A Dog is a Chien is a Perro is a Hund

_{Barry Arrington

February 11, 2013

Intelligent Design}

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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

He's looking for his doctoral certificate... Cut him a little slack. Axel

'Pass...' Axel

Gregory:
Let’s get this straight. You are a lay IDist; you promote ‘ID theory.’ Are you saying that *all* teleological arguments are by definition ‘ID’ arguments?
Lazy IDist might be more accurate. You asserted that anthropic arguments are a far cry from "IDM-ID arguments." I said they are not a far cry from ID arguments and in #363 I demonstrate the truth of what I said.
They are based upon probabilistic and inductive reasoning appealing to “inference to the best explanation” and they invoke the mantle of science.
Do you have a counter-argument or would you rather change the subject? Mung

"No, they aren’t. They are teleological arguments." - Mung (#353) Let's get this straight. You are a lay IDist; you promote 'ID theory.' Are you saying that *all* teleological arguments are by definition 'ID' arguments? Gregory

And Joe Felsenstein chimes in:
I think there still is reason to refute ID arguments (unless they find one that actually works). Because although we have drawn our conclusions, they are still using these arguments, and those arguments look sciency to undecided people. Granville Sewell is still proving plants can’t grow, and lots of ID commenters are still saying that if CSI can be found (basically if organisms are adapted a lot better than they would be if formed by a “tornado in a junkyard”) then it means that this could not have happened by natural selection. And semiotic something-or-other semi-proves something-or-other. So there is a need for repeated, and ever-clearer explanations of why none of those arguments work. Otherwise it will be easier for them to say that no one has ever refuted their arguments.
The way to refute our arguments are by supporting yours. And seeing that you cannot support yours then you have a serious issue with trying to refute ID. Show us blind and undirected processes producing a semiotic system of communication. Show us blind and undirected chemical processes producing CSI. However it is obvious that you will NEVER do either of those. And your current strategy is easily rebutted and your ID ignorance easily exposed. So good luck with your plan to refute ID. Too bad the way you are going about it won't work. Joe

Gregory:
My colleagues apply ‘anthropic’ arguments regularly. But these are a far cry, thankfully so, from IDM-ID arguments.
Really?
: New Proofs for the Existence of God : Robert J. Spitzer : Chapter 2 : Indications of Supernatural Design in Contemporary Big Bang Cosmology This chapter will summarize some of the results upon which physicists base their belief in design by a supernatural intelligence. The general form of the argument used by some physicists to justify belief in a supernatural designing intelligence may be set out as follows: 1) The values of the universal constants controlling the interrelationship among space, time and energy in the universe must fall within a very narrow, closed range in order to allow any life form to develop. [high specificity] 2) But the possible values that these universal constants could have had that would have disallowed any life form from developing are astronomically higher (falling within a virtually open range). [in a huge space] 3) Therefore, the odds against an anthropic condition occuring are astronomically high, making any life form (or universal condition allowing a life form) exceedingly improbable. This makes it highly, highly unlikely that the conditions for life in the universe occurred by pure chance, which begs for an explanation (cause) - physical or metaphysical. [vast improbability given the chance hypothesis] As can be seen, this argument turns on the values of universal constants, and is therefore different from the arguments constructed by the Intelligent Design Movement.
How so? Mung

RB: Just remember, we live in a digital age, where symbolic representations, mappings and codes -- even layercake comms protocols [or at least names!] -- are household concepts. So, in today's day and age, it will not be esoteric to notice the force of what Crick had to say in 1953:
Sir Francis Crick, March 19, 1953: “Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)“
Back then, digital technologies and comms protocols were exotic beyond exotic, but now, they are as close as your friendly Wi Fi network or your browser, or even ASCII text on a screen. The dismissive rhetoric has long since passed sell-by date. D/RNA serves as a molecular code-carrying medium, and mRNA acts as a control tape in the Ribosome, with tRNA acting to assemble proteins step by step, using code-recognising anti-codons at one end and pre-loaded amino acids locked to CCA coupler universal connector tips at the other. All under complex and sophisticated regulatory control involving chicken-egg causal loops. Which means a self replicating going concern depending on irreducibly complex systems and processes, has to be explained in a different way on its origin. Which points to the known cause of algorithms, coded and expressed through info processing and involving functionally specific complex information: design. Involving, per observation and related needle in haystack analysis alike -- yes, AF, Venter et al (who happen to be intelligent and purposeful, skilled agents) show this already in the primitive stages: skilled and intelligent designers. KF kairosfocus

Why is it that purported empiricists and 'skeptics' refuse to look at the facts? Mung

Bill, if I was describing a horse and included a large horn in the middle of its head, you'd have every right to question the validity of my observations. But I wasn't describing a horse, I was describing the material conditions of information transfer. You are welcomne to attack those observations whenever you're ready. Simply claiming they're not observations is a silly distraction, and won't suffice to refute them. Upright BiPed

Reciprocating Bill:
A description does not an observation make.
Alan is taking a break and a new (old) comedian has taken his place. Lucky us. Mung

And Alan and his kind in denying agency deny reality. They in fact deny themselves, and in so doing display the utter incoherence of their world view. Mung

UB:
Allow me to cut my “definition” in half and see if we can find an observation: ”A representation is _________________________________________.” Well no, apparently that’s not an observation. There is no “observation” there whatsoever. In fact, one could easily suggest that the sentence above is literally defined by being devoid of an observation. So let’s try the other half: ”_________________ is an arrangement of matter that evokes an effect within the system, and is materially arbitrary to the effect it evokes.” To any rational person, this is clearly an observation of the object being described (what else would describe it, if not descriptions). It’s an observation that imparts certain qualities on the object.
A description does not an observation make. The function of the description in your definition is to provide criteria for deciding, by means of observation, whether the defined entity is present. It is not itself an observation. This should make it clear: "A unicorn is a horse with a single straight spiraled horn projecting from its forehead." Let's parse this as well: "A unicorn is..." Obviously, this states the term to be defined. "...a horse with a single straight spiraled horn projecting from its forehead." My definition of unicorn. It is obviously not an observation (no one has ever observed a unicorn). Rather, it is the description, provided by the definition, of what one would observe were a unicorn present, as so defined. Nothing wrong with definitions - of course, they are indispensable. But a definition is not an observation. Nor does it necessarily "carve nature at its joints" ("unicorn," for example does not). That's an empirical determination. Reciprocating Bill

Alan Fox runs back to the TSZ and proclaims:
Now the religious nature of ID is openly admitted (even UB is happy to talk about “agency”), ID loses its raison d’être and will continue the slide into obscurity.
You have some serious mental issues, Alan. "Agency" does not = religion and ID is gaining ground, not sliding into obscurity. Just because you and your ilk can live in denial doesn't mean anything to us. As for ID's raison d’être, well that is still alive and doing very well. And it will stay alive as long as people like you refuse to ante up and support teh claims of your position. IOW materialism and evolutionism are losing their raison d’être and will slide into comedic obscurity. Joe

Gregory contiues with his 'human analogy' objection. But he steadfastly refuses to test his complaint against the physical evidence. Upright BiPed

Gregory:
Mung, Have you ever met a ‘professional semiotician’? I doubt most Americans even know what the word means!
What kind of argument is that? From the earlier posted link: Building on a range of disciplines from biology and anthropology to philosophy and linguistics this book draws on the expertise of leading names in the study of organic, mental and cultural codes brought together by the emerging discipline of biosemiotics. The book's 18 chapters present a range of experimental evidence which suggests that the genetic code was only the first in a long series of organic codes, and that it has been the appearance of new codes - organic, mental and cultural that paved the way for the major transitions in the history of life. While the existence of many organic codes has been proposed since the 1980s, this volume represents the first multi-authored attempt to deal with the range of codes relevant to life, and to reveal the ubiquitous role of coding mechanisms in both organic and mental evolution. This creates the conditions for a synthesis of biology and linguistics that finally overcomes the old divide between nature and culture. Mung

Gregory:
My colleagues apply ‘anthropic’ arguments regularly. But these are a far cry, thankfully so, from IDM-ID arguments.
No, they aren't. They are teleological arguments. They are based upon probabilistic and inductive reasoning appealing to "inference to the best explanation" and they invoke the mantle of science. Mung

Mung, Have you ever met a 'professional semiotician'? I doubt most Americans even know what the word means! My colleagues apply 'anthropic' arguments regularly. But these are a far cry, thankfully so, from IDM-ID arguments. Gregory

Gregory:
Well, I don’t know who my other ‘ilk’ are supposed to be here, but I am an Abrahamic mono-theist anti-Big-IDist. I don’t agree with the supposed ‘bankruptcy’ of this position and instead find it to be both morally and intellectually robust.
As if that position doesn't employ design arguments or inductive reasoning as part of it's robustness. Yeah right. Mung

Gregory: You will see that immediately Joe was corrected and has acknowledged it, expressing regrets. You, while complaining over what has been corrected and regretted [Joe sometimes falls off the wagon], show nowhere the faintest remorse over false accusations of fraud and idolatry. Please, think again, very seriously; and do better. KF PS: BA, there is a saying in my neck of the woods about monkeys that climb too high and expose themselves. Thwack, monkey stew for lunch. Let us hope G will wake up and see what he is doing to himself and his ilk. kairosfocus

Gregory:
“DNA is not “like” a semiotic code, it “is” a semiotic code.” – Barry Arrington This quite obviously confuses human-made things with non-human made things. It shows that a lawyer is not a professional semiotician.
By implication a professional semiotician would never say or even imply such a thing. But that's just absurd. The Codes of Life: The Rules of Macroevolution (Biosemiotics) Mung

F/N: It should be noted that just to name a "simple" case, the three body gravitational problem -- after 300 years -- remains unsolved analytically for the general case. Similar situations obtain in Quantum mech, etc. But of course, the cases we can solve analytically and those we may make suitable conditions on and solve numerically are good enough to do a lot. That's why one of my old profs was so fond of the joke about physicists being comparable to the two drunks under the lamp post. One found the other searching, and asked what is going on; lost my contacts. So, he tried to help. After quite a while, he asked, are you sure you lost your contacts here? Oh, no, over there in the dark, but this is where the light is. The real world is often beyond the reach of our state of the art mathematical and related techniques, but in truth we are a tad better off, we can throw some light with the cases we can solve or simulate. In the case in view, what we really need is some reasonable assurance that we are beyond a conservative threshold, beyond which we can be quite convinced on the signs we can see that chance and/or necessity absent design cannot be reasonably held to be causally adequate. 500 functionally specific bits, is reasonable for our practical universe for chemical level interactions, and if you want we can push to 1,000 bits for he observed cosmos. Makes no practical difference for the relevant cases, which have already been shown to lie at the heart of life and to be pervasive across cell based life. As for the notion that human designs are being projected, we have the evidence of beavers, as has been discussed with the one making the objections, that shows that designing intelligence, however limited, is not confined to humans. And, the case of software design in the context of discrete state control shows that it is skill and knowledge not humanity that are pivotal. Finally, to accept that inference to design as process is what the evidence in hand permits, is obviously not to indulge in "idolatry," etc. It has long since been shown that the attempt to make a mountain out of a mole hill over caps vs lower case, has failed; and is all too often involved in some pretty tendentious assertions that have no merit. KF kairosfocus

"he and his ilk spew." - Barry Arrington Well, I don't know who my other 'ilk' are supposed to be here, but I am an Abrahamic mono-theist anti-Big-IDist. I don't agree with the supposed 'bankruptcy' of this position and instead find it to be both morally and intellectually robust. In regard to lawyers, Barry, you might be pleasantly surprised to hear they/you are highly regarded in the institution where I work. While otoh PR people, which are to be found in abundance at the DI, are generally maligned. My semiotician colleagues have helped me to see how important that field is to science, philosophy, theology/worldview conversations. But just as unwilling as I am to accept R. Triver's and E.O. Wilson's claims about plant or insect 'societies' (theiving without qualms from social sciences as they do) I am also unwilling to accept the claims you make here about DNA 'semiotics.' That is a rational and educated choice. You and I are much more as persons (created by a higher power) than simply our DNA, Barry. We don't (reduce ourselves to) do DNA talk, but instead speak human language. This is why I reject your 'like/is' claim. Gregory

Gregory:
“I design, therefore the world is Designed; though I am not the designer or Designer of the world.” This is typical IDM idolatry.
Is not. Is all inductive reasoning idolatrous? How about all deductive reasoning? All reasoning period? Mung

Momentary lapse- Barry (or kf?) please edit out my line to Alan in comment 341 that starts "So either..." Joe

Gregory:
I could easily name 100 things that KF could not give an empirical FSCO/I value for. Easily.
So? I could easily name 100 things that you could not give an empirical Shannon information value for. Easily. Do you really think that this talking point of yours is meaningful? You must, because you keep repeating it, but you seem to be the only one who finds value in it. Perhaps it's time to move on. Mung

KF, I was tempted to ban Gregory on account of his outrageous assertions in 337. Then I thought, better to keep him around to continue to demonstrate the bankruptcy (both moral and intellectual) of the views he and his ilk spew. Barry Arrington

Joe: Language, please. KF kairosfocus

Note to Alan Fox: If you don't like ID nor FCSO/I, then all you have to do is step up and produce positive evidence for your position! And it is very telling that neither you nor any other anti-ID clown can do so. You can argue against ID, although you don't argue, you just spew, but that ain't going to produce positive evidence for your position. Joe

Gregory:
I could easily name 100 things that KF could not give an empirical FSCO/I value for.
It is doubtful that you can count to 100.
This quite obviously confuses human-made things with non-human made things.
Same principles involved, duh- it is all based on cause and effect relationships. I am sure glad that Gregory isn't an investigator. Joe

Gregory, you are here indulging in personal and unwarranted attack, in this case via patently false accusation. This in itself points to your consistent inability to actually address the matter on its merits. I call on you to apologise therefor [and not only to the undersigned, what you have been doing to Timaeus and others on a consistent basis is inexcuasable], and -- yet another time -- I call on you to address matters on the merits. KF kairosfocus

F/N: Do I need to explicitly say that design theory, qua theory, from the early 1980's on, makes no inference whatsoever that beyond any threshold of complexity, that what is, has been designed by God? Well, I have said it. Yet another strawman. KF kairosfocus

In one word: fraud. "FSCO/I is an objective, easily observable phenomenon; a commonplace in fact." - KF I could easily name 100 things that KF could not give an empirical FSCO/I value for. Easily. An applied physicist faking as a universalist based on religious principles. That's the name of kairosfocus' Big-ID game. Just let him say, like Peter, that religion and faith have nothing to do with it! “I design, therefore the world is Designed; though I am not the designer or Designer of the world.” This is typical IDM idolatry. “DNA is not “like” a semiotic code, it “is” a semiotic code.” - Barry Arrington This quite obviously confuses human-made things with non-human made things. It shows that a lawyer is not a professional semiotician. The category difference doesn't seem to matter in universal Big-IDism. UD Editors: And your comment shows that you know how to make ad hominem arguments (he’s a lawyer!) and bald unsupported assertions (Did anyone else notice the total absence of anything even resembling an argument in this comment?) Good for you. Now, do you care to actually try to advance the debate by making logical arguments based on warranted premises? If not, that’s OK. I understand. Really I do. When all of the evidence is against you, ad hominem and bloviating is all you’ve got. Gregory

AF: First, please get the descriptive abbreviation correct: functionally specific complex organisation and/or information. (With all due respect, your consistent inability/ unwillingness to accurately simply cite what you are discussing, after years of discussing design issues, speaks volumes, and none of it to your good. Whether inadvertently or not, you are erecting strawmen to knock over. In addition, your endless recycling of long since adequately answered objections speaks volumes on the underlying weakness of your case. If you had a real answer you would have given it, instead of indulging in strawman tactic sniping and dismissive bluster. For the sake of the onlooker, I will write again, and you are hereby warned that you have just earned poster-boy status.) Second, FSCO/I is an objective, easily observable phenomenon; a commonplace in fact. For specific instance, posts in this thread in English, are cases in point. Let's put it in these terms: anytime an object or phenomenon can be represented by a Wicken wiring diagram (= nodes and arcs pattern, which per the techniques of say AutoCAD can be reduced to a set of strings so to speak of strings is WLOG) and is such that moderate perturbation of same would destroy the function, where the information content of same is above 500 bits, we have a case of FSCO/I. (This obviously includes a string data or physical structure, i.e. one of form . . . -x-x-x-x- . . . Also, it is obvious that quite often, for something complicated to work,a great many parts have to be properly arranged, interfaced and combined. Otherwise the function will collapse or never emerge. Indeed, in many cases, without each and every member of a core cluster of parts being so present, arranged and interfaced, there can be no function of the relevant kind. And further, with a whole solar system to arrange 10^57 relevant atoms in, or at least the surface of a whole planet, there are vastly many more ways for such parts to be disorganised and non-functional than to be organised to function. That is, we see irreducible complexity, the emergence of islands of function in large configuration spaces of possible arrangements, and we see the needle in the haystack or monkeys at keyboards challenge to attempts to suggest emergence of function on blind chance and/or mechanical necessity.) You will observe that I have given a specific name, one of the two names that are foundational to the concept. And, I again must remind you of what you seem so eager to ignore or overlook, that the concepts, FSCO/I and the broader one specified complexity, are NOT -- repeat, NOT -- produced by any commenter online, or Dembski et al, or design theorists etc, but instead emerged as a needed concept to distinguish the way that observed cell based life forms differed from either order or randomness in their organisation that was specific in order to function. You have continued to indulge in empty dismissive bluster. So, let me note the score: 1 --> CSI and FSCO/I are terms/abbreviations that summarise concepts required to clarify how life forms are distinct from things that show the sort of low information order in a crystal, and the low specificity complexity in a random pattern. 2 --> It also turns out that this framework aptly describes a great many things in the world of language, computer programming, electronics, and engineered technology as a whole. 3 --> This is already suggestive of the credible source of FSCO/I. Design, which is in fact the only empirically well-warranted causally adequate source. 4 --> This point is analytically backed up by the needle in the haystack/monkeys at keyboards blind sampling of the config space challenge that shows why arriving at islands of function without intelligent direction is not credible. 5 --> Notice, the following result from the Monkey Shakespeare Simulator, on blind text generation from Wikipedia speaking against known ideological agenda, noting again, that an analysis of strings is WLOG:
it produced this partial line from Henry IV, Part 2, reporting that it took "2,737,850 million billion billion billion monkey-years" to reach 24 matching characters: RUMOUR. Open your ears; 9r"5j5&?OWTY Z0d...
6 --> 24 ASCII characters or so has a config space of ~ 10^50 possibilities. 73 or so characters, a space of ~ 10^150, a factor of 10^100 beyond. This is of course, the scope of the config space for 500 bits. That's just the solar system limit. For the cosmos as a whole, we would go to 1,000 bits. 7 --> There is no practical difference, as the genomes for the simplest cell based life forms are of order 100,000 bases - 1 million bases, i.e. config spaces of order 9.98 * 10^60,205 at the lower end, utterly swamping the resources of the observed cosmos to search them out blindly. 8 --> So, when you dismissively speak of published cases of information-content measures for proteins, that has to be held in the context that those proteins are examples from the hundreds and thousands in even the simplest life forms, and the associated regulatory circuitry and organised execution machines that must be in place for the information to function. (As in, chicken and egg causal circles aplenty.) 9 --> From the initial discussions in the 1970's by Orgel (1973) and Wicken (1979), that is the context that has been on the table. 10 --> Indeed, as far back as March 19, 1953, Sir Francis Crick went on utterly clear record to his son:
"Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)"
_____________ AF, your quarrel in the end is not with the design theory movement, it is with sixty years of multiple Nobel Prize winning microbiology and related research. Research that shows that beyond reasonable doubt, to moral certainty [the degree that empirical facts can access], the living cell is based on functionally specific complex organisation that is information bearing, and in quantities that stagger the capacities of blind chance and mechanical necessity on the gamut of the observed cosmos. Where also, there is just one empirically -- and routinely -- observed, known causally adequate source for such FSCO/I. (And this, after decades of attempts to find something, anything else that is a plausible substitute; all of which have failed or end up smuggling or letting the known cause in the back door.) In one word: Design. KF kairosfocus

FSCO/I = functional specified complex "O" (organisation?) information. It has been pointed out on innumerable occasions that attaching some numerical probability to some arbitrary property of (the only example I have seen even attempted is the number of residues in a protein) some aspect of a biological entity only gives the result that beyond some arbitrary threshold everything is designed by God (come on guys, let's not beat around the bush). I have nothing to say about such beliefs except I am the last person to prevent other people believing what they want (as if I could!) I am strongly in support of freedom of conscience and the free exchange of ideas. Anyway, I'm over my bug, the sun is shining and my wife gets back home tomorrow, so there'll be no more trolling from me unless events conspire to create those initial conditions again. That may not be before the next ice age but qui sait? Alan Fox

AF: Given your earlier fairly dismissive remarks on the term, I am going to ask you directly to read and respond to 260 above [won't take 2 mins to read], specifically on the roots of the concepts and terminology behind the abbreviation FSCO/I, and especially the role of Wicken and Orgel; you may wish to mix in Hoyle's remarks in the early 1980's also. KF kairosfocus

O: Right on, again. Your point that he denial we seem to be seeing is most plausibly explained by inability to empirically warrant a materialistic model of cause for codes and algorithms joined to execution machinery, is sobering food for thought. KF kairosfocus

EA @ 328 Your criticism is right on the mark. The avalanche of empirical knowledge that information and coding systems originate from intelligent agency, combined with the emphatic lack of any evidence that purely materialistic forces possess causal adequacy in this respect, shows that the burden of proof rests with the materialist. And furthermore, what is to be proved must be properly understood. The materialist must not only show that material processes are capable of producing information and coding systems, but that material processes are a more probable explanation than intelligent agency. Indeed, the materialist is fighting a losing battle. Incidentally, if there were abundant evidence to suggest that purely material causes were perfectly able to create the genetic code etc., I don't think materialists would have any objection to the term "genetic code." On the contrary they would be tripping over themselves to point out how material causes had produced an actual coding system comparable with what we humans create! Optimus

O: Actually, oddly, it is the logical consequence of selective hyperskepticism. In order to dismiss what you should not -- here, the blatant evidence of a digital, algorithmically functional machine code in D/RNA, you have to accept what you should not -- that such a code is illusory and/or that it is all explained by chemistry and the wonderful powers of chance variation and differential success. (Remember, the FSCI threshold of 500 bits for our solar system is equivalent to pulling just one straw at chance from a cubical haystack 1,000 light years thick, and coming up on the jackpot. Even if such a haystack were superposed on our galactic neighbourhood, we are so far beyond a reasonable threshold here that anything but a straw under the circumstances is vanishingly different from practically impossible.) What instead is needed is balanced understanding of what makes reasonable warrant, and how that leads to an appreciation of the variety in legitimate views on important subjects. Such as this one. But, the point is, that those who are trying to insist on the blind watchmaker thesis far too often want those who raise the slightest question on their scheme radically marginalised, derided and dismissed. That is telling. KF kairosfocus

Isn't there something tragically ironic about a guy from The Skeptic Zone criticizing ID proponents because of their incredulity (skepticism)? Optimus

EA: "Charges of people being incredulous (which seems to be your primary debating tactic — just count how many times you have made that charge in this thread alone) are useless bluster." AF leveled the charge seven different times in this one thread by my count. Barry Arrington

Alan Fox:
That there is the possibility that the origin of the genetic code did not require “an agency”.
Sure. And there is a possibility that the sun will cease shining today at noon or that gravity will fail tonight at midnight. However, thinking that these won't occur doesn't mean that one is inappropriately "incredulous." Science doesn't deal in sheer possibilities, but in realistic probabilities. Significant evidence has been presented that (i) we are dealing with a semiotic system in biology, (ii) semiotic systems are known, to our present state of knowledge, to only arise from intelligent designing beings. Further, neither you -- nor anyone else in the world, despite decades of diligent efforts -- has presented any solid evidence that such a system can arise through purely material and natural processes. You are the ones claiming that this system we see in biology goes against all other experience. The burden is squarely on you to show that this is a realistic possibility, not just some sheer logical possibility for debating purposes. Charges of people being incredulous (which seems to be your primary debating tactic -- just count how many times you have made that charge in this thread alone) are useless bluster. If you have some evidence for a purely natural origin of the semiotic system found in living cells, by all means please present it (and go claim your Nobel Prize, while you're at it). In the meantime we will continue to be properly and objectively incredulous of the materialist creation myth for this semiotic system. And our rational position in this regard will continue to stand in sharp contrast to those who, in order to justify their a priori materialistic philosophy, seem to be willing to believe almost anything . . . Eric Anderson

Alan Fox:
But I still would like to know what “an agency” is WRT protein synthesis.
The Intelligent Designer who designed the system, ie the gentic code and the transcription/ translation process. Joe

Alan Fox:
We are at cross purposes.
That is what happens when you spew unsupportable nonsense and refuse to follow along.
You appear to be referring to the origin of the code.
That is what the debate is about, Alan- how did it come to be. We say by intelligent design.
The code is well nigh universal across all extant species. There are subtle clues about possible simpler versions may have pre-dated the current code but not much hard evidence to decide between the various proposals.
Alan you don't even have a way to test the claim that blind and undirected chemical processes produced the genetic code. You lose. Joe

Alan Fox:
Essentially, it remains a classical example of an argument from incredulity.
And what does your position have besides arguments from incredulity, arguments from ignorance and imagination?
That there is the possibility that the origin of the genetic code did not require “an agency”.
Is there? Good luck finding evidence for that. Geez Alan will accept anything just as long as it doesn't have anything to do with ID. You are pathetic Alan Joe

Alan Fox said:
Rubbish, William. It’s the invention of one commenter here.
Says the guy who admits that he doesn't even know what the acronym means. William J Murray

F/N: Bit busy, as the meteorite impact is a biggie, and there is to be an asteroid flyby. From VJT's responsive post, clipping Chaitin -- yes THAT one:
[P]eople often talk about DNA as a kind of programming language, and they mean it sort of loosely, as some kind of metaphor, and we all know about that metaphor. It’s especially used a lot, I think, in evo-devo. But it’s a very natural metaphor, because there are lots of analogies. For example, people talk about computer viruses. And another analogy is: there is this sort of principle in biology as well as in the software world that you don’t start over. If you have a very large software project, and it’s years old, then the software tends to get complicated. You start having the whole history of the software project in the software, because you can’t start over… You … can try adding new stuff on top… So the point is that now there is a well-known analogy between the software in the natural world and the software that we create in technology. But what I’m saying is, it’s not just an analogy. You can actually take advantage of that, to develop a mathematical theory of biology, at some fundamental level… Here’s basically the idea. We all know about computer programming languages, and they’re relatively recent, right? Fifty or sixty years, maybe, I don’t know. So … this is artificial digital software – artificial because it’s man-made: we came up with it. Now there is natural digital software, meanwhile, … by which I mean DNA, and this is much, much older – three or four billion years. And the interesting thing about this software is that it’s been there all along, in every cell, in every living being on this planet, except that we didn’t realize that … there was software there until we invented software on our own, and after that, we could see that we were surrounded by software… So this is the main idea, I think: I’m sort of postulating that DNA is a universal programming language. I see no reason to suppose that it’s less powerful than that. So it’s sort of a shocking thing that we have this very very old software around… So here’s the way I’m looking at biology now, in this viewpoint. Life is evolving software. Bodies are unimportant, right? The hardware is unimportant. The software is important…
As in, wake up and smell the coffee time! KF kairosfocus

good night Alan. Upright BiPed

What part of that conclusion do you think I’m incredulous about?
That there is the possibility that the origin of the genetic code did not require "an agency". But I still would like to know what "an agency" is WRT protein synthesis. Alan Fox

Well, have you flounced or not, Upright Biped? What do you mean by "an agency" WRT protein synthesis? Is "an agency" a real entity WRT to proein synthesis? Alan Fox

Alan, (again) the conclusion of the argument is that a mechanism capable of establishing a semiotic state is required prior to the onset of information transfer since information transfer is wholly dependent on it. Try to be specific. What part of that conclusion do you think I'm incredulous about? And which part is a "default" answer? Upright BiPed

Joe: There is another level of the "game," and one key to it is the constant allusion to "presentation" by AF. A short list of talking points that manipulate emotions, ideological loyalties and perceptions that may well have been manipulated already, all reflect a pattern of failure to do due diligence to think through and address matters substantially and fairly on the merits of warrant. This in turn reflects the breakdown of rigour in post modern education and discourse. Let's pull back to basics:
Q: Arguments persuade, how? ANS: By appealing to one or more of emotions [and underlying perceptions, expectations and attitudes], to authorities (including presenters), and to fact and logic. Of these, our emotions are no better than the accuracy of underlying perceptions and warrant for judgements, where also they are notorious for blinding and leading to foolish and irrational behaviour. Next, no authority -- including no presenter, no matter how confident and smoothly polished his manner -- is better than his underlying facts, assumptions and reasoning. Thus, we see that in the end, it is warrant on reason in light of evident facts that is decisive. So, at some point, while it is also the case that Pareto's principle of the 10% or 20% of effort that yields 80 - 90% of results is applicable, there is also a need for the working out of reasonable details. Not, to persuade those who are not yet sufficiently broken from their locked in systems and selectively hyperskeptical dismissals of that which does not line up, and who are sufficiently benumbed to brush aside duties of care to truth and fairness through Alinsky type nihilistic tactics, but for the onlooker who is genuinely in need to a reasoned explanation. For such, the obvious duck, dodge and divert game will soon enough reveal itself as unreasonable and possibly deceptive.
In the case above, AF shows that after years he has either failed to learn, ponder and understand fairly the basic history of the roots of the concepts of complex specification and complex functionally specific organisation and information, or else that he is being willfully deceitful in spire of knowing better. And, he has shown by playing the ignore game, that he has again utterly failed to address the matter on the merits, once corrected. By now, sadly, this pattern goes to character, and one hopes that he will wake up and realise that he is exposing something that is, one way or another, very ugly and destructive. But again, this is one slice of the cake that has in it all the ingredients. We are suffering a widespread breakdown of the life of reason in our civilisation, and it portends sobering consequences in a world where one of the grim lessons of history is that folly, irrationality, unsound decisions and policy, selfish divisiveness and ruthless power-seeking and manipulation games in that cause lead to ruin. (Ever wondered why the Vikings were able to get launched on their raiding? Inadequate defences. Why? Internal in-fighting that distracted resources and focus. Similarly, after the initial Arab-led Islamic onslaught [itself invited by the mutual exhaustion of the wars between Byzantium and the Persians culminating in a patently hollow victory for the former in 628], the Byzantine empire gradually recovered and pushed back its frontier lines, actually all the way to Syria and Mesopotamia. But then in the 1070's someone had come to power in a very divisive fashion and a major defeat followed by civil strife allowed the Seljuk Turks to lay waste to the heartland of Anatolia. Byzantium never recovered from the blow. Our civilisation is playing these sorts of march of folly games, now. And the injection of radical a priori materialism wearing the holy lab coat and speaking falsely and destructively in the name of science, is a big part of the trouble.) What this thread has done is that it has shown that a prominent representative of the party of unyielding objection, is unable or unwilling to coherently and fairly address basic history, key concepts and ideas, much less evidence on the merits. After years and years. We can therefore freely draw the conclusion that the evidence is not pointing he way they desire. It is patent in an information age that information is real and is often used in information processing technology. Information has a sufficiently clear conceptual description, and is capable of being quantified, with the binary digit or bit as the commonest unit. Let us use the UD glossary definition, which is simply the Wiki definition cited as testifying against known interest:
“ . . that which would be communicated by a message if it were sent from a sender to a receiver capable of understanding the message . . . . In terms of data, it can be defined as a collection of facts [i.e. as represented or sensed in some format] from which conclusions may be drawn [and on which decisions and actions may be taken].”
The specifically organised sequencing of DNA monomers falls well within this definition. It is also instantly recognisable to someone who say knows how a Yale lock works: prong height in combination allows choosing of a functional pattern from a large set of possible patterns. This is a message that says "pass me, I am the authorised user." We see a four-state digital information system, used to construct a control tape by an organised process that is itself highly complex and functionally specific. That control tape, mRNA is then fed to a NC machine, the Ribosome, to construct a functional and highly specific object, a protein molecule. [BTW, the very fact that simply mixing and reacting AA molecules in a test tube and allowing them to react reliably will not lead to forming useful proteins is testimony to the isolation of the functional clusters of configs in the space of possibilities, even before we deal with cross reactions, chirality/handedness of molecules, etc etc. Darwin's warm little pond and the like OOL scenarios are dead.] That NC machine initialises, then uses a carrier, position-arm device with a universal carrier tool tip, tRNA, to assemble proteins. Which are then released and folded, often with chaperoning to fold in ways that are less stable than prion states, but are functional. Mad cow disease is eloquent testimony that we are dealing with isolated structures, and metastable ones that function. The computational challenge to specify folds and 3-d functional forms from linear chains and interaction forces, is only too eloquent in highlighting the functional specificity involved in the organisation. All of this and much more is easily accessible to AF. None of it even piques his interest, much less his serious examination. That speaks volumes, loud and telling volumes. None of it to his benefit. Or to that of the side that he represents as a seasoned objector to the design inference. That is a very important take-away lesson. Let us hope that sufficient of these objectors have sufficient sense of duty to truth, evidence and fairness left that they will wake up and rethink what they are and have been doing. And if not, then we can look on and draw lessons as to what we can and should avoid at all costs. For our own sakes and that of our civilisation, now sorely, nay, mortally wounded. By our very own selves. We need a miracle. Like as of yesterday. Otherwise, what lies ahead on inner dissentions and conflicts multiplied by ruthless assaults from without occasioned by now patent strategic failure, does not bear thinking about; it is beyond our worst nightmares. It is time to sober up, now. Before we find ourselves int eh position of France on May 10, 1940. The day when the bailiff's panzers came rolling in to collect the unpaid debts that had been so foolishly built up since 1919. This is not just a little rhetorical parlour game, we are seeing a slice of the wider, deeper ills of our whole civilisation. Where, as at now, I think it is too late to avert rivers of blood. The question is, whether we are in August 1914 or May 1940. (Both cost France about the same magnitude of casualties [rather roughly about 1/4 millions in the initial attacks], the difference is: in 1914, they were able to hold the line and hang on until they could win with the help of allies, at ruinous cost. But in 1940, things moved too fast for minds and systems conditioned to the rhythms of war techniques of a generation previous. And the cost of defeat on the initial onslaught was horrific beyond reckoning.) I trust I have been clear enough on the historical parallels that are at stake. So, let us close off by focusing on the expose of materialism and its self-refuting follies; as Plato highlighted 2350 years ago in The Laws, Bk X. That is, we can hardly say we were not warned on the consequences of clutching this asp to our bosom, in good time. Plato here speaks in the voice of the Athenian Stranger, in the aftermath of Athens' ruin:
Ath. . . . [[The avant garde philosophers and poets, c. 360 BC] say that . . . The elements are severally moved by chance and some inherent force according to certain affinities among them-of hot with cold, or of dry with moist, or of soft with hard, and according to all the other accidental admixtures of opposites which have been formed by necessity. After this fashion and in this manner the whole heaven has been created, and all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only. [[In short, evolutionary materialism premised on chance plus necessity acting without intelligent guidance on primordial matter is hardly a new or a primarily "scientific" view! Notice also, the trichotomy of causal factors: (a) chance/accident, (b) mechanical necessity of nature, (c) art or intelligent design and direction.] . . . . [[Thus, they hold that t]he Gods exist not by nature, but by art, and by the laws of states, which are different in different places, according to the agreement of those who make them; and that the honourable is one thing by nature and another thing by law, and that the principles of justice have no existence at all in nature, but that mankind are always disputing about them and altering them; and that the alterations which are made by art and by law have no basis in nature, but are of authority for the moment and at the time at which they are made.- [[Relativism, too, is not new; complete with its radical amorality rooted in a worldview that has no foundational IS that can ground OUGHT. (Cf. here for Locke's views and sources on a very different base for grounding liberty as opposed to license and resulting anarchistic "every man does what is right in his own eyes" chaos leading to tyranny. )] These, my friends, are the sayings of wise men, poets and prose writers, which find a way into the minds of youth. They are told by them that the highest right is might [[ Evolutionary materialism leads to the promotion of amorality], and in this way the young fall into impieties, under the idea that the Gods are not such as the law bids them imagine; and hence arise factions [[Evolutionary materialism-motivated amorality "naturally" leads to continual contentions and power struggles], these philosophers inviting them to lead a true life according to nature, that is, to live in real dominion over others [[such amoral factions, if they gain power, "naturally" tend towards ruthless tyranny], and not in legal subjection to them . . .
Those who refuse to learn the lessons of history are doomed to repeat its worst chapters. (Santayana, paraphrased, I believe.) Why are we so insistently foolish, in light of the horrific cost that has been paid over and over and over again? Why, why, why? AF, do you see what sort of folly you are serving by giving yourself over to this sort of self-refuting, nihilism-inviting materialism? (never mind the current disguise in the holy lab coat not the philosopher's cloak.) Do you not see where it leads, predictably and consistently leads? KF kairosfocus

Thus far, I’ve pointed out this same model (at one time or another during the conversation) in human and animal communications, music boxes, traffic systems, bees, ants, gestures, a night light, computers, automated fabric looms, vision, sensory systems, bacteria, and protein synthesis. Each and every one using recorded information to bring about a concrete physical effect.
And I interpret you as concluding that thus all the examples that you list, including protein synthesis are the result of "an agency". (Therefore ID, I guess) Alan Fox

And now Upright Biped tells Reciprocating Bill
Months wasted. They all end up the same way. I don’t care to make time for it right now...
And there we have it! So we await further developments in due course. Though I still have to point out that I haven't seen any indication of UB's conjecture gaining much traction outside the echo chamber. Essentially, it remains a classical example of an argument from incredulity. Alan Fox

Just to save wear on scroll fingers Upright Biiped offers to answer my questions, so I ask:
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.
Sothat prompts me to ask
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?
and I get this from Upright Biped
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.
Whether he/she intended to or not, UB does not address my query. Perhaps the best thing, as I and others have been suggesting, is for Upright Biped to write up his argument and publish it. I am sure there are appropriate veues. What about Evolution News and Views or BioInformatics? Alan Fox

Bill, we've been off on your definitional derbies before. Months wasted. They all end up the same way. I don't care to make time for it right now, so please enjoy the last word. Upright BiPed

Bill at #310
there are no observations in the OP above. Instead, we find a definition followed by a string of assertions. Specifically, “A representation is an arrangement of matter which evokes an effect within a system” is a definition, not an observation. Everything that follows in the OP is built one way or another upon that definition.

I’m glad you now agree: “A representation is an arrangement of matter which evokes an effect within a system” is a definition, not an observation.
Good grief. One opponent complains about not getting any definitions, while another complains that definitions are all I’ve given. I've been having conversations about a particular type of system, those that do the work of transferring recorded information into concrete physical effects. I’ve talked about the material demands on such systems, named objects, and described how those objects operate in order for the system to function. Your reply to this, is that my words are only definitions, not observations. Allow me to cut my “definition” in half and see if we can find an observation: ”A representation is _________________________________________.” Well no, apparently that’s not an observation. There is no “observation” there whatsoever. In fact, one could easily suggest that the sentence above is literally defined by being devoid of an observation. So let’s try the other half: ”_________________ is an arrangement of matter that evokes an effect within the system, and is materially arbitrary to the effect it evokes.” To any rational person, this is clearly an observation of the object being described (what else would describe it, if not descriptions). It’s an observation that imparts certain qualities on the object. These qualities identify the object among others in the system. One such quality is that it (the object) obviously operates within a system that produces effects. Another is that it evokes the effect in that system. And yet another is that it is materially-arbitrary to the effect it evokes. These observations, taken with others (i.e. protocols, evoke, information, arbitrary) provide a model for the transfer of recorded information. Thus far, I’ve pointed out this same model (at one time or another during the conversation) in human and animal communications, music boxes, traffic systems, bees, ants, gestures, a night light, computers, automated fabric looms, vision, sensory systems, bacteria, and protein synthesis. Each and every one using recorded information to bring about a concrete physical effect. Thus far, none of the observations have been demonstrated to be false. You cannot do so either. Your complaint is the nonsense that stems from that fact. Upright BiPed

petrushka on February 4, 2013 at 1:17 am said:
Anybody home?
Recent Comments: Patrick on Sandbox OMTWO on Sandbox Robin on Sandbox Patrick on Sandbox OMTWO on Sandbox Robin on Sandbox Joe Felsenstein on Sandbox Reciprocating Bill on Sandbox rhampton7 on Sandbox Reciprocating Bill on Sandbox Allan Miller on Sandbox Dave L on Sandbox petrushka on Sandbox Dave L on Sandbox Toronto on Sandbox Neil Rickert on Sandbox petrushka on Sandbox Mung

What better way to deal with observations than to simply say they are definitions? Mung

UB @ 304:
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”.
(My emphases.) As I said in the "UB Sets it Out" thread:
UB has characterized his opening post as presenting “observations” followed by logical conclusions. But there are no observations in the OP above. Instead, we find a definition followed by a string of assertions. Specifically, “A representation is an arrangement of matter which evokes an effect within a system” is a definition, not an observation. Everything that follows in the OP is built one way or another upon that definition.
UB, you objected at the time.
Ah yes. Let us not forget another round of the ridiculously-strained and notoriously-idiosyncratic parsing of words. What better way to deal with observations than to simply say they don’t exist?
I'm glad you now agree: "A representation is an arrangement of matter which evokes an effect within a system” is a definition, not an observation. Carry on! Reciprocating Bill

"It seems to me that an additional strong argument for the arbitrary nature of the genetic codes is the existence of anti-sense transcription."
Anti-sense transcription aids error correction, which aids survival.
Proofreading DNA Replication ...Ultimate precision is achieved by two separate stages of sensory-based proofreading: - The first stage occurs during polymerization. When an incorrect nucleotide has been incorporated into the new growing DNA strand, mispairing between the new and old strands distorts the structure of the growing double helix. The polymerase senses the distortion and interrupts polymerization. While polymerization is halted, another activity of the replication apparatus removes the incorrect base from the end of the new strand, relieves the distortion to the double helix, and allows polymerization to resume, replacing the incorrectly inserted nucleotide. In this process, known as exonuclease proofreading, the polymerase itself serves as the sensor that detects mistakes and activates the correct functions.... Exonuclease proofreading increases replication accuracy 100 to 1000-fold (two or three orders of magnitude).... - Evolution: A View from the 21st Century, James A. Shapiro, Kindle location 511.
Organisms exhibiting this feature exhibit a distinct survival advantage, and are more likely to successfully reproduce. Hence, natural selection provides a parsimonious explanation for such features -- for any feature, really. Why else would we expect to see features that contribute to, enhance, or are necessary for survival? Chance Ratcliff

"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

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

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

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

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

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

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 nuit Alan Fox

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

@ 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

lis S/B lies Alan Fox

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

Alan, would you please explain why you think the concept of CSI is applicable only to functional proteins? Mung

Let’s do anything but address the matter on the table.
And that would be? Alan Fox

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

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

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

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

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

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

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/32145998 bornagain77

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

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

'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

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

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

@ 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

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

@ 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

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

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

There isn’t any chemical reactions that determine the code.
We are at cross purposes. You appear to be referring to the origin of the code. The code is well nigh universal across all extant species. There are subtle clues about possible simpler versions may have pre-dated the current code but not much hard evidence to decide between the various proposals. Alan Fox

Phinehas
Who is this “you?” Does information require a “you” to “know” something?
I hesitated to use the impersonal pronoun "one". It's a little pretentious these days. Try it in the passive voice. Alan Fox

Alan Fox:
DNA transcription and translation is a chemical chain of reactions that depends on the spacial conformation and inherent chemical properties of atoms and molecules.
No, it isn't. That is the whole point. There isn't any chemical reactions that determine the code. 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 is like asking someone who has never seen technology to tell you how a PC is built.
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. Joe

In what way is the genetic code not a “set of symbols and a rule for converting information from one form to another?” In what way is it only analogous to a “set of symbols and a rule for converting information from one form to another?”
In the sense that there is no giver or receiver of information in a communicative sense. DNA transcription and translation is a chemical chain of reactions that depends on the spacial conformation and inherent chemical properties of atoms and molecules. Alan Fox

contd @ Eric Anderson: 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. I have just responded to other points as they came up. Alan Fox

Alan:
I have no problem calling the gentic code the genetic code.
In what way is the genetic code not a "set of symbols and a rule for converting information from one form to another?" In what way is it only analogous to a "set of symbols and a rule for converting information from one form to another?" Phinehas

So is your issue that you feel “information” has not been adequately defined at the beginning of this thread? Or have you switched the concern to “complex specified information”? Or is the concern still back at “code” which is where things started early in the thread?
My issue with CSI is tht it presented as a quantifiable entity which is, to understate the issue, undemonstrated. Alan Fox

Eric Anderson:
So can we take this to mean that you accept that the “genetic code” really is a code?
I have no problem calling the gentic code the genetic code. And... Alan Fox

Alan:
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.
Who is this "you?" Does information require a "you" to "know" something? Phinehas

<blockquoteAlan Fox @259: And what do you mean by “an agency”?
Seriously? Yes, seriously!
It appears you’re just playing the child’s game of the endless regress of asking “what does that mean” with every additional explanation. It seems there are three possibilities: (i) You haven’t spent much time reading up on or thinking about the design/evolution debate; (ii) You don’t understand what you’ve read; or (iii) You are being deliberately obtuse.
I'll concede that (i) and (ii) are likely contributory factors but I reject (iii) and suggest you have overlooked (iv) with regard to "an agency". I haven't yet had a satisfactory or consistent answer. Joe is working with me but I am not convinced Joe is an authoritative source on ID concepts. If there is a general consensus to endorse Joe as a reliable spokesman for ID then I would have to take that into account, of course. What I would really like to know is whether we are talking about reality or are agency's immaterial when manipulating nature? Alan Fox

Anything that can produce counterflow*, for example anything that can produce an artifact. Anything that can manipulate nature for its own purpose.
OK, so are we talking about a real thing that can manipulate nature. I can conceive of humans manipulating nature collectively on a large scale and beavers, say, on a smaller scale. How is your agency manipulating nature? In an observable measurable way or are we looking at suspensions of the laws of physics, discontnuities, miracles? Alan Fox

Alan Fox @259:
And what do you mean by “an agency”?
Seriously? It appears you're just playing the child's game of the endless regress of asking "what does that mean" with every additional explanation. It seems there are three possibilities: (i) You haven't spent much time reading up on or thinking about the design/evolution debate; (ii) You don't understand what you've read; or (iii) You are being deliberately obtuse. This whole tactic is no different that the ridiculous diversionary tactic we recently witnessed on another thread over the definition of the word "arbitrary" -- a 1000+ comment distraction from the real substantive issues. Eric Anderson

kairosfocus- You are playing the wrong game- or playing the game the wrong way. Alan isn't here to be convinced. He's here because the septic zone has dried up and he wants to muddy things around here. Joe

BA77: @237 I had just that "simulation" in mind. I should have said something closer to “...if one could simulate the simplest single cell lifeform AND with an adequately sized population AND with an adequately sized/complex environment...” etc. But I imagine we’re a ways off from that- since we apparently can’t yet even almost model a true-to-life interactome via simulation, of the whole organism [single instance] with all of its constituent parts. MrMosis

Alan Fox @218:
There is not the same issue with “code”. I have no problem with this as the context clarifies the usage.
Good. So can we take this to mean that you accept that the "genetic code" really is a code?
An ad hoc definition at the beginning of any discourse of new or unfamiliar terms is all that is necessary.
Fine. So is your issue that you feel "information" has not been adequately defined at the beginning of this thread? Or have you switched the concern to "complex specified information"? Or is the concern still back at "code" which is where things started early in the thread? Eric Anderson

Also nature doesn’t select- that requires an agency. Alan Fox:
And what do you mean by “an agency”?
Anything that can produce counterflow*, for example anything that can produce an artifact. Anything that can manipulate nature for its own purpose. *Counterflow refers to things running contrary to what, in the relevant sense, would (or might) have resulted or occurred had nature operated freely. Del Ratzsch page 5 of Nature, Design and Science: The Status of Design in Natural Science Joe

Perhaps from now on your could define every word you are using and tell us how you are using it.
Let's adopt it as a rule for everyone! Alan Fox

Onlookers ( and AF): It has been several years that you, AF, have been debating -- that seems to be the proper word -- back and forth on design issues, and yet it seems you refuse to do, or read when someone else does basic homework. Despite the fact that the meaning of FSCO/I has been defined for you many times, you either don't know what the abbreviation means or are pretending that you don't for rhetorical purposes. FYI, yet again, this is a descriptive phrase, abbreviated: functionally specific, complex organisation and associated information. (There is even an equation that you obviously do not want to review.) Now, you also want to dismissively assert that the concept FSCO/I is a creation of a presumably dubious design-supporting blog commenter. That does not even address the basic issue that we can all easily tell the difference between: (a) AAAAAAAA -- orderly sequence; (b)I3RGIHEQYWES -- random sequence (overwhelmingly likely to look like that more or less); (c) AN ORGANISED, FUNCTIONALLY SPECIFIC SEQUENCE. But in fact it has repeatedly been put within easy reach that the concepts of (I) specified complexity and that of (II) functionally specific complex information/organisation are not produced by the design theory movement at all. Indeed they are earlier than the movement. Just, conveniently ignored or willfully distorted. As in, yet again, let us hear from Orgel and Wicken, discussing a pivotal observation from OOL research in the 1970's (which was a part of the underlying developments that gave rise to design theory in the 1980's and 90's):
ORGEL, 1973: >> . . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity. [[The Origins of Life (John Wiley, 1973), p. 189.] >> WICKEN, 1979: >> ‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)] >>
The roots of the terms CSI and FSCO/I are obvious. By the time he wrote his No Free Lunch, Dembski picked this up:
p. 148: “The great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence. My aim throughout this book is to dispel that myth . . . . Eigen and his colleagues must have something else in mind besides information simpliciter when they describe the origin of information as the central problem of biology. I submit that what they have in mind is specified complexity [[cf. here below], or what equivalently we have been calling in this Chapter Complex Specified information or CSI . . . . Biological specification always refers to function . . . In virtue of their function [[a living organism's subsystems] embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specificity criterion . . . the specification can be cashed out in any number of ways [[through observing the requisites of functional organisation within the cell, or in organs and tissues or at the level of the organism as a whole] . . .” p. 144: [[Specified complexity can be defined:] “. . . since a universal probability bound of 1 [[chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [[the cluster] (T, E) constitutes CSI because T [[ effectively the target hot zone in the field of possibilities] subsumes E [[ effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ”
By 2005, he had derived a fairly complex expression, which in response to the challenges of the sock-puppet MG, several of us brought down to the following:
xix: Later on (2005), Dembski provided a slightly more complex formula, that we can quote and simplify, showing that it boils down to a "bits from a zone of interest [[in a wider field of possibilities] beyond a reasonable threshold of complexity" metric: ? = – log2[10^120 ·?S(T)·P(T|H)]. --> ? is "chi" and ? is "phi" xx: To simplify and build a more "practical" mathematical model, we note that information theory researchers Shannon and Hartley showed us how to measure information by changing probability into a log measure that allows pieces of information to add up naturally: Ip = - log p, in bits if the base is 2 . . . xxi: So, since 10^120 ~ 2^398, we may "boil down" the Dembski metric using some algebra -- i.e. substituting and simplifying the three terms in order -- as log(p*q*r) = log(p) + log(q ) + log(r) and log(1/p) = – log (p): Chi = – log2(2^398 * D2 * p), in bits, and where also D2 = ?S(T) Chi = Ip – (398 + K2), where now: log2 (D2 ) = K2 That is, chi is a metric of bits from a zone of interest, beyond a threshold of "sufficient complexity to not plausibly be the result of chance," (398 + K2). So, (a) since (398 + K2) tends to at most 500 bits on the gamut of our solar system [[our practical universe, for chemical interactions! ( . . . if you want , 1,000 bits would be a limit for the observable cosmos)] and (b) as we can define and introduce a dummy variable for specificity, S, where (c) S = 1 or 0 according as the observed configuration, E, is on objective analysis specific to a narrow and independently describable zone of interest, T: Chi = Ip*S – 500, in bits beyond a "complex enough" threshold . . . . xxii: So, we have some reason to suggest that if something, E, is based on specific information describable in a way that does not just quote E and requires at least 500 specific bits to store the specific information, then the most reasonable explanation for the cause of E is that it was designed. The metric may be directly applied to biological cases: Using Durston’s Fits values -- functionally specific bits -- from his Table 1, to quantify I, so also accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold: RecA: 242 AA, 832 fits, Chi: 332 bits beyond SecY: 342 AA, 688 fits, Chi: 188 bits beyond Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond xxiii: And, this raises the controversial question that biological examples such as DNA -- which in a living cell is much more complex than 500 bits -- may be designed to carry out particular functions in the cell and the wider organism.
Now, in the case of protein synthesis, digitally coded information stored in the DNA -- yes this is a memory, storing coded information, no new vocabulary needs to be manufactured to suit those who are uncomfortable with the evident facts -- is transcribed and adjusted to form messenger RNA, which is transferred to the Ribosome. In the ribosome, AUG serves as a start codon, and the start-from tRNA sets up the first AA. In succession, three letter codons are read by tRNA's and the ribosome clicks them together to form the elongated protein chain. This happens until a stop codon is reached which triggers termination and release. The protein folds under its internal, complex pattern of forces, in many cases aided by chaperone molecules (as the existence of prions shows, there are other possible and non-functional folds in many cases.) Where, as has been painstakingly pointed out the coupler to the tRNA is a universal one, CCA, and the loading can in fact be modified. Has been modified. This is not a physical link here it is an informational one. Based in a code, stored in the same sort of prong height system that makes a Yale-type lock work. There is nothing physical that determines that a given DNA base hall be followed int he same strand by another of a specific type from the set ACGT, and if there were DNA could not store information, it would be a fixed order crystal. Similarly, the sequence in the DNA string, is not random, or there would be no functional protein, with almost certain outcome. (Just start with that three of the 64 possible codons are stops, i.e. nearly 5% of the time a random codon will be a stop. Next the coded for AA's vary in their affinity for water, and this can easily derange folding. So, folding sequences are by no means easily found, indeed the evidence is that there are several thousand of these fold domains and they are isolated in the space of possible sequences. All of this, GP has repeatedly taken time to explain, all just simply ignored or brushed aside as it does not fit the demands of a priori materialism, it seems, or at least is hard to accommodate to it. And of course, there is the further fact that -- cf Axe et al -- there is published research that points to that viable protein sequences are something like 1 in 10^70 of the A sequence space. More broadly, once we have function dependent on proper configuration of many parts, it is a general and empirically easily supported expectation that only a few configs will be functional, as can be seen from something so simple as the three letter-chains above.) So, we see the use of a case of machine code stored in a control tape, driving what is in the end a numerically controlled automatic assembly machine, the ribosome. And, the applicaiton of concepts such as informaiton, meaningfulness of coded sequences, funciton resulting from algorithmic step by step processes, etc is natural and empirically well supported. It is increasingly obvious that the objections are ideological, not substantial, and as this very post highlights, either some of these objectors have not done even basic homework or something as simple as actually reading what is easily accessible to them, for literally years, or else they are being profoundly mischievous and dishonest. Sorry if that sounds strong, but this is more than warranted by the stunt we just saw above. kairosfocus

Sorry messed up HTML in 257 Should read: Joe G:
Also nature doesn’t select- that requires an agency.
And what do you mean by “an agency”? Alan Fox

Alan Fox:
Speaking generally, a code is a set of symbols and a rule for converting information from one form to another.
How are you defining "information"? Also define "set", "symbol", "rule", "converting" and "form".
In this context information is something you didn’t know before but know after.
We don't know that because you have failed to define your words. Perhaps from now on your could define every word you are using and tell us how you are using it. Joe

Also nature doesn’t select- that requires an agency. And what do you mean by "an agency"? Alan Fox

So propose one. A code is…?
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. Alan Fox

Alan:
An ad hoc definition at the beginning of any discourse of new or unfamiliar terms is all that is necessary
So propose one. A code is...? Phinehas

You are lecturing me on honesty??? YOU??? Thanks for the belly laugh!
You really can't comprehend that people might hold views that differ from your own, honestly? Well, I can't do anything about that but there's not much point in my responding to you further. Good day, Sir! *stalks off huffily* Alan Fox

@ Optimus You are are under no obligation to me nor I to you. I have no problem with general usage of "information" or "code". You say:
Inevitably when someone offers some reasonable definition, you then throw a semantic hissy fit, and the main point gets lost in the smoke.
I have repeatedly made the point, that, in a scientific or logical discussion, it is the proposer of an idea who is best equipped to define his terms. I am not a mind reader and it's a darn sight easier for someone to tell me what they mean than for me to guess. You think that is unreasonable? Information describes facts conveyed from source to recipient. Code has such a wide range of meanings it is better to think of the word qualified with an adjective. Bar code, civil code, morse code, genetic code, highway code.
...if you yourself can’t define ‘information’ or ‘code’, then how can you be so sure that these are not integral features of biological systems?
You can be sure that whenever I use either word in a comment from now on I will append my contextual definition to avoid ambiguity. You illustrate my complaint beautifully in that remark, conflating the use of a word into implying some unintended correlation. Alan Fox

Alan Fox:
Well, that’s the point, environmental design does indeed select from what’s available.
And that means it doesn't design anything. Also nature doesn't select- that requires an agency.
Its the variation aspect of evolution that provides the raw material.
Yup, that's the claim. However there still isn't any evidence that natural selection can design.
Pleased you’re beginning to grasp the concept.
It is obvious that I grasp it better than you do. It is also obvious that you cannot support your claim. Joe

Mr. Fox, "It’s the honest thing to do one or the other." You are lecturing me on honesty??? YOU??? Thanks for the belly laugh! :) bornagain77

AF @ 186 When I say that the burden of proof rests with you, that means that you have to do the work. Why should I tire myself out defining terms ad nauseum that have already been explained to you? Inevitably when someone offers some reasonable definition, you then throw a semantic hissy fit, and the main point gets lost in the smoke. So why don't you establish the definitions for 'information', 'code', etc.? That way you won't have anything to complain about, and the actual substantive, adult discussion can take place. If you cannot supply a rigorous definition of these terms, then your ability to say anything meaningful in this venue is practically nonexistent. After all, if you yourself can't define 'information' or 'code', then how can you be so sure that these are not integral features of biological systems? Optimus

Except differential survival doesn’t design anything. It relies on existing designs.
Well, that's the point, environmental design does indeed select from what's available. Its the variation aspect of evolution that provides the raw material. Pleased you're beginning to grasp the concept. Alan Fox

BA77:
Mr. Fox, claims...
Wrong! Mr Fox asked you to support your assertion that Mr Fox denies that design happens in living organisms. Please produce the evidence or withdraw the assertion. It's the honest thing to do one or the other. Alan Fox

StephenB
In this context, I define “information” as the substance of the message communicated to the cell that tells it what role it is to play and how to carry it out. I define “instruction” as the relevant set of directions. Do we agree that those two elements reside in the DNA molecule? If we do not agree on the use of the words “information” and “instruction,” what words would you use?
I'm no expert, so this is idle speculation, but I don't think that a distinction between "information" and "instructions" is necessary or accurate with regard to the process that results in adult organism from zygote. However I can agree that the information necessary for development of the organism must reside in the genes and the cytoplasm of the oocyte (mitochondria, for example). Although I should add that some external influences (maternal control being a major example) occur. Sex determination in some reptiles (turtles and crocodiles is controlled by temperature for instance.
You mean the zygote does not unfold according to a pre-existent plan? If no plan orders its development and outcome, what does? If no plan determines its traits and features, what does? We understand that chemical and physical processes are involved, but what, if not a plan, determines the way in which they are ordered. You can’t say that the chemical and physical elements are the cause of the form they take–they are the thing being formed.
I was being literal. Development proceeds by cell division and differentiation. A lot of this depends on cascades of gene switches that control how sheets of cells fold and turn into specific cell types. I am sure you have heard of Hox genes. The instructions for growing a human being are not read off a blueprint. It is a dynamic process and a rapidly expanding field of knowledge generally referred to as evo-devo. But, essentially, it is all chemistry!
Why would you expect to “find” a plan? The plan is a conception that shapes the reality of an ordered outcome. We infer the conception from the outcome. I realize that you don’t accept that proposition, but the point is that an ordering principle is, by definition, an abstract concept. It has no physical parts. There is nothing there to find. We can only know it exists by observing its effects.
I can't recall that I ever expected that genetic material would contain a plan and I don't think that now. I used to think that penetrating the mysteries of how DNA sequences that only represented RNA and amino-acid sequences (there are no nonsense codes, any possible triplet codes for an amino-acid or "stop") could notwithstanding cause an organism to develop as necessary would be impossible but progress has been astonishing.
What is inexcusable, as it wastes everyone’s time and marks some as dishonest, is to continue to equivocate over meanings when a misunderstanding over use of words occurs.
I agree and I share your frustration when people do that.
Thanks and I appreciate that. I like to argue but abhor violence! ;) Alan Fox

Joe and BA77 your recent comments are noted. Alan Fox

@ ciphertext I am unsure whether you are highlighting or falling into the trap of anthropomorphism in your comment 235. All the issues you raise fade away if people explain what they mean when asked. Alan Fox

RSCO/I is an integral part of the challenge presented to your arguments/worldview
Rubbish, William. It's the invention of one commenter here. Alan Fox

StephenB
Alan Fox, I realize that you are trying to play chess with several people at once, so I will economize my points as best I can.
Appreciated, Stephen. I seem to have defaulted into the rôle of resident token ID sceptic for which I am not at all well qualified but there is a tide in the affairs of men which taken at the flood... Detailed response in preparation... Alan Fox

Moreover,, More from Ann Gauger on why humans didn’t happen the way Darwin said - July 2012 Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population. You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect. Facing Facts But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes. https://uncommondesc.wpengine.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/ If that wasn't bad enough,, Haldane's Dilemma Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift - creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors - it surely would have killed us. Since Haldane's dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation - but has obtained identical results. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 159-160 Kimura's Quandary Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most 'evolution' must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom's (neo-Darwinism's) very validity. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 161 - 162 A graph featuring 'Kimura's Distribution' is shown in the following video: Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086 The Frailty of the Darwinian Hypothesis "The net effect of genetic drift in such (vertebrate) populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,” http://www.evolutionnews.org/2009/07/the_frailty_of_the_darwinian_h.html Thou Shalt Not Put Evolutionary Theory to a Test - Douglas Axe - July 18, 2012 Excerpt: "For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be 'neutral'). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years). My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they're in the position of insisting that something is a scientific fact without having the faintest idea how it even could be." Doug Axe PhD. http://www.evolutionnews.org/2012/07/thou_shalt_not062351.html bornagain77

Inconsistent Nature: The Enigma of Life's Stupendous Prodigality - James Le Fanu - September 2011 Excerpt: Many species that might seem exceptionally well adapted for "the survival of the fittest" are surprisingly uncommon. The scarce African hunting dog has the highest kill rate of any predator on the savannah, while cheetahs may have no difficulty in feeding themselves thanks to their astonishing speediness -- but are a hundred times less common than lions. http://www.evolutionnews.org/2011/09/inconsistent_nature051281.html bornagain77

Alan Fox:
That’s what natural selection is – a process of design by the environment.
So you keep sayin' yet never can support.
Now by “environment” I mean all the various effects that environment, including but not exclusively, weather, climate, catastrophe, prey, predators, parasites, etc. that contribute to differential survival.
Except differential survival doesn't design anything. It relies on existing designs. You lose, again. Joe

Mr. Fox, claims "where have I denied that design happens in living organisms? That’s what natural selection is – a process of design by the environment. Now by “environment” I mean all the various effects that environment, including but not exclusively, weather, climate, catastrophe, prey, predators, parasites, etc. that contribute to differential survival." Yet, Mr. Fox is severely deluded in what he imagines his proposed 'designer substitute' of Natural Selection can actually do: Darwin proven wrong, again! Experimental Evolution Reveals Resistance to Change (Fruit Flies) Excerpt: Our work provides a new perspective on the genetic basis of adaptation. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. https://uncommondesc.wpengine.com/intelligent-design/darwin-proven-wrong-again-experimental-evolution-reveals-resistance-to-change/ At Why Evolution Is True, the Chewbacca Defense – David Klinghoffer – December 13, 2012 Excerpt: “There is no compelling empirical or theoretical evidence that complexity, modularity, redundancy or other features of genetic pathways are promoted by natural selection….Mmany aspects of complexity at the genomic, molecular and cellular levels in multicellular species are likely to owe their origins to these non-adaptive forces, representing little more than passive outcomes.” (Lynch, “The evolution of genetic networks by non-adaptive processes,” Nature Rev. Gen., 8:803-13, (October, 2007)) So if the “complexity, modularity, redundancy or other features of genetic pathways” and “many aspects of complexity at the genomic, molecular and cellular levels in multicellular species” aren’t easily explained by natural selection, that’s a lot. http://www.evolutionnews.org/2012/12/at_why_evolutio_5067451.html Evidence for Creation now banned from UK religious education classes - July 2012 Excerpt: (In 2008) Professor Massimo Piattelli-Palmarini spoke for a number (of top university academics) in stating simply that natural selection ‘is not the way new species and new classes and new phyla originated.’ http://creation.com/creation-religious-education Darwin’s Legacy – Donald R. Prothero – February 2012 Excerpt: In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. http://www.skeptic.com/eskeptic/12-02-15/#feature “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 Oxford University Admits Darwinism's Shaky Math Foundation - May 2011 Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years. http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html Are We Reaching a Consensus that Evolution is Past its Prime? By Doug Axe - October 2012 Excerpt: By this classically Darwinian view (of natural selection), all that was needed for our ape ancestors to evolve the intellectual capabilities that distinguish us so dramatically from apes was the right “conditions of life.” It follows that any ape population of today, if placed in those conditions, should evolve in the same way—not becoming human per se, but rather human-like in every respect that we benefit from being un-ape-like. And similarly, all it should take for one member of a protein family to transition to a new function is the right selective environment. As old-fashioned as this classical view sounds in a day when very few biologists are proudly waving the flag of natural selection, it did at least have its place in the time-honored scientific tradition of making claims that can be tested today. So, to Moran I say, regale us with heroic stories of magically evolvable apes and magically evolvable enzymes if you must, but when you’re finished with the stories, be sure to join us in doing the science that should convince everyone one way or the other as to their plausibility. It’s the same challenge I put to James Shapiro at the beginning of the year:,,, http://www.biologicinstitute.org/post/34190339725/are-we-reaching-a-consensus-that-evolution-is-past-its This following study is very interesting for the researcher surveyed 130 DNA-based evolutionary trees to see if the results matched what 'natural selection' predicted for speciation and found: Accidental origins: Where species come from - March 2010 Excerpt: If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve.,,, Instead, Pagel's team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution. Like the bell curve, the exponential has a straightforward explanation - but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen.,,,To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak." http://www.newscientist.com/article/mg20527511.400-accidental-origins-where-species-come-from.html?page=2 Did Natural Selection Construct Metazoan Developmental Sequences? - Paul Nelson - July 2011 The necessary and sufficient conditions of the process of natural selection (Endler, Natural Selection in the Wild, 1986) are (1) variation, (2) selection or fitness differences, and (3) inheritance. These conditions impose evidential demands on any investigator who wishes to employ natural selection in evolutionary (i.e., historical) explanation. Data from model systems (e.g., C. elegans, Drosophila, and Danio), as well as theoretical analyses, raise challenges for the use of natural selection as the causal process responsible for the origin of developmental sequences. In particular, the conditions of (2) selection differences and (3) inheritance have not been adequately described in current theories of the evolution of the Metazoa. http://www.evolutionnews.org/2011/07/paul_nelson_jonathan_wells_tak048301.html Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated) Casey Luskin April 12, 2011 Excerpt: This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn't create....[N]eo-Darwinists say that new species emerge when mutations occur and modify and organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence. http://www.evolutionnews.org/2011/04/lynn_margulis_criticizes_neo-d045691.html bornagain77

Alan Fox:
How many times do you get told that science advances by the testing of competing hypotheses?
And we are still waiting for your position to produce a testable hypothesis.
Had I a position and you were able to shred it by wielding your mighty intellect, it would not improve the strength of any alternative hypothesis.
Perhaps not. But in this case SCIENCE mandates that we eliminate necessity and chance before even considering design. So it is part of the process.
ID proponents need to start advancing testable hypotheses of their own if they want to be taken seriously.
We have. You just don't know what a testable hypothesis is as your position can't muster one. Alan Fox:
However, when someone proposes a new idea like, say, complex specified information, the onus is on the proposer to make it clear what he means by the phrase.
We have. That you choose to be obtuse is not our problem. Joe

as to: " if one could simulate the simplest single cell lifeform of an adequately sized population," To Model the Simplest Microbe in the World, You Need 128 Computers - July 2012 Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,, The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,, ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,, http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/ bornagain77

Alan Fox, I realize that you are trying to play chess with several people at once, so I will economize my points as best I can. [“Do we agree that the “instructions” providing the necessary “information” for the organism’s development reside in the cell’s nucleus as a DNA molecule? If the words “instruction” and “information” are too strong (too anthropomorphic) to express that relationship, what words would you use?”]’
I think you should be able to work out what my answer is here. Years ago there was a BBC radio program called “The Brains Trust” where a panel of experts answered question from the audience. One panel member, Professor C. M. Joad, was noted for often prefacing his answers with “It all depends what you mean by [some key word in the question]“. So, in any discussion where the intent is to communicate effectively and honestly, first define your terms.
In this context, I define “information” as the substance of the message communicated to the cell that tells it what role it is to play and how to carry it out. I define “instruction” as the relevant set of directions. Do we agree that those two elements reside in the DNA molecule? If we do not agree on the use of the words “information” and “instruction,” what words would you use? [“Do we agree that a DNA molecule “encodes” a detailed set of plans for building different parts of the cell. If “encode” is too strong (human-like) of a verb, what verb would you use?”]
Most assuredly, not! Talking of “building plans” is a total misunderstanding in what goes on when a zygote develops into an adult organism (though there is no reason to limit this to sexually reproducing eukaryotes).
You mean the zygote does not unfold according to a pre-existent plan? If no plan orders its development and outcome, what does? If no plan determines its traits and features, what does? We understand that chemical and physical processes are involved, but what, if not a plan, determines the way in which they are ordered. You can’t say that the chemical and physical elements are the cause of the form they take--they are the thing being formed.
There is nowhere in the genetic material where anything resembling an overall plan can be found.
Why would you expect to “find” a plan? The plan is a conception that shapes the reality of an ordered outcome. We infer the conception from the outcome. I realize that you don’t accept that proposition, but the point is that an ordering principle is, by definition, an abstract concept. It has no physical parts. There is nothing there to find. We can only know it exists by observing its effects.
What is inexcusable, as it wastes everyone’s time and marks some as dishonest, is to continue to equivocate over meanings when a misunderstanding over use of words occurs.
I agree and I share your frustration when people do that. StephenB

It seems to me, from reading through the postings, that each "camp" (for lack of a better term) has "staked out" their positions based upon perceived strategies associated with the use of the english lexicon. The one camp sees a strategy to the use of "code" as indicative of an external intelligence to the system. The other camp sees a strategy to downplay the use of "code" to something more benign, like simply an"abbreviation" or "shortcut" for a more complex process. I know, that is a huge over-simplification of the "camps'" respective positions, but that is how I (an interested onlooker, sometimes participator to a degree) have come to understand the arguments. I also understand that depending on the camp, there are particular merits/demerits to each use of the various words. Here is the Merriam-Websters definitions of "genetic code" and "code" respectively. <a href="http://www.merriam-webster.com/dictionary/genetic+code?show=0&t=1360861037"genetic code: the biochemical basis of heredity consisting of codons in DNA and RNA that determine the specific amino acid sequence in proteins and appear to be uniform for nearly all known forms of life code: a system of signals or symbols for communication (there are several definitions, here I am using #3a.) In studying the history of the genetic code, what is useful to remember (at least for me) is that most likely the operational definition that I list for "code" was the one being used during the time during which the relevant research was being conducted. This is because the definition of "genetic code" as we have it defined, didn't exist prior to its (the genetic code) discovery and subsequent refinement. So at the very least, the "code" in "genetic code" owes its existence to the definition which "includes a system of signals or symbols for communication". Now, we should probably also include definitions for the term communication. That, also, seems to be a loaded term with respect to the various "camps". Here are three definitions (four technically), all from Merriam Websters, which are most likely the ones being used by the different camps. It should be obvious which ones based upon the idea being proposed by each camp. communication: 1) an act or instance of transmitting 2a) information transmitted or conveyed 2b) a verbal or written message 3) a process by which information is exchanged between individuals through a common system of symbols, signs, or behavior ; also : exchange of information What I find curious, is that the definition of "genetic code" (from Merriam Websters at least) makes no mention of communication, which typically goes hand-in-glove with the use of code. If no communication takes place, then shouldn't we rename the genetic code? If for no other reason than to avoid the issues of lexicon we experience here? Though the names "Genetic Abbreviations", "Genetic Shorthand", "Genetic Symbols" (which is really a "code" in another word) don't seem to fit as a representation of what "it" is. I find it interesting that the history of the research indicate that the scientists themselves did in fact believe the DNA to be "communicating" or part of a larger "communication" apparatus associated with heredity. Which is likely why they chose the word "code" as opposed to "representative" or some other category descriptor. They could have made one for their own purposes it seems. Yet they chose "code". The term "communication" to most persons implies an intelligence does it not? Though the act of communication as defined above in definition "1" doesn't necessarily require one. It is the physical process of transmission. That definition occurs every day millions of times a second. Both in the biological world (as evidenced by my participation in the prior posts about B-Cells and antibodies) and in the physical world (financial transactions for instance). The question is then begged, the transmission of what? That question itself, won't definitively "prove" the existence of an intelligent, external (to the system being viewed) agent, but it could strengthen a case for such a position. Another question that I have about communication is "why"? I like the question "the transmission of what?". It is much more interesting to me than the "how". Though, how is interesting in its own right. That is where another word with a polymeaning enters into the discussion. Rather than clarifying, the word causes each camp to sharpen their swords, insure the reinforcement of their barricades, and "circle the wagons". Usually, it boils down to a difference of opinion as to what definition of such a word should be applied. The word in question here is information. I, once again, return to Merriam Websters and have selected the following definition as appropriate. You may disagree, but you must provide another definition for use. It is definition #2b. information: 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 In light of these definitions, it would seem to me that the genetic code is the total of all "codes" (def #3a); which are representatives of information (inherent attributes per above definition) that is "communicated" (def #1, or act of transmission) between cellular systems. Notice, I haven't described the communication system (the RNA, tRNA, ribosomes, etc...). Nor have I described the information being communicated (the amino acids etc...). Interesting questions that follow are "what" is being communicated? The answer being simply "nucleotides". Though a longer, more technical discussion could take place about that. Seemingly, the nucleotides are themselves "codes" that represent an instruction set are they not? Specifically instructions to the cell on which amino acids to use in constructing a specific protein, correct? My question is what leads "us" to believe that heredity and natural selection would be sufficient to generate the "codes", "information", and "communication" as I have them defined? I understand that the codes could be preserved through the mechanism of inheritance. That is loosely the equivalent of obtaining an ability to parse an ASC EDI X12 purchase order specification from a "library" class. I'm less confident that natural selection would be the genesis of such specifications (i.e. the ASC EDI X12 or metaphorical equivalent in biology) or even of the metaphorical equivalent to the library class (though that would seem to be an easier hurdle than the specification). I'm not unwilling to entertain the hypothesis, however. It is easy to relate the concept of "intelligence" to cellular automata, once you use terms like "code", "information", and "communication". The reason being, is that there are, I argue, default assumptions about those particular words; which are held by the general public. Namely, the computer technology we enjoy today are almost always associated with those words. The general populace will make an implicit assumption about topics that use "code", "information", and "communication" regularly as descriptors. The assumption is that an intelligent agent defined those systems. The information systems employed today were designed by mankind, so that association is made (design association at least). The hard question for the "design hypothesis" camp is how do you associate a more "abstract" intelligence to the "codes", "information", and "communication" exhibited by the biological machinery? The approach you are "stuck with" will be a hard sell to the scientist community that uses the a materialistic (Popper?) Philosophy of Science, rather than meta-physical (Aristotelian?) Philosophy of Science. Though, the individuals who dislike the study of Philosophy, will no doubt not enjoy that the prominence of their position rests upon the philosophical foundation of their choosing. Which, at base, is largely a matter of preference. ciphertext

Answer a simple question if you will, G. Is functional sequence complexity the same concept as your FSCO/I (what do these initials stand for, BTW)?
Really? This far into several debates where RSCO/I is an integral part of the challenge presented to your arguments/worldview ... and you haven't even bothered to find out what it means? Like so many others, AF is not serious about any debate here, he's only serious about preserving his own worldview via willful ignorance and denial. William J Murray

PS @ KF 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. Alan Fox

Answer a simple question if you will, G. Is functional sequence complexity the same concept as your FSCO/I (what do these initials stand for, BTW)? If so, why use a different acronym? If not why is Durston's paper relevant? Alan Fox

JWT, shoot me an email (follow the link) and I will pass to you a PDF. Sorry on eqn formats, I did that in part to get around the formatting headaches that crop up in so many situations and to avoid the problem of using GIFs (which are actually just displayed in the page, they "live" elsewhere). KF kairosfocus

AF: Playing at the "let's object on style (one can ALWAYS do that . . . ) if we cannot answer on substance" game I see; sadly. And, trying the switcheroo that Durston et al were not speaking about functionally specific bits, and providing a metric of complexity for same. (Perhaps, you need to be aware of this earlier work (observe the diagram) by them and what FSC -- functional sequence complexity -- stands for, which is what the paper is providing a metric for with specific application to protein sequences, which is what they report. Note, that the nodes-arcs analysis means that anything that has functionally specific organisation can be reduced to strings, so this is WLOG. Remember, too, H is a metric of avg info per symbol in light of the observed statistics for a given system, where any real world system will have some redundancy. KF kairosfocus

...had AF bothered to simply scan down...
Hey, don't blame me for your inadequacies in blog layout! ;) Durston doesn't cut it. Firstly its not FCSI in his paper. FCSI is not referred to anywhere. Secondly Durston's "fits" produce no new insight into protein structure. I note there are zero citations showing on Google Scholar for this paper. Alan Fox

@kairosfocus: Is there any way you could make your paper "On Information, Design, Science, Creation & Evolutionary Materialism" available as a nice-looking (tex-based) pdf-file one could read on an e-book (Btw. have you ever thought about printing your article as a book? :-) I'd buy it.)? Maybe it's just me, but the website is really hard to read, especially with the unfriendly formatting of equations. JWTruthInLove

So Mr. Fox are you really that self deceived to see that you are directly refuted by empirical evidence, or are you just being purposely dishonest to the evidence that was presented to you because you don’t like the implications of admitting design in biology?
But Phil, where have I denied that design happens in living organisms? That's what natural selection is - a process of design by the environment. Now by "environment" I mean all the various effects that environment, including but not exclusively, weather, climate, catastrophe, prey, predators, parasites, etc. that contribute to differential survival. Alan Fox

* If evolution is true! Alan Fox

Can the simplest structure possible that copies itself, while being able to take in/accumulate changes (probably necessarily of a truly random, stochastic nature initially), transition to a state where both the copying and updating/modifying functions rely on/utilize a coded system, without disrupting the process along the way?
There are* upper and lower limits for any population of replicators. If copying is too perfect, there is nothing for natural selection to work on and if copying results in too many mutations the population will become extinct with natural selection too slow to eliminate the deleterious changes. There are many on-line resources and communities who can be of help in getting more information than I as a layman can provide. Talkorigins.org is a good starting point.
I was wondering if you had a chance to check out the link to the more recently discovered spider...
Yes. Most impressive! The evolutionary explanation involves the assumption that the innate behaviour patterns that result in decoy building (and, essentially, all other innate behaviour that occurs in metazoans) must exist in the fertilized egg. I happen to think the only possible candidate is DNA sequences (though I have no idea remotely how this happens precisely) and thus this is passed on as "alleles" (different versions of the genetic sequences) which will then be subject to natural selection. Each spider builds its decoys to according to its programmed behaviour. Where a variation gives a survival advantage, that allele will proliferate. I'm not sure I'm convincing myself here but there is no better competing hypothesis that I am aware of. Alan Fox

Correction/Update @221: Of course, if one could simulate the simplest single cell lifeform of an adequately sized population, along with an adequately sophisticated/detailed environment, one would be tasked with demonstrating that a code/dialect in use could transform to a different code/dialect- as obviously the cell requires that an initial code already exist. So this would address a different but related question: Can codes change "naturally", as opposed to can codes arise "naturally"? (Or for that matter, can codes in living systems be engineered to change by human minds, and if so, what types of changes are possible?) MrMosis

Onlookers, another couple of dodges. First, the burden of proof game is appropriate to courtrooms where since the Govt has overwhelming resources it is safer to have the defendant presumed innocent. In scientific matters, everyone who makes a claim, has a burden of evidence-based warrant, even if the claim is negative. As one experienced with machine code and its use in discrete state control context, and communication contexts, I state that I find that the coded information that fits on the Codon table and commonly appears in mRNA is an obvious and well known INSTANCE of a control tape; one using prong height as coding mechanism. There has been no cogent, empirically based answer. If AF wants to reject that evidence, let him bring forth his evidence based reasons, and while he is at it, correct from Crick on down. Similarly, had AF bothered to simply scan down and notice the indented list (never mind, actually attending to the relevant chain of reasoning, which inter alia gives in outline what info measured in bits is about), he would have observed the following information measured in functional bits (which should itself have been a clue), the basis of which has been in the peer-reviewed literature for some five years:
Using Durston’s Fits values -- functionally specific bits -- from his Table 1, to quantify I, so also accepting functionality on specific sequences as showing specificity giving S = 1, we may apply the simplified Chi_500 metric of bits beyond the threshold:
RecA: 242 AA, 832 fits, Chi: 332 bits beyond SecY: 342 AA, 688 fits, Chi: 188 bits beyond Corona S2: 445 AA, 1285 fits, Chi: 785 bits beyond

This is in the end based on the view of informational entropy as specifying the average information per symbol [cf discussion here], which is linked to thermodynamic entropy from an informational view as measuring the average missing information on the specific microstate facing us if we only have the state info that gives the macrostate of a system. I highlight this, to underscore that the quantifiable concepts of information we are dealing with are now embedded in a serious school of thought in thermodynamics. KF kairosfocus

Mr. Fox states: "Argument from incredulity! You must skip Joe’s and BA77?s comments!" Yet Mr. Fox was the one who originally 'incredulously' claimed: ”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.” And yet Mr. Fox was shown that, among other things such as storing massive amounts of 'digital' information directly on DNA, that,, Passing the baton of life – from Schrödinger to Venter – July 2012 Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said Venter. “We are now using computer software to design new DNA software.” – Craig Venter http://www.newscientist.com/blogs/culturelab/2012/07/passing-the-baton-of-life---from-schrodinger-to-venter.html So Mr. Fox are you really that self deceived to see that you are directly refuted by empirical evidence, or are you just being purposely dishonest to the evidence that was presented to you because you don't like the implications of admitting design in biology? bornagain77

Alan Fox: Thank you for the reply. I gathered that some were disputing the adequacy of the descriptor altogether. I suppose the real disagreement concerns whether or not anything meaningful can be said about whether or not such systems (those using codes as defined here) can arise “naturally”. I would think a rigorous mathematical system/model that tightly corresponds with reality and has a limited set of assumptions could address this- similar but not identical to the matter of FSCO/I. Can the simplest structure possible that copies itself, while being able to take in/accumulate changes (probably necessarily of a truly random, stochastic nature initially), transition to a state where both the copying and updating/modifying functions rely on/utilize a coded system, without disrupting the process along the way? (putting aside for the moment the issue of how the original system came to be) This may not be practical, in large part because to my [limited] knowledge, the only known, imagined, or contemplated system that is capable of doing this is the cell, which is still too big and complicated to model with enough specificity. ALSO slightly OT: I was wondering if you had a chance to check out the link to the more recently discovered spider I posted @145. It is mind boggling to consider what form of mutation could have facilitated the spider’s “knowing” how to model itself in its web. Stochastic point mutations at random locations do not seem to be up to the task. But if that is true, what would that entail? What if the spider’s web making-related knowledge is stored in such a manner that it is oriented towards enabling some form of change? Such that the spider and its instincts have a predisposition towards taking in “suggestions” for how to do web decoys “better”. And even if so, it is hard to imagine how the spider could wind up putting legs on its decoys. At the very least, the appearance of purposes seems to emerge from some very strange places of late. MrMosis

Eric Anderson:
It is hard to imagine a more clueless statement.
Argument from incredulity! You must skip Joe's and BA77's comments! :) Alan Fox

...real world cases on measuring FSCI...
As I am sure many here will agree, I am not the most assiduous reader. However can anyone else spot a "real world case" in the piece KF links to? Alan Fox

Please define for us what you mean by “code” and “information”. Make sure you are using watertight definitions. And not just based on what scientists generally ‘consent’ to the words meaning.
You miss my point but I'll indulge you. Firstly I am not the one using the word "information" as if it imbues a concept with, well, information. Information has a generally accepted common usage. However, when someone proposes a new idea like, say, complex specified information, the onus is on the proposer to make it clear what he means by the phrase. There is not the same issue with "code". I have no problem with this as the context clarifies the usage.
We want to hear definitions that apply across all boundaries and without relying on dictionaries.
That is what I have been saying is impossible. Impossible and pointless. Impossible, pointless and misleading. An ad hoc definition at the beginning of any discourse of new or unfamiliar terms is all that is necessary Alan Fox

EA: That would be interesting to see, especially if the said definitions can be backed up by technical usage, beyond Shannon's metric of info carrying capacity. (For those wishing to see some real world cases on measuring FSCI, cf. here and onward in light of the source of the cited, published results in functional bits). KF kairosfocus

Alan Fox:
The genetic code is called the genetic code by general consent. We shouldn’t read any more into its name than that. Claims about its function and origin should be made using evidence based on research and not based on poor analogy with other things called codes.
It is hard to imagine a more clueless statement. The reason it is called a code is because it is -- based on evidence and research -- not because of some analogy. You've been a great Exhibit A for the inability of materialists to play semantic games and not engage the evidence. But I'll play along one last time. Please define for us what you mean by "code" and "information". Make sure you are using watertight definitions. And not just based on what scientists generally 'consent' to the words meaning. We want to hear definitions that apply across all boundaries and without relying on dictionaries. Either put up or shut up. Eric Anderson

Programming of Life - Biological Computers - video http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/5/hRooe6ehrPs Introducing "Bi-Fi": The Biological Internet - October 3, 2012 Excerpt: They already achieved 5 petabits per cubic millimeter! That's 1,000 terabits of data -- nearly twice the entire volume of digital records at the Library of Congress1 -- in a cube the size of the space between your thumb and forefinger when you hold them slightly apart.2 There are more reasons they think DNA storage is the wave of the future: "DNA is particularly suitable for immutable, high-latency, sequential access applications such as archival storage. Density, stability, and energy efficiency are all potential advantages of DNA storage, although costs and times for writing and reading are currently impractical for all but century-scale archives. However, the costs of DNA synthesis and sequencing have been dropping at exponential rates of 5- and 12-fold per year, respectively--much faster than electronic media at 1.6-fold per year. Hand-held, single-molecule DNA sequencers are becoming available and would vastly simplify reading DNA-encoded information." Hand-held? You mean your smartphone might read and write documents in DNA? Why not? Well, if DNA is the ideal storage medium, how about using it for the Internet? In fact, "Bi-Fi: The Biological Internet" is in development at Stanford School of Medicine. (links provided at site) http://www.evolutionnews.org/2012/10/introducing_bi-064781.html As well, The Ribosome of the cell is found to be very similar to a CPU in a electronic computer: Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf Also of interest is that a cell apparently seems to be successfully designed along the very stringent guidelines laid out by Landauer's principle of 'reversible computation' in order to achieve such amazing energy efficiency, something man has yet to accomplish in any meaningful way for computers: Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf bornagain77

Mr. Fox claims: " 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." Huh??? You are, once again, 'not even wrong',,, Passing the baton of life - from Schrödinger to Venter - July 2012 Excerpt: "All living cells that we know of on this planet are 'DNA software'-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions," said Venter. "We are now using computer software to design new DNA software." - Craig Venter http://www.newscientist.com/blogs/culturelab/2012/07/passing-the-baton-of-life---from-schrodinger-to-venter.html Information Theory, Evolution, and the Origin of Life - Hubert P. Yockey, 2005 Excerpt: “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” http://www.cambridge.org/catalogue/catalogue.asp?isbn=9780521802932&ss=exc Every Bit Digital DNA’s Programming Really Bugs Some ID Critics - March 2010 Excerpt: In 2003 renowned biologist Leroy Hood and biotech guru David Galas authored a review article in the world’s leading scientific journal, Nature, titled, “The digital code of DNA.”,,, MIT Professor of Mechanical Engineering Seth Lloyd (no friend of ID) likewise eloquently explains why DNA has a “digital” nature: "It’s been known since the structure of DNA was elucidated that DNA is very digital. There are four possible base pairs per site, two bits per site, three and a half billion sites, seven billion bits of information in the human DNA. There’s a very recognizable digital code of the kind that electrical engineers rediscovered in the 1950s that maps the codes for sequences of DNA onto expressions of proteins." http://www.salvomag.com/new/articles/salvo12/12luskin2.php ID Vindicated - August 17, 2012 Excerpt: Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. Here, we develop a strategy to encode arbitrary digital information in DNA, write a 5.27-megabit book using DNA microchips, and read the book using next-generation DNA sequencing. https://uncommondesc.wpengine.com/intelligent-design/id-vindicated/ DNA Computer Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today’s most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours. http://www.tech-faq.com/dna-computer.html The Digital Code of DNA and the Unimagined Complexity of a ‘Simple’ Bacteria – Rabbi Moshe Averick – video (Notes in Description) http://vimeo.com/35730736 Even the leading "New Atheist" in the world, Richard Dawkins, agrees that DNA functions exactly like digital code: Richard Dawkins Opens Mouth; Inserts Foot - video http://www.evolutionnews.org/2010/06/richard_dawkins_opens_mouth_in035861.html Human DNA is like a computer program but far, far more advanced than any software we've ever created. Bill Gates, The Road Ahead, 1996, p. 188 Bill Gates, in recognizing the superiority found in Genetic Coding compared to the best computer coding we now have, has now funded research into this area: Welcome to CoSBi - (Computational and Systems Biology) Excerpt from early 2010 (of note the following heading is now changed on the site): Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas. http://www.cosbi.eu/index.php/component/content/article/171 bornagain77

Alan Fox (and allies)
Plural? Allies? Where?
How is it possible to in any meaningful way dispute the notion of “code” being a fitting descriptor of these systems?
I don't dispute that. The genetic code is called the genetic code by general consent. We shouldn't read any more into its name than that. Claims about its function and origin should be made using evidence based on research and not based on poor analogy with other things called codes. Alan Fox

@ MrMosis Sorry, I did miss your earlier comment, I suspect I might have skipped it assuming the whole was addressed to kairosfocus. so:
Alan Fox: For my own benefit if nothing else, from your view and adopted philosophies, how have you dealt with the significance of this matter? I am curious how given the above from KF, one can still discount that there are instantiations of codes in biology. I might be able to allow for some wiggle room and quibbling had the translation information been inherent within the design of the ribosome itself. But if ribosomes need to in effect be programmed to use the same code, to in essence be speaking the same language, as the DNA, I am not sure how one can conceptually get way from it not just being similar to a code, but in fact being a code- in the sense as described in the OP and UB’s original post.
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. Alan Fox

Alan Fox (and allies): I am wondering if you noticed my reply @170. I would be most appreciative if you wouldn’t mind offering me your thoughts. I have tried to read through most of the comments here, so I apologize if it has been addressed full on previously- if so, I must have missed it. How would you describe your thought processes as relates to the matter of DNA sequences storing codes, given that the arbitrary relationship of the code (symbols to actions, or symbols to AAs) exists at both ends of the “communication”? Or if you prefer, the same arbitrary relationship existing at both the “reading and writing” functions. Here the reading function would be of course the mRNAs being translated by the ribosome, itself having been programmed by tRNAs. And the writing, taking place by whichever mechanisms, utilizing the same arbitrary assignments(although it seems to me that point mutations are increasingly losing their share of responsibility for overall change, and their scope for actualizing potential change is turning out to be more constrained than previously imagined.) Take horizontal transfer for instance. How is it possible to in any meaningful way dispute the notion of “code” being a fitting descriptor of these systems? I will truly understand your position whenever I can fully articulate it. As of yet I am unable to do so- so I seek to learn. MrMosis

The main thrust of the OP is twofold: (1) life is information based, and (2) when it comes to demonstrating how that information could have originated through blind directionless physical forces the materialists have exactly bupkus.
Can't argue with either (1) or (2). (BTW thanks for translating "bupkus". Who knew you were Jewish!) There is no scientific consensus on the origin of life on Earth and you are absolutely right to say that there is no current explanation worth the name. While there are plenty of competing hypotheses and the incontrovertible fact is that the origin of life occurred sometime between the Earth becoming cool enough for liquid water to be present and the first fossil evidence, it remains an elusive goal of science to make any real progress beyond speculation. Are ID researchers working on the problem? Alan Fox

Thanks Barry *blushes* Thank-you for allowing me back into this fold of reason and enlightenment. Alan Fox

Alan, you are truly priceless. Thank you, thank you, thank you for posting here at UD. The main thrust of the OP is twofold: (1) life is information based, and (2) when it comes to demonstrating how that information could have originated through blind directionless physical forces the materialists have exactly bupkus. And you come on here and repeatedly and enthusiastically demonstrate proposition (2). Wonderful. Thank again. To those of you who might believe that Alan is a sock puppet for ID who only pretends to be an obstinately clueless foil, I can assure you that it isn’t so. [“Bupkus” = Yiddish for “nothing”] Barry Arrington

Why are you referring to ‘kairosfocus’ as ‘G’?
It feels less formal than Mr. M. Alan Fox

You sure as hell don’t have any real evidence to support the claims of your position.
How many times do you get told that science advances by the testing of competing hypotheses? Had I a position and you were able to shred it by wielding your mighty intellect, it would not improve the strength of any alternative hypothesis. ID proponents need to start advancing testable hypotheses of their own if they want to be taken seriously. Alan Fox

Alan, Why are you referring to 'kairosfocus' as 'G'? Gregory Gregory

Alan Fox:
Likewise, the observed evidence that blind chance plus mechanical necessity is able to spontaneously originate FSCO/I (especially digital code beyond 500 bits) without intelligent direction is word salad[which BTW, takes hill-climbing algorithms off the table for good reason)
What a joke. Just saying something is "word salad" doesn't make it so. IOW Alan, it appears all you have is word salad. You sure as hell don't have any real evidence to support the claims of your position. BTW "hill-climbing algorithms" are all Intelligently Designed and the hills are climbed by design. Joe

word salad though woed salad does equally well! Alan Fox

Now Alan proves that he lacks the ability to read. Joe

Oh right. Fill in the blanks. Your presentation skills are abysmal G. ...the warrant for OOL on chance plus necessity is (a) not computable, it was not published and the Nobel Prize was not awarded. Likewise, the observed evidence that blind chance plus mechanical necessity is able to spontaneously originate FSCO/I (especially digital code beyond 500 bits) without intelligent direction is word salad[which BTW, takes hill-climbing algorithms off the table for good reason) and this can be seen as more woed salad. Voilà! Alan Fox

Please, please, please, show my prediction false. KF
What prediction? Clearly state your prediction without excess verbiage and I'll comment on it. Alan Fox

Joe, looks like AF likely dresses a priori materialist ideology up in a lab coat and calls it science, rather than philosophy. KF kairosfocus

AF: You have again manged to duck the substantial matter, and play at side track games. The need for the correction above is, sadly, evident -- and evidently unheeded. However, it should be fairly clear to the onlooker who has dealt with the substantial matters and who has consistently been evasive and selectively hyperskeptical, also -- as Joe just pointed out -- excessively credulous in absence of sound warrant regarding his preferred view. Let's hear again, the warrant for OOL on chance plus necessity is (a) ________, it was published (b) _________ and the Nobel Prize was awarded (c ) ________. Likewise, the observed evidence that blind chance plus mechanical necessity is able to spontaneously originate FSCO/I (especially digital code beyond 500 bits) without intelligent direction is (d) _______ [which BTW, takes hill-climbing algorithms off the table for good reason) and this can be seen (e) __________ . I predict that you will not be able to fill in the blanks a through e, but will find some excuse for not doing so. Please, please, please, show my prediction false. KF kairosfocus

Alan Fox:
The third choice is not to toss over all of science and to accept there is good empirical evidence for many real phenomena and reject FSCO/I as a personal foible of one commenter on a blog.
Exactly what "science" is being "tossed over" and what " good empirical evidence for many real phenomena" is there to accept wrt evolutionism? That said, the functionality observed in biological organisms is real. It doesn't matter what it is called, your position cannot account for it. Joe

Pardon me but at this point the turnabout tactics begin to wear, and I will speak fairly directly but I hope with a modicum of respect due to you as a human being. In so doing, I am asking you to reflect on what you have done and what it has demanded of others in terms of time and effort in response. Then, I am asking you to do better, for surely you are a reasonably educated and intelligent person. The evidence in front of me, with all due respect, says willful evasiveness via selective hyperskepticism; working by demanding definitions in a context where over several months such have been provided over and over, with adequate basis. Similarly, to keep on asserting that you don’t see info in the face of digital code routinely represented in code tables, and the obvious consensus of the science; is not a commendation of your view. What you really need to be doing is providing a basis for warranting the claim that such a system can arise in some warm little pond or other by chance and necessity, or in a like OOL environment. This neither you nor anyone else on your side, for years, has done. That instead you are resorting to all sorts of definitionitis games and denials, is now saying — here comes semiotics again, I am saying here that actions speak as loudly as words — that you cannot answer on the merits so you are trying to play selectively hyperskeptical you prove it to me while I assume the mantle of default games.
Such piffle is not worthy of a response, G.
We have in hand things that plausibly trace from the origins of cell based life and from the origin of body plans. We see that functionally specific complex information, including digitally coded info and algorithms, are deeply emb3edded in life. We cannot directly observe the actual deep past of origins, so we are forced to model it scientifically based on observing adequate and evidently characteristic causes int eh present that produce sufficiently similar effects that we can identify cause on an inference to best current explanation basis. This is a commonplace in scientific work when we cannot directly observe objects or phenomena.
This is actually trivially about right! Why do need to keep repeating such mantras? Try and be a little bit specific.
It turns out that the high contingency manifest in FSCO/I — especially evident in digital code — is first not credibly a product of necessity, as that makes low contingency. Similarly, functional specificity and complexity make chance a maximally implausible explanation for such phenomena. The only observed — and we routinely observe such — cause adequate to create FSCO/I is design.
Back to piffle! FSCO/I is your own imaginary construct. Harping on it will not make it real.
That makes the traces from the past credibly point to design as their source.
In some cases it might. Stonehenge would be a case in point. So what? Are we extrapolating from particular to general here?
If you object to this inference then either toss over all of science that works with objects and phenomena that cannot be directly observed (which will be a big chunk of physics and chemistry as well as other things) or else provide good empirically grounded evidence that FSCO/I can reasonably be the product of blind chance and/or mechanical necessity.
The third choice is not to toss over all of science and to accept there is good empirical evidence for many real phenomena and reject FSCO/I as a personal foible of one commenter on a blog.
Absent such, and in a context where for instance it is a safe bet that you accept the cosmological and geochronological standard timelines, to reject the above chain of reasoning is a plain case of selective hyperskepticism.
If you are asking me is dedrochronology a useful scientific tool, of course it is! Is cosmology a useful branch of science? Arguable but it's certainly fascinating.
Good day, sir.
G'day to you, G! Alan Fox

AF: Pardon me but at this point the turnabout tactics begin to wear, and I will speak fairly directly but I hope with a modicum of respect due to you as a human being. In so doing, I am asking you to reflect on what you have done and what it has demanded of others in terms of time and effort in response. Then, I am asking you to do better, for surely you are a reasonably educated and intelligent person. The evidence in front of me, with all due respect, says willful evasiveness via selective hyperskepticism; working by demanding definitions in a context where over several months such have been provided over and over, with adequate basis. Similarly, to keep on asserting that you don't see info in the face of digital code routinely represented in code tables, and the obvious consensus of the science; is not a commendation of your view. What you really need to be doing is providing a basis for warranting the claim that such a system can arise in some warm little pond or other by chance and necessity, or in a like OOL environment. This neither you nor anyone else on your side, for years, has done. That instead you are resorting to all sorts of definitionitis games and denials, is now saying -- here comes semiotics again, I am saying here that actions speak as loudly as words -- that you cannot answer on the merits so you are trying to play selectively hyperskeptical you prove it to me while I assume the mantle of default games. Sorry, that is not how science works. We have in hand things that plausibly trace from the origins of cell based life and from the origin of body plans. We see that functionally specific complex information, including digitally coded info and algorithms, are deeply emb3edded in life. We cannot directly observe the actual deep past of origins, so we are forced to model it scientifically based on observing adequate and evidently characteristic causes int eh present that produce sufficiently similar effects that we can identify cause on an inference to best current explanation basis. This is a commonplace in scientific work when we cannot directly observe objects or phenomena. It turns out that the high contingency manifest in FSCO/I -- especially evident in digital code -- is first not credibly a product of necessity, as that makes low contingency. Similarly, functional specificity and complexity make chance a maximally implausible explanation for such phenomena. The only observed -- and we routinely observe such -- cause adequate to create FSCO/I is design. That makes the traces from the past credibly point to design as their source. If you object to this inference then either toss over all of science that works with objects and phenomena that cannot be directly observed (which will be a big chunk of physics and chemistry as well as other things) or else provide good empirically grounded evidence that FSCO/I can reasonably be the product of blind chance and/or mechanical necessity. Absent such, and in a context where for instance it is a safe bet that you accept the cosmological and geochronological standard timelines, to reject the above chain of reasoning is a plain case of selective hyperskepticism. Good day, sir. KF kairosfocus

Alan Fox:
Give me a clear operational definition of “information” and I will be able to give you a clear answer which could be “yes”, “no”, “perhaps”, “I don’t know” or “your definition is unworkable” depending on how “information” is defined in the context. In everyday speech, I would have no hesitation in agreeing that any – any – DNA sequence contains information.
OK: information- 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 Ya see Alan, not just any DNA sequence will encode for the required proteins. That takes specific sequences. Joe

The genetic CODE is a CODE by DEFINITION. And it is semiotic, again by definition. Codons REPRESENT amino acids, they do NOT become them. And blind and undirected chemical processes cannot account for that. If they could Alan and others would have posted that evidence by now. Joe

Alan Fox:
I see no communicative element in the chemical processes that occur when DNA sequences are transcribed into RNA and translated into polypeptide sequences. It’s all a result of the inherent physical and chemical properties of the interacting molecules.
Except there isn't any physical and chemical properties that DETERMINE which codon REPRESENTS what amino acid. So either you are being very obtuse, like Zachriel, or you are just very dishonest.
Talking of “building plans” is a total misunderstanding in what goes on when a zygote develops into an adult organism (though there is no reason to limit this to sexually reproducing eukaryotes).
Good luck supporting that bit of trope.
There is nowhere in the genetic material where anything resembling an overall plan can be found.
Perhaps we just don't know where to look nor what to look for. Joe

G Have posted a reply to you in the thread you link to. I puzzles me why you have to lace your comments with general slurs apparently directed to people who's views differ from your own.It's hardly encouraging to a free exchange ideas but perhaps that's the point! Alan Fox

F/N: Rather than double thread again, here is the link where I point out the essentially informational character of what is going on. Those are not exactly obscure results, so I am beginning to move to the conclusion that the issues raised as objections at this point are mainly rhetorical flak intended to protect a key vulnerable spot for those who do not wish to address the issues raised by having to face the evident fact of an information system in the living cell based on digital code (as was spotted by Crick as early as March 19, 1953 -- long before the details were worked out), not genuinely substantial. KF kairosfocus

One thing some folks (Raevmo, for example in the thread you linked to) have failed to understand is that information of the kind we are discussing does not exist simply by virtue of a physical object existing.
Curiosity piqued, looked at thread (goodness, what has happened to Telic Thoughts these days? The last few comments by "Guts", who confirms he still runs it day-to-day, are fascinating! But I digress) and déjà-vu kicks in. Five years on, not much has changed. One hypothesis made me smile. Shame commenters like Zachriel have left the scene. Like Lizzie Liddle, he seemed to have almost limitless patience with obtuse commenters. Alan Fox

At this point it strikes me that what we are really dealing with is putting up heavy flak to protect a critical vulnerability, through selective hyperskepticism.
And sometimes everyday speech just fails at making any sense! :) Alan Fox

For example, if there is a cube sitting on my desk, it does not “contain” or “have” information. Now if I observe the cube and then describe for someone else the cube’s appearance, colors, size position, and so on, then I by my mental act have created information. All of those aspects of my description — embedded the language or code I used — are information.
But have you said anything useful here? What have you communicated? It's either trivially right or trivially wrong, depending on what you mean by "mental act", "created" and "information". Alan Fox

...absolutely the onus is on you [KN and me, I'm assuming] to clearly articulate WHY the sequences in DNA are not really information. As EA commented earlier, the absolute refusal to acknowledge the patently obvious is telling.
Here is a classic illustration of the problem. Agreeing or disagreeing about whether DNA sequences have some property called information depends absolutely on the meaning of "information" in the context. Give me a clear operational definition of "information" and I will be able to give you a clear answer which could be "yes", "no", "perhaps", "I don't know" or "your definition is unworkable" depending on how "information" is defined in the context. In everyday speech, I would have no hesitation in agreeing that any - any - DNA sequence contains information. Alan Fox

F/N: Since this is playing out across threads, I will post substantially the same content here as elsewhere, by way of a challenge to objectors to address on the merits. Identity of indiscernibles, SEP. Second, observe the issue of different specific instantiations of an underlying general pattern or type. Where, as has been REPEATEDLY highlighted across the months since UB has put the issue on the table:
code (kd)n. 1. A systematically arranged and comprehensive collection of laws. 2. A systematic collection of regulations and rules of procedure or conduct: a traffic code. 3. a. A system of signals used to represent letters or numbers in transmitting messages. b. A system of symbols, letters, or words given certain arbitrary meanings, used for transmitting messages requiring secrecy or brevity. 4. A system of symbols and rules used to represent instructions to a computer; a computer program. 5. Genetics The genetic code. 6. Slang A patient whose heart has stopped beating, as in cardiac arrest. v. cod·ed, cod·ing, codes v.tr. 1. To systematize and arrange (laws and regulations) into a code. 2. To convert (a message, for example) into code. v.intr. 1. Genetics To specify the genetic code for an amino acid or a polypeptide. 2. Computer Science To write or revise a computer program. 3. Slang To go into cardiac arrest. [Middle English, from Old French, from Latin cdex, book; see codex.] The American Heritage® Dictionary of the English Language, Fourth Edition copyright ©2000 by Houghton Mifflin Company. Updated in 2009. Published by Houghton Mifflin Company. All rights reserved.
A reasonable dictionary will summarise typical usages. It should be quite clear, from what a code is and does, that the genetic code is just that. Those who want to put up heavy clouds of rhetorical flak in objection need to take up an argument with, say, Sir Francis Crick, from as early as 1953:
"Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)" [March 19, 1953 remarks to his son.]
Indeed, let us note that the notoriously ideological Wikipedia, on this subject, against what seems to be the obvious interest of fending off implications of semiotics, is forced to speak as follows on the genetic code:
Genetic code The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. Biological decoding is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms, and can be expressed in a simple table with 64 entries. The code defines how sequences of these nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions,[1] a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid . . . . Not all genetic information is stored using the genetic code. All organisms' DNA contains regulatory sequences, intergenic segments, chromosomal structural areas, and other non-coding DNA that can contribute greatly to phenotype. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code.
In short, there are multiple codes involved in the genetic process that creates the specific body plan of a given organism in a given environment and also supports the associated key life processes. And, on biosemiotics, the same Wikipedia is reduced to saying:
Biosemiotics (from the Greek bios meaning "life" and semeion meaning "sign") is a growing field that studies the production, action, and interpretation of signs and codes[1] in the biological realm. Biosemiotics attempts to integrate the findings of scientific biology and semiotics, proposing a paradigmatic shift in the occidental scientific view of life, demonstrating that semiosis (sign process, including meaning and interpretation) is its immanent and intrinsic feature . . . . To define biosemiotics as “biology interpreted as sign systems study” is to emphasize not only the close relation between biology as we know it (as a scientific field of inquiry) and semiotics (the study of signs), but primarily the profound change of perspective implied when life is considered not just from the perspectives of molecules and chemistry, but as signs conveyed and interpreted by other living signs in a variety of ways, including by means of molecules. In this sense, biosemiotics takes for granted and respects the complexity of living processes as revealed by the existing fields of biology – from molecular biology to brain science and behavioural studies – however, biosemiotics attempts to bring together separate findings of the various disciplines of biology (including evolutionary biology) into a new and more unified perspective on the central phenomena of the living world, including the generation of function and signification in living systems, from the ribosome to the ecosystem and from the beginnings of life to its ultimate meanings. Furthermore, by providing new concepts, theories and case studies from biology, biosemiotics attempts to throw new light on some of the unsolved questions within the general study of sign processes (semiotics), such as the question about the origin of signification in the universe. Here, signification (and sign) is understood in a very general sense, that is, not simply the transfer of information from one place to another, but the generation of the very content and meaning of that information in human as well as non-human sign producers and sign receivers. Sign processes are thus taken as real: They are governed by regularities (habits, or natural rules) that can be discovered and explained. They are intrinsic in living nature, but we can access them, not directly, but indirectly through other sign processes (qualitative distinction methods, for instance) – even though the human representation and understanding of these processes (in the construction of explanations) builds up as a separate scientific sign system distinct from the organisms’ own sign processes. One of the central characteristics of living systems is the highly organized character of their physical and chemical processes, partly based upon informational and molecular properties of what came to be known in the 1960s as the genome. Distinguished biologists, such as Ernst Mayr and Manfred Eigen have seen these informational aspects as one of the emergent features of life as a process that distinguish life from anything else in the physical world, except, perhaps, man-made computers. However, whereas the informational teleology of computer programmes is derived, by being designed by humans to achieve specific goals, the teleology and informational characteristics of organisms are intrinsic to them and evolve naturally. Traditional biology (and philosophy of biology) has seen such processes as being purely physical and, being influenced by a reductionist and mechanistic tradition, has adopted a very restricted notion of the physical as having to do with only efficient causation. Biosemiotics uses concepts from semiotics (in the sense of C.S. Peirce as the broad logical and scientific study of dynamic sign action in humans as well as elsewhere in nature) to answer questions about the biological emergence of meaning, intentionality and a psychical world. These questions are either hard to answer or completely incoherent within a purely mechanist and physicalist framework.
Obviously, Wikipedia is trying to absorb the implications of sign systems in its typical materialistic context, but that does not detract from the force of what it has had to concede. At this point it strikes me that what we are really dealing with is putting up heavy flak to protect a critical vulnerability, through selective hyperskepticism. KF kairosfocus

As you point out, it suggests, “I can’t conceive of any other explanation,” but it also asks, “can you conceive of one?” Do you think it is not a fair question?
Fair, yes. But... We are all deeply into semantic a communication issues here. This is why in a factual or scientific discussion, it is imperative do define the concepts we are talking about. Depending on how "code" is defined, both "A DNA sequence is a code" and "A DNA sequence is not a code" could be factually correct. I see no communicative element in the chemical processes that occur when DNA sequences are transcribed into RNA and translated into polypeptide sequences. It's all a result of the inherent physical and chemical properties of the interacting molecules.
You are saying that no such thing as communication takes place because that kind of activity is something that only humans do (mutual exchange of thoughts and ideas) and we should not be using that kind of language to describe cell activity. Is that a fair account of your objection?
Sort of. The problem here, as with "semiotic" and "code" is how you define the concept. That gives us the set boundaries so we can then decide what is and isn't a member of the set we have defined. To lump chemical processes in with aspects of linguistics is such a stretch that any set that encompasses both is large enough and fuzzy enough to be meaningless.
Do we agree that cells need to be (informed?-instructed?-prompted?) to know which role to play and how to play it. Or are the words “informed” and “know” too strong (too human-like)? If so, what words would you use?
At the cellular and sub-cellular level and consequently and cumulatively at the level of the organism there is a huge amount of communication going on. It is chemical communication. Evo-devo is a fascinating subject and how embryos develop by orchestrated cell growth, death and differentiation is a very fertile area of research. I am sure the field has plenty of jargon now and one would need to be aware of contextual use of words and be aware of operational definitions when reading the primary literature. Obviously I think using "know" in relation to chemical processes is anthropomorphic but defining the term in context is acceptable.
Do we agree that the “instructions” providing the necessary “information” for the organism’s development reside in the cell’s nucleus as a DNA molecule? If the words “instruction” and “information” are too strong too anthropomorphic) to express that relationship, what words would you use?
I think you should be able to work out what my answer is here. Years ago there was a BBC radio program called "The Brains Trust" where a panel of experts answered question from the audience. One panel member, Professor C. M. Joad, was noted for often prefacing his answers with "It all depends what you mean by [some key word in the question]". So, in any discussion where the intent is to communicate effectively and honestly, first define your terms.
Do we agree that a DNA molecule “encodes” a detailed set of plans for building different parts of the cell. If “encode” is too strong (human-like) of a verb, what verb would you use?
Most assuredly, not! Talking of "building plans" is a total misunderstanding in what goes on when a zygote develops into an adult organism (though there is no reason to limit this to sexually reproducing eukaryotes). There is nowhere in the genetic material where anything resembling an overall plan can be found. Evo-devo again. "Encode" could be used as a defined shorthand for some step in the chemical processes that go on in the cell, of course. Maybe there is a scientific definition in the context of biochemistry. Ther'es no reason not to use a word so long as it is clearly defined at the start. The problem is when words are bandied around and party A and party B have completely different concepts in mind. What is inexcusable, as it wastes everyone's time and marks some as dishonest, is to continue to equivocate over meanings when a misunderstanding over use of words occurs. Alan Fox

Mung @181: One thing some folks (Raevmo, for example in the thread you linked to) have failed to understand is that information of the kind we are discussing does not exist simply by virtue of a physical object existing. For example, if there is a cube sitting on my desk, it does not "contain" or "have" information. Now if I observe the cube and then describe for someone else the cube's appearance, colors, size position, and so on, then I by my mental act have created information. All of those aspects of my description -- embedded the language or code I used -- are information. But an object does not have information or contain a code by its mere existence. This distinction is critical. Otherwise folks get off on all sorts of red herring tangents -- arguing that distant stars, the rings of Saturn, solar flares and so on contain "information." So what is so special about the information in DNA, the faulty thinking goes . . . Eric Anderson

Amazon Mung

Definition of a code: Given a source with probability space [Omega, A, p(A)] and a receiver with probability space [Omega, B, p(B)], then a unique mapping of the letters of alphabet A onto letters of alphabet B is called a code. Here p(A) is the probability vector of the elements of alphabet A and p (B) is the probability vector of the elements of alphabet B. (Perlwitz, Burks and Waterman, 1988) http://telicthoughts.com/misusing-natural-selection/#comment-205035 Yockey Mung

@ AF & KN That DNA relates to polypeptide sequence through a code (I.e. the "genetic code") is a basic, empirically know fact of biology. Additionally it is also known that there are variant genetic codes, so the basic point of Barry's post is known by direct observation to be true. There is nothing in chemistry or physics that forces the code to be what it is. Specific permutations of the four nucleotide bases taken three at a time are mapped to specific amino acids (of the twenty available). That is a code by any reasonable definition, consistent correspondencies between distinct character sets. That DNA is a molecule in no way detracts from the fact that it is part of a coding system. That is emphatically distinct from the order commonly seen to arise spontaneously in the natural world (snow flakes, convection currents, water funnels, etc.) Asserting that the genetic code is mere order (as opposed to a form of complex, specified organization) is to evince a fundamental lack of comprehension concerning the relationship of information theory to biology.You're free to challenge that knowledge, but absolutely the onus is on you to clearly articulate WHY the sequences in DNA are not really information. As EA commented earlier, the absolute refusal to acknowledge the patently obvious is telling. Optimus

Alan Fox @174: You are correct, of course, that DNA itself is not a code. It contains information that is written in a code. The information stored on it is stored according to the requirements of the code. When people say DNA is a code, that is probably not the best way of describing it. However, when I read such statements I realize the individual means that DNA contains sequences coded according to the genetic code. A code itself is non-physical (although it can be stored/represented in physical media). -----
DNA sequences translate to specific protein sequences by chemical interactions.
I hope you aren't saying that specific protein sequences arise automatically by chemical reactions once the sequence of nucleotides is exposed? There is a whole system in place that takes the 4-character digital code and translates it on the basis of the genetic code into a subsequent physical chain of amino acids. This does not just happen by chemistry. The translation (and it is not just called that by analogy, it is really what is going on) is precisely one of the things that highlights the semiotic nature of the system we are dealing with. Eric Anderson

Alan Fox
"What else” uttered in a rhetorical way simply suggests “I can’t conceive of any other explanation so my preferred explanation is true by default”.
Well, it's a question, so it suggests two things: As you point out, it suggests, "I can't conceive of any other explanation," but it also asks, "can you conceive of one?" Do you think it is not a fair question?
What else” was the phrase Stephen. Your list is not exhaustive.
Very true. I limited my number of questions to only those subtopics that speak to your objection.
"c) is anthropomorphizing nonsense. DNA sequences translate to specific protein sequences by chemical interactions. d) ditto. Nonsense"
OK, I think I understand. You are saying that no such thing as communication takes place because that kind of activity is something that only humans do (mutual exchange of thoughts and ideas) and we should not be using that kind of language to describe cell activity. Is that a fair account of your objection? That prompts a few follow-up questions. Do we agree that cells need to be (informed?-instructed?-prompted?) to know which role to play and how to play it. Or are the words "informed" and "know" too strong (too human-like)? If so, what words would you use? Do we agree that the "instructions" providing the necessary "information" for the organism's development reside in the cell's nucleus as a DNA molecule? If the words "instruction" and "information" are too strong too anthropomorphic) to express that relationship, what words would you use? Do we agree that a DNA molecule "encodes" a detailed set of plans for building different parts of the cell. If "encode" is too strong (human-like) of a verb, what verb would you use? StephenB

Alan Fox:
c) is anthropomorphizing nonsense. DNA sequences translate to specific protein sequences by chemical interactions.
Please tell us of the chemical interactions that determined the gentic code. Or just admit that bit is just nonsense. And yes Alan, "what else" proved your position had nothing OR ELSE you would have posted some evidence to refute SB. Joe

Hopefully Joe will understand too! Alan Fox

And just to explain it so Joe can undertand: "What else" uttered in a rhetorical way simply suggests "I can't conceive of any other explanation so my preferred explanation is true by default". Alan Fox

But a) is wrong. DNA is a molecule, not a code. b) is right but it is also almost universal among all living organisms and another important property of the genetic code is that there is no ambiguity. Any DNA sequence will in principle translate to a protein sequence c) is anthropomorphizing nonsense. DNA sequences translate to specific protein sequences by chemical interactions. d) ditto. Nonsense e) depends what you mean by communicative systems. Sounds like "only red things are red". Alan Fox

Alan Fox:
“What else” was the phrase Stephen. Your list is not exhaustive.
Trying to get through to you and your ilk is getting exhaustive. There are singularities that are less dense than you. Just sayin'... Joe

"What else" was the phrase Stephen. Your list is not exhaustive. Alan Fox

StephenB: "What else, other than a communicative semiotic system, could communicate assembly instructions?" Alan Fox: "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”. The word "that" doesn't tell me what it is that you disagree with. Pronouns are hard to follow. Which of the following do you dispute: [a] DNA is a code. [a] the code is arbitrary. [b] the code communicates by issuing assembly instructions. [d] assembly instructions require communication. [e] only a communicative system can communicate. Please be specific. StephenB

KF: @168 & @169 Awesome, thanks for that insight. I will research this further. As I mentioned @116, It seems to me that either scenario (ribosomes, the design of which IS the translation information/mechanism OR ribosomes that can be programmed/reprogrammed) would be difficult [impossible] to account for in neo-Darwinian terms- Particularly in light of differences in the code throughout various lifeforms. For such a tangible manifestation of the arbitrary nature of the code's symbol-to-action relationship to exist on both ends of the message's sending and receiving compounds the difficulties for neo-Darwinists it seems to me. Alan Fox: For my own benefit if nothing else, from your view and adopted philosophies, how have you dealt with the significance of this matter? I am curious how given the above from KF, one can still discount that there are instantiations of codes in biology. I might be able to allow for some wiggle room and quibbling had the translation information been inherent within the design of the ribosome itself. But if ribosomes need to in effect be programmed to use the same code, to in essence be speaking the same language, as the DNA, I am not sure how one can conceptually get way from it not just being similar to a code, but in fact being a code- in the sense as described in the OP and UB's original post. MrMosis

F/N: the genetic code is blatantly a code save to those whose view pivots on not admitting the fact. Instantiation, not analogy. Providing instructions acted upon informationally -- recall the key is that the tRNA is loaded with an enzyme at a universal CCA- coupler, and once there is a key-lock prong fit, the correct tRNA sits on the mRNA and clicks to the AA chain. Next in sequence etc. However, at this stage I am fairly sure that we are dealing with those who will go down screaming that it is different as it MUST be different, or their view crashes in flames. So, tell us AF, WHY, specifically and without begging questions, should this be different from what we commonly use codes in machines for? In so doing, kindly explain why from 1953 on starting with Crick, it was seen as a code and why this view that is so common, is mistaken. KF kairosfocus

MM: In brief, the assignment is not in the Ribosome at all. This is only the machine that sets the framework. It is the universal CCA- coupler in the tRNA that is loaded with the relevant amino acid. The loading on this, is in the "loading" enzyme. That is, if the tRNA is reprogrammed by a different loading enzyme -- hard to build as this is a complex protein -- there will be a different loading. However, that in turn will require reprogramming of the DNA. If you observe, all along the key linkages are informational, especially the CCA- coupler. KF kairosfocus

Alan Fox:
Thanks for the responses, Joe. As it is Upright Biped’s “argument”, I will wait and let him answer for himself.
I understand the argument, Alan. Why do you want to make this into something personal with UB? That makes you sound like a spoiled brat... Joe

Thanks for the responses, Joe. As it is Upright Biped's "argument", I will wait and let him answer for himself. Alan Fox

Re: bornagain77 Thank you very much for the links and comments. I have done a quick perusal and I am eager to review the material in depth. That's quite a homework assignment you gave me! NeilBJ

Alan Fox:
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”.
How can you dispute that when it is obvious to everyone else that codons REPRESENT amino acids, they do not become them? IOW your "dispute" is nothing but your personal incredulity- "I don't believe the genetic code is semiotic!" Joe

Alan Fox:
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.
Yes, by design, Alan. Joe

Alan Fox:
Now tell me why this is not a default argument.
Because it doesn't match the definition of the word "default".
“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.
Geez, Alan, you could always just step forward and demonstrate otherwise. You have all the power to refute Intelligent Design! But I will ammend what you posted: 1- There isn't any law that determines the genetic code 2- We can't demonstrate that blind and undirected processes can put such a thing together 3- We have direct observation of and experience with, agencies creating and using arbitrary codes
Can I find anything out about this “agency”?
Maybe. As I have been telling you for years, reality dictates that in the absence of direct observation or designer input, the only possible way to say anyting scientific about the designer(s) or the specific process(es) used, is by studying the design (and all relevant evidence) in question. Write that down, Alan. And guess what? ID is all about the detection and then study of design in nature. The DESIGN, Alan.
Is this agency subject to the same “laws” that the rest of reality is subject to?
The DESIGNS appears to be. Don't know how studying the DESIGNS will help us answer that. Can your position even explain those "laws"? Joe

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.
Now that's funny. Alan Fox takes issue with a perceived insult to an individual by insulting an entire nation! It's OK Alan, I forgive you. Nighty night! ;) Chance Ratcliff

No that's really OK, Phil. I understand and forgive you. Night now. Alan Fox

It's well past my bedtime here. I'll look in tomorrow if I have time. Alan Fox

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_M bornagain77

Thanks for the apology, Phil. Now hush while I listen to Biped. Alan Fox

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

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

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

"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

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

...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

correction: I think you got your whose canards are whose canards mixed up, bornagain77

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 organelle Alan Fox

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

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

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

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

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

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

This is the very thing that I dispute about UB’s “argument”.
Feel free to engage the details. Upright BiPed

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

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

@ 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

...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

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://uncommondesc.wpengine.com/intelligent-design/jerry-coyne-and-poisoning-the-well/#comment-441150 bornagain77

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

...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

@ 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

@ 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

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

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

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. KF kairosfocus

@ 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

In the curious case of the recently discovered spider that builds a model of its self in its web (a model of a bigger, scarier version of itself, wasn't it?), that serves some purpose I am not entirely sure about, I couldn't help but wonder.... Of all possible scary [effective] designs, why should one that even remotely resembles the spider itself ever be arrived at? How many designs need to be searched to allow the feedback mechanism of selection to arrive there? When its ancestors were first inclined to start putting bits of trash into their webs, I wonder what sorts of messes they made of things. I wonder how many quadrillions upon quadrillions of spiders had to die along the way to today, because their instincts were stupid enough to think that a green scarecrow spider made of bits of plant material would not suffice? Or mock dismembered spiders, scattered about the web. MrMosis

MM: Hard to believe that was not so long ago. 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? KF kairosfocus

#118,
Here’s an early one of mine that UB picks up on here: Interactions between molecules involve their chemical properties; charge, conformation, level of hydrophilic and lipophilic residues etc. Nothing analogous to language goes on here.
Alan, if you'll take a moment to write your name across a piece of paper, you will find that the ink adheres to the paper as a product of their physical and molecular properties. There is nothing analogous to language that goes on there. But then again, no one is suggesting otherwise. The semicoductors in your computer are following physcal law. Your eardrums and vocal chords follow physical law. The teletype and the piano follow physcial law. The trivial fact that all matter (including information systems) conforms to natural law is hardly an impediment to my argument. Perhaps in place of simply repeating empty retorts, you could attempt to understand why they are empty. Upright BiPed

RE: Alan Fox post #114 So if the bees have an innate ability to recognize the communication signals from the dance, that would imply pre-programming wouldn't it? Assuming that information such as distance and direction are conveyed by the dance, that would require the bees have at least; knowledge of self, knowledge of others (implicit with knowledge of self, a.k.a. if not self, then others), and a knowledge of abstract concepts. At least to a small degree. The bee would need to know how to recognize the proximate (assuming the dance doesn't provide exact measurements) distance and direction (abstract concepts associated with spatial relations) of food with respect to itself (knowledge of self), as is communicated by the dance. The bee who is performing the communication, must be sophisticated enough to obtain the necessary measurements to communicate to the crowd. Assuming inheritance as the mechanism to preserve and transfer programming, and natural selection as a means for deriving new algorithms; wouldn't it be required that natural selection have the necessary fore-knowledge to generate the needed algorithms? Or at the very least enough knowledge of the existing algorithms to adapt the algorithms for use? ciphertext

AF quoted by Axel:
‘The behaviour is innate, therefore heritable and subject to natural selection.’

No. Their behaviour would be the product of unreflective intelligence, infused by the Creator. What we are pleased to call ‘instinct’.
Instinctive and innate are synonyms. If you think about it for one moment, you must surely agree that all multicellular sexually reproducing organisms pass through the bottleneck of the zygote and it must follow that innate (or if you prefer instinctive) behaviour is stored somewhere in the zygote. Alan Fox

RE: Alan Fox post #108 & 109 So based upon my limited knowledge of immunology, an antibody has been created by a "B Cell" that can attach itself to one of many "kinds" of antigens. A "novel" antibody is one that has been created by a "B Cell" that can attach to an antigen that until now, would migrate through the human body unmolested by the immune system. Is this considered novel because previously there were no B-Cell's in existence which could generate this antibody? If so the question then becomes, did the B-Cell operated outside its programming by generating an antibody that it isn't supposed to generate? I'm a bit fuzzy on whether the helper t-cells can trigger a B-Cell to produce an antibody other than the antibody for which it (B-Cell) was constructed to produce. Or, if the Bone Marrow must first generate a B-Cell specific to an antigen encountered by other cells in the immune system. Either one of those (helper t-cell or bone marrow) would be vectors for the instruction set to generate novel antibodies. ciphertext

Alan Fox:
the bit about the genetic code being semiotic seemed pretty much nonsense to me.
Yes, facts and reality do appear to be nonsense to you. Strange, that. Do codons become their respective amino acids or do they represent them? Joe

OK, Frenchie... Renard, it shall be. Axel

'The behaviour is innate, therefore heritable and subject to natural selection.' No. Their behaviour would be the product of unreflective intelligence, infused by the Creator. What we are pleased to call 'instinct'. Axel

No, Reynard. Just the application of reason. Zen is the antithesis.
Well I am as sceptical of William's ability to reason without reference to the real world as I am badly versed in the tenets of Zen Buddhism. BTW my old pseudonym was Renard. Alan Fox

Here's an early one of mine that UB picks up on here:
Interactions between molecules involve their chemical properties; charge, conformation, level of hydrophilic and lipophilic residues etc. Nothing analogous to language goes on here.
Alan Fox

'That’s very Zen.' No, Reynard. Just the application of reason. Zen is the antithesis. Axel

KF: @25 you replied to my comment @17 for which I am most appreciative. But I believe I did an insufficient job wording my question initially. I am not 100% confident that I am interpreting your reply correctly, so I am therefore not certain that I got my point across @17. Let me add/rephrase: In whichever context makes this question most accessible (perhaps eukaryotic mRNA and ribosome complex (and constituent parts) doing their thing in cytoplasm) If the hypothetical lookup table (whether an actual table, or instead, something analogous which accomplishes the same- a mapping of codons to AAs, stop/start control, etc.) in the ribosome actually exists, (1) could one or more values of the table be altered with the effect of changing said mappings, without altering the fundamental design of the ribosome itself? OR Rather, (2) is the mapping instead inherent within the given model of ribosome in question, such that the given design/model of ribosome in fact IS the lookup table itself? In the latter case, a change to the mappings would mean a change to the design of the ribosome in the given context. In the case of the former, it seems to me that the ribosome's design could remain wholly or at least partially unchanged when the mappings are changed. In either scenario, it seems to me that most types of changes to the codes/mappings whether within a population or even just an individual organism are wholly intractable conceptually. And either case is difficult to give a naturalistic/stochastic account for, whether you receive: (2)deterministic/mechanistic, hardware decoding machines (ribosomes) from your mother, along with instructions and facilities to synthesize more of the same hardware decoders (which will abide by the same code), OR (1)pre-programmed, non-deterministic, programmable decoding machines (ribosomes) from your mother, along with instructions and facilities to synthesize and program more of same, of course programmed to use the same code/mappings. I used to think these might be dumb questions, but it now seems to me that the knowledge needed to answer them is not as widely disseminated as I'd imagined. And of course all of this putting aside for the moment that mere sequences are increasingly seeming to tell less and less of the story of the organism, as far as I can tell. MrMosis

Alan Fox, who on numerous occasions has both admitted and demonstrated ignorance concerning Upright BiPed’s argument, now says it’s the same as the one presented by Kantian Naturalist. Something stinks.
I think we can track down enough of my comments here and elsewhere to establish that while I couldn't grasp the rest of his argument, the bit about the genetic code being semiotic seemed pretty much nonsense to me. Alan Fox

[Bees]possess the ability to both learn and teach the technique to other bees.
It is easy to observe that bees neither learn nor teach the "bee dance" communication (that incidentally happens in complete darkness and is transferred by touch (smell may also be involved). The behaviour is innate, therefore heritable and subject to natural selection. Alan Fox

Alan Fox, who on numerous occasions has both admitted and demonstrated ignorance concerning Upright BiPed's argument, now says it's the same as the one presented by Kantian Naturalist. Something stinks. Mung

RE: Kantian Naturalist at post #102 It might be possible to weaken (3) where “linguistic artifact” is replaced with something like “semiotic system”. But then I’m not sure MAID really works. Honeybees communicate through a semiotic system, where the wiggles and circles in their dances communicate the direction and distance of flowers, and they don’t need to be at all intelligent in order to do this, nor need we posit from long-extinct Genius Bee who thought it all up.[sic] Why would the bees not "need to be at all intelligent" to ascribe and derive meaning from the "wiggles and circles" in bee "dances"? It would seem to me that, rudimentary as it may be, the communication established by the dances would require a certain degree of intelligence to be understood, would it not? We could say that such recognition of the "wiggles" and "circles" was an instinctual response, but that would require that the bee was programmed beforehand. However, with the bees ability to discern approximate distance and direction with the dance maneuvers; whatever performed the programming would need to provide each unit (bee) with at least: a universal "bee" standard communication protocol; an understanding of what we commonly refer to as "distance" and "direction"; an algorithm for calculating distance and direction that takes into account characteristics of each unit's environment. This seems to suggest that the pre-programming was accomplished with fore knowledge about the bee specifically, and about the bee's environment generally (concepts of spacial relations). In this view, the bee is not a true "intelligent" being, rather it is just an automaton which has received its programming from an external entity. We could also say that both the recognition of and generation of the "wiggles" and "circles" were emergent communication phenomena (for lack of a better term). That would require the bees to have developed this communication technique on their own, and also to possess the ability to both learn and teach the technique to other bees. This would indicate to me, that the bees are imbued with a level of intelligence. ciphertext

I took the claim to be (3) because I couldn't see how else to get (4) from (1) and (2). Suppose we replaced (3) with the weaker claim, (3'), that the genetic code is a semiotic system, and adjust (1) and (2) accordingly: (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. Likewise for (2'). But (1') is problematic, because while (1') is true, it is surely false that (1'') We have direct, observational knowledge that semiotic systems are only created by intelligent beings 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. 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. Kantian Naturalist

Kantian paraphrases Biped's argument: (1) We have direct, observational knowledge that linguistic artifacts are created by intelligent beings; (2) We have no good reason to believe that the interaction of random events and natural laws can create linguistic artifacts; (3) The genetic code is a linguistic artifact; (4) So, it is overwhelmingly likely that the genetic code was created by an intelligent being. 3 is indeed the point at which the UB argument becomes utterly incoherent. Unfortunately I am constantly told that this is not his argument and that he is misinterpreted. Alan Fox

Or it could mean that a mutated protein occurs that has an entirely different serendipitous function as must happen if evolutionary theory is correct. Alan Fox

What constitutes a “novel functional protein”?
With regard to antibody proteins, that would be a mutated (changed peptide sequence) protein that now binds to a different antigen, as happens as we develop resistance to a new strain of bug. Alan Fox

AF: Once you have to engage core questions of warrant of claims in science, you are inevitably addressing philosophical results and concerns. It is unavoidable and those of us educated in science need to be aware of it. KF kairosfocus

KN: The RNA string is instantly recognisable to those who have had to work at machine code level. It is object code, machine code, here stored in in effect a pattern of Yale Lock like prongs where patterns of prong height store information. And yes, in a very relevant sense, it is a code, complete with dialects and now with intelligent mods used to create artificial proteins. KF kairosfocus

The discussion of antibodies in posts #37 and #38 intrigued me. I'm not familiar with the literature that describes an antibody. What constitutes a "novel functional protein"? If it is indeed an antibody, what about antibodies would be a novel function? Isn't the functionality of an antibody the same regardless of its particular target pathogen or its (antibody) particular shape? ciphertext

Alan Fox:
Nobody I know seems to have grasped it.
Yes, reality is lost on you and your ilk, so you have to pretend to not "grasp" it. And Alan, the literature bluff is that not one of those articles has anything to do with blind and undirected chemical processes producing a termite from a non-termite. Again reality eludes you. Go figure... Joe

Alan Fox:
Honed and perfected by the design process also referred to as natural selection.
Natural selection is just differential reproduction due to heritable random variations. It doesn't design anything. It is incapable of designing. Joe

The discussion has moved on, alas, but I shall attempt to pick up with the discussion that ensued in response to my (6) above. I shall be concerned with three questions: in what sense, if any, is "the genetic code" really a code? if it is a code, what follows? and what is the relation between language and intelligence? (I shall also respond to Bornagain's (10) at the bottom of this comment.) First, I challenged Arrington's assertion that the genetic code is really a code. Now, I don't know semiotics, but I do know a little bit about philosophy of language, and in particular, I know the normative functionalism approach developed by Lewis, Sellars, and Brandom. So that's how I'll approach these issues. When we say "'Hund' means dog," what are we really saying? On the normative functionalist approach to meaning, what we're saying is this: the rules that govern the use of 'Hund' in German are the same as the rules that govern the use of 'dog' in English. (These rules include correctly applying the term to perceived items, drawing the right inferences from the term, and acting correctly. If Heinrich were to say, "Kein Hund ist ein Tier", his conversants would believe that he had failed to master the correct usage of 'Hund', or of 'Tier', or perhaps had failed to understand negation.) Many codes are derivative of their 'home' languages: Morse code follows the rules of English; the Enigma ciphers followed the rules of German. But I'm not sure if that's a sense of 'code' that's relevant here. Point is, in order for something to be a language, there must norms of correct and incorrect use, ways of enforcing those norms, and a community of speakers to do so. There must be an iterative grammar. And so on. One might complain that I'm taking the analogy too seriously. But I think that the defender of intelligent design must take the analogy this seriously in order to introduce the second premise: that, so far as we know, linguistic artifacts are only created by intelligent agents. By "linguistic artifact" I mean some text or document that conveys linguistic information, and that can only be understood if one knows the relevant language. Now, if the claim is taken that way, I have no objection at all. What I was objecting to was the claim that languages themselves are created by intelligent agents. Shakespeare invented Hamlet, not Elizabethan English. Elizabethan English is what Shakespeare used (and, in the process, modified) in order to create Hamlet. Thus construed, the Master Argument for Intelligent Design (MAID) would look like this: (1) We have direct, observational knowledge that linguistic artifacts are created by intelligent beings; (2) We have no good reason to believe that the interaction of random events and natural laws can create linguistic artifacts; (3) The genetic code is a linguistic artifact; (4) So, it is overwhelmingly likely that the genetic code was created by an intelligent being. Reconstructed in this way, my complaint is with (3), not with (1) or (2). If the genetic code is a linguistic artifact, what is its grammatical structure? What are the norms of correct and incorrect use? How are those norms enforced? Who speaks it, and for what purposes? It might be possible to weaken (3) where "linguistic artifact" is replaced with something like "semiotic system". But then I'm not sure MAID really works. Honeybees communicate through a semiotic system, where the wiggles and circles in their dances communicate the direction and distance of flowers, and they don't need to be at all intelligent in order to do this, nor need we posit from long-extinct Genius Bee who thought it all up. Finally, in response to Bornagain at (10): Kim's critique of "non-reductive physicalism" works in response to his targets -- Donald Davidson and Hilary Putnam -- but my view is not theirs. My view comes out of Merleau-Ponty's transcendental phenomenology of embodied perception and to dynamical systems theory. For a response to Kim informed by neurophenomenology and DST, I recommend Embodied Minds in Action by Robert Hanna and Michelle Maiesse. Kantian Naturalist

More evidence that you didn’t read his argument, or if you did, you failed to comprehend it.
Nobody I know seems to have grasped it. Can you dumb it down for me? Alan Fox

Is Alan trying to do philosophy again?
Only inadvertently. Philosophy is hard to avoid on this site. Alan Fox

Alan Fox:
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”).
More evidence that you didn't read his argument, or if you did, you failed to comprehend it. Mung

Is Alan trying to do philosophy again? Has he finally abandoned his self-refuting nonsense? Mung

PS: As for instance Hippocrates of Cos and others have used, sign may be used in the sense of an observable feature, behaviour or the like that helps ground inference to an underlying state, to one who is observant and knowing, such as a clinical diagnostician. kairosfocus

F/N: Re semiotics: Merriam- Websters: >> : a general philosophical theory of signs and symbols that deals especially with their function in both artificially constructed and natural languages and comprises syntactics, semantics, and pragmatics >> AmHD: >> se·mi·ot·ics also se·mei·ot·ics (sm-tks, sm-, sm-) n. (used with a sing. verb) The theory and study of signs and symbols, especially as elements of language or other systems of communication, and comprising semantics, syntactics, and pragmatics. semi·o·tician (--tshn) n. The American Heritage® Dictionary of the English Language, Fourth Edition copyright ©2000 by Houghton Mifflin Company. Updated in 2009. Published by Houghton Mifflin Company. All rights reserved. >> Collins: >> semiotics, semeiotics [?s?m???t?ks ?si?m?-] n (functioning as singular) 1. (Linguistics) the study of signs and symbols, esp the relations between written or spoken signs and their referents in the physical world or the world of ideas See also semantics, syntactics, pragmatics 2. (Medicine) the scientific study of the symptoms of disease; symptomatology Also called semiology semeiology Collins English Dictionary – Complete and Unabridged © HarperCollins Publishers 1991, 1994, 1998, 2000, 2003 >> David Chandler: >> The concept of the 'code' is fundamental in semiotics. Whilst Saussure dealt only with the overall code of language, he did of course stress that signs are not meaningful in isolation, but only when they are interpreted in relation to each other. It was another linguistic structuralist, Roman Jakobson, who emphasized that the production and interpretation of texts depends upon the existence of codes or conventions for communication (Jakobson 1971). Since the meaning of a sign depends on the code within which it is situated, codes provide a framework within which signs make sense. Indeed, we cannot grant something the status of a sign if it does not function within a code. Furthermore, if the relationship between a signifier and its signified is relatively arbitrary, then it is clear that interpreting the conventional meaning of signs requires familiarity with appropriate sets of conventions. Reading a text involves relating it to relevant 'codes'. Even an indexical and iconic sign such as a photograph involves a translation from three dimensions into two, and anthropologists have often reported the initial difficulties experienced by people in primal tribes in making sense of photographs and films (Deregowski 1980), whilst historians note that even in recent times the first instant snapshots confounded Western viewers because they were not accustomed to arrested images of transient movements and needed to go through a process of cultural habituation or training (Gombrich 1982, 100, 273). As Elizabeth Chaplin puts it, 'photography introduced a new way of seeing which had to be learned before it was rendered invisible' (Chaplin 1994, 179) . . . Semioticians argue that, although exposure over time leads 'visual language' to seem 'natural', we need to learn how to 'read' even visual and audio-visual texts (though see Messaris 1982 and 1994 for a critique of this stance). Any Westerners who feel somehow superior to those primal tribesfolk who experience initial difficulties with photography and film should consider what sense they themselves might make of unfamiliar artefacts - such as Oriental lithographs or algebraic equations. The conventions of such forms need to be learned before we can make sense of them. >> In short, UB and BA have a serious point. KF kairosfocus

PS: BTW, no satisfactory and comprehensive precising definition of "life" exists. Should we therefore consign biology -- the study of life -- to the status of pseudoscience? Patently, we do not and for good reason. We can sufficiently identify cases and extend the cases by material family resemblance, and so we use ostensive definition. Going back to the point of the OP, saying does not make it so or not so, but we can be reasonable and seek to align what we say and our conventions to what we find to be real per experience of the world. Intelligence exists, and can be described on sufficient cases and with sufficient precision to be used in a great many scientific and day to day contexts. Design, similarly is real, as real as the design evident in the posts of the objectors. And, we are now down to the point of dealing with self-referential absurdities, as has had to be discussed here. kairosfocus

F/N: As AF and Gregory know or should know, it is in fact reasonably quantifiable and empirically testable to stipulate a threshold of behaviour that per known cases of intelligence and per known limits of accessible atomic resources for blind chance based contingency, will reliably distinguish intelligent and unintelligent cause (where for instance we routinely are understood to be intelligent). Dismissive mockery will not change that fact, but it does underscore that we seem to be dealing with those who have little to say, but an ideological determination to avoid where the evidence is pointing. Per the just linked, we can examine the metric: Chi_500 = I*S - 500, bits beyond the solar system threshold, . . . and stipulate that should Chi_500 go positive, the cause is best explained on intelligence. As for definitions of intelligence, a good enough point of departure is in the UD Glossary, per a rearranged statement in Wiki speaking against known ideological biases:
“capacities to reason, to plan, to solve problems, to think abstractly, to comprehend ideas, to use language, and to learn.”
Let's just say that the attempts to dismiss the reality of intelligence above, require the use of that which is being dismissed. Reductio ad absurdum, driven by ideological a priori. That speaks volumes about the balance of the case on the actual merits when objectors to the design inference are desperately clinging to absurdities, and are resorting to personalities and ridicule. Volumes. KF kairosfocus

By definition, a person who refuses to acknowledge the law of non-contradiction is not reasonable.
Oh, I think unreasonableness manifests itself more broadly. UD Editors: Indeed it does Alan. But refusing to acknowledge the law of non-contradiction is the very acme of unreasonableness. Here’s something else that’s unreasonable: Continuing to comment in a thread when you’ve already tacitly admitted you have nothing to say. Alan Fox

>blockquote>Intelligence: The ability to match means towards an end. That's very Zen. William. Not a measurable property then? You have it or you don't. Or could you have more or less of such an ability? Alan Fox

Alan Fox: “Ban all reasonable people . . .” Actually, I banned only those who refused to acknowledge the law of non-contradiction. By definition, a person who refuses to acknowledge the law of non-contradiction is not reasonable. Barry Arrington

Alan Fox: Intelligence: The ability to match means towards an end. William J Murray

Alan, thank you for confirming in comments 84-88 that you are in fact struck speechless when it comes to making an argument that even addresses (far less rebuts) the argument I made in the OP. You can move along now. Barry Arrington

Oops scuse typo. Trying again:
Alan, the first rule of getting out of holes: “When your in one, stop digging.”
But I notice you didn’t supply a meaningful definition of intelligence. Does anyone else want to try? Alan Fox

>blockquote>Alan, the first rule of getting out of holes: “When your in one, stop digging.” But I notice you didn't supply a meaningful definition of intelligence. Does anyone else want to try? Alan Fox

You have demonstrated that your side quite literally has nothing to say (or at least you, as a representative of your side, has nothing to say).
I am on nobody's side here and I represent nobody but myself. You reap what you sow, Barry. Ban all reasonable people (I wince to recall the treatment meted out to serious and well-meaning professional scientists in OPs and comments here over the years) and you get left with the loonies like me. :) Alan Fox

You’ve spewed a lot of invective into this combox. You’ve sneered. You’ve made several literature bluffs about unrelated topics (all of which have been called). You’ve impugned motives. You’ve attempted to distract attention away from the topic and have tried to change the subject.
Several literature bluffs? One link to Google Scholar? Papers about eusociality in termites. They exist. Where's the bluff? I agree it was off-topic for which I apologise. But I was only responding to other commenters. Alan Fox

“over 3,000? Wow. Now, I’m convinced. Alan, you are addicted to the literature bluff. I call your bluff. Those articles don’t say what you say they say. Now what?
Well, I guess we could examine what I said about what those articles said. All I said was "That link was to Google Scholar listing over 3,000 articles relating to the evolution of eusociality in termites." Just skimming through a sample of the most recent ones gives me no reason to think there is not a huge body of work on the subject. Do you want to argue that it is not so? Shall we take a few examples and look more closely? Alan Fox

Alan Fox writes: “Much has already been said.” That is my very point Alan. You’ve spewed a lot of invective into this combox. You’ve sneered. You’ve made several literature bluffs about unrelated topics (all of which have been called). You’ve impugned motives. You’ve attempted to distract attention away from the topic and have tried to change the subject. Yes, as you say, much has been said. What has not been said is anything even approaching an argument that rebuts the OP. If you had an argument that rebutted the OP, surely you would have made it by now. Thus, the fact that you’ve made no argument demonstrates quite nicely that you have no argument to make. You have demonstrated that your side quite literally has nothing to say (or at least you, as a representative of your side, has nothing to say). Thank you again. Barry Arrington

I agree. Phil, you are a great asset to this site. Alan Fox

No problem MR. Arrington. As they say in the military, it is a target rich environment we are engaging. :) ,,, Thus even someone who makes as many mistakes as I do is bound to hit something no matter where I aim! :) bornagain77

Oops "his argument". Alan Fox

I take your silence as an admission that you’ve got nothing to say.
Much has already been said. Even Upright Biped didn't wish to add anything remotely new to his argument. He simply hasn't made a case for an aspect of DNA synthesis to be grouped in a set of "things that are semiotic". We await operational definitions and the like. We also wonder how is argument is related to the concept of "Intelligent Design". Alan Fox

That you would use your own intelligence (i.e., type a paragraph) to express your incredulity at the concept of your own intelligence shows that you are simply not to be taken seriously.
I merely pointed out the word is meaningless in any objective context. Refute me by giving a meaningful definition. UD Editors: Alan, the first rule of getting out of holes: "When you're in one, stop digging." Alan Fox

BTW Alan Fox and Gregory, I note that neither of you has responded to the argument in the OP other than to sneer at the concept of semiotics. I take your silence as an admission that you’ve got nothing to say. Thank you. Barry Arrington

Barry The voice-in-the-ceiling is a technique reminiscent of David Springer. I am surprised you would want to emulate him. ;) Alan Fox

BA77, thank you for calling Alan Fox’s literature bluffs. You are a treasure.
That's rather a harsh interpretation of my comment in response to Joe claiming there was no work examining Darwinian processes in the development of eusociality in termites. There does appear to be some. Are you agreeing with Joe that there is NO literature supporting the idea that termites evolved from a common ancestor shared with modern cockroaches? Alan Fox

Moreover, it is interesting to note that many (most?) proteins are now found to be multifunctional depending on what overall context (or cell type) that the protein happens to be involved in. Thus, the sheer brick wall that Darwinian processes face in finding ANY novel functional protein to perform any specific single task in a cell is only exponentially exasperated by the fact that proteins are multifunctional, and serendipitously, perform several different 'context dependent' tasks within the cell: Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought: Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival. http://www.sciencedaily.com/releases/2008/11/081102134623.htm Genes Code For Many Layers of Information - They May Have Just Discovered Another - Cornelius Hunter - January 21, 2013 Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms." http://darwins-god.blogspot.com/2013/01/genes-code-for-many-layers-of.html http://www.fasebj.org/content/23/7/2022.full Explaining how a protein can perform multiple roles - Cell Biology - December 18, 2009 Excerpt: It’s been known for more than a decade that some cell proteins can carry out multiple functions. For example, it was discovered in 1999 that the protein TyrRS (explained shortly) participated not only in the building of enzymes, but also could function to stimulate the growth of blood vessels. Discovering that the same protein could perform very different roles opened one of the great new chapters in molecular biology. http://scitechstory.com/2009/12/18/explaining-how-a-protein-can-perform-multiple-roles/ related notes: Epigenetics and the "Piano" Metaphor - January 2012 Excerpt: And this is only the construction of proteins we're talking about. It leaves out of the picture entirely the higher-level components -- tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players. http://www.evolutionnews.org/2012/01/epigenetics_and054731.html With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory - November 2011 Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,, http://www.evolutionnews.org/2011/11/with_a_startling_candor_oxford052821.html What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: "Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements ... take unique meaning from their context.[3]",,, http://www.thenewatlantis.com/publications/what-do-organisms-mean bornagain77

BA77, thank you for calling Alan Fox's literature bluffs. You are a treasure. Barry Arrington

Their behaviour is designed in, Alan, duh.
Ah progress! Of course it was designed in. Termites hatch with their innate behaviours programmed in. Designed, indeed! Honed and perfected by the design process also referred to as natural selection. Alan Fox

Is that photo visible in the public domain?
No comment ;) Alan Fox

Moreover, Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723 ID Scientist Douglas Axe Responds to His Critics - June 2011 - Audio Podcast http://intelligentdesign.podomatic.com/entry/2011-06-01T15_59_43-07_00 Doug Axe Knows His Work Better Than Steve Matheson Excerpt: Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance. http://www.evolutionnews.org/2010/06/doug_axe_knows_his_work_better035561.html Evolution vs. Functional Proteins - Doug Axe - Video http://www.metacafe.com/watch/4018222 It is simply comical to try to envision a Darwinian process trying to find a functional protein in such a rare (1 in 10^77) sequence space: How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html bornagain77

Alan, We already know that you have nothing but snide remarks and cowardly innuendos. Do you really think that helps make your case?
Where do termites go to learn to behave like termites, Joe?
Their behaviour is designed in, Alan, duh. Joe

Mr. Fox, you claim:
Variation in a genetic sequence or allele will result in a novel protein. It may only vary by a single residue but, in my book, that makes it a novel protein.
Well my oh my that's just so very generous of you to grant that for your preferred answer of Darwinian evolution (amazingly the binding proteins are still classified under the same name though). If you could also only be 100th as generous in your considerations for ID you may eventually stop getting egg on your face! 8) Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, http://www.ncbi.nlm.nih.gov/pubmed/19765975 “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009 Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. http://www.evolutionnews.org/2009/10/nature_paper_finally_reaches_t026281.html Wheel of Fortune: New Work by Thornton’s Group Supports Time-Asymmetric Dollo’s Law – Michael Behe – October 5, 2011 Excerpt: Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection. http://www.evolutionnews.org/2011/10/wheel_of_fortune_new_work_by_t051621.html When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://www.biologicinstitute.org/post/18022460402/when-theory-and-experiment-collide Corticosteroid Receptors in Vertebrates: Luck or Design? – Ann Gauger – October 11, 2011 Excerpt: if merely changing binding preferences is hard, even when you start with the right ancestral form, then converting an enzyme to a new function is completely beyond the reach of unguided evolution, no matter where you start. http://www.evolutionnews.org/2011/10/luck_or_design051801.html On top of the lack of proteins to evolve into new shapes and functions What does the recent hard evidence say about novel protein-protein binding site generation. i.e. about the ability of protein with novel functions to combine with other proteins in a meaningful way to do something useful for the cell? “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.” Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”) Waiting Longer for Two Mutations – Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. Generally, when the results of a simple model disagree with observational data, it is an indication that the model is inadequate. http://www.discovery.org/a/9461 “Why Proteins Aren’t Easily Recombined, Part 2? – Ann Gauger – May 2012 Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.” http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2 ,,, This seems to be a severe problems since several binding sites, in the following video, seem to be required in the joining of the domains into a novel functional protein: Two Domain Protein – photo/video (several binding sites seem to be required in the joining of the domains in the photo) http://www.facebook.com/photo.php?v=421708024519477 bornagain77

I am asking about the organism itself, not its behaviour. Keep on like this, Joe, and you are really going to blow your cover! Where do termites go to learn to behave like termites, Joe? Alan Fox

"We may claim to be intelligent though you can’t define intelligence meaningfully and much less can you quantify it." Sure, he's an applied physicist; he can do anything he wants! Pretty much everything looks 'quantifiable' to his eyes. Just don't accuse him of physicalism. "Of course you and I are real. I’ve seen your photo!" Is that photo visible in the public domain? Gregory

…the “theory” of evolution isn’t quantifiable… Alan Fox:
Joe, you are priceless. I swear you must be an evilutionist secret agent!
Typical cowardly non-sequitur. Joe

...the “theory” of evolution isn’t quantifiable...
Joe, you are priceless. I swear you must be an evilutionist secret agent! Alan Fox

And BTW Alan, eusociality is a BEHAVIOUR. I am asking about the organism itself, not its behaviour. How many mutations did it take to get a termite from a non-termite- quantify it, Alan. Joe

Alan Fox:
That link was to Google Scholar listing over 3,000 articles relating to the evolution of eusociality in termites.
Yeah, it's called a "citation bluff". So please point out just ONE article tat demonstrates accumulations of genetic accidents can account for roaches and then termites. So your bluff has been called and we all know how you will respond. Joe

Alan Fox:
We may claim to be intelligent though you can’t define intelligence meaningfully and much less can you quantify it.
Yet "intelligence" has been defined meaningfully and seeing that the "theory" of evolution isn't quantifiable I do not understand Alan's point wrt "quantify it".
It does not follow that “Intelligent Designers” (Sorry, Gregory, not sure where we are with capitalization) float about incorporeally interacting with the real world at opportune moments.
True, THAT follows from the evidence. And if you had any evidence that blind and undirected processes can produce what we say is designed, then you win and we lose. So perhaps you should get to work. Joe

...there wasn’t anything in your link that says anything about blind and undirected processes producing a termite from a non-termite. No one even knows how to test the claim.
That link was to Google Scholar listing over 3,000 articles relating to the evolution of eusociality in termites. That you can skim through and dismiss 3,000 articles in the space of a few minutes is pretty impressive, Joe. I don't need to speculate further about the quantity of your intelligence! UD Editor: "over 3,000" Wow. Now, I'm convinced. Alan, you are addicted to the literature bluff. I call your bluff. Those articles don't say what you say they say. Now what? Alan Fox

I guess this means AF, author of the cited, is imaginary, too.
KF conflates the real and the imaginary again! Of course you and I are real. I've seen your photo! We may claim to be intelligent though you can't define intelligence meaningfully and much less can you quantify it. It does not follow that "Intelligent Designers" (Sorry, Gregory, not sure where we are with capitalization) float about incorporeally interacting with the real world at opportune moments. That's imagination at work. UD Editor: That you would use your own intelligence (i.e., type a paragraph) to express your incredulity at the concept of your own intelligence shows that you are simply not to be taken seriously. Alan Fox

Alan Fox:
Variation in a genetic sequence or allele will result in a novel protein.
Maybe and maybe not. However your position cannot account for genetic sequences nor alleles nor proteins. It needs to start with all of those already in place. Joe

Darwinian processes can’t account for termites. Alan Fox:
Oh really?
Really and there wasn't anything in your link that says anything about blind and undirected processes producing a termite from a non-termite. No one even knows how to test the claim. So perhaps you should stop with your equivocations already. Joe

PPS: "likely" and "may have" and "particularly persuasive" and "likely" again are just so story markers, not the sort of empirical warrant required. (I cite the first link in the above linked.) kairosfocus

BTW I don't mind discussing aspects of evolution but it does seem almost a deliberate distraction from the OP, semiotics and whether there is any substance to a semiotic argument relating to DNA. Alan Fox

No novel functional proteins listed there
Back we go to "it all depends what you mean by..." semantics. Variation in a genetic sequence or allele will result in a novel protein. It may only vary by a single residue but, in my book, that makes it a novel protein. And if it has some function, the same or different from its alleles then it is functional. If it has a new function it is doubly novel! Alan Fox

PS: Just so stories do not hack it. Start from empirically warranted chem evo then go up from there to empirically grounded blind watchmaker origin -- step by functional, fixed advantageous step up Mt Improbable -- of multicellular body plans including arthropods, then onwards to termites. kairosfocus

Re AF:
“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.
I guess this means AF, author of the cited, is imaginary, too. Or at least his intelligence and agency that equip him to design and effect that bit of FSCI. In short, self-referentially incoherent. Cf here, this morning, for more. As for definition, ostensive definition by pointing out key examples is valid. Case A, humans who write, case two, beavers that build dams adapted for specific circumstances, case gamma, computer designers. On Gamma, I move to the case in the living cell and hold that per what we know of capabilities of chance, necessity and intelligence, and what we can show on monkeys at keyboards, this is best explained on design. Trying to exert his own personal incredulity about the possibility of design in places and times inconvenient for a priori materialism, does not make the cogency of or warrant for that inductive inference conveniently go up in a poof of blue magician's smoke. KF KF kairosfocus

Darwinian processes can’t account for termites.
Oh really? Alan Fox

Alan Fox:
So you’re happy that the selection aspect of biological evolution is occurring with antibody production,
What "selection"? Please be specific. Natural selection doesn't select- you knew that, right?
it’s just the God is directing the variation in plasma B cells.
Nope- 1- ID does NOT require God and 2- The internal programming does the directing- just as it did with "weasel". Joe

Mr. Fox you ask:
Phil, are new antibodies novel functional proteins or not?
And from the reference you cited we find:
Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections - 2012 Excerpt: The mutational patterns revealed recurrent evolution of biofilm specialists from generalist types and multiple adaptive alleles at relatively few loci.,,, two independent mutations in the promoter sequence of bacterioferritin led to an ecological revolution that remodeled the community (Figs. 3 and 4). New mutants of S with up-regulated bacterioferritin (Fig. S2) likely succeeded in other niches (Fig. 3C) because of their enhanced competitive ability for limiting iron, and the mutations enabling invasion were novel wsp alleles,,, Seemingly identical genetic relatives isolated from the same lung at the same time may display distinct differences in the ability to form biofilms and may occur within multiple patients http://www.pnas.org/content/110/3/E250.full
No novel functional proteins listed there,, and from my references we find,,,
Response to Edward Max on TalkOrigins Immunity Article Donald L. Ewert - November 19, 2010 Excerpt: Furthermore no significant new information is being generated by SHM. The nucleotide changes are limited to replacing amino acids that alter the electric forces between two proteins. The specificity of the antigen receptor must remain unaltered or the B cell would be destroyed by cell-suicide or apoptosis. http://www.evolutionnews.org/2010/11/response_to_edward_max_on_talk040661.html
Thus Mr. Fox, why do you misleadingly claim that new functional proteins are being generated in the immune system when even your own reference listed no examples novel proteins but only bounded variations to existing proteins??? If you are having trouble understanding what a new functional protein would actually be, here are some references to help you out: Protein Excerpt: Proteins (pron.: /?pro??ti?nz/ or /?pro?ti.?nz/) are large biological molecules consisting of one or more chains of amino acids.,,, The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass, which is normally reported in units of daltons (synonymous with atomic mass units), or the derivative unit kilodalton (kDa). Yeast proteins are on average 466 amino acids long and 53 kDa in mass.[5] The largest known proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids.[8] http://en.wikipedia.org/wiki/Protein A New Guide to Exploring the Protein Universe "It is estimated, based on the total number of known life forms on Earth, that there are some 50 billion different types of proteins in existence today, and it is possible that the protein universe could hold many trillions more." Lynn Yarris - 2005 http://www.lbl.gov/Science-Articles/Archive/sabl/2005/March/02-protein-universe.html Shoot, no one even really has a firm clue as to exactly how many different proteins reside in a single cell much less all of life; Go to the Cell, Thou Sluggard - March 2011 Excerpt: Calculations indicate that each human cell contains roughly a billion protein molecules.,,, These proteins have a kind of address label, a signal sequence, that specifies what place inside or outside the cell they need to be transported to. This transport must function flawlessly if order is to be maintained in the cell, http://www.creationsafaris.com/crev201103.htm#20110302a Even the most generous of protein classifications, 'folds and superfamilies' yields several thousand completely unique proteins: SCOP (Structural Classification of Proteins) site - gpuccio Excerpt: However we group the proteome, we have at present at least 1000 different fundamental folds, 2000 “a little less fundamentally different” folds (the superfamilies), and 6000 totally unrelated groups of primary sequences. https://uncommondesc.wpengine.com/intelligent-design/uh-oh-is-he-going-to-get-gould-ed/#comment-367564 And despite the abject poverty for evolutionists to produce EVEN ONE example of a single protein being generated by purely material processes, completely unique "Orphan" proteins/genes are found to be ubiquitous (widespread): Orphan Genes (And the peer reviewed 'non-answer' from Darwinists) - video http://www.youtube.com/watch?v=1Zz6vio_LhY Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these "orphan genes" are high achievers (are just as essential as 'old' genes),,, But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn't be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven't-quite the opposite, in fact.,,, The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, "the probability that a functional protein would appear de novo by random association of amino acids is practically zero".,,, Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing. http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf bornagain77

tyhe variation needs to be by chance/ happenstance, in order for it to be darwinian. If the variation arises by design, then it ain’t darwinian.
So you're happy that the selection aspect of biological evolution is occurring with antibody production, it's just the God is directing the variation in plasma B cells. Is that what you are saying? Alan Fox

So humans, beavers, ants, bees, termites, etc., are all imaginary? Alan Fox:
No. But are they all intelligent?
Yes, and I have explained why- they can all manipulate nature for their own purpose.
Are the complex and cleverly designed termite mounds orchestrated by imaginary agents or are they the result of Darwinian processes acting on termite populations over time?
Termite mounds are the result of a designed agency's designing process. Darwinian processes can't account for termites. Wouldn't even know how to test such a claim. Joe

Alan Fox:
are new antibodies novel functional proteins or not?
Yes, but there isn't any evidence to suggest they arose via darwinian mechanisms. Ya see, Alan, tyhe variation needs to be by chance/ happenstance, in order for it to be darwinian. If the variation arises by design, then it ain't darwinian. Joe

Oops just noticed an ommission in my previous comment n° 43 which should read Phil, are new antibodies novel functional proteins or not? The way novel antibodies [form] has been closely studied and widely reported. Reiterated variation and selection is quite obviously at the heart of the process. See here for instance. Alan Fox

So humans, beavers, ants, bees, termites, etc., are all imaginary?
No. But are they all intelligent? And how intelligent is a termite, speaking quantitatively? Are the complex and cleverly designed termite mounds orchestrated by imaginary agents or are they the result of Darwinian processes acting on termite populations over time?
Are you daft, Alan?
Depends what you mean by daft, Joe. Daft enough to respond to one of your comments, anyway :) Alan Fox

Well by golly you are just a treasure trove of cited references instead of bald face assertions aren't you Mr Fox??
Phil, are new antibodies novel functional proteins or not? The way novel antibodies has been closely studied and widely reported. Reiterated variation and selection is quite obviously at the heart of the process. See here for instance. Alan Fox

Alan Fox:
Anyone not emotionally predisposed towards imaginary “explanations”.
LoL! All your position has are imaginary explanations. Your "science" = imagination, Alan. Who do you think you are fooling? Everyone knows that if your position had something, ID would fade away. Yet ID is here are still going strong. Go figure... Joe

Barry: This in turn is important because there is only one known source for a semiotic code: intelligent agency. Alan Fox:
This is the standard argument from incredulity, Barry.
It is a FACT, Alan. How are FACTS an "argument from incredulity"?
But it is not the beginnings of any sort of logical or scientific argument.
YOU, Alan, don't seem to know anything about science nor logic.
A definition of “intelligent agency” that distinguishes between reality and imagination might help.
Something that can manipulate nature for its own purpose.
I simply point out that “intelligent designers” and “intelligent agents” are imaginary, products of the human imagination.
So humans, beavers, ants, bees, termites, etc., are all imaginary? Are you daft, Alan?
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”).
Your only "answer" for anything is to accuse your opponents of being religious. IOW you are just another evo-coward. Joe

HMMM, could you please provide us with the ‘pathetic detail’ of Darwinian evolution producing JUST ONE novel functional protein???
Alan Fox: Antibodies!
How did you determine tat darwinian processes didit? Joe

Well by golly you are just a treasure trove of cited references instead of bald face assertions aren't you Mr Fox?? :) It is interesting to note that many times evolutionists will try to use the highly choreographed mutation/selection process of the immune system itself, claiming that the brilliantly designed immune system is actually proof of evolution. Yet the immune system is almost exactly what we have with the evolutionists claims for 'evolutionary algorithms' in that the immune system is carefully designed from the outset to converge on a solution. It would be surprising, and deadly, if the immune system did not do exactly what it was 'designed' to do: Falk’s fallacy - Feb. 2010 Excerpt: This (the immune system) is one of the most amazing processes ever described.,,, Whatever may be said about it, it is a highly regulated, specified, directed and choreographed process. It is obviously the product of overwhelmingly brilliant design,,, https://uncommondesc.wpengine.com/intelligent-design/falks-falacy/ Response to Kathryn Applegate - Caroline Crocker PhD.- cell biologist and immunologist - October 2010 Excerpt: Diversity of antibodies generated by B cells is due to deliberate, cell-engineered changes in the DNA sequence, not random mutations. In fact, I have never before heard the process whereby functional antibodies are formed (before they encounter antigen) described as mutation. And it is well-known that the appearance of functionality as a result of a mistake-mutation is extremely rare. Of course, after encountering antigen the hypervariable regions of the antibody DNA do undergo somatic hypermutation, but again this is in particular places and is controlled by enzymes.,,, https://uncommondesc.wpengine.com/intelligent-design/comments-on-kathryn-applegate%E2%80%99s-may-posts-on-biologos/#more-15176 Generation of Antibody Diversity is Unlike Darwinian Evolution - microbiologist Don Ewert - November 2010 Excerpt: The evidence from decades of research reveals a complex network of highly regulated processes of gene expression that leave very little to chance, but permit the generation of receptor diversity without damaging the function of the immunoglobulin protein or doing damage to other sites in the genome. http://www.evolutionnews.org/2010/11/response_to_edward_max_on_talk040661.html "A Masterful Feat of Courtroom Deception": Immunologist Donald Ewert on Dover Trial - audio http://intelligentdesign.podomatic.com/player/web/2010-12-20T15_01_03-08_00 In this following podcast, Casey Luskin interviews microbiologist and immunologist Donald Ewert about his previous work as associate editor for the journal Development and Comparitive Immunology, where he realized that the papers published were comparative studies that had nothing to do with evolution at all. What Does Evolution Have to Do With Immunology? Not Much - April 2011 http://intelligentdesign.podomatic.com/entry/2011-04-06T11_39_03-07_00 Irreducible complexity meets multifunctionality in the immune system: Immune system molecule with hidden talents - January 22, 2013 Excerpt: The human immune system is made up of some half a dozen different cell types that are all working in tandem. Team work is key since each cell type has a single unique job to perform, which is central to its ability to help defend the body against invaders and ward off disease. If one of these players is taken out of commission, the entire system is thrown out of whack. This is precisely what Dr. Siegfried Weiss, head of HZI Department of Molecular Immunology, and his team of researchers observed when they looked at immunodeficient mice. "Our 'RAG' mice are lacking adaptive, or acquired immunity," explains Weiss. "Basically, what this means is they are missing their antibody-producing B cells, among others." The dendritic cells belong to a different branch of the immune system - innate immunity, which, although far less pliable, is capable of a fairly rapid response. Which is why these cells should not be affected by a defect in acquired immunity. Still, the scientists noticed that DCs obtained from this particular murine strain were not working properly - their maturation process was faulty and instead of breaking down a pathogen into small pieces, they ended up destroying the pathogen altogether.,,,, "We had no idea that B cells and dendritic cells use immunoglobulins to communicate with each other. It just goes to show you how complex the immune system really is and how we are a long way from truly grasping the full scope of its complexity," http://medicalxpress.com/news/2013-01-immune-molecule-hidden-talents.html Of related note: Immunity bacteria are shown to be species specific (Regardless of the surprising result, Darwinists still insist evolution did it.) Our Microbes, Ourselves: Billions of Bacteria Within, Essential for Immune Function, Are Ours Alone - ScienceDaily (June 21, 2012) Excerpt: Chung repeated the experiment, only this time populating a third group of mice with microbes common to rats. This new group showed the same immune system deficiency as the humanized mice. "I was very surprised to see that," Chung said. "Naturally, I would have expected more of a half-way response." http://www.sciencedaily.com/releases/2012/06/120621130643.htm "Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No. Philip S. Skell - (the late) Professor at Pennsylvania State University. Podcasts and Article of Dr. Skell http://www.evolutionnews.org/2010/11/giving_thanks_for_dr_philip_sk040981.html List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria: http://www.trueorigin.org/bacteria01.asp bornagain77

HMMM, could you please provide us with the ‘pathetic detail’ of Darwinian evolution producing JUST ONE novel functional protein???
Antibodies! Alan Fox

"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.html bornagain77

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

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

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_A bornagain77

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

"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

...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

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

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

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=1111 bornagain77

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

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.) KF kairosfocus

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.) KF kairosfocus

Taken seriously by whom?
Anyone not emotionally predisposed towards imaginary "explanations". Alan Fox

and: scintilla, not scintillation,,, sorry, I must really start to check more carefully before posting,,, bornagain77

correction : even THOUGH they have not one scintillation of evidence that material processes can produce as such?? bornagain77

"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

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

Barry: Great post and good job calling out the "we can't understand what arbitrary means" nonsense. Eric Anderson

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=qTChu5vX1VI bornagain77

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

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 Life bornagain77

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-code bornagain77

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 clarity Optimus

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

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

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

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

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

Wow. Kantian Naturalist just provided reason and proof that I can ignore his/her comments from now on without fear of missing anything important. Mapou

KN writes: “(1) Languages are not codes.” Of course they are. What an absurd statement. The word “dog” is not a dog. It is code for dog. “(2) The genetic code is a code in a metaphorical sense, not a literal one. (The genetic code is not a code in the sense that Morse code is a code.)” Nonsense. The genetic code is an actual code for precisely the reason I explained in the last two paragraphs. You make an assertion (not an argument) to the contrary. Why should anyone heed your assertion when you do not deign to support it with any argument? “(3) There is a causal relation between genes and proteins, because the specific molecular commonalities between triplets and amino acids. This is not obviously the case between the word “cat” and the little critters themselves.” No again. You again make a bald unsupported assertion in place of an argument. You assert that there is some physical relationship between the arrangement of the codons and the amino acids they represent. NO, THERE IS NOT. KN, you are entitled to your own opinions. You are not entitled to your own facts. “(4) There are insurmountable problems with what Ryle called “the ‘Fido’-Fido account” of language . . .” Another bald unsupported assertion. This is a literature bluff. I call your bluff. No, Ryle does not do what you say he does. “(5) Languages are not the products of intelligent agency . . .” Unbelievable. This statement is absurd on its face and requires no rebuttal. “(6) Design, chance, and necessity is a false trichotomy.” OK; I’ll bite. If you are the first one since Aristotle to discover a new causal pathway (a quartum quid) do tell. I’m all ears. Barry Arrington

There are some serious problems here. (1) Languages are not codes. (2) The genetic code is a code in a metaphorical sense, not a literal one. (The genetic code is not a code in the sense that Morse code is a code.) (3) There is a causal relation between genes and proteins, because the specific molecular commonalities between triplets and amino acids. This is not obviously the case between the word "cat" and the little critters themselves. (4) There are insurmountable problems with what Ryle called "the 'Fido'-Fido account" of language, whereas something like that account works perfectly well for explaining the molecular affinities between nucleotides and amino acids. (5) Languages are not the products of intelligent agency, although intelligent agents can deliberately create new languages (Elvish, Klingon, etc.), create codes (e.g. Morse code, Navaho code), and create formal languages (e.g. computing languages). But no one sat down to create Greek, Latin, French, Chinese, or English. So while languaging is something that intelligent agents do, it is not something that they deliberately create, and I would say that no one could create a new language if she didn't already possess one learned at her parents' knees. (6) Design, chance, and necessity is a false trichotomy. Kantian Naturalist

Orlando:
Sorry, but a symbol is not a sign.
It certainly can be.
A symbol cannot be changed without changing its representation (what it represents);
There can be more than one symbol for any given thing. Heck Valentine's Day is coming and there are many symbols of affection.
a sign can be arbitrarily changed independently of what it means.
So "Eat at Joe's" can be changed to "No Parking" and the meaning remains the same? A symbol is something that represents an idea, a process, or a physical entity. A sign is a representation of an object that implies a connection between itself and its object. Signs contain symbols and symbols are a sign of communication. Joe

Orlando Braga brings out an excellent point. Without prior knowledge or a Rosetta stone, it is impossible to extract useful information from signs (arbitrary codes). However, it is possible to extract information from symbols (metaphors, really) through careful analysis. UD: Thread diversion deleted. Mapou

Barry, The semiotic, ie genetic, code refers to the codons (triplets) of RNA that represent an amino acid or STOP (START is represented by an amino acid (met) coding codon). Represent is key because there isn't any physical connection, meaning the codon does not become an amino via some chemical reaction(s). And that means there isn't any law that determines which codon represents what amino acid. There isn't even any law that requires a codon, ie a triplet, to do the job. So that is also arbitrary. What isn't arbitrary is the number of different codons we can get given 4 different nucleotides. That is set at 64- determined by law. And all 64 are spoken for, which could be arbitrary, ie determined by something other than law-> design efficiency perhaps. Joe

Great post, WJM! Optimus

Sorry, but a symbol is not a sign. A symbol cannot be changed without changing its representation (what it represents); a sign can be arbitrarily changed independently of what it means. The symbol has a content in which a determined representation is meant; but the signs are chosen arbitrarily. The symbol, besides the cultural significance which the sign can also have, has a spiritual significance — related to a subjective human experience that acquires an intersubjective meaning — that the sign does not possess. A sign would only be transformed in a symbol when it possesses a content in relation to a representation. A symbol cannot be changed without the disappearance or elimination of its meaning (for example, the Christian Cross); a sign can be changed without loosing its meaning (for example, a traffic sign). UD Editors: The OP has been adjusted to reflect the distinction to which Orlando alludes. Orlando Braga

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