The Amylome: More Constraints on Protein Design and Evolution

DrREC, you can define whatever you want to mean whatever you want, so that you can believe whatever you want, because, as far as I have seen of your 'science', that is what you always do anyways, in spite of what the ANY evidence says to the contrary.,,, As for myself I will follow the evidence where it leads! further notes on falsifying neo-Darwinism: Materialistic neo-Darwinism contends that all the functional information found in life, including 'transcendent' quantum information, merely emerges from material particles. Yet quantum teleportation, which is a extension of quantum entanglement/information,,,,

Quantum Entanglement and Teleportation - Anton Zeilinger - video http://www.metacafe.com/watch/5705317/

,,, teleportation reduces material particles to 'transcendent' quantum information in the process of 'instantaneous' quantum teleportation of the material particles. Thus how can quantum information 'emerge' from material particles, when material particles reduce to transcendent quantum information in the first place???:

The following articles show that even atoms (Ions; 'material particles') are subject to teleportation:

Of note: An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. 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

======================= Of related note: Chuck Missler makes a interesting comment at the beginning in this following video about how atheists/materialists have hijacked modern science, from the Christian Theists who originally founded modern science, And have turned tried their best to turn 'science' into a 'tool of indoctrination' instead of a tool for revealing God's glory.

God's Science Quiz To Job - Chuck Missler http://vimeo.com/28967695

bornagain77

Ok, maybe a simpler question. Can we agree realism in physics is not the same thing as metaphysical realism? DrREC

Well DrREC, as usual, you do your dead level best to obfuscate the obvious, but to put it even more clearly and highlight, for others, the levels of irrationality you will delude yourself with just to deny the obvious Theistic implications.,,, Entanglement is now conclusively shown to be 'instantaneous', regardless of how far apart two entangled particles may be in the universe. Einstein himself argued for the materialistic position against quantum mechanics with what were termed 'hidden variables',, these 'hidden variables were postulated so that quantum entanglement would not violate what Einstein felt were insuperable space-time barriers of the speed of light, Parameters that he had layed out in General, and Special, Relativity. Yet Quantum Mechanics, to borrow from Laplace, has 'no need of that hidden variable hypothesis' and thus no need for any space-time constraints whatsoever:

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

Yet DrREC, though quantum entanglement/information defies space-time constraints, material particles are STILL strictly constrained to space-time (speed of light) constraints. i.e. It is impossible for the material particles to be the 'cause' of a 'effect' that defy space-time. i.e. A cause which is not limited to space-time must be supplied in order to explain a effect which defies space-time. The 'cause' for quantum entanglement is simply not within the ability of material particles to supply: Further notes;

Wheeler's Classic Delayed Choice Experiment: Excerpt: Now, for many billions of years the photon is in transit in region 3. Yet we can choose (many billions of years later) which experimental set up to employ – the single wide-focus, or the two narrowly focused instruments. We have chosen whether to know which side of the galaxy the photon passed by (by choosing whether to use the two-telescope set up or not, which are the instruments that would give us the information about which side of the galaxy the photon passed). We have delayed this choice until a time long after the particles "have passed by one side of the galaxy, or the other side of the galaxy, or both sides of the galaxy," so to speak. Yet, it seems paradoxically that our later choice of whether to obtain this information determines which side of the galaxy the light passed, so to speak, billions of years ago. So it seems that time has nothing to do with effects of quantum mechanics. And, indeed, the original thought experiment was not based on any analysis of how particles evolve and behave over time – it was based on the mathematics. This is what the mathematics predicted for a result, and this is exactly the result obtained in the laboratory. http://www.bottomlayer.com/bottom/basic_delayed_choice.htm 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 http://henry.pha.jhu.edu/aspect.html "As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter." Max Planck - The Father Of Quantum Mechanics - Das Wesen der Materie [The Nature of Matter], speech at Florence, Italy (1944)

bornagain77

Well, you answered neither of me questions. Let me provide you a reference: http://arxiv.org/pdf/quant-ph/0607057v2 "Of course, whether users of the phrase ‘local realism’ are misusing and/or abusing the term ‘realism’ can only be established if we know (which, by the way, requires that they know) what they mean by it. Since, unfortunately, they typically don’t tell us what they mean, we will survey four di?erent senses of realism that one might plausibly think could be relevant." So what do you mean by 'local realism' Hint: http://www.youtube.com/watch?v=G2y8Sx4B2Sk DrREC

Well DrREC, since you never believe anything I have to say anyway, here it is from the mouth of the scientist who was at the forefront of empirically falsifying local realism (reductive materialism), with quantum entanglement:

Quantum Entanglement – The Failure Of Local Realism (Reductive Materialism) – Alain Aspect – video http://www.metacafe.com/w/4744145

i.e. DrREC, all you have to do to explain finding quantum entanglement in molecular biology, in materialistic neo-Darwinian terms, is explain how material particles can 'cause' a non-local (beyond space and time) quantum entanglement 'effect'. Yet in order to do so you will have to falsify Alain Aspect, and company's work, which falsified 'local' realism! ,,,, Good luck with that! :) bornagain77

"quantum entanglement is not reducible to material processes" How so? Define quantum entanglement in your own words. Then explain how it it immaterial. DrREC

DrREC, perhaps it is necessary to strongly impress upon you just how 'spooky' it is to find quantum entanglement/information in molecular biology on such a massive scale:

Light & Quantum Mechanics Reflect Some Of God's Characteristics - video http://www.metacafe.com/watch/4102182/

bornagain77

DrREC you, as usual, avoid presenting anything to counter the the direct empirical observation of extreme rarity for functional proteins, and acts as if Darwinian evolution is somehow immune to actually prove itself directly. Pseudo-science at its peak!!! Moreover you ask:

What the deuce does quantum entanglement have to do with anything?

Yet quantum entanglement/information is now EMPIRICALLY shown, by direct observational evidence, which is far more than I can say about anything in Darwinism, to be inside functional proteins. Thus since neo-Darwinism purports to explain everything in life solely by reference to purely material processes, and yet quantum entanglement/information is not reducible to material processes, I would say this has EVERYTHING to do with the matter at hand!!! For you to play this all this off as if it does not matter reveals the extraordinary, and irrational, lengths you will go to to deny the obvious implications of design that we find in life. As Dr. Hunter says, Religion drives science and it matters! bornagain77

The big numbers game is just that. If the nature of the first proteins in life is unknown, it is a guessing game played with big numbers that ignore early evolution. What the deuce does quantum entanglement have to do with anything? Unless someone else jumps in, I'll stop here-the links you toss up are far too diffuse a mess to have a conversation about. DrREC

Further note: To dovetail 'Functional Quantum Information' into Dembski and Marks's work on Conservation of Information;,,, Dembski and Marks outline the conservation of 'classical' information here;

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/

Yet,,,Encoded classical information that Dembski and Marks found to be 'conserved', classical information such as what we find in computer programs, and yes like the classical information we find encoded on DNA, is found to be a subset of 'transcendent' quantum information by the following method:,,,

This following research provides solid falsification for Rolf Landauer’s contention that 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 '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

bornagain77

Well now DrREC, you simply are restating that 'big big numbers', against the plausibility of finding functional proteins by neo-Darwinian means, are a game, and yet, without reference, you claim this is not so and offer no 'small small numbers' to counter the work of Doug Axe and others (Sauer; MIT), or even to counter the critique of Szostak's 1 in 10^12 number for simple ATP binding.,,, But DrREC, aside from this 'playing games' with 'big big numbers', the materialistic framework, of the neo-Darwinian evolution of functional proteins by PURELY material processes, is falsified, by a completely different angle, by the finding of 'non-local' quantum information/entanglement in functional proteins: First here is the falsification of local realism (reductive materialism) by quantum entanglement:

Quantum Entanglement – The Failure Of Local Realism - Materialism - Alain Aspect - video http://www.metacafe.com/w/4744145 The falsification for local realism (reductive materialism) was recently greatly strengthened: 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 Quantum entanglement is shown to be related to ‘functional information’ by the following evidence; 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/

And yet, to the chagrin of atheistic materialists, but to the delight of the rest of us, quantum entanglement is now found, on a massive scale, in molecular biology, even though just a few years ago, because of 'noisy high temperature' concerns in living creatures, it was considered completely impossible for quantum entanglement to exist in living creatures;

Quantum Information/Entanglement In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/ 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/ 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 Here's another measure that strongly implicates quantum information in protein structures: Proteins with cruise control provide new perspective: Excerpt: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.” http://www.princeton.edu/main/news/archive/S22/60/95O56/ The preceding is fairly solid confirmation that far more complex functional information resides in proteins than meets the eye, for the calculus equations used for ‘cruise control’, that must somehow reside within the quantum information that is ‘constraining’ the entire protein structure to its 'normal' state, is anything but ‘simple classical information’. For a sample of the equations that must be dealt with, to ‘engineer’ even a simple process control loop like cruise control along a entire structure of the protein, please see this following site: PID controller Excerpt: A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal. http://en.wikipedia.org/wiki/PID_controller

i.e. 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, 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 falsify Alain Aspect, and company’s, falsification of local realism (reductive materialism)! bornagain77

As for the rest of the links, I think they just go to showing the issues with Hunter's critique, and the game of big big numbers. To get those big big numbers have to assume the only functional protein is a large modern one like we see today. But functional amyloids, catalytic peptides, peptides that assemble into larger domain-like architectures, are observed and experimentally made. DrREC

Thanks for the link-but I think it reinforces my point. It was the fifth "here" off a link off the post. DrREC

Here you go DrREC on the 10^21 number;

Natural Selection Doesn’t Help, Gradualism is Out, and so is Evolution Excerpt: To defend their second claim, that evolution can easily search the entire protein sequence space, the evolutionists present upper and lower bound estimates of the number of different sequences evolution can explore. Their upper bound estimate of 10^43 (a one followed by 43 zeros) is ridiculous. It assumes a four billion year time frame with 10^30 bacteria constantly testing out new proteins. First, even for an upper bound estimate their time frame is about two to three orders of magnitude too large. And furthermore, from where did these bacteria come? Bacteria need thousands of, yes, proteins. You can’t use bacteria to explain how proteins first evolved when the bacteria themselves require an army of proteins. The lower bound of 10^21 is hardly any more realistic. The evolutionists continue to use the four billion year time frame. And they also continue to rely on the pre existence of an earth filled with a billion species of bacteria (with their many thousands of pre existing proteins). So with these two claims in hand, the evolutionists conclude that the evolution of new proteins is no big deal. “We hope,” they explain, “that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.” This shifting of attention to “divine intervention” does not remedy their several scientific errors. The scientific fact is that the numbers are big. This isn’t a “game.” http://darwins-god.blogspot.com/2011/07/response-to-comments-natural-selection.html

DrREC, does it not bother you in the least that neo-Darwinists continually refer to hypothetical worlds in which evolution is forever searching for new functional proteins, so as to be able to evolve more complexity 'in the future', but that they never actually demonstrate the evolution of any novel functional proteins in the present for those of us who are skeptical of their hypothetical worlds??? It seems to me that this little matter of having ZERO empirical evidence, for the origination of novel proteins by neo-Darwinian processes, should be taken far more seriously by you instead of you just accepting any conjecture that is dreamed up and then calling that conjecture science!

Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 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 How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html Signature In The Cell - Review Excerpt: Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. http://www.fourmilab.ch/documents/reading_list/indices/book_726.html

bornagain77

From the article Dr. Hunter references: "Eisenberg, Dobson and others have speculated that the self-complementary stickiness of these short segments might have made them useful building blocks in the earliest stages of life on Earth. Moreover, reports have started to emerge of proteins that function normally in the amyloid state, for example some pituitary hormones. "We know by now of over two dozen native amyloids, so this state is clearly used by biology in a functional way as well as a dysfunctional way," says Eisenberg" On another note, could Dr. Hunter include more references in his posts? It is often difficult to trace the claims being made when "elsewhere, evolutionists..." is the norm, often with only a link to a former post that links to another post.... I bring this up, because one estimate of the total number of evolutionary experiments possible in the history of life 10^21 is so inane, I wanted to see where it came from. There are 10^30 or greater bacteria on earth, now, each harboring multiple mutations, so i was puzzled. I can't trace the origin of this number through the post. DrREC