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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
Mr. Fox, I did not apologize. I pointed out that it was Live Science that owed you an apology! Moreover, how does a materialistic atheist, such as yourself and Richard Dawkins, justify being morally outraged at the drop of a hat when you have no basis in which to ground morals in the first place??? The Knock-Down Argument Against Atheist Sam Harris' moral landscape argument – William Lane Craig – video http://www.youtube.com/watch?v=xL_vAH2NIPc Richard Dawkins and the Moral Argument for God by William Lane Craig - video http://www.youtube.com/watch?v=4f3I2QGpucs R.C. Sproul and Stephen Meyer Explain Ethics – video – 2013 http://www.youtube.com/watch?v=NzQwyq_e9fI Stephen Meyer - Morality Presupposes Theism (1 of 4) - video http://www.youtube.com/watch?v=uSpdh1b0X_Mbornagain77
February 12, 2013
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Thanks for the apology, Phil. Now hush while I listen to Biped.Alan Fox
February 12, 2013
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Editing out the preamble, Biped says:
Agency is a capable mechanism. It is the only capable mechanism known to exist. It is a universal observation. There are no counter-examples. Therefore, the opposing argument is necessarily based on personal incredulity; generally, that agency involvment was impossible prior to the onset of life on earth.
Now tell me why this is not a default argument. "I can only think of an agency that could produce the protein synthesis system that we find in cellular life" unless I am not paraphrasing you correctly, in which case can you amend it accordingly. Can I find anything out about this "agency"? Is this agency subject to the same "laws" that the rest of reality is subject to?Alan Fox
February 12, 2013
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Hey Alan don't get mad at me, I'm only following Live Science's lead,: “Meet your Mama” http://www.livescience.com/26929-mama-first-ancestor-placental-mammals.html why aren't you mad at them Mr. Fox for insinuating that was your original Mama? You ought to be upset at such insanity, but be righteously upset at the source, don't be falsely upset at me for making fun of your insane theory!bornagain77
February 12, 2013
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what if anything has your argument to do with “Intelligent Design”
Ahh, strategy. Curiously, not a strategy employed to get to the evidence, but one to stay away from it. I've answered this question numerous times. The reason it keeps coming back up is because the material evidence of semiosis is intractable and overwhelming. Notice that Alan repeatedly claims that the argument is false (i.e. genetics has nothing to do with semiosis) then when challenged to enage the details and evidence, he quickly switches to argue about its implications instead. This does indeed, "cut to the chase" for Alan because the truth value of the observations themselves are meaningless to him. The conclusion of the argument is that a mechanism capable of establishing a semiotic state is required prior to the onset of the semiotic systems in biology. That is the conclusion. What that conclusion has to do with ID is obvious. Agency is a capable mechanism. It is the only capable mechanism known to exist. It is a universal observation. There are no counter-examples. Therefore, the opposing argument is necessarily based on personal incredulity; generally, that agency involvment was impossible prior to the onset of life on earth.Upright BiPed
February 12, 2013
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"you would find it a little more nuanced" Which current mainstream presentation would that be? Would it be the current one that admits that the modern synthesis of neo-Darwinism is dead or did you have another one in mind that says the modern synthesis of neo-Darwinism is only in a coma on life support?,,, Which current presentation do you favor???bornagain77
February 12, 2013
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And, Phil, it may be the American way to insult the memory of the mothers of people you encounter on a blog site, but I find it rather distasteful. You are a Christian, aren't you?Alan Fox
February 12, 2013
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...it is evolutionists who dogmatically insist that it is true that this rat looking creature is their Mama...
I was referring to the creationist strawman of dogs turning into cats. I think, if you were ever motivated to look at a mainstream presentation of the theory of evolution, you would find it a little more nuanced.Alan Fox
February 12, 2013
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correction: I think you got your whose canards are whose canards mixed up,bornagain77
February 12, 2013
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For an organelle* that performs such a universally basic function across all cellular life, there is a (to me) surprising amount of variation across species, to the extent that phylogenetic hierarchies can be resolved in some related species such as rodents. *more strictly, a non-membranous organelleAlan Fox
February 12, 2013
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Mr. Fox at 138 "Reiterating old creationist canards is not going to bring new people into the fold, now, is it?" creationist canard??? I think you got your whose canards or whose canards mixed up, it is evolutionists who dogmatically insist that it is true that this rat looking creature is their Mama, not people who believe God created all life: http://i.livescience.com/images/i/000/036/470/original/ancestor-placental-mammals.jpg?1360252387 This just came out as a matter of fact,,, Meet Your Evolutionary Propagandists – February 11, 2013 Excerpt: When Science Magazine announced “The Placental Mammal Ancestor” on February 8, the evolutionary propagandists went on a media blitz to promote it (see 2/07/13), with titles like “Meet your earliest common mammalian ancestor” (New Scientist), “Meet your Mama” (Live Science), and “You’re descended from a fuzzy, bug-eating, scampering critter” (Christian Science Monitor). Few seemed concerned about the problems with evolving giraffes, whales and humans from a shrew-like animal.... Although Yoder bluffed that “The fossil record has always lent veracity to the classical account,” she then undermined it with some important questions: “Why did virtually all placental groups—such as primates, bats, ungulates, and whales—appear so abruptly in the fossil record? Where are the transitional forms that must link the diminutive insectivores of the Mesozoic to today’s multitude of mammals?” http://crev.info/2013/02/meet-your-evolutionary-propagandists/ I'm sorry Mr. Fox, I think I may have killed a few critters that look a lot like your Mama :)bornagain77
February 12, 2013
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kf @127
What we have is a case structure, where on case X, action 1 is taken Case Y triggers action 2 etc. A case structure is formally equivalent to a lookup table. Have you ever used log or sine tables?
I imagine I have used log or sine tables at some point. I find your statement that a case structure is formally equivalent to a table matching codons with actions entirely compatible with my imaginings related to these matters. I am still not sure if I was clear enough previously though. What I want to know is if the case + action relationship is inherent and fixed within the design of the ribosome or if it would be possible to alter the ribosome minimally to change case-to-action assignments, thereby "re-programming" the ribosome with a new/altered code. OR... would an entirely new ribosome need to be architected to achieve a change to the code? Or does the answer lie somewhere in between?MrMosis
February 12, 2013
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edit for 145: I necessarily remain agnostic as to the sources of this new information and function in terms of the molecular mechanisms that give rise to, store, and facilitate it ("it" being the instinct to make a large decoy spider, at least some of the time with 8 legs, in this case).MrMosis
February 12, 2013
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Alan Fox @ 133
A lot of spiders would indeed have to die if the evolutionary explanation is correct. Is there an alternative hypothesis that explains the phenomenon?
I was actually referring to a more recent discovery, publicized at the end of 2012. This one actually does legs: http://www.wired.com/wiredscience/2012/12/spider-building-spider/ I remain necessarily agnostic as to the sources of this new information in terms of the molecular mechanisms that store and facilitate it. I have some ideas about what kinds of originating entities and mechanisms can be ruled out though.MrMosis
February 12, 2013
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What would you like to know?
Cutting to the chase, Upright Biped, what if anything has your argument to do with "Intelligent Design"? That will do for a start.Alan Fox
February 12, 2013
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I don’t present facts about your argument. I ask you what you mean and you don’t tell me;
What would you like to know?Upright BiPed
February 12, 2013
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This is the very thing that I dispute about UB’s “argument”.
Feel free to engage the details.Upright BiPed
February 12, 2013
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Then you no longer have reason to present this fact as being of some decisive importance when it comes to my argument. It’s not.
I don't present facts about your argument. I ask you what you mean and you don't tell me;Alan Fox
February 12, 2013
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What else, other than a communicative semiotic system, could communicate assembly instructions?
That's a blatant argument from incredulity, Stephen and also presumes that DNA synthesis has anything in common with signs and symbols. This is the very thing that I dispute about UB's "argument".Alan Fox
February 12, 2013
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@ Upright Biped 126 I certainly adhere to the principle that the observed physical properties of the observable universe are, well, universal and continuous. No need to labour the point. So what?
Then you no longer have reason to present this fact as being of some decisive importance when it comes to my argument. It's not.Upright BiPed
February 12, 2013
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...rats can turn into bats, whales and shrews...
You ought to know better than that, Phil. Reiterating old creationist canards is not going to bring new people into the fold, now, is it? An dplease call me Alan.Alan Fox
February 12, 2013
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Yes ciphertext, believe it or not, ignoring the fact that the mutations in the immune system aren't really random (they are 'directed' mutations), and that 'new protein domains (Axe)' aren't really being generated, and that natural selection is not really occurring, in that the binding proteins revert back to there basic shape after the infection has passed (and even the 'remembered' immunity to a particular infection in a organism persists for only a few generations at most with many infections requiring exposure every generation: i.e. chicken pox), and ignoring the fact that the functional information generated in the responce to the infection is well within Dr. Dembski's Universal Probability Bound for functional information generation, as well as being well within Dr. Behe's limit of protein-protein binding site generation, then yes ciphertext, ignoring all those 'minor' details then Mr. Fox has evidence that rats can turn into bats, whales and shrews,,, :) Notes: It is important to point out that mutations to DNA, such as what we have with the immune system, are, by far, found to be 'non-random' mutations that are induced by the information processing machinery of the cell. Thus undermining a main tenet of the Central Dogma of neo-Darwinism i.e. Mutations to DNA are overwhelmingly found not to be 'accidental/random' as is required by a strict interpretation of the materialistic theory of neo-Darwinism but are found to be directed! Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf Majority of mutations are directed - Jonathan Bartlett - video http://www.youtube.com/watch?v=YJwWhhpua_o Non-Random and Targeted Mutations (Epigentics to the level of DNA) - video http://www.youtube.com/watch?v=qTChu5vX1VI Moreover, Natural selection, despite its hype as this great creative engine, is found to severely wanting of any confirmational evidence that it has actually occurred: "...but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have..." Maciej Marian Giertych - Population Geneticist - member of the European Parliament - EXPELLED EXPELLED - Natural Selection And Genetic Mutations - video http://www.metacafe.com/watch/4036840 List of various major problems with natural selection https://uncommondescent.com/intelligent-design/jerry-coyne-and-poisoning-the-well/#comment-441150bornagain77
February 12, 2013
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Kantian Naturalist (reviewing the revised form of the argument)
1?) We have direct, observational knowledge that semiotic systems are created by intelligent beings; (2?) We have no good reason to believe that the interaction of random events and natural laws can create semiotic systems (3?) The genetic code is a semiotic system; (4) So, it is overwhelmingly likely that the genetic code was created by an intelligent being.
(3?) could be true, though I’m not entirely sure.
You are not sure? What else, other than a communicative semiotic system, could communicate assembly instructions? Feel free to use your imagination.
Likewise for (2)
If you “are not sure” that we have no good reason to believe that the interaction of random events and natural laws can create semiotic system, what is your good reason for thinking otherwise?
But (1?) is problematic…… because we have ample evidence of semiotic systems throughout the biological world which are used by animals, plants, and microbes that we would not regard as ‘intelligent’ in whatever sense that we and the higher mammals are intelligent.
Why did you inject the strawman term “used by” into the discussion? Are you trying to quietly reframe then argument in order to make it appear unreasonable? We are not speaking of anything and everything that might interact with a semiotic system, such as plants and microbes--we are concerned with its cause. In that context, the ID meaning of causal intelligence includes animal instinct and the attendant capacity to design artifacts. In keeping with that point, the forces of wind, air, and erosion have never been known to produce a spider’s web. If you think that proposition is “problematic,” try arguing the other way.
Clearly, there is a real and interesting problem here: what is the origin of biosemiotic systems? I just don’t see how intelligent design works as an even plausible answer to that question.
If you don’t tamper with or reframe the argument in order to invalidate it as you did with (3’) and if you try to actually give reasons for rejecting (1’) and (2’), as opposed to the vague claim that “you are not sure,” you will find that your objections do not hold much water.StephenB
February 12, 2013
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...the outrageous idea that particles bumping into each other over time can produce the information we see in biology.
Now if that weren't a strawman that would be an argument from incredulity. :)Alan Fox
February 12, 2013
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@ Upright Biped 126 I certainly adhere to the principle that the observed physical properties of the observable universe are, well, universal and continuous. No need to labour the point. So what?Alan Fox
February 12, 2013
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@ MrMosis 128 I guess you are referring to this. A lot of spiders would indeed have to die if the evolutionary explanation is correct. Is there an alternative hypothesis that explains the phenomenon?Alan Fox
February 12, 2013
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Wow. I just glanced through the flood of posts over the past 24 hours. Too many to comment on, but this early one caught my eye: ----- Alan Fox @20:
This is the standard argument from incredulity, Barry.
No. It is the observable and objective fact. Contrasted sharply with, for example, folks who demonstrate near-unlimited credulity and the ability to believe almost anything -- even the outrageous idea that particles bumping into each other over time can produce the information we see in biology. Now, if that is what you are accusing us of being incredulous of, I for one accept the title with honor.Eric Anderson
February 12, 2013
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Ciphertext at 125 How innate behaviour might be coded for in the genome is a very interesting question but one that is yet to be addressed anywhere by anyone as far as I know. Further research is needed. A lot of further research! Mind you, there's a lot of "junk" still to be accounted for. :)Alan Fox
February 12, 2013
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AF: If I were to describe how the forces in a Yale Lock work by electron cloud polarisation leading at first to attraction then sharp repulsion etc, you would make the same error of distraction and miss the material issue of info stored in prong heights. (Contact forces are complex.) The material point is that info is coded in the sequence of bases [as is utterly uncontroversial, save to those desperate not to see the fact of coded D/RNA information that then gives rise to protein folding potential, that may require chaperoning . . . cf. prions], and that info comes out in essentially the same prong height effect. That is why you have complementarity of bases in the two strands of DNA; matching prongs. KFkairosfocus
February 12, 2013
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@ ciphertext Nort being an immunologist, I am not the best person to answer your questions but somatic hypermutation and affinity maturation reinforce and build on the recombination variations and mutations that occur in the B cells. Wikipedia has articles on both subjects with references to the primary literature.Alan Fox
February 12, 2013
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