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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
"Speaking generally, a code is a set of symbols and a rule for converting information from one form to another. In this context information is something you didn’t know before but know after."
That sounds a lot like a representation and a protocol. In essence, the rule F(a) = b, or F:A→B maps elements in A to elements in B, where a ∈ A and b ∈ B, F: being some arbitrary onto mapping, serving the purpose of a protocol. And it's entirely appropriate to give information an ontology, as the image of A under F, with no need of reducing it to merely an epistemic category. After all, information in the context of a functional system produces its effect irrespective to what one knows about the input or the output, or the relationship between the two. Of course, it's tempting to think of information as an anthropomorphism since, excepting its presence in biology, it's a product of human agency. This is only a problem if one rejects that information implies intelligence. However that appears to be a sound premise -- falsifiable, yet unfalsified (straining over definitions of information and intelligence notwithstanding). Information: 2b : the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects... Intelligence: 1a (2) : the ability to apply knowledge to manipulate one's environment or to think abstractly as measured by objective criteria (as tests)... That said, the DNA to polypeptide mapping function is in the form F:A→B, where F: is performed essentially by RNA polymerase, aminoacyl trna synthetase, and the ribosome, and works by mechanism to convert elements of A (codons) into elements of B (amino acids). This is exactly the sort of thing that intelligence does; we have no viable candidate hypothesis that implicates another cause. Notice the two corollary claims: a positive inference to design, based on isomorphic informational quantities (codes); and a negative claim, that there exist no known unguided processes to produce such. The positive claim is empirical. The negative claim is eminently falsifiable, yet unfalsified.Chance Ratcliff
February 14, 2013
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It seems to me that an additional strong argument for the arbitrary nature of the genetic codes is the existence of anti-sense transcription. Am I wrong?Mung
February 14, 2013
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Au contraire my fuzzy french friend. There is no claim here that representations are not material entities and that they cannot arise by material means.Mung
February 14, 2013
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What are the requirements for the transfer of recorded information in a material system? Let's pretend like we don't know and that the very question appears meaningless to us. Is it possible to transfer recorded information in a material system without a representation which is likewise instantiated in matter? Representations are immaterial things, the constructs of minds. So the obvious answer is no.Mung
February 14, 2013
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Alan, I have already given my definitions in purely material terms. For instance, I refer to one of the critical objects in my argument as a "representation" but then immediately define it as "an arrangement of matter that can evoke a physical effect within a system, where the representation is physicochemically arbitrary to the effect it evokes". That is what a representation is a mechanical system which transfers information into an effect. Both the medium, and its arbitrary nature, are fundamental requirements of the system. You simply don't recognize these facts yet. If you ever come to a point where you are capable of arguing the details of my argument instead of issuing dismissals, let me know.Upright BiPed
February 14, 2013
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Mung: Let’s do anything but address the matter on the table. Alan Fox: And that would be? Go back and read the text in bold at the top of the post to which you were responding. You see how utterly simple the question is that was posed by Upright BiPed? Even I could grasp it.Mung
February 14, 2013
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It’s close enough.
Call me a pedant but if that's your attitude, I doubt there is going to be much point in continuing. Bonne nuitAlan Fox
February 14, 2013
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Alan Fox:
Now that’s not what I said, is it.
It's close enough. But you'd probably need to understand the underlying concepts in order to grasp the meaning.Mung
February 14, 2013
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@ mung Oh and there is the other issue of proteins evolving stepwise from already viable proteins. Evolutionary theory does not involve tornado-in-junkyard scenarios. But carry on.Alan Fox
February 14, 2013
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lis S/B liesAlan Fox
February 14, 2013
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Alan, would you please explain why you think the concept of CSI is applicable only to functional proteins?
Because that is the only attempt at calculating that I have seen with gpuccio, kairosfocus and indeed with Dembski. The issue of what lis in unsearched space is never addressed, only assumed as empty of functional proteins. If you think you can apply the concept to something else then have at it.Alan Fox
February 14, 2013
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Alan, would you please explain why you think the concept of CSI is applicable only to functional proteins?Mung
February 14, 2013
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Let’s do anything but address the matter on the table.
And that would be?Alan Fox
February 14, 2013
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What are the requirements for the transfer of recorded information in a material system? Let's confuse this with an argument about the origin of life. Let's confuse this with an argument over the genetic code. Let's pretend we don't understand the question. Let's just call it "word salad" and talk about something else. Let's debate the meaning of the word arbitrary. Endlessly, if possible. Let' claim that question is irrelevant because the answer doesn't lead to intelligent design. Let's do anything but address the matter on the table. Please.Mung
February 14, 2013
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Given your self-admitted ignorance and lack of comprehension regard his argument, and your subsequent demonstrated confusion over it, you should have just considered keeping your mouth shut.
Physician, heal thyself!Alan Fox
February 14, 2013
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Alan Fox:
But my initial interest in the thread was to do with the repetition of the representation of Upright Biped’s assertions as some kind of unrefuted coherent argument.
Given your self-admitted ignorance and lack of comprehension regard his argument, and your subsequent demonstrated confusion over it, you should have just considered keeping your mouth shut.Mung
February 14, 2013
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Now Alan want’s us to believe, based upon his word alone, that it’s not possible to measure information content absent some arbitrary level of “rarity”!
Now that's not what I said, is it. I said that until you (not you personally, mung, you as in any ID proponent who thinks CSI is a valid concept) can show that functional proteins are rare in sequence space, you cannot calculate CSI.Alan Fox
February 14, 2013
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Joe:
Alan Fox: How is your agency manipulating nature?
No one said that ID’s designer is still manipulating nature. And as I told you before unless we see the designer or have the designer’s input, we may never know exactly how. Heck we don’t know exactly how Stonehenge was built. So something above our capabilities may be close to impossible to resolve.
It may surprise you to learn that what we see now at Stone Henge is partly due to restoration in the early twentieth century involving steam cranes and excavators directed by a Colonel Crawley! But there's no question people built Stone Henge. Their bodies and other artefacts are all over the site and in the surrounding area.
It is like asking someone who has never seen technology to tell you how a PC is built.
Fruitless, then; :(
In an observable measurable way or are we looking at suspensions of the laws of physics, discontnuities, miracles?
Discontinuities work and we see that between living organisms and inanimate matter. BTW the laws of physics are evidence for an agency.
I should have defined what I mean by discontinuity. I mean the result of an intervention by an imaginary agency. In my thought experiment, this would involve an effect without a cause. For example our agency decides to kick a soccer ball. I, as a bystander, see a soccer ball deform and fly off into the air. You say discontinuities work? Are we on the same page or planet here? Your final remark about physics and agency... I just don't follow.Alan Fox
February 14, 2013
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Alan Fox:
And until you can show that functional proteins are rare in sequence space, there is no possible way to calculate CSI or it’s imaginative variants.
LOL!!! And the laughs keep coming. Now Alan want's us to believe, based upon his word alone, that it's not possible to measure information content absent some arbitrary level of "rarity"! oh man. har har har. thanks alan! you're a barrel o' laughs today.Mung
February 14, 2013
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Mr. Fox, before you walk away from your lecture on 'honesty' to me, I have a very simple question for you. Since truth cannot be grounded within your materialistic/naturalistic worldview, how is it possible for a atheist, such as yourself, to even know if he is being 'honest' towards the truth or not? "But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?" - Charles Darwin - Letter To William Graham - July 3, 1881 Evolutionists Are Now Saying Their Thinking is Flawed (But Evolution is Still a Fact) - Cornelius Hunter - May 2012 Excerpt: But the point here is that these “researchers” are making an assertion (human reasoning evolved and is flawed) which undermines their very argument. If human reasoning evolved and is flawed, then how can we know that evolution is a fact, much less any particular details of said evolutionary process that they think they understand via their “research”? http://darwins-god.blogspot.com/2012/05/evolutionists-are-now-saying-their.html The following interview is sadly comical as a evolutionary psychologist realizes that neo-Darwinism can offer no guarantee that our faculties of reasoning will correspond to the truth, not even for the truth that he is purporting to give in the interview, (which begs the question of how was he able to come to that particular truthful realization, in the first place, if neo-Darwinian evolution were actually true?); Evolutionary guru: Don't believe everything you think - October 2011 Interviewer: You could be deceiving yourself about that.(?) Evolutionary Psychologist: Absolutely. http://www.newscientist.com/article/mg21128335.300-evolutionary-guru-dont-believe-everything-you-think.html Scientific Peer Review is in Trouble: From Medical Science to Darwinism - Mike Keas - October 10, 2012 Excerpt: Survival is all that matters on evolutionary naturalism. Our evolving brains are more likely to give us useful fictions that promote survival rather than the truth about reality. Thus evolutionary naturalism undermines all rationality (including confidence in science itself). Renown philosopher Alvin Plantinga has argued against naturalism in this way (summary of that argument is linked on the site:). Or, if your short on time and patience to grasp Plantinga's nuanced argument, see if you can digest this thought from evolutionary cognitive psychologist Steve Pinker, who baldly states: "Our brains are shaped for fitness, not for truth; sometimes the truth is adaptive, sometimes it is not." Steven Pinker, evolutionary cognitive psychologist, How the Mind Works (W.W. Norton, 1997), p. 305. http://blogs.christianpost.com/science-and-faith/scientific-peer-review-is-in-trouble-from-medical-science-to-darwinism-12421/ Alvin Plantinga - Evolutionary Argument against Naturalism - video http://www.youtube.com/watch?v=r34AIo-xBh8 The Historical Alliance of Christianity and Science - Kenneth Richard Samples Excerpted quote: "Modern science was conceived, and born, and flourished in the matrix of Christian theism. Only liberal doses of self-deception and double-think, I believe, will permit it to flourish in the context of Darwinian naturalism." ~ Alvin Plantinga “One absolutely central inconsistency ruins [the popular scientific philosophy]. The whole picture professes to depend on inferences from observed facts. Unless inference is valid, the whole picture disappears… unless Reason is an absolute, all is in ruins. Yet those who ask me to believe this world picture also ask me to believe that Reason is simply the unforeseen and unintended by-product of mindless matter at one stage of its endless and aimless becoming. Here is flat contradiction. They ask me at the same moment to accept a conclusion and to discredit the only testimony on which that conclusion can be based.” —C.S. Lewis, Is Theology Poetry (aka the Argument from Reason) C.S. Lewis, Reason, and Naturalism: An Interview with Dr. Jay Richards - audio http://www.idthefuture.com/2012/12/cs_lewis_reason_and_naturalism.html The Argument From Reason - resource page http://www.reasonsforgod.org/the-argument-from-reason/ The Argument from Reason - video http://www.youtube.com/watch?v=xKX-QtEo2fI “If you do not assume the law of non-contradiction, you have nothing to argue about. If you do not assume the principles of sound reason, you have nothing to argue with. If you do not assume libertarian free will, you have no one to argue against. If you do not assume morality to be an objective commodity, you have no reason to argue in the first place.” - William J Murray “Atheism turns out to be too simple. If the whole universe has no meaning, we should never have found out that it has no meaning...” CS Lewis – Mere Christianity Do the New Atheists Own the Market on Reason? - On the terms of the New Atheists, the very concept of rationality becomes nonsensical - By R. Scott Smith, May 03, 2012 Excerpt: If atheistic evolution by NS were true, we'd be in a beginningless series of interpretations, without any knowledge. Yet, we do know many things. So, naturalism & atheistic evolution by NS are false -- non-physical essences exist. But, what's their best explanation? Being non-physical, it can't be evolution by NS. Plus, we use our experiences, form concepts and beliefs, and even modify or reject them. Yet, if we're just physical beings, how could we interact with and use these non-physical things? http://www.patheos.com/Evangelical/Atheists-Own-the-Market-on-Reason-Scott-Smith-05-04-2012?offset=1&max=1 Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer - video – (Notes in description) http://vimeo.com/32145998bornagain77
February 14, 2013
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Alan Fox:
The genetic code is called the genetic code by general consent. We shouldn’t read any more into its name than that.
Well, that's a science stopper! I guess biosemiotics is up a creek.Mung
February 14, 2013
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Alan Fox:
All I am pointing out that it is fine to refer to the genetic code as a code. It is not fine to assume that merely by using a convenient descriptive, this somehow gives credence that there is more than analogy between the genetic code and, say, computer language.
Unbelievable! It is fine to refer to the genetic code as a code, if it is in fact a code. For why say of a thing that it is what it is not? It is fine to refer to the genetic code as a code. Is it likewise fine to say the genetic code is not a code? Is it likewise fine to say both that the genetic code is not a code and that it is a code? If the genetic code is in fact a code, then your second sentence is just pure ignorance. If the genetic code is not in fact a code, then why on earth would you assert that it is "fine" to refer to it as if it is? What sort of nonsense are you peddling? This is just the sort of thing I'd expect from someone who maintains that philosophy is "bunk."Mung
February 14, 2013
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'or are we looking at suspensions of the laws of physics, discontuities, miracles?' To you, atheists, Renard, quantum mechanics would be all of the above. To the Christian scientist, everything in Creation is a miracle, created out of nothing. He or she can look at quantum mechanics with its imponderable anomalies of physics, as well as its laws, and, instead of denying its miraculous nature, as you must, merely take the paradoxes as just more mysteries of God's creation. Ironically, Newton, himself, wasn't mug enough to discount the possibility of the existence of more than three dimensions. Y'all would still be toiling away with your mechanistic scientism, because you surely wouldn't have considered quantum mechanics. If their theoretical work wasn't immediately provable mathematically, I doubt if Bohr or Einstein, who had his own major paradoxes, would have managed to persuade the establishment of their day to even consider their discoveries.Axel
February 14, 2013
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Alan:
I should have prefaced my comment to you with the general observation that I refer to objects, people, processes etc that are discernible or are somehow based in reality. I am generally sceptical about imaginary things or processes. Does that help?
I can't say whether it helps you or not, but since it doesn't appear to addresses any of the questions I asked @279, I'm afraid it doesn't particularly help me.Phinehas
February 14, 2013
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But it is still reasonable to say the the old ideas have been shown to be inadequate, isn’t it?
That's my impression too. But that's progress. If we didn't question old dogma we might still be in the stone age!Alan Fox
February 14, 2013
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@ Phinehas 279 I should have prefaced my comment to you with the general observation that I refer to objects, people, processes etc that are discernible or are somehow based in reality. I am generally sceptical about imaginary things or processes. Does that help?Alan Fox
February 14, 2013
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Sorry, clipped the "post" button prematurely. S/B But once you assume the behavioural pattern is heritable and variation exists in the population (I e different genes – alleles – that produce slightly different behaviours), the possibility then arises that better decoy builders will on average survive to reproduce more often than those with genes that result in decoys less distracting to potential predators and selection will shift the allele frequency accordingly.Alan Fox
February 14, 2013
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@ MrMosis You ask:
It’s the Random Mutation part I call into question when it comes to the spider’s decoy in its web.
I understand your scepticism. How innate behaviour is passed on through parent to offspring in organisms sch as spiders is little understood. Simpler behaviour patterns in molluscs for example have been studied and specific genes identified as paramount in instigating egg laying for instance. But once you assume the behavioural pattern is heritable and variation exists in the population (I e different genes - alleles - that produce slightly different behaviours, the possibility that better decoy builders will on average survive to reproduce more often than those with genes that result in decoys less distracting to potential predators, then selection will shift the allele frequency accordingly.Alan Fox
February 14, 2013
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Alan Fox: @226 you said:
* If evolution is true!
… in reference to your comment @125. I think everyone accepts some forms of evolution as being true, depending on what one means by “evolution”. But I assume you have in mind RM+NS w/ CD. It’s the Random Mutation part I call into question when it comes to the spider’s decoy in its web. If the knowledge enabling the spider to create a realistic decoy in its web is encapsulated in DNA sequences (for the sake of argument, although I doubt it is entirely so simple myself), then the question becomes, how do those changes get introduced to those sequences? It seems to me that it can be more or less known that “random” point mutations (combined with whichever dispersal mechanisms, even generous ones, with generous time) will not suffice to introduce the necessary changes, or new “information”. It also seems to me that recent discoveries shed light on the fact that to whatever degree and in whatever circumstances changes are introduced, there are much more rapid mechanisms for change at work (which on a not unrelated note seem to be quite constrained and purposeful, strangely.)
I’m not sure I’m convincing myself here but there is no better competing hypothesis that I am aware of.
I am an agnostic when it comes to the as yet undiscovered or pinned down efficient-causal mechanisms introducing new information (particularly of the complex and specified variety). But it is still reasonable to say the the old ideas have been shown to be inadequate, isn’t it?MrMosis
February 14, 2013
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Alan:
I hesitated to use the impersonal pronoun “one”.
One what?
In the sense that there is no giver or receiver of information in a communicative sense.
What do you mean by, "in a communicative sense?" Can information be transmitted in a non-communicative sense? What does that look like? Unfortunately, you've introduced some new terms that need clarifying. What is required to qualify as a giver or receiver of information? In what way does the genetic code not have a giver or receiver?
DNA transcription and translation is a chemical chain of reactions that depends on the spacial conformation and inherent chemical properties of atoms and molecules.
And this is never true of other codes that are codes in fact and not merely analogous?Phinehas
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