The Finely Tuned Genetic Code

_{Jonathan McLatchie

November 19, 2011

Intelligent Design}

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Francis Crick regarded the genetic code found in nature as a “frozen accident.” Yet more and more it is looking to be the case that this code is exquisitely finely tuned — with features suggesting it is indeed one in a million. Therefore ought not purposive or intelligent design be regarded as a legitimate inference, as the best explanation for how the code came into existence?

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Comments

Thanks, bornagain77, for the thoughts on error-minimization. Like I said, I think we'll find even additional things as we gain more understanding of DNA. Given that DNA is designed and the code was selected from among possible codes, it is very likely that the code (and related DNA structure) will turn out to be a remarkably efficient and capable code that performs its task beautifully from an engineering standpoint. My point is simply that, by definition, the code is arbitrary. Therefore, to support design it does not have to be better than other codes or the best possible. There may be design constraints, as with any design process, that impose limitations and make the code less than perfect, or even less than other hypothetical possible codes. Stated another way, the idea that the DNA code is "the best" or is "perfect" (I'm not saying this is your position) is really another example of the "perfect design" requirement that design critics try to impose. Then the argument is opened up to all kinds of attack, based on some alleged design shortcoming or some other possible "better" design. We shouldn't get caught in that rhetorical trap. I agree that the DNA code is impressive. I am also confident that the more we learn we will find that it is extremely finely tuned to the task at hand and that it will turn out to be another example of exquisite design, like so many things we see in biology. My point is more narrow: (1) by definition the code is arbitrary, and therefore, there are other possible codes, including some that could turn out to be quite close in terms of function and capability; (2) the code can be functional and fill its task beautifully without meeting some arbitrary definition of "best" or "perfect" (in other words, the code can be imperfect and still be exquisitely functional); (3) the very existence of a complex functional code is the key evidence for design, not the particular code selected.Eric Anderson_{November 22, 2011
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As to 'thought experiments': Moving away from the face of a clock at the speed of light happens to be the 'thought experiment' that gave Einstein his breakthrough insight into e=mc2 and opened up a new era in physics.
Albert Einstein - Special Relativity - Insight Into Eternity - 'thought experiment' video http://www.metacafe.com/w/6545941/
As well, Einstein used a thought experiment of falling in a elevator to gain his breakthrough insight into general relativity:
Einstein – General Relativity – video http://www.youtube.com/watch?v=vyVUbUrB2YY
As well a thought experiment was used to verify that the beginning of the universe must be absolute:
"The conclusion is that past-eternal inflation is impossible without a beginning." Alexander Vilenkin - from pg. 35 'New Proofs for the Existence of God' by Robert J. Spitzer (of note: A elegant thought experiment of a space traveler traveling to another galaxy, that Borde, Guth, and Vilenkin, used to illustrate the validity of the proof that the beginning of the universe must be absolute, is on pg. 35 of the book as well.)
Thus DrREC, thought experiments, though poisonous, and very unfruitful when in the hands of neo-Darwinists, are actually very fruitful, in the field of physics, for discerning the Theistic foundation of reality = Further note on how Atheists have twisted the preceding proof:
How Atheists Take Alexander Vilenkin Out Of Context - William Lane Craig - video http://www.youtube.com/user/drcraigvideos#p/u/1/-aemfYmusSY
bornagain77_{November 22, 2011
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DrREC, as to this comment:
Again, that paper is a thought experiment without experimental verification, despite your claim that “since probabilities are now ruled out.” I also don’t think their hypothesis is decisively anti-materialist.
Yet, although you, and the authors of the paper, are not aware of it yet, there actually is experimental verification that quantum waves are in fact 'physically real';
It is important to note that the following experiment actually, conclusively, proved that information can be encoded into a photon while it is in its quantum wave state, thus destroying the notion, that was/is held by many materialists/atheists, that the wave function was not ‘physically real’ but was merely ‘abstract’. i.e. How can information possibly be encoded into a entity that is not physically real but is merely abstract? It simply would not be possible! Ultra-Dense Optical Storage – on One Photon Excerpt: Researchers at the University of Rochester have made an optics breakthrough that allows them to encode an entire image’s worth of data into a photon, slow the image down for storage, and then retrieve the image intact.,,, Quantum mechanics dictates some strange things at that scale, so that bit of light could be thought of as both a particle and a wave. As a wave, it passed through all parts of the stencil at once, carrying the “shadow” of the UR with it. http://www.physorg.com/news88439430.html
It is also interesting to note that materialists/atheists, instead of dealing forthrightly with the Theistic implications of quantum wave collapse, postulated quasi-infinite parallel universes, i.e. Many-Worlds, in which any absurdity would not be prevented from happening in the infinite parallel universes i.e. Elvis could be president, pink elephants, etc.. etc.. in the Many-Worlds model;
Quantum mechanics Excerpt: The Everett many-worlds interpretation, formulated in 1956, holds that all the possibilities described by quantum theory simultaneously occur in a multiverse composed of mostly independent parallel universes.[43] This is not accomplished by introducing some new axiom to quantum mechanics, but on the contrary by removing the axiom of the collapse of the wave packet: http://en.wikipedia.org/wiki/Quantum_mechanics#Philosophical_implications Finely Tuned Big Bang, Elvis In The Infinite parallel universe, and the Schroedinger Equation - Granville Sewell - audio http://www.metacafe.com/watch/4233012
A closer look at the 'physically real' quantum wave state, reveals some very interesting things:
Wave function Excerpt "wave functions form an ~~abstract~~physically real vector space",,, This vector space is infinite-dimensional, because there is no finite set of functions which can be added together in various combinations to create every possible function. http://en.wikipedia.org/wiki/Wave_function#Wave_functions_as_an_abstract_vector_space Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh Excerpt: In contrast to a classical bit, the description of a (photon) qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) http://www.cas.umt.edu/phil/faculty/duwell/DuwellPSA2K.pdf Quantum Computing – Stanford Encyclopedia Excerpt: Theoretically, a single qubit can store an infinite amount of information, yet when measured (and thus collapsing the Quantum Wave state) it yields only the classical result (0 or 1),,, http://plato.stanford.edu/entries/qt-quantcomp/#2.1 Dr. Quantum – Double Slit Experiment & Entanglement http://www.metacafe.com/watch/4096579/
Moreover, quantum wave collapse is found to be instantaneous, and universal, to each unique point of observation in the universe:
Centrality of Each Individual Observer In The Universe and Christ’s Very Plausible Reconciliation Of General Relativity and Quantum Mechanics https://docs.google.com/document/d/17SDgYPHPcrl1XX39EXhaQzk7M0zmANKdYIetpZ-WB5Y/edit?hl=en_US
Now, I find all of the preceding, that we have briefly gone over, to be absolutely fascinating! A photon, in its quantum wave state, is found to be mathematically defined as a ‘infinite-dimensional’ state, which ‘requires an infinite amount of information’ to describe it properly , which can be encoded with information in its ‘infinite dimensional’ state, and this ‘infinite dimensional’ photon is found to collapse to each individual point of observation in the universe, instantaneously, and thus ‘non-locally’, to just a 1 or 0 state, out of a infinite number of possibilities that the photon could have collapsed to instead!!!,,, Now my question to the materialistic atheists is this, “Exactly what ’final cause’ has been postulated throughout history to be completely independent of any space-time constraints, as well as possessing infinite knowledge and power, so as to be the ‘sufficient cause’ to explain what we see in the 'effect' of quantum wave collapse of a photons to each unique observer in the universe???
John 1:1-5 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. In him was life, and that life was the light of all mankind. The light shines in the darkness, and the darkness has not overcome it. Jeremy Camp – Walk By Faith http://www.youtube.com/watch?v=BgWOcYpHm0o
bornagain77_{November 22, 2011
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corrected link:
NP-hard http://en.wikipedia.org/wiki/NP-hard
bornagain77_{November 22, 2011
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DrREC, Oh goody more derision and false accusation as to my true intention for posting the 'quantum dot/quantum comoputation' paper. I believe they call this type of argumentation 'straw man'. Once again this is par for the course in dealing with a neo-Darwinist who is dogmatically committed to atheism! Moreover you act as if quantum computation in the DNA repair paper is not readily apparent. OK DrREC, if this massive 'traveling salesman' computation is being done 'materially' in the DNA, as you hold that it is,; The traveling salesman problem is an:
NP-hard (read: very hard) problem in computer science http://en.wikipedia.org/wiki/NP-hardNP-hard (read: very hard) problem in computer science; it involves finding the shortest possible route between cities, visiting each city only once. "Traveling salesman" problems keep supercomputers busy for days.
,,,so as to allow the DNA to 'materially' (locally) calculate how to fix 'every pothole in America before next rush hour', where exactly in the DNA's A, T, C, and Gs is this calculation being done??? Please point me to the CPU in the DNA so that I may see the DNA busily, materially, carrying this calculation out in a local (within space-time), material, fashion.
Quantum Computing in DNA - Hameroff Excerpt: Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.,,, We can then consider DNA as a chain of qubits (with helical twist). Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement. http://www.quantumconsciousness.org/views/QuantumComputingInDNA.html Quantum Information/Entanglement In DNA & Protein Folding – short video http://www.metacafe.com/watch/5936605/
I'm all ears DrREC! Please show me where the 'material' calculation is being done!bornagain77_{November 22, 2011
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Ok...well, thanks for answering your own question before I had a chance to reply. I'm not sure why you asked me to interpret a sentence in plain English in such insulting terms. I could do without "as if you had a clue" and "try to be honest just once." Others have been banned for less-but the hypocrisy of the blog moderators is a discussion for another day. This, especially on a thread where the vacuousness of your links was pointed out. You literally searched for "quantum + DNA" and came up with a experiment where DNA repair was experimentally observed using quantum dots (semi-conducting nanocrystals) and advertised it as quantum computing of DNA! So instead of admitting you were wrong, you start insulting me about some other link you found. Again, that paper is a thought experiment without experimental verification, despite your claim that "since probabilities are now ruled out.” I also don't think their hypothesis is decisively anti-materialist.DrREC_{November 21, 2011
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DrREC this statement means that quantum waves are physically real instead of abstract. In case you did not know, the position of materialists was that the quantum wave state was abstract. In fact Everett developed his entire Many Worlds (infinite parallel universes) hypothesis off of that very premise!,,, Night!bornagain77_{November 21, 2011
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DrREC, you state ( i mean pontificate as if you had a clue): “distinct quantum states must correspond to physically distinct states of reality” Now do you really think you know what this means DrREC? This is going to be real good! :)bornagain77_{November 21, 2011
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"DrREC, try to be honest just once, (it may just grow on you), and honestly answer this question." My replies here are always honest. You first-will you retract your interpretation of the quantum dots paper? Your question here is a bit mangled. Are you asking about non-local realism? "Non-local materialistic cause" isn't exactly a phrase with meaning, or one you'll find in the scientific literature. Google it. As it stands, this paper is a hypothetical, a Gedankenexperiment: "given only very mild assumptions, the statistical interpretation of the quantum state is inconsistent with the predictions of quantum theory. This result holds even in the presence of small amounts of experimental noise, and is therefore amenable to experimental test using present or near-future technology. amenable to experimental test are confirmed, " See the "mild assumptions.... amenable to experimental test.... if the predictions are confirmed." Bit of a reading comprehension fail from "since probabilities are now ruled out." And the last line of the abstract answers your question: "distinct quantum states must correspond to physically distinct states of reality" in a direction I don't think you like, given your interesting interpretation of QM.DrREC_{November 21, 2011
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“How this system works is an important unanswered question in this field,” I guarantee you the answer for how DNA is figuring out how to 'fix potholes on every street corner in America" ain't a materialistic one!!!!bornagain77_{November 21, 2011
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DrREC, try to be honest just once, (it may just grow on you), and honestly answer this question. Since this
The quantum state cannot be interpreted statistically – November 2011 http://lanl.arxiv.org/abs/1111.3328
shows that you can’t have an interpretation of a quantum state as probabilistic, exactly what is your non-local materialistic cause for a quantum state since probabilities are now ruled out?bornagain77_{November 21, 2011
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Article: "quantum dots, which are semi-conductor nanocrystals that light up in different colors" used to image DNA repair. You: "DNA repair evidence I cited is solid for highlighting impressive quantum computation in the DNA no matter what you may say to the contrary" Sorry, but you're just making stuff up. The cited article is not about quantum computation in the DNA. Is is about using quantum dots (quantum confined semiconductors) as fluorescent tracers to image DNA repair.DrREC_{November 21, 2011
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DrREC, so apparently you can now read my mind as to my intent for posting the link? But reading minds would be another falsification of materialism wouldn't it be?? :) ,,, instead of honestly addressing the overwhelming evidence for quantum non-locality in the DNA, you belittle me! Should figure it is par for the course in dealing with a dogmatic neo-Darwinists to hurl insults instead of honestly addressing the evidence!!!. The DNA repair evidence I cited is solid for highlighting impressive quantum computation in the DNA no matter what you may say to the contrary, or how much you may proclaim yourself to be wiser than everybody else.bornagain77_{November 21, 2011
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"Moreover DrREC, the ‘quantum dot’ link is quoted as to draw attention to the quantum computation" No, it isn't a "quantum computation." It is a method used by the researchers to image the process. From your article: "The researchers sought to unravel the mystery by tagging two repair proteins, called UvrA and UvrB, with quantum dots, which are semi-conductor nanocrystals that light up in different colors. They also stretched the usually clumped DNA into multiple "tightropes" to see the process more clearly." I really don't have time to go over how bogus most of your links are--but you seem to have a almost willful misunderstanding of them.DrREC_{November 21, 2011
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Moreover DrREC, the 'quantum dot' link is quoted as to draw attention to the quantum computation of 'It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.”,bornagain77_{November 21, 2011
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DrREC, you state:
'Your inability to grasp that realism in physics does not equate with metaphysical realism'
and yet it is your very own cherished atheistic philosophy of reductive materialism which is directly falsified by quantum entanglement. And yet quantum entanglement is found on a massive scale in molecular biology. Science at its best DrREC!!! Thus apparently it is you who ignores the scientific fact that you now have no materialistic basis in science in which to make any solid neo-darwinian conjectures that will bear fruit to the truth. Go figure?!? But then again it was never about the science, or truth, in the first place was it DrREC!?! and just to drive another nail in the materialistic coffin that you have chosen to lay in:
Quantum Theory's 'Wavefunction' Found to Be Real Physical Entity: Scientific American - November 2011 Excerpt: David Wallace, a philosopher of physics at the University of Oxford, UK, says that the theorem is the most important result in the foundations of quantum mechanics that he has seen in his 15-year professional career. "This strips away obscurity and shows you can't have an interpretation of a quantum state as probabilistic," he says. http://www.scientificamerican.com/article.cfm?id=quantum-theorys-wavefunction The quantum (wave) state cannot be interpreted statistically - November 2011 http://lanl.arxiv.org/abs/1111.3328
A song for you DrREC:
Creed - My Own Prison http://www.youtube.com/v/iBBqjGd3fHQ&fs=1&source=uds&autoplay=1
bornagain77_{November 21, 2011
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"DrREC, please reference your claims DrREC!" If you google either of the phrases genetically incorporating artificial amino acids or four base coding ribosome without quotes, and read the first article, you'll be fine. "Quantum Dots Spotlight...." Wow. Do you just do a google search for quantum and biology? Your inability to grasp that realism in physics does not equate with metaphysical realism notwithstanding, this one is the most hilarious yet. Quantum dots are man-made semi-conductors (quantum confined semiconductors to be precise, hence the name) that are really bright fluorophores used in cell biology as "tags" to follow certain processes. This highlights the depth to which you try to understand something before it becomes one of your links. Maybe stick to the youtube videos and Bible quotes.DrREC_{November 21, 2011
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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
I would like to reiterate just how ‘spooky’, to use Einstein’s infamous word, it is to find something that blatantly defies our concepts of time and space, on a massive scale, within our bodies;
Light and Quantum Entanglement Reflect Some Characteristics Of God – video http://www.metacafe.com/watch/4102182
At the 6:05 minute mark, of this following video, cells are photographed as they pull themselves together, from a distance, to form flawless blood vessels. The commentator on the video refers to the 'at a distance' action of the cells, to form flawless blood vessels, as a 'miracle';
Fearfully and Wonderfully Made - Glimpses At Human Development In The Womb - video http://www.metacafe.com/watch/4249713 Psalm 139:13-14 For you created my inmost being; you knit me together in my mother's womb, I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well. Jeremiah 1:5 "Before I formed you in the womb I knew you, before you were born I set you apart;,,,
we also find that non-local quantum information/entanglement is also necessary for dictating the final shape that proteins will take upon protein folding;
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
etc.. etc.. Another very interesting piece of evidence, that non-local’ quantum information/entanglement is dictating the shape of a organism, comes forth when we realize that the ‘shape’ of a organism fairly quickly disintegrates to thermodynamic equilibrium upon the death of the organism:
The Unbearable Wholeness of Beings – Steve Talbott Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings
As well it is very interesting to note that this quantum information/entanglement, which will assuredly be 'totally missing’ from the organism, once the organism disintegrates to complete thermodynamic equilibrium, is shown to be ‘conserved’. i.e. This transcendent non-local quantum information, though missing from the dead, and now disintegrated, organism must reside somewhere 'in the universe' (this provides a mechanism for the 'eternal soul' of man):
Quantum no-hiding theorem experimentally confirmed for first time – March 2011 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. 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
Music and verse:
Job 19:26 And after my skin has been destroyed, yet in my flesh I will see God; Kutless - Take Me In (Holy Of Holies) – http://www.metacafe.com/w/4716801
bornagain77_{November 21, 2011
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DrREC, please reference your claims DrREC! So that we may a little fun seeing how jerry-rigged your supposed 'evidence' is!(And by the way I don't even consider atheistic materialists as true scientists in the first place since number 1, quantum mechanics has shown reductive materialism to be false, and 2, science is impossible without God guaranteeing our perceptions and reasoning in reality are trustworthy in the first place!)
Epistemology - Why Should The Human Mind Even Be Able To Deeply Comprehend Reality? - Stephen Meyer http://vimeo.com/32145998
But to further critique the sheer absurdity of the atheist's foundationless materialistic conjectures, for the ability of purely undirected material processes to generate function information, as well as parallel integrated coding that far, far, outclasses anything man has ever devised, I want to point out that the highest level of information in the DNA is not even the information that is encoded on the DNA in the first place, but is the transcendent quantum information which is holding the DNA together, is directing the shape of the DNA to be in the form it is in, and is preforming very impressive 'quantum computation" in/on the DNA: Notes: First DNA does not control body plan morphogenesis:
‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009) The next evolutionary synthesis: Jonathan BL Bard (2011) 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 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
Here are a few comments on ‘non-local’ epigenetic information being a very plausible solution to 3-D spatial organization of Body Plans,,, (as well as in quantum computation): Although when many people speak of epigenetic information they are mainly focused on information flow in the cell that is not DNA centric in its basis, such as the many examples of epigenetic information flow Dr. Shapiro lists on page 22 of this following paper: ,,,
Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009 http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
,,,There is a particular type of extra ‘epigenetic’ information in life, that is not listed in Dr. Shapiro’s paper, that is very important for people to consider. This information is transcendent quantum information. To build on the last two references of post 4.1:
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/
Quantum Action confirmed in DNA by direct empirical research;
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 Does DNA Have Telepathic Properties?-A Galaxy Insight - 2009 Excerpt: 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. http://www.dailygalaxy.com/my_weblog/2009/04/does-dna-have-t.html
further note on non-local quantum computation within DNA:
Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm
bornagain77_{November 21, 2011
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"don’t you find it even a little bit suspicious that neo-Darwinists have NOT randomly evolved EVEN ONE CODE from scratch to begin with???" Make life de novo you darn scientists!!! And do it without design or selection! Actually, new codon functions (e.g. genetically incorporating artificial amino acids) and even a four base coding ribosome have been developed using directed evolution.DrREC_{November 21, 2011
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DrREC, in your characteristic severe lack of skepticism towards anything of a atheistic neo-Darwinian persuasion, don't you find it even a little bit suspicious that neo-Darwinists have NOT randomly evolved EVEN ONE CODE from scratch to begin with???
The DNA Code - Solid Scientific Proof Of Intelligent Design - Perry Marshall - video http://www.metacafe.com/watch/4060532 Codes and Axioms are always the result of mental intention, not material processes https://docs.google.com/document/pub?id=1PrE2Syt5SJUxeh2YBBBWrrPailC3uTFMdqPMFrzvwDY
Nor even a single protein from scratch???
Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723
DrREC, perhaps your skepticism would carry much more weight if you had any foundation in science to argue from in the first place, rather than just you insisting that materialism is true?!?~!?! Further note
Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement - 2009 Excerpt: A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. http://pre.aps.org/abstract/PRE/v79/i6/e060901 Quantum Information/Entanglement In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/ Falsification Of Neo-Darwinism by Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US
bornagain77_{November 21, 2011
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I'm unconvinced the genetic code is really optimal. One of your major sources: "Freeland et al. (2000) show that the genetic code is highly optimized -- indeed "the best of all possible codes" -- taking into account two parameters: first, the relative likelihood of transitions and transversions; and second, the relative impact of mutation." Has been highly questioned in the literature. In particular, DiGullo finds "the origins of the genetic code cannot be studied using measurements based on the PAM matrix because this matrix reflects the code itself, making any such analysis tautologous" which seems pretty self-explanatory. http://www.sciencedirect.com/science/article/pii/S0022519300922069 Other work has suggested the genetic code is stuck in a local, not global minimum, and that codes equally and more fit are easily obtained, calling into question the statistical approaches you cite. "Simulated evolution applied to study the genetic code optimality using a model of codon reassignments" http://www.biomedcentral.com/1471-2105/12/56 "Knight RD, Freeland SJ, Landweber LF: Adaptive evolution of the genetic code. In The Genetic Code and the Origin of Life. Volume 80. Edited by Lluís Ribas de Pouplana. Kluwer Academic/Plenum Publishers; 2004:175-184."DrREC_{November 21, 2011
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From page 175; 'The Cell's Design'; Fazale Rana:
"The genetic code's error-minimization properties are far more dramatic than these (one in a million) results indicate. When the researchers calculated the error-minimization capacity of the one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution. Researchers estimate the existence of 10^18 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This means of 10^18 codes few, if any have an error-minimization capacity that approaches the code found universally throughout nature."
bornagain77_{November 21, 2011
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Chas D: You are certainly right that there are alternative codes. Indeed we see different codes at work in other areas of the cell. I'm not sure the idea that the existing DNA code being better than other codes is a good argument. "One in a million" who know? That sounds more like just a rhetorical statement to me. As you point out, if it is one in a million, that still leaves a lot of potential codes on the table, and we may never know why this particular code was chosen. That said, there are lots of interesting things we have learned about DNA. For example, why a 4-bit digital code? We can get come inkling, perhaps: Coding for 20 amino acids requires more than a 2-bit code. A 3-bit code would not permit a complementary strand, which is critical to DNA function (this is a structural requirement, not a "coding" requirement). Therefore, the 4-bit code appears to be the minimal or the "most efficient" code that could accomplish the basic objectives. Are there other things, say structural elements, beyond the code itself that make DNA more optimal than other approaches? I suspect we'll find additional things as we gain more understanding of DNA and the interactions between the various components. Nevertheless, I don't think a "one-in-a-million" type argument is particularly persuasive from a standpoint of design. Rather, the focus needs to be on the fact that *any* rational and functional code exists in life. That is the distinguishing factor for design, much moreso than being able to argue that it is the "best code" or the "only possible code that could work", etc.Eric Anderson_{November 21, 2011
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Chas you are extremely biased in your reading of this for Freeland et al:
Ode to the Code - Brian Hayes The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code. It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we'll never see again in the modern world. https://www.americanscientist.org/issues/pub/ode-to-the-code/4
Found that the genetic code is the best out of 1 million compared. Yet even though they found no superior code out of 1 million, you assume that the 10^64 they did not search are superior to the one code. Where in fact the best you could say is that for each million of the 10^64 codes there may be one code that is equal to or better than the one we find. But you don't know that for sure and it is extremely biased of you, to put it mildly, for you to assume that all 10^64 codes not surveyed are superior to the ones they checked. As for this comment of yours,,,
"You may or may not realise that the origin of life and the crystallisation of the modern genetic code are two completely separate phenomena."
Really???
Was our oldest ancestor a proton-powered rock? - Oct. 2009 Excerpt: “There is no doubt that the progenitor of all life on Earth, the common ancestor, possessed DNA, RNA and proteins, a universal genetic code, ribosomes (the protein-building factories), ATP and a proton-powered enzyme for making ATP. The detailed mechanisms for reading off DNA and converting genes into proteins were also in place. In short, then, the last common ancestor of all life looks pretty much like a modern cell.” http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html
Further notes:
Shannon Information - Channel Capacity - Perry Marshall - video http://www.metacafe.com/watch/5457552/ “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life
Moreover besides such severe constraint on 'evolvability' of the 'optimal' code, the protein machinery that replicates DNA is found to be vastly different in even the most ancient of different single celled organisms, thus exacerbating the Darwinists insurmountable problems once over again:
Did DNA replication evolve twice independently? - Koonin Excerpt: However, several core components of the bacterial (DNA) replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic (DNA) replication apparatus. http://nar.oxfordjournals.org/cgi/content/full/27/17/3389
There simply is no smooth 'gradual transition' to be found between these most ancient of life forms, bacteria and archaea, as this following articles and videos clearly point out:
Was our oldest ancestor a proton-powered rock? Excerpt: In particular, the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea,... Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common (between the bacteria and the archaea). http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html?page=1 Bacteria Too Complex To Be Primitive Eukaryote Ancestors - July 2010 Excerpt: “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola. “Obviously, this misperception must be modified.... There is a whole process going on that we have been blind to.”,,, For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote. http://www.creationsafaris.com/crev201007.htm#20100712b
As for your swipe at Yockey's 'atomic bomb' credentials, Well considering your sheer lack of integrity thus far in being forthright with the math of the evidence, I will take his word over your word 24 hours a day 7 days a week, and then some!!!bornagain77_{November 20, 2011
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Further notes:
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 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm 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
Verse and Music
1 Corinthians 1:25 For the foolishness of God is wiser than man's wisdom, and the weakness of God is stronger than man's strength. Jotta A.-Agnus Dei - HQ.mp4 http://www.youtube.com/watch?v=e6cDQcLkprk
bornagain77_{November 20, 2011
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Oh, for goodness' sake! Yockey helped develop the atomic bomb? What an excellent grounding for a career in molecular biology! Yockey's musings on the prebiotic soup have absolutely no relevance to the evolution of the genetic code. You may or may not realise that the origin of life and the crystallisation of the modern genetic code are two completely separate phenomena. That is the whole point. I am suggesting that the first cell with a 20 amino acid genetic code was not the first cell.
Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature.
You really didn't grasp what I was saying, did you? All your quote says is that there are > 10^70 codes, and selection would have to explore 'em all to find the best. He does not say that the one we have is the best. I too think that selective optimisation of the genetic code is impossible - but that is not the only means by which the apparent fault-tolerance can be achieved, as I argued in my first post. However, you are at odds with Jonathan M and his quoted sources if you think that the code is the best out of 10^70, rather than one in a million. With you and Yockey's deep knowledge of molecular biology, no doubt you can pull up some basis for your assertion. That's what Freeland et al have tried to do - compare codes by various metrics, and they come up with about 1 in a million. I don't see it in your quotes - by what heuristic have Yockey, and you as his disciple, concluded that this code is the best? And where has this result been published?Chas D_{November 20, 2011
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Chas you ask:
Do you have some evidence to back up your assumption that it is the best of all 10^70 possibilities?
Well Hubert Yockey
Professor Hubert P. Yockey (b. April 15, 1916), PhD is a physicist and information theorist. He worked under Robert Oppenheimer on the Manhattan Project, and at the University of California, Berkeley. He has studied the application of information theory to problems in biology and published his conclusions in the Journal of Theoretical Biology from 1974 onwards. He is very critical of the primordial soup theory of the origin of life, and believes that "the origin of life is unsolvable as a scientific problem".
asserts on pages 180-83 in,,
Information Theory and Molecular Biology http://www.amazon.com/Information-Theory-Molecular-Biology-Hubert/dp/0521350050
That,,,
Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell's Design - 2008 - page 177) DNA - The Optimal Genetic Code - Error Minimization & Parallel Codes - video http://www.metacafe.com/watch/4491422/
Thus Chas unless you have concrete evidence that Professor Hubert Yockey, who helped develop the atomic bomb, was wrong. I guess I'll stick with his assessment that the DNA code is optimal out of 10^70 possible codes; further notes:
The coding system used for living beings is optimal from an engineering standpoint. Werner Gitt - In The Beginning Was Information - p. 95 Collective evolution and the genetic code - 2006: Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes. http://genome.cshlp.org/content/17/4/405.full The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy 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). "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 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/ 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
Verse and music
Isaiah 40:28 Do you not know? Have you not heard? The LORD is the everlasting God, the Creator of the ends of the earth. He will not grow tired or weary, and his understanding no one can fathom. Third Day - Tunnel http://www.youtube.com/watch?v=S7V5t9ECZXo
bornagain77_{November 20, 2011
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And, besides your blanket assertion that there are 10^64 better codes than the DNA code, what is your actual evidence to prove there is ANY conceivable DNA code better than the optimal one we find in life??
If you read Jonathan's article really carefully, he will tell you that there are 10^70 possible codes, and will also quote you papers with Freeland as co-author that assess the variant codes by various error-tolerance metrics - the very assessments that persuade many in the Creationist/ID community that it must be designed. One of Freeland's papers is entitled the genetic code is one in a million. 10^64 is not a blanket assertion, it is simply the result of dividing 10^70 (all possible codes) by 10^6 (the fraction that is better, on those metrics, than the one we have). Do you have some evidence to back up your assumption that it is the best of all 10^70 possibilities?Chas D_{November 20, 2011
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Of note: not only is DNA code found to be 'optimal', the programming of the cell exceeds what man has accomplished in computers. i.e. A cell apparently seems to be successfully programmed along the very stringent guidelines laid out by Landauer's principle of 'reversible computation':
Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus (computers), dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a
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