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A Dog is a Chien is a Perro is a Hund

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File:RNA-codons.png

Photo courtesy of Wikipedia

In his “UB Sets It Out Step-By-Step” UprightBiped argued that the transfer of recorded information in the genome is like any other form of recorded information – i.e., it is an arbitrary relationship instantiated in matter.

After several months and over 1,400 combox comments, UB’s argument has withstood a barrage of attacks from our materialist friends.  This post is a response to one such attack.

UB’s opponents argue they cannot understand what he means by “arbitrary” in his argument.  Of course, UB has good responses to this objection, and I invite you to read them in the combox.  But as I was thinking about the matter this morning, it occurred to me that there is a very simple definition of “arbitrary” that, I think, makes the matter so clear that only the willfully obtuse could deny it.  Here it is:  An arrangement of signs is arbitrary when the identical purpose could be accomplished through a different arrangement of signs if the rules of the semiotic code were different.  [“Semiotics” is the study of how signs are used to represent things, such as how a word in a language represents a particular object.]

Here’s an example of an arbitrary arrangement of signs:  DOG.  This is the arrangement of signs English speakers use when they intend to represent Canis lupus familiaris. In precise semiotic parlance, the word “dog” is a “conventional sign” for Canis lupus familiaris among English speakers.  Here, “conventional” is used in the sense of a “convention” or an agreement.  In other words, English speakers in a sense “agree” that “dog” means Canis lupus familiaris.

Now, the point is that there is nothing inherent in a dog that requires it to be represented in the English language with the letters “D” followed by “O” followed by “G.”  If the rules of the semiotic code (i.e., the English language) were different, the identical purpose could be accomplished through a different arrangement of signs.  We know this because in other codes the same purpose is accomplished with vastly different signs.  In French the purpose is accomplished with the following arrangement of signs:  C H I E N.  In Spanish the purpose is accomplished with the following arrangement of signs:  P E R R O.  In German the purpose is accomplished with the following arrangement of signs:  H U N D.

In each of the semiotic codes the purpose of signifying an animal of the species Canis lupus familiaris is accomplished through an arbitrary set of signs.  If the rules of the code were different, a different set of signs would accomplish the identical purpose.  For example, if, for whatever reason, English speakers were collectively to agree that Canis lupus familiaris should be represented by “B L I M P,” then “blimp” would accomplish the purpose of representing Canis lupus familiaris just as well as “dog.”

How does this apply to the DNA code?  The arrangement of signs constituting a particular instruction in the DNA code is arbitrary in the same way that the arrangement of signs for representing Canis lupus familiaris is arbitrary.  For example, suppose in a particular strand of DNA the arrangement “AGC” means “add amino acid X.”  There is nothing about amino acid X that requires the instruction “add amino acid  X” to be represented by  “AGC.”  If the rules of the code were different the same purpose (i.e, instructing the cell to “add amino acid  X”) could be accomplished using “UAG” or any other combination.  Thus, the sign AGC is “arbitrary” in the sense UB was using the word.

Why is all of this important to ID?  It is important because it shows that the DNA code is not analogous to a semiotic code.  It is isometric with a semiotic code.  In other words, the digital code embedded in DNA is not “like” a semiotic code, it “is” a semiotic code.  This in turn is important because there is only one known source for a semiotic code:  intelligent agency.  Therefore, the presence of a semiotic code embedded within the cells of every living thing is powerful evidence of design, and the burden is on those who would deny design to demonstrate how a semiotic code could be developed though blind chance or mechanical law or both.

Comments
HMMM, could you please provide us with the ‘pathetic detail’ of Darwinian evolution producing JUST ONE novel functional protein???
Antibodies!Alan Fox
February 12, 2013
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"it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories." HMMM, could you please provide us with the 'pathetic detail' of Darwinian evolution producing JUST ONE novel functional protein??? Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 Following the Evidence Where It Leads: Observations on Dembski's Exchange with Shapiro - Ann Gauger - January 2012 Excerpt: So far, our research indicates that genuine innovation, a change to a function not already pre-existent in a protein, is beyond the reach of natural processes, even when the starting proteins are very similar in structure. http://www.evolutionnews.org/2012/01/observations_re055171.html Whereas, on the other hand, I can provide you the 'pathetic detail' of Intelligent Design doing as such: Viral-Binding Protein Design Makes the Case for Intelligent Design Sick! (as in cool) - Fazale Rana - June 2011 Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required: "...cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2" If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely? In other words, the researchers from the University of Washington and The Scripps Institute have unwittingly provided empirical evidence that the high-precision interactions required for PPIs requires intelligent agency to arise. Sick! http://www.reasons.org/viral-binding-protein-design-makes-case-intelligent-design-sick-cool Computer-designed proteins programmed to disarm variety of flu viruses - June 1, 2012 Excerpt: The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.,, These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, "to leapfrog over bottlenecks" to improve the activity of the binder. http://phys.org/news/2012-06-computer-designed-proteins-variety-flu-viruses.htmlbornagain77
February 12, 2013
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I see. Suggesting a little more clarity and precision with definitions is "a nonstop game of semantics". I must remember that ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories.Alan Fox
February 12, 2013
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33 Alan FoxFebruary 12, 2013 at 4:41 am As I said, Jammer, if you are already disposed towards the religious explanations for things like the presence of life on Earth and the existence of the Universe then I guess it will make sense.
Yes, and if you have a worldview bias that abhors the notion of design being true, you'll sink to any level to deny it, including self-delusion and a nonstop game of semantics.Jammer
February 12, 2013
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Your objections Mr. Fox are hypocritically ludicrous, for one thing consciousness is shown to be fundamental to material reality thus falsifying your reductive materialistic presupposition in neo-Darwinism: “No, I regard consciousness as fundamental. I regard matter as derivative from consciousness. We cannot get behind consciousness. Everything that we talk about, everything that we regard as existing, postulates consciousness.” (Max Planck, as cited in de Purucker, Gottfried. 1940. The Esoteric Tradition. California: Theosophical University Press, ch. 13). “Consciousness cannot be accounted for in physical terms. For consciousness is absolutely fundamental. It cannot be accounted for in terms of anything else.” (Schroedinger, Erwin. 1984. “General Scientific and Popular Papers,” in Collected Papers, Vol. 4. Vienna: Austrian Academy of Sciences. Friedr. Vieweg & Sohn, Braunschweig/Wiesbaden. p. 334.) "In any philosophy of reality that is not ultimately self-defeating or internally contradictory, mind – unlabeled as anything else, matter or spiritual – must be primary. What is “matter” and what is “conceptual” and what is “spiritual” can only be organized from mind. Mind controls what is perceived, how it is perceived, and how those percepts are labeled and organized. Mind must be postulated as the unobserved observer, the uncaused cause simply to avoid a self-negating, self-conflicting worldview. It is the necessary postulate of all necessary postulates, because nothing else can come first. To say anything else comes first requires mind to consider and argue that case and then believe it to be true, demonstrating that without mind, you could not believe that mind is not primary in the first place." - William J. Murray and another thing that makes your objections ludicrous is that if anything is 'fuzzy' in its operational definition that would be Darwinian evolution, not ID: Science and Pseudoscience – Imre Lakatos “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture Nobel Prize-Winning Physicist Wolfgang Pauli on the Empirical Problems with Neo-Darwinism – Casey Luskin – February 27, 2012 Excerpt: “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’” Wolfgang Pauli (pp. 27-28) - Murray Eden, as reported in “Heresy in the Halls of Biology: Mathematicians Question Darwinism,” Scientific Research, November 1967, p. 64. “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109. “No human investigation can be called true science without passing through mathematical tests.” Leonardo Da Vinci Whereas, in contrast to there being no identifiable falsification criteria for neo-Darwinism (at least no identifiable falsification criteria that neo-Darwinists will accept), ID, on the other hand, does provide a fairly rigid framework for falsification: Dembski’s original value for the universal probability bound is 1 in 10^150, 10^80, the number of elementary particles in the observable universe. 10^45, the maximum rate per second at which transitions in physical states can occur. 10^25, a billion times longer than the typical estimated age of the universe in seconds. Thus, 10^150 = 10^80 × 10^45 × 10^25. Hence, this value corresponds to an upper limit on the number of physical events that could possibly have occurred since the big bang. How many bits would that be: Pu = 10-150, so, -log2 Pu = 498.29 bits Call it 500 bits (The 500 bits is further specified as a specific type of information. It is specified as Complex Specified Information by Dembski or as Functional Information by Abel to separate it from merely Ordered Sequence Complexity or Random Sequence Complexity; See Three subsets of sequence complexity) Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors http://www.tbiomed.com/content/2/1/29 This short sentence, “The quick brown fox jumped over the lazy dog” is calculated by Winston Ewert, in this following video at the 10 minute mark, to contain 1000 bits of algorithmic specified complexity, and thus to exceed the Universal Probability Bound (UPB) of 500 bits set by Dr. Dembski Proposed Information Metric: Conditional Kolmogorov Complexity – Winston Ewert – video http://www.youtube.com/watch?v=fm3mm3ofAYU Michael Behe on Falsifying Intelligent Design – video http://www.youtube.com/watch?v=N8jXXJN4o_Abornagain77
February 12, 2013
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As I said, Jammer, if you are already disposed towards the religious explanations for things like the presence of life on Earth and the existence of the Universe then I guess it will make sense.Alan Fox
February 12, 2013
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"I design, therefore the world is Designed; though I am not the designer or Designer of the world." And because of this revolutionary idea, 'Intelligent Design Natural Scientific Theory' (copyright Seattle think tank) must be true and should be accepted by all scientists and citizens who are not 'ignorant, stupid or insane'! ;) "I am an 'intelligent agent,' therefore an 'Intelligent Agent' made the world, biological information and human beings and the proof comes not just by analogy." Such logic is of course infallible. And goodness No, I don't need *any* sacred scripture(s) to tell me this. I just need 'Science.' I just need...semiotics. "DNA is not “like” a semiotic code, it “is” a semiotic code."Gregory
February 12, 2013
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...why do you “imagine” that unguided material processes can produce functional information that is orders of magnitude greater than what man has ever produced in his most sophisticated computer programs?
False dichotomy, Phil. I don't have an answer for the origin of life on Earth (which presumably is what is at the centre of UB's "argument"). I am not swayed emotionally by the various religious explanations advanced here however, especially when they are presented as logical explanations.Alan Fox
February 12, 2013
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Alan Fox breaking out the immense "close your eyes, stick your fingers in your ears, and play stupid" counterargument. I don't know about the rest of you, but I find such a powerful counterargument completely convincing. Alan Fox has solved the origin-of-information problem by merely pretending it doesn't exist. Brilliant! I.D. is truly dead!Jammer
February 12, 2013
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You need for example in order to progress UB's "argument" an operational definition of semiosis that can develop the concept into a construct. Operationalization is key to starting to develop a coherent argument.Alan Fox
February 12, 2013
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Mr. Fox you state: "Anyone not emotionally predisposed towards imaginary “explanations”. And since you yourself, in your own post, by your own intelligence, are the one who is producing more meaningful information than has ever been witnessed being produced by unguided, purposeless, material processes of the universe, why do you "imagine" that unguided material processes can produce functional information that is orders of magnitude greater than what man has ever produced in his most sophisticated computer programs? Incredibly, and ironically, the charge that you make against ID, "Anyone not emotionally predisposed towards imaginary “explanations”, applies full force to you in this matter! Stephen Meyer - The Scientific Basis Of Intelligent Design https://vimeo.com/32148403 Moreover,,, 1. Consciousness either preceded all of material reality or is a 'epi-phenomena' of material reality. 2. If consciousness is a 'epi-phenomena' of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality. 3. Consciousness is found to have a special, even central, position within material reality. 4. Therefore, consciousness is found to precede material reality. Three Four intersecting lines of experimental evidence from quantum mechanics that shows that consciousness precedes material reality (Wigner’s Quantum Symmetries, Wheeler’s Delayed Choice, Leggett’s Inequalities, Quantum Zeno effect): https://docs.google.com/document/d/1G_Fi50ljF5w_XyJHfmSIZsOcPFhgoAZ3PRc_ktY8cFo/edit "It will remain remarkable, in whatever way our future concepts may develop, that the very study of the external world led to the scientific conclusion that the content of the consciousness is the ultimate universal reality" - Eugene Wigner - (Remarks on the Mind-Body Question, Eugene Wigner, in Wheeler and Zurek, p.169) 1961 - received Nobel Prize in 1963 for 'Quantum Symmetries' Eugene Wigner receiving his Nobel Prize for Quantum Symmetries in 1963 - video http://www.nobelprize.org/mediaplayer/index.php?id=1111bornagain77
February 12, 2013
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I simply point out that "intelligent designers" and "intelligent agents" are imaginary, products of the human imagination. Such concepts will remain so unless someone makes some effort at definition that amounts to more than the usual default via incredulity.Alan Fox
February 12, 2013
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AF: Are you willing to assert or imply that posts in this thread are only designed in our imaginations? Or that it is only imaginary that we can intuitively and quantitatively distinguish: (i) AAAAAAAA . . . from (2) fgq328wgies . . . from (3) this is a complex statement in English text . . . ? That, is what all of this boils down to, once we see that we can reduce functionally specific complex organisation, per some code of representation, to a string data structure via a nodes and arcs model. (As in, how AutoCAD etc in effect work on our PCs.) KFkairosfocus
February 12, 2013
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BA: Great job of boiling down to essentials. Pareto would be proud. BA 77: Some really nice clips and links. More, more, more like this . . . ! KN: Oh, dear. A target-rich environment. In particular, if by objecting to the concept that aspects of objects or phenomena can fruitfully be causally analysed on chance/ necessity/ design, you imply the reality of a-causal events and effects, I suggest that it would be interesting to see the fourth way instantiated. (Just as I recently responded to questions on the recent UK vote, "Say 'square circle.' Now, draw me one." can't be done. Or, in Mr Lincoln's terms, if we say the tail is a leg, how many legs does a sheep have? If you guess five, on grounds that "leg" can mean anything you please, note his response: a tail cannot be the same as a leg so merely saying a tail is a leg cannot change reality. that is, while verbal symbols are somewhat arbitrary: dog- dawg- [I here underscore the role of various dialects in English] chien- perro- hund- etc, the language systems using such have to be anchored down to reality or they become useless. (We can say all sorts of things that come down to being incoherent and impossible or confused; or worse, willfully obtuse or outright deceitful. And yes, I here hint at the Kantian point that evils expose themselves by needing to parasite off the fact that in a viable society we cannot universally act like that. If everyone lies and uses verbal symbols in arbitrary, agenda-driven and malicious ways, language and what language enables will collapse, leading to utterly destructive chaos.)) I suspect you may be hinting at the usual causeless events game commonly motivated on a misreading of the role of cause in quantum theory. To such, I point out that an a-causal event or effect inter alia would have no necessary enabling factors. That is, once there are on/off factors that must be on for an event or effect to be possible, there are identified causal factors. E.g. no U-238 nucleus, and no "tension" between repulsive and binding forces, as well as no tunnelling effect etc, no alpha decay of same. To examine such on/off factors, I again commend the fire tetrahedron. (And of course this leads onwards to the case of necessary being candidates, which if possible will be actual; having no beginning and no possibility of ending. Down that road lies the challenge that atheism -- as opposed to agnosticism -- ends up implying the stance that God is held impossible; though of course that is often overlooked, dismissed or hotly denied.) On the Q-T issue, I suggest the UD WAC here. NeilBJ Near optimality says the actual code is pretty clever. BTW another point of comparison is the evidence of "dialects" that play off the standard form to do odd things, as well as the recent designed in extensions done by experimenters. MrMosis Lookup tables can be implied by algorithms that respond by mapping a definite case to a definite response. Do they still teach sequence, branch, loop and case control structures these days? [In my intended Hello World based intro to pgg, I plan to use HW to bring in these control structures, never mind if they are unfashionable.] Algorithms of reasonable complexity, of course, are another case of functionally specific complex organisation and associated info [FSCO/I] that lead us to see design as best causal explanation. As well, the issue is not the succession of replications and reproductions pivoting on the integration of a metabolic entity and a von Neumann self replicator facility, which uses codes and algorithms, but the ultimate origin of same. (This brings us back to the pivotal ID focal issue on the bio side: origin of cell based life.) KFkairosfocus
February 12, 2013
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Taken seriously by whom?
Anyone not emotionally predisposed towards imaginary "explanations".Alan Fox
February 12, 2013
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and: scintilla, not scintillation,,, sorry, I must really start to check more carefully before posting,,,bornagain77
February 12, 2013
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correction : even THOUGH they have not one scintillation of evidence that material processes can produce as such??bornagain77
February 12, 2013
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"Otherwise you are doomed to continue not having your arguments taken seriously." Taken seriously by whom? Taken seriously by those who dogmatically believe, no matter what, that unguided, purposeless, material processes can produce levels of integrated functional information that are orders of magnitude more complex than man has ever devised even they have not one scintillation of evidence that material processes can produce as such??,,, But who would take those who think as such seriously in the first place?? ,,, Should we have convinced every one who believed in a flat earth that it was round before we accepted the fact that the earth is round? http://theflatearthsociety.org/cms/bornagain77
February 12, 2013
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This in turn is important because there is only one known source for a semiotic code: intelligent agency.
This is the standard argument from incredulity, Barry. It works for those who want it to. But it is not the beginnings of any sort of logical or scientific argument. Define some terms* and maybe you can get on the first rung of the ladder. Otherwise you are doomed to continue not having your arguments taken seriously. *A definition of "intelligent agency" that distinguishes between reality and imagination might help.Alan Fox
February 12, 2013
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Barry: Great post and good job calling out the "we can't understand what arbitrary means" nonsense.Eric Anderson
February 11, 2013
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OT: These recently made videos are very well done and may be of particular interest to anyone who has debated Darwinists on these points: Orphan Genes (And the peer reviewed 'non-answer' from Darwinists) - video http://www.youtube.com/watch?v=1Zz6vio_LhY Phenotypic Plasticity - Lizard cecal valve (cyclical variation)- video http://www.youtube.com/watch?v=zEtgOApmnTA Non-Random and Targeted Mutations (Epigenetics to the level of DNA) - video http://www.youtube.com/watch?v=qTChu5vX1VIbornagain77
February 11, 2013
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One thing I have been wondering: (in the overly simple scenario of the say, a eukaryotic mRNA and ribosome) Where is the ribosome's lookup table? Or, is the ribosome's work more mechanistic, such that the arbitrary-ness must precede the particular ribosome in questions's synthesis? (in which case the arbitrary relationship between the codons and what they represent was inherited from the mother presumably?)MrMosis
February 11, 2013
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Though the DNA code is found to be optimal from a error minimization standpoint, it is also now found that the fidelity of the genetic code, of how a specific amino acid is spelled, is far greater than had at first been thought: Synonymous Codons: Another Gene Expression Regulation Mechanism - September 2010 Excerpt: There are 64 possible triplet codons in the DNA code, but only 20 amino acids they produce. As one can see, some amino acids can be coded by up to six “synonyms” of triplet codons: e.g., the codes AGA, AGG, CGA, CGC, CGG, and CGU will all yield arginine when translated by the ribosome. If the same amino acid results, what difference could the synonymous codons make? The researchers found that alternate spellings might affect the timing of translation in the ribosome tunnel, and slight delays could influence how the polypeptide begins its folding. This, in turn, might affect what chemical tags get put onto the polypeptide in the post-translational process. In the case of actin, the protein that forms transport highways for muscle and other things, the researchers found that synonymous codons produced very different functional roles for the “isoform” proteins that resulted in non-muscle cells,,, In their conclusion, they repeated, “Whatever the exact mechanism, the discovery of Zhang et al. that synonymous codon changes can so profoundly change the role of a protein adds a new level of complexity to how we interpret the genetic code.”,,, http://www.creationsafaris.com/crev201009.htm#20100919a A New Study Adds Further Depth to the Information Story - JonathanM - March 2012 Excerpt: The conventional genetic code involves 20 different amino acids, which map to 64 different triplets of nucleotides called codons. Since there are many more codons than amino acids, this means that there is an element of redundancy because amino acids can be specified by multiple codons. As I noted before, this redundancy allows the genetic code to be exquisitely fine-tuned to minimize error. The paper explains that "redundancy in the genetic code allows the same protein to be translated at different rates." In other words, even so-called silent substitutions (that is, those mutations that exchange a nucleotide for another without changing the amino acid specified by the codon) can have an impact on the rate of translation of the protein product. http://www.evolutionnews.org/2012/03/new_study_adds058051.html A hidden genetic code: Researchers identify key differences in seemingly synonymous parts of the structure - January 21, 2013 Excerpt: (In the Genetic Code) there are 64 possible ways to combine four bases into groups of three, called codons, the translation process uses only 20 amino acids. To account for the difference, multiple codons translate to the same amino acid. Leucine, for example, can be encoded in six ways. Scientists, however, have long speculated whether those seemingly synonymous codons truly produced the same amino acids, or whether they represented a second, hidden genetic code. Harvard researchers have deciphered that second code,,, Under some stressful conditions, the researchers found, certain sequences manufacture proteins efficiently, while others—which are ostensibly identical—produce almost none. "It's really quite remarkable, because it's a very simple mechanism," Subramaniam said. "Many researchers have tried to determine whether using different codons affects protein levels, but no one had thought that maybe you need to look at it under the right conditions to see this.",,, While the system helps cells to make certain proteins efficiently under stressful conditions, it also acts as a biological failsafe, allowing the near-complete shutdown in the production of other proteins as a way to preserve limited resources. http://phys.org/news/2013-01-hidden-genetic-code-key-differences.html Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. - Jan 2013 Excerpt: Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides.,,, Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. http://www.ncbi.nlm.nih.gov/pubmed/23293005 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 Moreover the first DNA code of life on earth had to be at least as complex as the current DNA code found in life: 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 Lifebornagain77
February 11, 2013
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NeilBJ, here are a few notes on the optimality of the 'digital' Genetic Code: The Digital Code of DNA - 2003 - Leroy Hood & David Galas Excerpt: The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html 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) With New Research, the Genetic Code Looks More and More Like a Deliberate Choice - July 11, 2012 Excerpt: Even though the natural genetic code is "conserved through all of life," experiments such as these show that other codes are possible. If natural DNA were the only solution to the problems posed by biological information storage and retrieval, it might be argued that nature had to converge on it. But the researchers concluded that natural DNA does not represent a one-and-only solution. Though they don't say this, it surely gives more the appearance of a deliberate choice. http://www.evolutionnews.org/2012/07/with_new_resear061911.html A Critique of Douglas Theobald’s - “29 Evidences for Macroevolution” by Ashby Camp Excerpt: There is yet another reason that the universality of the genetic code is not strong evidence for evolution. Simply put, the theory of evolution does not predict the genetic code to be universal (it does not, for that matter, predict the genetic code at all). In fact, leading evolutionists such as Francis Crick and Leslie Orgel are surprised that there aren’t multiple codes in nature. - Biophysicist Cornelius G. Hunter http://www.trueorigin.org/theobald1b.asp Does Life Use a Non-Random Set of Amino Acids? - Jonathan M. - April 2011 Excerpt: The authors compared the coverage of the standard alphabet of 20 amino acids for size, charge, and hydrophobicity with equivalent values calculated for a sample of 1 million alternative sets (each also comprising 20 members) drawn randomly from the pool of 50 plausible prebiotic candidates. The results? The authors noted that: "…the standard alphabet exhibits better coverage (i.e., greater breadth and greater evenness) than any random set for each of size, charge, and hydrophobicity, and for all combinations thereof." http://www.evolutionnews.org/2011/04/does_life_use_a_non-random_set045661.html 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 The Finely Tuned Genetic Code - Jonathan M. - November 2011 Excerpt: Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: "why is the genetic code the way it is and how did it come to be?," that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology. - Eugene Koonin and Artem Novozhilov http://www.evolutionnews.org/2011/11/the_finely_tuned_genetic_code052611.html DNA - The Genetic Code - Optimal Error Minimization & Parallel Codes - Dr. Fazale Rana - video http://www.metacafe.com/watch/4491422 Deciphering Design in the Genetic Code - Fazale Rana Excerpt: Sixty-four codons make up the genetic code. Because the genetic code only needs to encode 20 amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, up to six different codons specify some amino acids. Others are specified by only one codon.,,, Genetic code rules incorporate a design that allows the cell to avoid the harmful effects of substitution mutations. For example, six codons encode the amino acid leucine (Leu). If at a particular amino acid position in a polypeptide, Leu is encoded by 5? (pronounced five prime, a marker indicating the beginning of the codon). CUU, substitution mutations in the 3? position from U to C, A, or G produce three new codons, 5? CUC, 5? CUA, and 5? CUG, all of which code for Leu. The net effect produces no change in the amino acid sequence of the polypeptide. For this scenario, the cell successfully avoids the negative effects of a substitution mutation. Likewise, a change of C in the 5? position to a U generates a new codon, 5?UUU, that specifies phenylalanine, an amino acid with similar physical and chemical properties to Leu. A change of C to an A or to a G produces codons that code for isoleucine and valine, respectively. These two amino acids also possess chemical and physical properties similar to leucine. Qualitatively, the genetic code appears constructed to minimize errors that result from substitution mutations.,,, The genetic code’s error-minimization properties are actually more dramatic than these results indicate. When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution.18 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 finding means that of 10^18 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature. http://www.reasons.org/biology/biochemical-design/fyi-id-dna-deciphering-design-genetic-codebornagain77
February 11, 2013
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My bad @ 2 - must have read the author name too quickly:-/ Nice post, Barry. There's a lot to be said for its simplicity and clarityOptimus
February 11, 2013
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I hope my minimal knowledge as a layman doesn't get me in trouble here, but I remember reading quite some time ago that the DNA code was determined to be optimum. I'm not quite sure what that means and how that was determined. In other words in all the arbitrary ways that the codon truth table could be organized, the one that is observed is the best of all possible truth tables. The truth table could have been arbitrary, but apparently it was not. If so, what does this imply?NeilBJ
February 11, 2013
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BA @ 10. You know, I usually appreciate KN’s comments (while rarely agreeing with them). But his comments at 6 are beyond the pale. He should not expect to be treated gently when he spews that sort of nonsense into a combox attached to one of my posts.Barry Arrington
February 11, 2013
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Joe “So ‘Eat at Joe’s’ can be changed to ‘No Parking’ and the meaning remains the same?” Well, yes actually. It depends on the convention (agreement) of the speakers. Just as it is conceivable that all English speakers could use the word “blimp” to mean Canis lupus familiaris, it is conceivable that English speakers could agree that “no parking” means what “eat at Joes” used to mean. It is not likely, but it is possible, because both signs are equally arbitrary in the sense we are using the word here. We actually see this happening with certain words. Example: There was a time when the the sign “sick” signified an illness. When my kids use that sign, they usually are signifying something completey different (i.e., crazy, cool, insane) as in “Hey, that snowboarding trick was totally sick!” The other day I was playing poker and made what poker players call a "heroic call" and snapped up a gigantic bluff. A younger man at the table yelled "Man, that call was so sick!"Barry Arrington
February 11, 2013
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Mr. Arrington you write to KN:
You again make a bald unsupported assertion in place of an argument.
Welcome to KN fantasy land where 'bald face assertion' carries the same weight as a demonstrated cause and effect: Notes: The Myth Of Non-Reductive Materialism - Jaegwon Kim - 1989 http://ethik.univie.ac.at/fileadmin/user_upload/inst_ethik_wiss_dialog/Kim__J._1989_The_Myth_of_Nonreductive_Materialism.pdf Addressing emergentism (under the guise of non-reductive physicalism) as a solution to the mind-body problem Jaegwon Kim has raised an objection based on causal closure and overdetermination. Emergentism strives to be compatible with physicalism, and physicalism, according to Kim, has a principle of causal closure according to which every physical event is fully accountable in terms of physical causes. This seems to leave no “room” for mental causation to operate. If our bodily movements were caused by the preceding state of our bodies and our decisions and intentions, they would be overdetermined.bornagain77
February 11, 2013
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Sorry, but I do not have the time right now to participate in this thread. I will just say that this idea: "a symbol is not a sign" is a purely anthropocentric distinction. In the appropriate material terms, they both are "an arrangement of matter that can evoke a response within a system, but is physicochemically-arbitrary to the response it evokes". Also, KN, I am one of the many here who enjoy your thoughtful comments. I can only say that in each of your numbered assertions above, you simply could not be more wrong. It would not be possible. I think there is perhaps a profound significance that it is this subject that causes you to put your foot down, and exposes how far off the mark you are. Best regards...Upright BiPed
February 11, 2013
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