darwinism. http://www.evolutionnews.org/2014/03/its_a_shame_rea083441.html William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.html Eyeballing Design by Casey Luskin - December 2011 Excerpt:,,, the team of scientists who determined the function of glial cells concluded that the "retina is revealed as an optimal structure designed for improving the sharpness of images." http://www.salvomag.com/new/articles/salvo19/19luskin.php Evolution Vs. The Miracle Of The Eye - Vision Cascade Molecular Animation https://www.youtube.com/watch?v=AuLR0kzfwBU Could the eye have evolved by natural selection in a geological blink? March 18, 2013 Excerpt: Let us return to the question, how do we see? Although to Darwin the primary event of vision was a black box, through the efforts of many biochemists an answer to the question of sight is at hand. When light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein’s metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin. The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water. A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision. If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state; there are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration. However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration. Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall. Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate. The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon. Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle. To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol. Finally, a third enzyme removes the previously added hydrogen atoms to form 11-cis-retinal, and the cycle is complete. https://uncommondescent.com/intelligent-design/could-the-eye-have-evolved-by-natural-selection-in-a-geological-blink/ The Vision Cascade is Initiated Not by Isomerization but by Force Field Dynamics - July 2011 Excerpt: 'In addition to designing the opsin protein, evolution must now design the electric field surrounding the chromophore, and how it responds to photon interaction. And while it is busy with that task, it must also specify the correct amino acids at the correct locations within the opsin, that will be influenced by the chromophore’s dynamic electric field.' http://darwins-god.blogspot.com/2011/06/vision-cascade-is-initiated-not-by.html
bornagain77_{May 24, 2014
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For someone asking questions, citing the 'evolution' of 'blind' cave fish is hardly an example that will bolster any confidence in the molecules to man narrative of Darwinists. We want to know how the eye, and everything else, evolved in the first place! We already know that Darwinian processes are excellent at breaking things!
Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
Not a single novel gene are protein was seen to 'evolve' in 4 decades of laboratory evolution experiments! Moreover the odds of a gene or protein evolving by Darwinian processes are astronomical:
"In light of Doug Axe's number, and other similar results,, (1 in 10^77), it is overwhelmingly more likely than not that the mutation, random selection, mechanism will fail to produce even one gene or protein given the whole multi-billion year history of life on earth. There is not enough opportunities in the whole history of life on earth to search but a tiny fraction of the space of 10^77 possible combinations that correspond to every functional combination. Why? Well just one little number will help you put this in perspective. There have been only 10^40 organisms living in the entire history of life on earth. So if every organism, when it replicated, produced a new sequence of DNA to search that (1 in 10^77) space of possibilities, you would have only searched 10^40th of them. 10^40 over 10^77 is 1 in 10^37. Which is 10 trillion, trillion, trillion. In other words, If every organism in the history of life would have been searching for one those (functional) gene sequences we need, you would have searched 1 in 10 trillion, trillion, trillionth of the haystack. Which makes it overwhelmingly more likely than not that the (Darwinian) mechanism will fail. And if it is overwhelmingly more likely than not that the (Darwinian) mechanism will fail should we believe that is the way that life arose?" Stephen Meyer - 46:19 minute mark - Darwin's Doubt - video https://www.youtube.com/watch?v=Vg8bqXGrRa0&feature=player_detailpage#t=2778
Yet, despite such consistent evidence against their theory, we have Darwinists continually, and insanely, insisting that their theory is true. When asked for solid evidence for why they believe their theory to be true they will cite such evidence as blind cave fish (or some other such ludicrous example). It would be absolutely funny if it weren't for the fact that so much (i.e. their soul) was riding on it. But what can a person do???? It is much like trying to talk a drug addict out of using drugs. It never works until the addict personally decides the cost is too great to continue the charades and then reaches out for help. Only then, when the willingness is finally there, can recovery begin! Of related interest to sight and souls: One of the more fascinating branches of Near Death Studies have been the studies of people who were born blind who have had NDE’s, who could see for the first time in their life during their NDE. This simply has no explanation within the materialistic framework, whereas, in the theistic framework, this is expected:
Blind Woman Can See During Near Death Experience (NDE) - Pim von Lommel - video https://www.youtube.com/watch?v=gKyQJDZuMHE Kenneth Ring and Sharon Cooper (1997) conducted a study of 31 blind people, many of who reported vision during their Near Death Experiences (NDEs). 21 of these people had had an NDE while the remaining 10 had had an out-of-body experience (OBE), but no NDE. It was found that in the NDE sample, about half had been blind from birth. (of note: This 'anomaly' is also found for deaf people who can hear sound during their Near Death Experiences(NDEs).) http://www.newdualism.org/nde-papers/Ring/Ring-Journal%20of%20Near-Death%20Studies_1997-16-101-147-1.pdf
Verse and Music:
2 Corinthians 5:7 For we walk by faith, not by sight. Jeremy Camp - Walk By Faith http://www.youtube.com/watch?v=BgWOcYpHm0o
bornagain77_{May 24, 2014
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Querius:
For example, the cave fish you mentioned have lost their sight, but they have not been observed evolving sonar. Not even a little.
Why would blind cave fish need to 'evolve' sonar? The increased size, number, and sensitivity of their superficial neuromasts are more than adequate for their survival in dark environments. In fact when compared to their surface-dwelling sighted-relatives they out perform them on many tasks/challenges such as the detection of current, vibration, and prey.franklin_{May 24, 2014
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Querius: There are many different cave fish and I don't know much about most of them, but blind Mexican tetras, for example, have developed a type of echolocation. They create waves of suction by opening their mouths continually, and detect the reflected waves with their skin sensors. It's a simple system, but it works. Have you ever seen blind tetras in an aquarium? I have, many times. They swim gracefully in schools and don't bump into things. Blind tetras are recently evolved cave forms of two different Astyanax species (both of them have surface-dwelling forms with fully developed eyes). Give them a few million years and they'll come up with a more advances system of orientation.Piotr_{May 24, 2014
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Great observation, bogart! Natural selection works extremely well for reducing complexity. In fact, ALL observed contemporary changes due to evolution have resulted in a reduction of complexity. For example, the cave fish you mentioned have lost their sight, but they have not been observed evolving sonar. Not even a little. Under natural selection, fixation of genes results in reduced genetic diversity. Many species are evolving toward extinction, but none have been observed evolving back again. -QQuerius_{May 24, 2014
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I get fed up with these axioms. From now on, I will interpret: "There are many examples of complex features evolving more than once." as: "There are many examples of complex features being designed in more than one way." Only seems fair if we are going to all make assumptions.Dr JDD_{May 24, 2014
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