Semiotic theory of ID

Upright BiPed has been proposing what he has called a “semiotic” theory of Intelligent Design, for a while, which I have found confusing, to say the least.  However, he is honing his case, and asks Nick Matzke

…these three pertinent questions regarding the existence of information within a material universe:

  1. In this material universe, is it even conceivably possible to record transferable information without utilizing an arrangement of matter in order to represent that information? (by what other means could it be done?)
  2. If 1 is true, then is it even conceivably possible to transfer that information without a second arrangement of matter (a protocol) to establish the relationship between representation and what it represents? (how could such a relationship be established in any other way?)
  3. If 1 and 2 are true, then is it even conceivably possible to functionally transfer information without the irreducibly complex system of these two arrangements of matter (representations and protocols) in operation?

… which I think clarify things a little.

I think I can answer them, but would anyone else like to have a go? (I’m out all day today).

1,027 thoughts on “Semiotic theory of ID

  1. Upright BiPed on May 14, 2012 at 4:09 pmsaid:

    Dr Liddle,

    Nobody is claiming that A implies B means that B does not imply A, merely that A implies B does not mean B implies A.”

    I am not sure where you’ve been, but Bill’s entire counter-argument is that “B does not imply A”. He began his counter-argument with this observation:

    “Murder victims invariably entail a dead person who does not walk, talk, respirate, or exhibit a heartbeat. In every instance of a murder the world over, throughout all history, these entailments have invariably obtained. Therefore every time we encounter a dead person, who does not walk, talk, respirate, or exhibit a heartbeat, we can conclude the person has been murdered.”

    And after several rounds of discussion, his counter-argument has come to this:

    BIPED : (talking about Bill’s objection) “Then he suggests that the physical entailments of recorded information cannot confirm the existence of a semiotic state. This is the crux of his objection.”

    BILL: Correct.

    And none of that is at odds with what I said, which is that if we know that A implies B, and we observe B, we cannot confirm A.  We cannot refute A either, of course, but the relevant point is that we cannot confirm A.

    Of course if you define “A state” to mean “anything with property B” then you are, a priori, saying that not only does A imply B but B also implies A.

    In which case, obviously, observing B implies A! 

     

    We are merely saying that pointing out that A implies B does not alone allow us to conclude that B implies A.

    What allows us to conclude that B implies A is material evidence. As crazy as it sounds, that is how all empirical disputes are resolved. But this has not been Bill’s gameplan. Bill’s entire goal is to build a box around the semiotic argument so that he does not have to argue over the validity of the material evidence. On one side of the box is a “fatal logical flaw” created just by making the claim (after all, ‘wet ground can’t confirm that it rained’ and ‘not all males are bachelors’). And on the other side of the box is the bald assertion that I am assuming my conclusions. His first objection would result in a situation where claims cannot even be made, and his second objection is wholly unsustainable based upon the content of the argument. 

    It seems to me that you have completely misunderstood what Bill, and everyone else, has been saying.

    Clearly, if it is the case that the only possible cause of wet ground is rain, and if the only possible result of rain is wet ground, then wet ground is evidence for rain, and rain is evidence for wet ground.

    And so, if you define a “semiotic state” as being the state in which A and B are present, then if you observe A and B, then yes, you have evidence of a “semiotic state”. 

    But we have all been willing to grant this.  What we want to know is what you can conclude from defining “semiotic state” in such a way that it embraces both genetic translation and linguistic communication. 

    If we agree to define “a cat” as “a mammal that purrs”, then any mammal that purrs will, by definition, be called, by us, “a cat”.

    You are doing the same thing Bill has been doing, using a loaded analogy to sell a point which does not reflect the actual argument. If you want to argue that the definition of semiosis used in the argument is false, then do it straight up without the false analogies. Otherwise, acknowledge it is correct.

    Well, a number of us consider your use of the word “semiosis” to be a highly loaded analogy!  But leaving that aside, I’m not the slightest bit bothered by your definition of “semiotic state” as long as it does not lead to the fallacious argument-by-analogy that because linguistic “semiotic states” exist between intelligent agents, somehow the genetic transcription process must have something to do with intelligence.

    If that’s not the argument you are making, fine.  If it is, then there’s a problem.

    We are prepared, for the purpose of this discussion, to call such a process “semiotic” (because the tRNA molecules “translate” a “code” into a “meaning”, rather as in language).

    Who is this “we” Dr Liddle? Bill entire argument is that the process cannot be termed “semiotic”. He has been joined in that by every defender on your side of the argument. But does this “we” include you Dr Liddle? Are these not your words: “I do dispute that there is anything “semiotic” about the genetic code.” Elizabeth Liddle 4/18/2012.

    Well, perhaps I should not have used such an inclusive pronoun. My own view is that the word “semiotic” is wildly inappropriate to describe the genetic code.  However, for the purposes of this discussion, I am personally happy to accept your definition of “semiotic state”, as long as you don’t then extrapolate from properties of human symbol usage to biochemical processes.

    The only reason you are “prepared” to call the process “semiotic” is because you have no logical or evidentiary means to deny it – just like the entire remainder of the argument. In fact, within the course of our conversations, you have step-by-step conceded virtually every point made in the argument. Yet, you still don’t exhibit the intellectual integrity to concede that the argument has merit, nor can you sustain a viable argument that it doesn’t.

    Blimey

    Upright BiPed, the only reason I am “prepared” to call the process “semiotic” is because you have defined “semiotic” in such a way that it includes such a process

    You seem utterly confused about the difference between definitions and evidence.  We’ve had this problem right from the beginning of this conversation, when I tried to pin you down to a workable operational definition of information.   Yes, we can define “semiotic” so that the word includes the processes by which an mRNA molecule is part of a chain of catalytic processes, the endstate of which is a protein that it is completely specified by the specific sequence of that mRNA molecule.

    And not one person here denies the evidence that this cascade of processes, termed “translation”, takes place in a cell, nor that the sequence of mRNA bases determines the final protein.

    The only thing any of us disagree with you about is that that process must be Intelligently Designed.

    And you have provided no argument that I am aware of that it must be.

    Can you drop the other shoe?

    If I do, it will most certainly land on your head. Your defense of your position has been a total failure. Your apparent belief that you’ve had such a obvious success with it, is intractably incoherent to the facts.

    And to repeat, my “position” is simply that your argument for Intelligent Design is, at best, circular, and amounts to:

    • What exists between mRNA and a protein is a semiotic state, by my definition.
    • Some semiotic states are between intelligent agents.
    • Therefore the genetic code is intelligently designed.

    Which fallacious in exactly the way we have all been pointing out, NOT because we deny that the evidence implies that a semiotic state, by your definition, exists between mRNA and the protein it codes for, but because the only intelligent design argument that you seem to be building on that definition is circular.

     

    However, it is possible that this is not your argument.  If this is the case, please can you tell us what it is?

  2. Upright BiPed on May 14, 2012 at 4:42 pmsaid:

    I would like to also note that after tens of thousands of words and more than a dozen back-and-forth exchanges with a dozen or so objectors, the material evidence underlying the semiotic argument remains unchanged, and unrefuted.

    I agree that the argument remains unrefuted.  That is because it has not been made.

    ETA: to clarify – if the argument is as I just presented it, then it has been refuted. I am not aware of any other argument you have advanced.

    All you seem to have done is defined “semiotic state” in such a way that it includes translation [ETA: i.e. the genetic translation process]. Which whoever coined the term “translation” presumably already thought of.

  3. Yeah, if we say semiotic implies intelligence, and then we redefine semiotic as including gravitational attraction, we have “intelligent falling”. Piece of cake.

    I haven’t found a reason to change my suspicion that for Upright BiPed, his assumptions are taken so completely for granted that he regards them as manifest evidence. 

  4. I’ve been watching this for quite a few months, going back to UD. I haven’t seen anything to refute my opinion that UPB is simply assuming his conclusion.

    He abstracts the chemistry, “reducing” it to information processing, declares that information processing is something only done by intelligent agents, and declaring that the chemistry is therefore designed.

    As I have said elsewhere, it’s equivocation with lipstick.

  5. Dr Liddle,

    It appears that your last two posts are a haphazard attempt to reinstate your anthropocentric fallacies from before, with your imputing of “intelligence”, “human linguistics”, “human agency” etc., into the argument where they do not exist (and never have existed). All of these objections have already been dealt with on numerous occasions in numerous ways. So forgive me for having to repeat myself. Please pay attention:

    The semiotic argument argues that the transfer of any recorded information (form about something) has material consequences. To transfer form about something requires a material capacity to do so. Observation demonstrates that the capacity to transfer form about something through a material medium is facilitated by the transfer of a representation of that form instantiated in an arrangement of matter. This is complimented by a mechanism allowing a particular material representation to produce a particular effect within a system. The introduction of a representation into a physical system necessitates the physical establishment of arbitrary relationships between objects within that system. Representations are arbitrary to the form they represent because the medium they are transferred by is not the form they represent to the system. Observation also demonstrates that the arbitrary relationship (between the representation and its effect) is established by a second arrangement of matter within the system. This second arrangement of matter (referred to as a protocol in the argument) provides a mechanism by which the material (but arbitrary) representation can induce an effect based upon its material arrangement.

    A physical dynamic therefore exist between these material objects as a result of the arbitrary representation. That observed dynamic is that neither the representation nor the protocol ever becomes the effect, while together they determine what the effect will be. This dynamic is the necessary result of having a material effect determined by an arbitrary element within the system; it allows the establishment of an arbitrary relationship within a system otherwise operating by purely material forces. The material effect is induced by the representation while maintaining its arbitrary nature.

    Finally, there is a fourth observation (beyond that of representations, protocols, and their dynamic relationships) which is provided as a means to confirm the transfer of recorded information. That fourth element is the unambiguous observation of a functional effect being produced. Without that effect, we could not know with any confidence that any particular arrangement of matter was a representation of anything; we could not know that any particular arrangement of matter established an arbitrary relationship between two separate things. Only by the observation of a functional effect can the relationships of these other objects become discernible.

    Demonstrating a system that satisfies these material consequences confirms the transfer of recorded information and demonstrates a semiotic state, given that it is representations are protocols which are being demonstrated by their material existence. The conclusion of the semiotic argument in regards to genetic information is that protein synthesis demonstrates these exact material consequences and is therefore semiotic, requiring a mechanism capable of creating a semiotic state.

    As opposed to attacking the validity of the material observations, your claim is that this is circular reasoning. Please take the argument given above and demonstrate the circular reasoning involved in reaching the conclusion of the argument. Please do not impute subjects into the argument that are not a part of the material observations. Please do not imply that I have manufactured the definitions contained in the argument unless you can demonstrate that I have done so. Please do not argue in the abstract, given that the actual observations are provided. If you feel that additional information is required in order for you to demonstrate the circular reasoning you’ve claimed, then ask for it.

  6. Upright BiPed,

    As mentioned many times by Mike Elzinga, your semiotic argument fails because it does not take into account physics.

    No “code” has to obey “physics/chemistry” but biology does.

    If you take two bar magnets, throw them into a paper bag and shake, you will never end up with two like poles contacting each other.

    If chemistry was overruled by “semiotic code”, any chemical combination would be as likely as any other.

    There is no level of indirection at work in a cell.

     

  7. Toronto, as is typical of you, your argument is absolutely incoherent to the observations. All physical things must follow physical laws. Codes are physical things, they follow physical laws. Nowhere in the argument do I suggest otherwise. 

    Perhaps you should try understanding the argument you wish to refute. 

  8. Upright BiPed, rather than attempting to analyse my motives, I’d be grateful if you would actually address my posts. Or at least read them.

    You say:

    As opposed to attacking the validity of the material observations, your claim is that this is circular reasoning. Please take the argument given above and demonstrate the circular reasoning involved in reaching the conclusion of the argument.

    There is no circular reasoning in any argument you have made here, because you have made no argument.  All you have done is describe what is going on during the genetic translation process in linguistic terms. 

    At no stage have you attempted to argue that because the genetic translation process has these “semiotic” properties, they must have been intelligently designed.  You seem to think that this is self-evident.  It isn’t.  You need to make the case.  Most of us I think (I certainly) assumed that your case was: linguistic semiotic systems involve intelligent agents, so genetic ones must too, which would be fallacious, for reasons we gave.  But perhaps we have misunderstood you.  Perhaps this is not your argument.

    So I asked what it was.  You have provided nothing apart from yet another definition of “semiotic state” and a rationale for calling the genetic translation process “semiotic”.  Fine.  I will call it “semiotic” too, for exactly the reasons you give.

    But what has this got to do with an argument for intelligent design?

    Please do not impute subjects into the argument that are not a part of the material observations.

    I don’t know what this means.

    Please do not imply that I have manufactured the definitions contained in the argument unless you can demonstrate that I have done so.

    I don’t care whether you have manufactured them or transcribed them from some divine dictionary, the point is that a definition is not an argument. Your “semiotic argument” is supposed to be an argument for ID.  All I have seen is an argument that the translation process can be reasonably described as “semiotic”.  Fine.  I buy that.  Now, where is the argument for ID?

    Please do not argue in the abstract, given that the actual observations are provided. If you feel that additional information is required in order for you to demonstrate the circular reasoning you’ve claimed, then ask for it.

    What I need, Upright BiPed, is your argument.  I have told you I am perfectly happy to stipulate that by the definition of “semiotic” you have provided, the mRNA translation process is “semiotic”.  What I want to is how that makes your case for Intelligent Design.

     

     

  9. Upright BiPed on May 14, 2012 at 8:45 pmsaid:

    Toronto, as is typical of you, your argument is incoherent to the observations. All physical things must follow physical laws. Codes are physical things, they follow physical laws. Nowhere in the argument do I suggest otherwise. 

    Perhaps you should try understanding the argument you wish to refute. 

    If we are not understanding your argument, consider that you may need to make it more clearly.  I am not seeing an argument for Intelligent Design here, and the one that some of us have inferred appears to be one that you do not claim to be making.

    So please lay out what it is.

  10. Upright BiPed, everyone here has made an attempt to understand your argument. By astounding coincidence, everyone here has come to the same understanding. You have formulated your definitions in such a way as to assume your conclusions.

    Yes, chemistry follows laws, implicit in the periodic table. They are not following abstract codes, or encoded representations. They are following the rules of chemistry. There ARE NO CODES HERE. There is only chemistry, and the physical rules chemistry follows.

    If you wish to PROJECT some sort of intelligence into the rules of chemistry, note that chemistry follows these rules, and “deduce” intelligence (which you inserted by your own definition), you are going to get called on it. This is dishonest. Everyone sees it. You have assumed your conclusion.

    I think everyone is getting tired of telling you this, and you simply wrapping yourself up in verbose denial and repeating the error ad nauseum. You would probably be best advised to return to blathering at those who assume the same conclusions you do. That way, you’ll know you’re right.     

  11. Upright BiPed,

    UBP: “All physical things must follow physical laws. Codes are physical things, they follow physical laws.”

    No, “codes” are not things.

    Codes “represent” things, which is why we say information is “encoded”.

    I can send you the sound “ahhh” in an MP3 file or send you “a” with the same result.

    They both have to be “decoded” before use.

    Do you agree that a “code” for X is not the same as X?

    UPB: “Perhaps you should try understanding the argument you wish to refute. “

    Perhaps you should understand the difference between a “symbolic” code and the physical “thing” it represents.

     

     

     

  12. Dr Liddle,

    There is no circular reasoning in any argument you have made here, because you have made no argument.

    Odd isn’t it? You specifically claimed my argument was circular. Then when I asked you to substantiate your claim with details, suddenly there is no circularity because there is no argument.

    I gave you the etymology of the word “information” which I am working from. By your own estimation, I provided you with a very “defensible” definition of recorded information by defining its material existence. I then gave you the material description of a representation, and of a protocol. I provided the observations of these objects in terms of their material roles within the process of transferring recorded information. I provided a set of entirely coherent observations of these objects (without the slightest bit of ambiguity) from humans, animals, insects, and information-processing machinery. I even spoke to the logical necessity of these objects in the recording and transfer of information. I then provided the same observations of these objects at work during the process of genetic information transfer. Finally, I provided the widely-accepted definition of semiosis, which is a process involving the use of representations and protocols. I then offered the conclusion being made from these observations, and in order to avoid any misunderstanding, I presented those conclusions by specifically announcing that ‘these are the conclusions’ of the semiotic argument. I made the specific claim that protein synthesis is observationally semiotic given that it demonstrates the use of representations and protocols, as does all other forms of recorded information transfer. And as such, I also claimed that it would require a mechanism capable of creating a semiotic state.  

    And to this, all you can do now is say that no argument has been made.

    I am reminded of the very first time I became truly aware of the pejorative academic term “handwaiving” and the intellectual vacuity conveyed by its use. There could be no situation where that term is more appropriate than in your final response.

  13. You haven’t made an argument that this could not evolve. That’s the argument we are waiting for.

    What does all this have to do with ID?

  14. Toronto, all codes must be instantiated in a physical object in order for the code to exist. That physical object must follow physical law. This point has been explained to you before.

  15. Upright BiPed,

    Upright BiPed: “I made the specific claim that protein synthesis is observationally semiotic given that it demonstrates the use of representations and protocols, as does all other forms of recorded information transfer.”

    You have failed in your claim because you don’t understand the difference between a “code” and the “thing” that it represents.

     

  16. Upright BiPed,

    Upright BiPed: “Toronto, all codes must be instantiated in a physical object in order for the code to exist.”

    But what we are talking about are not “codes” for “things”, they are instead, the “things” themselves”.

    This point has been explained to you before.

     

  17. Upright BiPed,

    Odd isn’t it? You specifically claimed my argument was circular. Then when I asked you to substantiate your claim with details, suddenly there is no circularity because there is no argument.

    Dr. Liddle made her meaning quite clear in the very same comment to which you are replying:

    Most of us I think (I certainly) assumed that your case was: linguistic semiotic systems involve intelligent agents, so genetic ones must too, which would be fallacious, for reasons we gave. But perhaps we have misunderstood you. Perhaps this is not your argument. So I asked what it was. You have provided nothing apart from yet another definition of “semiotic state” and a rationale for calling the genetic translation process “semiotic”. Fine. I will call it “semiotic” too, for exactly the reasons you give. But what has this got to do with an argument for intelligent design?

    Like several other participants here, I have been following your “Semiotic Argument” for some time, frankly without ever seeing your point. Rather than playing rhetorical games, why don’t you simply reply to this question. If the fallacious argument everyone has assumed you are making is not your actual argument, what does anything you’ve written on this topic have to do with intelligent design?

  18. Upright BiPed,

    Upright BiPed: “That physical object must follow physical law.”

    Physical objects don’t actually “follow” laws as the analogy suggests.

    We come up with the “laws” of physics to describe the interaction of physical objects and sometimes we get it wrong.

    Before Einstein, light was said to travel in a straight line, but Einstein thought differently and he was right.

    So we changed the “law”.

    Light no longer “had” to travel in a straight line.

     

     

     

  19. Patrick you should keep an eye on reading comprehension. Dr Liddle stated that my argument was circular. I asked her for the details of that cicularity. She then responded that nothing was circular because there is no argument. So in the space of one post an argument existed, then didn’t exist. It was circular, then that circularity vanished. I understand your wish to come to her defense, but nothing in the quote you posted from her provides any details of the circularity she claimed existed in the argument – a claim she made immediately prior to me asking her for those details. 

  20. Upright BiPed on May 14, 2012 at 9:35 pm said: Edit

    Dr Liddle,

    There is no circular reasoning in any argument you have made here, because you have made no argument.

    Odd isn’t it? You specifically claimed my argument was circular. Then when I asked you to substantiate your claim with details, suddenly there is no circularity because there is no argument.

    Upright BiPed, I would much rather be addressed as Lizzie and treated with respect, than addressed as “Dr Liddle” and treated like a dishonest child.  No, it is not very “odd”.  I have, like others, apparently been under the illusion that your argument about what constituted a “semiotic state” was your semiotic argument for ID, and assumed that the point of your argument was that as “semiotic states” between language users involve intelligent agents, somehow this implied that “semiotic states” within cells must involve intelligent agents as well.  That’s why I tried to get you to say who the communicating agents were supposed to be in the cell.  Because if that had been your argument (as I thought it was) it would have been fallacious, for reasons we have given. 

    However, you have now made it clear that this is NOT your argument.  But in that case, I, like others, are at loss as to what your semiotic argument actually is (other than the circular argument that if we define “semiotic state” in such a way that it includes the biochemistry of a cell, then there is no surprise if we find that the biochemistry of a cell is semiotic) for ID.

    That’s why I asked you to “drop the other shoe”.

     

    I gave you the etymology of the word “information” which I am working from. By your own estimation, I provided you with a very “defensible” definition of recorded information by defining its material existence. I then gave you the material description of a representation, and of a protocol. I provided the observations of these objects in terms of their material roles within the process of transferring recorded information. I provided a set of entirely coherent observations of these objects (without the slightest bit of ambiguity) from humans, animals, insects, and information-processing machinery. I even spoke to the logical necessity of these objects in the recording and transfer of information. I then provided the same observations of these objects at work during the process of genetic information transfer. Finally, I provided the widely-accepted definition of semiosis, which is a process involving the use of representations and protocols. I then offered the conclusion being made from these observations, and in order to avoid any misunderstanding, I presented those conclusions by specifically announcing that ‘these are the conclusions’ of the semiotic argument. I made the specific claim that protein synthesis is observationally semiotic given that it demonstrates the use of representations and protocols, as does all other forms of recorded information transfer. And as such, I also claimed that it would require a mechanism capable of creating a semiotic state.  

     

    And to this, all you can do now is say that no argument has been made.

    No.  I have explicitly said that I am willing, for the sake of this discussion, to stipulate all that.  What I want to know is why this is an argument for ID. You have not given one.  All you have argued the case for is applying the word “semiotic” to the process of genetic transcription.

     

    I am reminded of the very first time I became truly aware of the pejorative academic term “handwaiving” and the intellectual vacuity conveyed by its use. There could be no situation where that term is more appropriate than in your final response.

    I think you mean “handwaving” ;)  However I profoundly disagree.  My request to you is absolutely on point and I have (yet again!) agreed to accept your terminology.  I am simply asking you to state why this makes any kind of case for ID.

    I refuse to waive this request ;)

  21. Again, I note…no one has attacked the material observations made within the argument.

  22. Upright BiPed,

     

    As amusing, productive, and not at all a waste of time as it would be to discuss the evidence for each other’s reading comprehension and to deconstruct Dr. Liddle’s most recent comment in excruciating detail, I’m going to suggest we skip that and focus on the actual issue she raised:

    If the fallacious argument everyone has assumed you are making is not your actual argument, what does anything you’ve written on this topic have to do with intelligent design?

  23. Upright BiPed on May 14, 2012 at 10:07 pm said:

    Patrick you should keep an eye on reading comprehension. Dr Liddle stated that my argument was circular. I asked her for the details of that cicularity. She then responded that nothing was circular because there is no argument. So in the space of one post an argument existed, then didn’t exist. It was circular, then that circularity vanished. I understand your wish to come to her defense, but nothing in the quote you posted from her provides any details of the circularity she claimed existed in the argument – a claim she made immediately prior to me asking her for those details.

    Upright BiPed, the reading comprehension problem appears to me to be on your side.

    Let me make my meaning still clearer: 

    1. The argument I thought you were making would have been circular.
    2. However, it appears that you are not making the argument I thought you were making, and what I thought was “circular” turns out merely to be a definitional preamble. 
    3. So now I am asking for your actual argument: why does the fact that the process of translation can be defined as “semiotic” imply an Intelligent Designer?

     

  24. Upright BiPed on May 14, 2012 at 10:14 pm said:

    Again, I note…no one has attacked the material observations made within the argument.

    No indeed we have not. All we are now waiting for is your actual semiotic argument for Intelligent Design.

  25. I think I answered that earlier. If we define gravitational attraction as semiotic, and say that semiosis involves intelligence, we come up with “intelligent falling.” UB seems to be saying that chemical reactions are semiotic, and therefore imply intelligence according to the same reasoning.

  26. Toronto on May 14, 2012 at 9:56 pmsaid:Edit

    Upright BiPed,

    Upright BiPed: “That physical object must follow physical law.”

    Physical objects don’t actually “follow” laws as the analogy suggests.

    We come up with the “laws” of physics to describe the interaction of physical objects and sometimes we get it wrong.

    Before Einstein, light was said to travel in a straight line, but Einstein thought differently and he was right.

    So we changed the “law”.

    Light no longer “had” to travel in a straight line.

    Yeah, Upright BiPed.  Don’t be misled by the word “law”.  A scientific law isn’t prescriptive like a human law, it is solely descriptive.  And sometimes only descriptive within certain ranges, or under certain conditions.  And sometimes only stochastically.

  27. I’ll ask Dr. Liddle a question to clarify things in my own mind. IF BiPed asserts that all semiotic processes imply intelligence, would he have made an argument as presented:
    1) Chemistry is semiotic
    2) Semiosis requires intelligent guidance
    3) therefore, chemistry is intelligently guided.  

  28. UBP says: “I made the specific claim that protein synthesis is observationally semiotic given that it demonstrates the use of representations and protocols, as does all other forms of recorded information transfer. And as such, I also claimed that it would require a mechanism capable of creating a semiotic state. ”

    What “representations and protocols” do atoms follow when they condense into stars?  What “representations and protocols” do stars follow in building up heavier elements from hydrogen and helium?  What “representations and protocols” do stars follow when they the go supernova and throw those new elements out onto space and generate additional heavier elements in the shock waves of the explosion?  What “representations and protocols” do these elements follow when they condense into second and third generation stars and are built up into even heavier elements?

     

    What “representations and protocols” do atoms follow when they combine into compounds?  What “representations and protocols” do atoms and molecules follow when condensing into solids and liquids?

     

    What “representations and protocols” do atoms and molecules follow then condensing into even more complex molecules?

     

    Where along the chain of complexity that we see in matter in the universe does the notion of “representations and protocols” start replace the laws of physics and chemistry?  Why do “representations and protocols” have to replace the laws of physics and chemistry?

     

    How do “representations and protocols” push atoms and molecules around?

     

    Are you suggesting that “representations and protocols” somehow “make use of” the laws of physics and chemistry?  How do they do that?  What physical mechanism(s) is(are) involved when “representations and protocols” push atoms and molecules around or “make use of” the laws of physics and chemistry?

     

    Aren’t you simply trying to replace “intelligence” and “information” with “representations and protocols?”  How does “information” push atoms and molecules around?

     

    What does semiotics have to do with any of this?

  29. Flint on May 14, 2012 at 10:24 pmsaid:Edit

    I’ll ask Dr. Liddle a question to clarify things in my own mind. IF BiPed asserts that all semiotic processes imply intelligence, would he have made an argument as presented:
    1) Chemistry is semiotic
    2) Semiosis requires intelligent guidance
    3) therefore, chemistry is intelligently guided.  

     

    Well as I understand it, the argument starts something like:

    1) The genetic transcription process can be described as semiotic for these reasons (entailments, protocols, transfer of information etc)

    2) ?

    3) ?

    I am happy to accept 1.  But if two and three are:

    2) Semiosis requires intelligent guidance

    3) therefore, the genetic transcription process is intelligently guided.  

    Then I would say that argument makes the fallacy of the excluded middle (All cats are mammals; this animal is a mammal; this animal is a cat), which is what we were all saying.  But Upright BiPed says that is not his argument.  He seems to think that his entire argument is the contents of 1).

    But if so, as an argument, it is circular (except in the trivial sense of being an argument that the two systems, language and genetic transcription, have something in common, which I think we all accept, and which Upright BiPed calls “semiosis”).  As a definitional preamble, it’s fair enough, but in that case, I want to hear the actual argument.

     

  30. Dr Liddle,

    No, it is not very “odd”.

    It’s not odd that you would repeat for the umpteen-millionth time that my argument is circular, only to claim there is no circularity and no argument the very moment I ask you to back up your claim? BS.

    I have, like others, apparently been under the illusion that your argument about what constituted a “semiotic state” was your semiotic argument for ID, and assumed that the point of your argument was that as “semiotic states” between language users involve intelligent agents, somehow this implied that “semiotic states” within cells must involve intelligent agents as well. 

    I have never (even once) deviated from the conclusion of the semiotic argument – that is that a semiotic state exists in protein synthesis, and would require a mechanism capable of creating a semiotic state. These are the conclusions which can be rationally drawn from the evidence at hand, i.e. they are appropriate to the evidence, and do not go beyond it. I have repeated them many, many, many times. Additionally, given my specific rebuttal to your “anthropocentric malaise” of several months ago, I find it virtually impossible that you could have understood the argument otherwise. Even in the original argument given to Dr Moran, I clearly stated:

    “Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state. It does so observationally. Yet, the descriptions of these entailments make no reference to a mind. Certainly a living being with a mind can be tied to the observations of information transfer, but so can other living things and non-living machinery. It must be acknowledged; human beings did not invent iterative representational systems, or recorded information. We came along later and discovered they already existed”.

    Consequently, when you claim that you’ve thought all along the argument was about human communication and intelligent agents, then I simply do not believe you. And if I am mistaken about that, then perhaps you might look back across the entire history of our conversation and recognize the sheer lack of any indication from me that I conveyed what you heard. I have been saying nothing of the sort, so you can assume the full responsibility of your position. I have done everything I could to divert you from the priori assumptions you’ve fallen into, just as you have resisted those efforts at every turn.

    I, like others, are at loss as to what your semiotic argument actually is (other than the circular argument that if we define “semiotic state” in such a way that it includes the biochemistry of a cell, then there is no surprise if we find that the biochemistry of a cell is semiotic) for ID.

    Surprise surprise! Circularity returns yet again! Amazing!

    You may make this claim of circularity when you demonstrate that the definition of semiosis is one I manufactured in order to fit the material observations. If not, then argument and definition are not circular, they’re simply accurate.

    What I want to know is why this is an argument for ID.

    We have already had this conversation as well. What I see here is a person who has struggled mightily to defend her position against a valid attack on material grounds, yet hasn’t demonstrated the integrity to acknowledge the argument being presented. (That’s all on you, by the way). And now you want nothing more than for me to get off the discussion of material evidence, and move into new territory without any acknowledgement of where we’ve been. I have no obligation to do so, and no intention of it. You may want to try and spin my unwillingness into a reason to quit. Certainly, no one could blame you.

    Alternatively, you can address the semiotic argument as it was actually presented, and either challenge those material observations or acknowledge the validity of the claim that protein synthesis is observable semiotic.

  31. Mike,

    UBP says: “I made the specific claim that protein synthesis is observationally semiotic given that it demonstrates the use of representations and protocols, as does all other forms of recorded information transfer. And as such, I also claimed that it would require a mechanism capable of creating a semiotic state.

    What “representations and protocols” do atoms follow when they condense into stars? 

    Who the hell thinks that atoms follow representations and protocols as they condense into stars? Moreover, why should I engage someone who obviously doesn’t understand the content of the argument, or whose only hope is to misrepresent it?

  32. Upright BiPed,

    Upright BiPed: “Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state. It does so observationally. Yet, the descriptions of these entailments make no reference to a mind.”

    But you need an “intelligence” that knows what to “do” with the “code”.

    If you “don’t” need a “mind” or any other “intelligence”, then the only thing at work is physics/chemistry and your semiotic theory is not supported.


  33. Upright BiPed,

    How is it possible that you missed this point?

    UPB: “Who the hell thinks that atoms follow representations and protocols as they condense into stars?”

    Mike’s point was, that just as “atoms” don’t need a protocol to condense into stars, neither do cells in biology require representations and protocols for their chemical activity.

    UPB: “Moreover, why should I engage someone who obviously doesn’t understand the content of the argument, or whose only hope is to misrepresent it?”

    You claim we don’t get your point, but you don’t seem to be able to connect two dots when they’re handed to you.

    Jumping to an unwarranted conclusion doesn’t help your cause or credibility.

    Read with respect and respond with less snark please.

     

     

     

     

  34. UB:

    Bill’s entire counter-argument is based upon the idea that something else could be causing the material entailments observed in the process of ‘transferring form though the use of an arrangement of matter.’ ….Bill suggests that this ‘something else’ could be non-semiotic and thereby cause the argument to be false. 

    No, my argument is that, owing to a fatal logical error, nothing in your semiotic argument excludes that possibility. As it is the purpose of your semiotic theory of ID to assert the impossibility of a non-semiotic origin for the process in question (the transcription of DNA ), this flaw results in the complete collapse of your argument.

    Nothing about the natural origins of the phenomena in question otherwise flows form “logical necessity.” In fact, I have stated the opposite from the beginning: “Of course, that is simply to state a starting assumption, not anything conclusory. It then becomes an empirical question, not one that can be decided in an armchair shuffling dictionary definitions. The science inheres in the work that follows: articulating how such complex biological systems arose by means of evolutionary processes. No trivial task.”

    UB: 

    Does the institution of science actually live by tenets of Bill objection?

    Yes, science often proceeds by invoking exactly the reasoning I describe. As I stated earlier, “wetted ground is an absolutely reliable entailment of (consequence of) rainstorms, in that wet ground always results from rainstorms. By modus tollens, if I hypothesize that it rained 15 minutes ago, I may test my hypothesis because rain 100% reliably entails wet ground. If I fail to find this entailment of rain, my hypothesis fails. If I do find wet ground my hypothesis is not disconfirmed, and indeed it is strengthened because a prediction that flowed from it has been confirmed. But it could still be wrong.”

    You will recognize this as the logic of hypothesis testing. Theoretical utterances, to be useful, must have operationalizable entailments, by means of which the theory may be tested. Those entailments must predict the outcome of observations, such that failure make the predicted observation places the theory at risk of disconfirmation (a form of entailment that is entirely absent from UB’s semiotic theory, as well as ID theory generally). You will also recognize the provisional nature of the support a scientific theory receives from observational success. It could still be wrong. It is by means of this logic of entailment that, in the real world, “judgments are made based on the evidence.”

    Simply repeating Bill’s disanalogy does not improve upon it. “A implies B does not mean B implies A” is a disanalogy for several reasons, but one of them is because it’s missing the logical possibility that B might imply A.

    Of course B might entail A for other reasons. But what does not obtain is “A entails B, therefore B entails A. And that is the logical form of your argument to date. Due to this error, your argument fails to accomplish what you so fervently wish it to accomplish.

    What allows us to conclude that B implies A is material evidence.

    Specifically, evidence that B exclusively entails A. But that is entirely what is at issue in this debate, and you’ve adduced no evidence whatsoever in support of the notion that B exclusively entails A – with the exception of the instances in which you state this by definition. Specifically, you’ve adduced no evidence whatsoever that the systems in question cannot have evolved by non-semiotic means through non-semiotic processes.

    Rather, you’ve assumed this conclusion throughout.

  35. You obviously didn’t get past the first sentence in my line of questions.

    The claim that I quoted from you apparently had no meaning either?

  36. I have never (even once) deviated from the conclusion of the semiotic argument – that is that a semiotic state exists in protein synthesis, and would require a mechanism capable of creating a semiotic state. These are the conclusions which can be rationally drawn from the evidence at hand, i.e. they are appropriate to the evidence, and do not go beyond it. I have repeated them many, many, many times.

    OK, let’s take it from here. As you define a semiotic state, it applies to protein synthesis. OK, people here are willing to allow your definition, and agree that a semiotic state exists in protein synthesis. So far so good.

    Next, you say this requires a mechanism capable of creating a semiotic state. No problem. The number of such mechanisms may well be very large, and include processes wildly different from one another.

    As a general principle, the wider your definition of a semiotic process, the more VERY different processes that this encompasses, the less your definition says about any particular process.

    So far, your definition applies broadly to ANY processes capable of producing proteins. So far, these are not “conclusions”, these are the definition of what you mean by semiotic – synthesized proteins and ANY AND ALL processes that might accomplish this.

    OK so far. Now, so what?

  37. I remember this argument’s origins at UD, and as I follow it, in the same sense that the specific binary sequence (100) shares no physical or chemical relationship with the number 4, the 4-ary dna base sequence (UGG) shares no physical or chemical relationship with Tryptophan. The relationship between the specific set of yes
    and no questions (100) and the number 4, and the specific set of dna bases (UGG) and the amino acid Tryptophan, is arbitrary. The relationships have been established by some separate protocol. Whereas the transfer of the sequence is simply the result of physics and chemistry,  the relationship between the sequence and the number or the amino acid is not necessarily bound by physics and chemistry, but rather some separate protocol.

    In this event, UB has been flanked by Alan and Bill. Alan’s simple precursor would refute the argument, as UB has already stated. If a plausible mapping as Alan suggests existed from some simple precurser to the genetic code, then Bill’s argument would simply follow from there. However, I’m not aware any plausible scenarios that currently exists.
     

  38. junkdnaforlife

    The relationship between the specific set of yes
    and no questions (100) and the number 4, and the specific set of dna bases (UGG) and the amino acid Tryptophan, is arbitrary.

    The relationship of UGG to Tryptophan is not arbitrary.  Arbitrary would mean that any codon could, at the whim of the designer, be used to produce any amino acid. We know that is not the case.

  39. Reciprocating Bill,

    No, my argument is that, owing to a fatal logical error, nothing in your semiotic argument excludes that possibility. As it is the purpose of your semiotic theory of ID to assert the impossibility of a non-semiotic origin for the process in question (the transcription of DNA ), this flaw results in the complete collapse of your argument.

    Nothing about the natural origins of the phenomena in question otherwise flows form “logical necessity.” In fact, I have stated the opposite from the beginning: “Of course, that is simply to state a starting assumption, not anything conclusory. It then becomes an empirical question, not one that can be decided in an armchair shuffling dictionary definitions. The science inheres in the work that follows: articulating how such complex biological systems arose by means of evolutionary processes. No trivial task.”

    I love the drama Bill. Unfortunately these two paragraphs are in a bit of a contradiction to one another. The first basically states that just making the claim causes a logical fallacy. The cause of the phenomenon in question could be this or that, and just by claiming its “this” causes all hell to break loose because it could be “that” instead. Is your judgment of logical turpitude on my part as silly as it sounds? Yes, entirely. It could only make sense if I said “it’s this” and walked away. But I didn’t, I made the case instead, just as it’s done in any other claim of any kind. On the other hand, your second paragraph claims that it’s the evidence itself which must mediate my claim. Great. Glad you could join me.

    Representations and protocols have material consequences which manifest themselves in a system. Representations induce effects within that system and protocols determine what those effects will be. A representation is an arrangement of matter which is physically arbitrary to the effect it induces in the system. It is not merely the physical presence of the representation that induces the effect; it is the arrangement itself, which a quality not inherent in its material make-up. A protocol is an arrangement of matter which physically establishes the otherwise arbitrary relationship which exists between the representation and the effect it induces. In order to facilitate in the arbitrary nature of the representation, the protocol must establish this relationship in material isolation from the effect.

    That describes a fairly unique material state, one that is not entirely lost on the intellectual world. Its uniqueness is widely understood, even as it exists in genetic information. Yockey tells us that that there is no other reaction in the physicochemical world “even remotely” like it; others have said much the same. Polanyi refers to it as a boundary condition, not reducible to its physical make-up. Yet, we find this incredibly unique material state occurring in every single instance of recorded information transfer ever known, but absolutely nowhere else. So an entirely exceptional material state in known only to manifest itself in an entirely singular phenomenon, the transfer of recorded information. And when we find it also appearing in the transfer of recorded genetic information, you want to suggest that it’s a fatal logical fallacy to think they share anything in common, beyond that unique material state of course. Or, do you want to suggest this is merely the assumption of a conclusion?

    I’m prepared to defend my claim in either case. The claim is that protein synthesis is observably semiotic and requires a mechanism capable of creating a semiotic state.

  40. “A representation is an arrangement of matter which is physically arbitrary to the effect it induces in the system.”

    Wait a minute. Nothing about chemical reactions is physically arbitrary.

    As far as I can decode your post, you seem to be saying that the molecules which are involved in these reactions somehow get translated into arbitrary symbols unrelated to the reactions themselves, and then somehow these arbitrary symbols are re-translated into something physically meaningful. And this happens according to some protocol somehow embedded in the way the molecules are shaped. Is that correct?

    I find the interpretation of a chemical reaction as involving protocols for encoding and decoding otherwise arbitrary symbols to be, uh, creative. But still, all you’ve produced is a highly imaginative description of a chemical process.

    I doubt anyone would disagree that chemical reactions happen, or that in biology those reactions are highly complex. I think many would doubt that they involve arbitrary symbols, and I still haven’t figured out who is the sender and who is the receiver of this symbolic information.

    But even if ALL of that is granted, so what? Where does the intelligent design come in? I’m left speculating that you believe that there is some threshhold of chemical complexity, beyond which you just can’t swallow the idea that billions of years of trial and error feedback processes could produce such a thing. 

    After all, to the best of my knowledge the physical translation process is well understood. You haven’t described any chemistry that’s different or unknown. And those who know these processes perhaps far better than you do, don’t see any intelligent design. Even if they are generous enough to grant that agreed-on processes are “semiotic”, so what? 

    Describing gravity in page after page of complex Einsteinian equations in order to creation the impression of a “semiotic process”, still means that the apple falls from the tree the same as ever. Emphasizing the complexity doesn’t change the nature of an unintelligent process.

    Maybe you could work backwards. Start with the intelligence. What does it do? How can you tell? Could biochemistry happen without it? Why not?     

  41. I’m prepared to defend my claim in either case. The claim is that protein synthesis is observably semiotic and requires a mechanism capable of creating a semiotic state.

    Yet you vehemently objected to nucleosynthesis in stars and supernovae as being examples of “representations and protocols.” What about the formations of compounds and complex macromolecules?

    Just where along the chain of complexity in matter interactions do you claim “representations and protocols” take over from the laws of chemistry and physics? Why in proteins and not in, say, urea or amino acids; or something even simpler like water molecules?

    Do you believe that molecules can have properties that their constituent atoms don’t have individually? If not, why? If so, why can’t more complex systems, responding to the same physical laws, have complex emergent behaviors that are not found in the constituents making up the system? Why deny what is actually observed in the universe?

    Why do you require “representations and protocols” instead of accepting the laws of chemistry and physics; which were derived from taking matter apart? Can you show us any laws of physics and chemistry that forbid the emergence of complex behaviors in complex systems of molecules, given the right environment?

    And you still haven’t answered the question of how “representations and protocols” push atoms and molecules around. How are “representations and protocols” any different from “information” pushing atoms and molecules around? How does “information” push atoms and molecules around? What is the mechanism?

    I have to agree with Flint; you seem to want to replace all of chemistry and physics with some imaginative “theory” that implies “only intelligence can do this.” But you can’t seem to articulate why.

    Just giving your “theory” some fancy name doesn’t solve the problem either; it only makes your effort seem like a naive and pretentious attempt to replace well-understood phenomena with something woo-woo. Why do that before you learn the physics and chemistry?

  42. Upright BiPed on May 14, 2012 at 11:40 pm said:

    You may want to try and spin my unwillingness into a reason to quit.

    I would not dream of it.  I’m going to be frank, here, Upright BiPed.  I find your posts to me extremely offensive.  You repeatedly suggest that I am trying to “quit” (when not suggesting that I set this blog up specifically to continue our conversation); you repeatedly suggest that I am evading your arguments, when I have specifically invited you here to continue them; you accused me of unstickying your thread because I thought you were “unreliably” present, when, conversely, I had stickied it precisely in consideration to your intermittent availability, and only unstickied it when I thought of a better way of keeping it visible for your, and others’ convenience.  I have pointed these things out, and have received no acknowledgement, let alone apology, from you. I have asked you to respond to the content of my posts, rather than attack my motives; I have even asked you not to refer, with faux civility, to me as “Dr Liddle”.  You ignore these requests.

    I am getting rather cross.

    Not so cross, however, that I have any intention of “quitting” a discussion I have made enormous efforts to sustain, despite the fact that you seem unable, or unwilling, to actually read my posts.

    harrumph.

    To content, briefly:

    I made the specific claim that protein synthesis is observationally semiotic given that it demonstrates the use of representations and protocols, as does all other forms of recorded information transfer.

    Yes, and, given your definition of “semiotic”, I agree that protein synthesis is “semiotic” according to your definition.

    And as such, I also claimed that it would require a mechanism capable of creating a semiotic state.  

    Indeed, there must have been a mechanism that resulted in the process that we know as “protein synthesis”, and which you classify as involving what you call a “semiotic state”.

    Can you tell me, as I have asked now several times, why this is, as you claim, an argument for Intelligent Design?

    As opposed to evolutionary processes?

     


  43. UB:

    The first [paragraph] basically states that just making the claim causes a logical fallacy.

    Yes. Your claim that “the entailments confirm semiosis” commits a logical error that is fatal to your argument.

  44. junkdnaforlife:

    If a plausible mapping as Alan suggests existed from some simple precurser to the genetic code, then Bill’s argument would simply follow from there.

    As Keiths pointed out above, UB’s claim that “the listed entailments confirm semiosis” remains fallacious regardless of the state of the evidence. Sayeth Keiths:

    “Apparently you are unaware that a logically invalid argument remains invalid regardless of the evidence. Here is an example:

    1. All floogs are sporgaceous.
    
2. Gorpins are sporgaceous. 

    3. Therefore, gorpins are floogs.

    That argument is logically invalid.  Its conclusion is unwarranted, and no amount of ‘material evidence’ regarding floogs, gorpins and sporgaceousness can change that.  Note that this does not mean that the conclusion is false: gorpins may in fact be floogs.  It’s just that we cannot conclude that gorpins are floogs based on this argument.  It’s logically invalid.”

    UB’s claim that “the listed entailments confirm semiosis” commits the same error.

  45. JunkDNAforlife,

    In this event, UB has been flanked by Alan and Bill. Alan’s simple precursor would refute the argument, as UB has already stated. If a plausible mapping as Alan suggests existed from some simple precurser to the genetic code, then Bill’s argument would simply follow from there. However, I’m not aware any plausible scenarios that currently exists.

    I’ll have to work on my communication skills, then! I did try to sketch a scenario that is entirely plausible.

    We simply need to generate a system of ‘translational’ mapping from one in which no translation occurs. That system only has to be reproductively competent. The obvious candidate for that is RNA. In an RNA world (even one in which peptides play a part), RNA has a dual role: as hereditary information, and as generator of phenotype, by direct catalysis (which does not preclude recruitment of metal ions or even amino acid cofactors). We have a complex system now – three-and-a-half billion years later – in which protein is intimately involved in its own generation – not least by implementing the codon-amino acid relationship in aaRS.

    But for all the elaborateness of protein catalysis, there are only about half-a-dozen basic chemical reactions involved. Most of the huge variety of modern enzymes reflects substrate specificity and control, not enormous variety of basic catalysis mechanism. We know that RNA can catalyse peptide bond formation – virtually every peptide bond in every cell on earth has been made that way, and that has likely been the case for 3+ billion years. That reaction is part of a more general class of condensation reactions that, with the reverse, hydrolysis, which RNA can also achieve, allows extensive opportunities for biosynthesis, rearrangement and catabolism.

    RNA life may have been a poor affair – chained amino acids offer much better catalysis – but it only had to compete with other RNA life. While I cannot offer a definitive role for non-catalytic peptides in RNA Life, we do have plenty of examples of modern non-catalytic peptides to lend plausibility to the idea that catalysts were not the primary product of early ribosomes. Once protein catalysis had evolved, competitive and predatory extinction of RNA-only life would leave us with no examples of the precursor, and a ‘locked-room’ mystery. No-one, as they decide that, Holmes-like, they have eliminated the ‘impossible’, notices the simple trap-door! And they refuse to believe that this provides a plausible answer unless they witness the entire history re-enacted.

    The RNA hypothesis answers the challenge: a mechanism by which the current state (call it ‘semiotic’ if you like) can have arisen ‘naturally’ from a non-semiotic one: one in which genotype and phenotype were tightly coupled.

  46. About six months ago, back on UD, I asked if this argument was about the origin of life. I received no response, and in the entire length of this thread, we have no response as to whether the argument is that this system could not have evolved.

    As others have pointed out, UPB may believe that the level of complexity is so great that it is obviously unevolvable. 

    But that question is the whole subject of OOL, and is being addressed experimentally. 

    I see the name Yockey invoked. I do know that Yockey went on record as saying we would never know the exact and full history of the origin of life. He did not say this because he argued it was a miracle. He said it because he thought there were so many possible pathways that we would never find the true historical path.  It would be a bit like reconstructing the history of a jigsaw puzzle from the completed solution.

  47. Elizabeth

    I’d very much like to see Upright BiPed address this post.

    We all would.

  48. Upright Biped

    I’m prepared to defend my claim in either case. The claim is that protein synthesis is observably semiotic and requires a mechanism capable of creating a semiotic state.

    Then please do so.  You’ve been making the same unsupported assertion since day 1.

    Please show where protein synthesis involves any level of abstract symbology that is required for a process to be semiotic.

  49. Wait a minute. Nothing about chemical reactions is physically arbitrary.

    Using my jigsaw puzzle analogy, UPB seems to be arguing that you have a puzzle in which all the pieces have the same shape, but we find the puzzle assembled to form a picture.

     If the pieces had unique shapes, we could imagine a non-intelligent sorting process that could end up with the puzzle “correctly” assembled. But since our hypothetical puzzle is physically arbitrary, the emergence of a picture is “miraculous.”

    I think UPB is arguing from the general statement that DNA and RNA can exist with any arbitrary sequence, and that no particular sequence is favored by energy states. I’m trying to understand his case, and perhaps he will correct me if I have this wrong.

  50. The situation here, as always, is that ALL jigsaw puzzle assemblies form a picture. So you need two things here: a process that fits puzzle pieces together arbitrarily, and a process that examines the resulting picture and uses some selection criteria to prefer some over others. Perhaps we can even posit some standard of “mininally picturesque.”

    But in any case, we’re back to the post facto “every bridge hand is a miracle” argument. Any particular picture is very unlikely. SOME picture is guaranteed. SOME minimally picturesque picture won’t be all that uncommon.

    Just looking at any of the potentially infinite number of acceptable pictures that can be generated by pieces all shaped alike and saying “this is too unlikely to have happened by chance” is a very tired argument, and if you’re right, UB is making it once again.

    Like a kaleidoscope, even very simple rules can produce endless forms most beautiful.     

  51. Seems to me that the central questions are: is the pictoral representation at all visible to selection? Is the arrangement replicable/heritable? If yes to both, interchangeability at the level of physical substrate isn’t relevant.

  52. As far as I can tell, this is what Upright is trying to argue:

    1. A system that transfers information by arbitrarily mapping a representation to an effect is a semiotic system.

    2. A semiotic system consists of a representation and a protocol.

    3. Remove either of these and you no longer have information transfer; therefore semiotic systems are irreducibly complex.

    4. Irreducibly complex systems can only be the result of intelligent design; therefore semiotic systems are the result of intelligent design.

    5. RNA-to-protein transcription arbitrarily maps nucleotide triplets to amino acids.

    6. Therefore, by #1, RNA-to-protein transcription is a semiotic system.

    7. By #3, RNA-to-protein transcription must be the result of intelligent design.

    It’s a problematic argument, to be sure, but it seems to be what UB is claiming.

  53. If that’s what his argument is, then this is a very clear exposition, and the argument seems quite compelling except that:
    a) natural processes regularly produce irreducible complexity, which is indeed one of the predictions of evolutionary theory; and
    b) transcription is not irreducibly complex anyway.  

  54. RB,

    The first [paragraph] basically states that just making the claim causes a logical fallacy.

    Yes. Your claim that “the entailments confirm semiosis” commits a logical error that is fatal to your argument.

    By your logic, the claim that “hominid footprints at Laetoli confirm bipedalism in the Pliocene” creates the same logical fallacy. As does the claim that the red shift in distant galaxies or the presence of CMBR confirms an expanding universe. As does the extrapolation that changes in allele frequencies over time results in speciation. And because these logical errors are “fatal”, (again following your logic) there is no need for any evidence to suggest the footprints at Laetoli confirm bipedalism, and no evidence need be considered regarding the wavelengths of light coming from distant galaxies. This is the operational consequence of your logic. Fortunately, no one lives by the untenable standard that the act of making a claim within an argument creates a fatal logical fallacy which cannot be overcome. Thankfully, evidence and rationale mediate claims, not partisan rhetoric.

    What confirms semiosis is the presence of the unique material consequences of representations and protocols within a system. Representations and protocols are instantiated in material objects, and are associated exclusively with the phenomena of transferring recorded information. This is a matter of universal observation. They are also found without equivocation in the transfer of recorded genetic information. There is no material evidence to suggest their appearance there is either functionally different or fundamentally discontinuous to their appearance in any other form of recorded information transfer. Your personal aversion to this valid observation is causing you to insist on arguments you don’t even follow yourself.

    By the way, I note that instead of responding to any criticism of your objection, you simply repeated it.

  55. Dr Liddle, it’s understandable that you find my posts offensive. Your posts started to become offensive to me last year, back when I was still singing your praises. One of the offensive attributes of your posts is the number of times you play dumb to the history of the conversation between us. For instance, you may want to ask me why the semiotic argument “is an argument for Intelligent Design?” You may even act as if you have no idea. I find this offensive, given that our conversation started with claims made about the ORIGIN of recorded information and its transfer. That conversation began in May of 2011 and lasted well into September, and even into October. In that conversation we repeatedly argued over the origin of the genetic information system. Over and over, I made reference to issues regarding “the rise of recorded information” from the simple (non recorded information bearing) chemical organizations which are fundamentally required by your beliefs. And even though you were forced to retract your claim to simulate the rise of information, you repeatedly argued that evolution would always somehow find a way. Therefore I reasonably find it disingenuous of you to now ask how I think this argument is tied to ID. Perhaps you can remember some of the back and forth:

    Mycoplasma genitalium is one of the least complex freely living organisms on Earth and it has 450+ genes consisting of 582,000 base pairs. How much of that required function do you think you can get to without a representation-translation-effect system in place; in other words, in the absence of the genuine recorded information processing we find in mycoplasma? And it really doesn’t matter where you put the mark Elizabeth, wherever it is, you’ll need the very simplest of chemical organizations to organically produce the immaterial [ed. arbitrary] representations and protocols you must have to get any further.  (OCT 27th, 2011)

  56. The following is such a tedious exercise, but it is one that must be done.

    As Keiths pointed out above, UB’s claim that “the listed entailments confirm semiosis” remains fallacious regardless of the state of the evidence

    Has it gone un-noticed that all those playing the logical fallacy card, particularly Bill and now Keiths, must repeatedly make their objection by arguing in the abstract? There is no mystery to this; arguing in the abstract provides the perfect amount of wiggle room to launch and cling to a false analogy. And the non-critical hangers-on will respond with applause.  

    This is how RB does it:

    Absent that assumed conclusion, your argument that DNA transcription is necessarily semiotic collapses due to a fatal error of logic. (A always causes B, therefore B is always caused by A.)

    And this is how Keiths does it:

    1 All floogs are sporgaceous.
    2 Gorpins are sporgaceous.
    3 Therefore, gorpins are floogs.
    That argument is logically invalid.

    For an abstract formulation to be valid, it must demonstrate the relationships it is said to be analogous to. I’ve already highlighted the fact that Bill’s analogy (among other major flaws) could only demonstrate the relationships between two elements, because it only has A and B. This is, of course, a problem because to be valid his analogy must demonstrate the relationships he is trying to refute – which includes three elements. Consequently his analogy is invalid on its face, yet he remains unfazed by this. He is also unfazed by the fact that no one has any evidence whatsoever of a non-semiotic process which could produce the material consequences of representations and protocols. Without that, his objection only serves a rhetorical purpose in the sake of argumentation, but it doesn’t actually reflect the real world. Keiths wants to save his cohort from these intractable problems, so he comes back with an abstract analogy of his very own, this time with three elements, each separated by the indicative verb “are”. To analyze Keiths abstraction, we should take a look at the three elements which must be demonstrated:

    a) The transfer of recorded information

    b) The physical consequences of that transfer (representations and protocols)

    c) The term “semiotic” or “semiotic state”

    So we have these three elements which must have their relationships demonstrated in order for Keiths’ analogy to demonstrate my claim is fallacious. But since he did not say, we must guess for ourselves as to how Keiths intended to place these three elements in his formulation. Here is the best guess:

    All transfers of recorded information are the physical consequences of the transfer

    The physical consequences of the transfer are semiotic

    Therefore, all transfer of recorded information are semiotic

    As any English-speaking person can see, the relationships provided by the indicative verb “are” do not form a coherent statement throughout, even though the elements themselves are where they need to be. It would be difficult to imagine a more clear demonstration that Keiths’ abstract analogy does not demonstrate the relationships required of it.

    In the first sentence the word “are” will have to be replaced entirely because not even a change in person/tense (is, be) can correct the sentence and demonstrate the appropriate relationship between the elements. In the second sentence the use of the word “are” is correct. The third sentence requires a change in tense at the very least, but can be more accurately stated. We end with:

    All transfers of recorded information entail physical consequences, i.e. representations and protocols

    Representations and protocols are semiotic

    Therefore, the transfer of recorded information demonstrates a semiotic state

    That fits very well with the statement Bill and Keiths would like to claim as a fallacy. I’m prepared to defend it with material evidence.

  57. Upright BiPed on May 16, 2012 at 7:00 amsaid:

    Dr Liddle, it’s understandable that you find my posts offensive.

    And yet I see no apology.

    Your posts started to become offensive to me last year, back when I was still singing your praises.

    And yet I have never treated you with the derisiveness with which you have treated me.  At the least, I would appreciate it if you would retract your entirely false accusation relating to the stickying of this thread.  This blog was not in fact created for the sole purpose of conducting this conversation, but far from trying to avoid the conversation, or let it die, I have gone to considerable lengths to keep it going, first by posting this thread, and subsequently by keeping it visible on the front page, and I will continue to do unless or until you let me know that you no longer wish to continue the conversation.  I have also asked you twice now, not to address me as “Dr Liddle”, but I see you have done so again.  It’s not very important, but it does indicate that you either do not read my posts properly, or that you don’t care whether you give needless offence.

    One of the offensive attributes of your posts is the number of times you play dumb to the history of the conversation between us.

    I do not “play dumb”.  I may make errors, and I may forget things, but I do not “play dumb”.  This accusation is technically against the rules of this site, but I will overlook it, as I try to err on the liberal side when the offendee is me.

    For instance, you may want to ask me why the semiotic argument “is an argument for Intelligent Design?”

    Not only do I want to, I have done so, repeatedly.

    You may even act as if you have no idea.

    Again, I don’t “act as if [I] have no idea”.  If I ask, it is because I want to know.  If you have already told me, then it is because I am either still, or no longer, clear.  In this case, it is the latter.

    I find this offensive, given that our conversation started with claims made about the ORIGIN of recorded information and its transfer. That conversation began in May of 2011 and lasted well into September, and even into October. In that conversation we repeatedly argued over the origin of the genetic information system.

    Yes, I know.

    Over and over, I made reference to issues regarding “the rise of recorded information” from the simple (non recorded information bearing) chemical organizations which are fundamentally required by your beliefs.

    And I still find your argument incomprehensible, for reasons that have also been given by others here.  I thought I knew what you were getting at, but your recent posts leave me baffled.  For the sake of those others, at the least, you need to restate your argument.

    And even though you were forced to retract your claim to simulate the rise of information,

    What I retracted, as I recall, Upright BiPed, and I would be grateful if you could actually link to the passage you are referring to, was a claim I made to be able to demonstrate that information could be readily generated by evolutionary processes.   My original claim was, as you will recall, based on Dembski’s definition of CSI.  I subsequently discovered that this was not the definition you were using, and so I said that I did not claim to be able to demonstrate the generation of information by your definition, but I’d be happy to have a go, if we could hammer out an operational definition.  Eventually, I gave up, because I ran out of time before we agreed on something we were both happy with.  At least that is my attempt at a summary.

    you repeatedly argued that evolution would always somehow find a way.

    I do not recall arguing this.  Please link to where you think I did so.

    Therefore I reasonably find it disingenuous of you to now ask how I think this argument is tied to ID. Perhaps you can remember some of the back and forth:

    Not disingenuous at all.  You claim to have “semiotic argument for ID”.  If so, it shouldn’t be very difficult for you to lay it out, or at least link to a clear exposition.

    Mycoplasma genitalium is one of the least complex freely living organisms on Earth and it has 450+ genes consisting of 582,000 base pairs. How much of that required function do you think you can get to without a representation-translation-effect system in place; in other words, in the absence of the genuine recorded information processing we find in mycoplasma? And it really doesn’t matter where you put the mark Elizabeth, wherever it is, you’ll need the very simplest of chemical organizations to organically produce the immaterial [ed. arbitrary] representations and protocols you must have to get any further.  (OCT 27th, 2011)

    I do not see here a “semiotic argument for ID”. 

    I am still waiting for you to make it.

  58. Upright BiPed on May 14, 2012 at 11:47 pmsaid:

    Mike,

    UBP says: “I made the specific claim that protein synthesis is observationally semiotic given that it demonstrates the use of representations and protocols, as does all other forms of recorded information transfer. And as such, I also claimed that it would require a mechanism capable of creating a semiotic state.

    What “representations and protocols” do atoms follow when they condense into stars? 

    Who the hell thinks that atoms follow representations and protocols as they condense into stars? Moreover, why should I engage someone who obviously doesn’t understand the content of the argument, or whose only hope is to misrepresent it?

    Upright BiPed, clearly none of us “understand the content of the argument”.  The reason why you should engage with us is to communicate that content.

    Please abandon your apparent default assumption that we are not posting in good faith.  It is one of the few rules I  have here.  Those of us who are querying your case are doing so because we are unable to parse it in any way that makes sense to us,  not because we are trying to annoy you, or make fun of you, or bury your argument, and we are not stupid, nor are we dishonest.  And even if we were, the rules of this site require that you assume that we are not. 

    Just as they require that we take your arguments seriously.

    Mike has raised a point that many of have raised, which is that the cascade of processes that make up the transcription and translation of DNA into a protein is not a symbolic process, nor is it “arbitrary”, given the DNA sequences that encode for the set of tRNA molecules we find in cells.  Which is why we do not find your use of the word “semiotic” appropriate.  Nonetheless some of us (me, for instance) are prepared to accept that it is “semiotic” by your definition of the word.

    What we want to know is why this amounts to an argument for design.

    Are you saying anything more than “transcription and translation is really really complicated and I don’t see how it could have evolved”?

    If so, what?

    (And FWIW, the reason I do not consider a DNA sequence “symbolic”, is that the whole DNA molecule, including the sequences that result in the production of a set of tRNA molecules, as well as ribosomes is, simply, a molecule, and, given the presence of that DNA molecule in a cell, and certain other molecules, a protein is simply the end product of a cascade of catalysed reactions, just as salt+water is the end product of an acid when confronted with a base.  It’s far more complicated, and includes catalysts, which are themselves products of the cascade of reactions,  but not symbolic.)

  59. It might be helpful to consider UB’s argument in a broader context.  He seems to be making the same argument seen in the putative science of Biosemiotics, or in the publications of Howard H Pattee, whom the notorious David L Abel has quoted extensively in his repetitive papers on “cybernetics” in biological phenomena.

    It all looks like woo to me, and a glimpse into the situation can be seen on the talk page of the Wikipedia article on Biosemiotics – and in the article itself! 

    “Biosemiotics attempts to integrate the findings of scientific biology and semiotics, representing 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.” 

  60. Pedant on May 16, 2012 at 12:59 pmsaid:

    It might be helpful to consider UB’s argument in a broader context.  He seems to be making the same argument seen in the putative science of Biosemiotics, or in the publications of Howard H Pattee, whom the notorious David L Abel has quoted extensively in his repetitive papers on “cybernetics” in biological phenomena.

    It all looks like woo to me, and a glimpse into the situation can be seen on the talk page of the Wikipedia article on Biosemiotics – and in the article itself! 

    “Biosemiotics attempts to integrate the findings of scientific biology and semiotics, representing 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.” 

    Well, woo or not, Upright BiPed still needs to make his argument explicit.  If he’s done so already, then he can provide a link.  If he thinks we have not understood it, then he needs to clarify it.

  61. This is quite helpful.

    And as I’ve been saying for a while, I’m willing to accept the application of the concept of semiotics to mechanical systems, at least for the sake of argument.

    It’s how it relates to ID that remains the puzzle.

  62. I’m thinking UPD has looked at a modern bacterial genome and concluded it is too complex to have poofed into existence,

    To complete his argument he needs to do what ID needs to do from any perspective: demonstrate it couldn’t have evolved. 

  63. Perhaps this will help re: Upright’s claim as he goes into some detail as to why it is an ID prediction. From UD. 

    Clearly, there is a huge group of people who carelessly throw around the word ‘information’ like it was a shapeless entity which can be taken for granted. Well, it can’t. Its existence imposes (observable) physical requirements on matter when it’s recorded and transferred (in any form). We live in a material universe, how could it be any other way?

    If the theory of material origins is actually true, then the idea itself predicts that the information in the genome is not semiotic – to borrow Dr Moran’s term – it is only ‘analogous’ to the kind of information transfer we as sentient beings use. One is symbolic and the other is chemical. Indeed, that position is argued by materialists (one way or another) ever day on this forum. The information transfer in the genome is said to be no more than a cascade of physical reactions, but of course, all information transfer is a cascade of physical reactions, so that is no answer, and it never has been. But why does the truth of materialism predict this (chemical-only transfer) anyway? Because the representations and protocols involved in semiosis would have only appeared on the map after billions of years of evolutionary advancement in organisms. An imaginative materialists may see a chemically non-complex origin of inheritable Life in his or her mind’s eye, but that image blows up if that heredity is accomplished by using representations and protocols. Ask a materialists “what came first on the great time-line of Life: a) molecular inheritance by genetics, or b) representations and protocols?” Typically confusions ensues, and the embattled assumptions of materialism are pushed to the very front of the defense.

    On the other hand, if ID is said to be true, then it’s own prediction is on the line. That prediction has been that the information causing life to exist is semiotic. And again, that is exactly what is argued (one way or another) on this board every day. When nucleic sequences were finally elucidated, we did not find an incredible new and ingenious way in which physical law could record and transfer information, we found the exact same method of information transfer that living agents use; semiosis. And as it turns out, if one properly takes into account the observable physical entailments of information transfer during protein synthesis, and compares it to the physical entailments of any other type of recorded information transfer (without exception), they are precisely the same. It requires an arrangement of matter to serve as a representation within a system, it requires an arrangement of matter to physically establish an immaterial relationship between two discrete objects within that system (the input and output), it requires an effect to be driven by the input of the representations, and it requires that all these physical things remain discrete. The semiotic state of protein synthesis is therefore confirmed by the material evidence itself, and with it, one of the predictions of ID theory.

    From here: http://www.uncommondescent.com/junk-dna/biochemist-larry-moran-responds-to-jonathan-m%e2%80%99s-junk-dna-post/#comment-403927

  64. “Ask a materialists “what came first on the great time-line of Life: a) molecular inheritance by genetics, or b) representations and protocols?”

     So we have the chicken and egg question. UPB’s nest of verbiage asks the same question that has been asked since Darwin. How did first life get started? There is no new question here, nor is there anything contributed to the understanding of the problem.

    It’s just a variation on irreducible complexity, pushed back to a era for which all historical traces have been erased. 

  65. The semiotic state of protein synthesis is therefore confirmed by the material evidence itself, and with it, one of the predictions of ID theory.\\

    Now we need a link to an independent, prior statement of the relevant ID theory.  Then some explanation of how a definition can be construed as a prediction, followed by a discussion of why this is interesting, new, or important.

  66. (And FWIW, the reason I do not consider a DNA sequence “symbolic”, is that the whole DNA molecule, including the sequences that result in the production of a set of tRNA molecules, as well as ribosomes is, simply, a molecule, and, given the presence of that DNA molecule in a cell, and certain other molecules, a protein is simply the end product of a cascade of catalysed reactions, just as salt+water is the end product of an acid when confronted with a base.  It’s far more complicated, and includes catalysts, which are themselves products of the cascade of reactions,  but not symbolic.)

    So from a purely material standpoint, a representation is not a representation if a protocol exist that can actualize that representation into the material effect it produces within a system. Great.

    By that standard, there are no representations anywhere in the cosmos. A music box does not contain a representation of a song because the presence of coordinated tines and pins within the music box can play that song. Likewise, a fawn nudging its mother’s flank is a not a sign of wanting to be fed, (sent to and recognized by the mother), because the doe has a protocol in her sensory system causing her to expose her teats for feeding. And the pheromone of an attacked ant is not a signal sent to the other ants in the colony, because the other ants have a protocol in their systems which causes them to respond by protecting the queen. Communication (the transfer of information) does not exist in the cosmos, because the material requirements for that communication exist. It all makes perfect sense.

    I once asked if you thought touching a warm object sent warmth up through your nervous system, or is it a representation of warmth, acting within a system which has the protocol to properly interpret it as warmth. You have now fundamentally removed that possibility; after all, it’s only molecules.

    What else can be said?

  67. From what I can tell Upright actually admits that it’s all about the origin of life.  

    Abstract representations and protocols are a formal system, Petrushka – a formal system. A system which must arise PRIOR to genetic heredity – prior to the onset of evolution by means of mutable genetic information. And it is also a sterling example of irreducibly complex (a physical representation and a physical protocol operating in a precise dynamic relationship, how could it be any other way, either object is useless without the other).

    http://www.uncommondescent.com/darwinism/4of-2011-for-id-community-stylus-computer-program-aims-to-bridge-gap-between-real-world-and-artificial-evolutionary-simulation/#comment-414379

    Here’s an actual example Upright gives of information transfer:

    When a wolf howls, he is recording information into an arrangement of matter to act as a representation within a system – to communicate (transfer) information. The other wolves perceive those representations and have the physical protocols in their brains to actualize their meaning. When a bee dances in flight on the way back to the hive, the other bees see the dance and can respond to it based upon its pattern. They can do so because they have a protocol in their sensory system which allows them to actualize that information. It is not I who has injected anthropomorphism into these observations, it is you. Clearly, you. Perhaps if you weren’t looking down your nose, you could see what was directly in front of you. One of the things you might find is the obvious.

    http://www.uncommondescent.com/evolution/simon-conway-morris-fossil-evidence-demands-a-radical-rewriting-of-evolution/#comment-422912 Here is what would disprove his claim, I think:

    I am not saying it is impossible, I am saying that no one can even provide a plausible conceptual pathway for making the jump to genuine recorded information, particularly one based upon the (entirely speculative) direct templating of relatively simple organic compounds.

    http://www.uncommondescent.com/intelligent-design/upright-biped-replies-to-dr-moran-on-information/#comment-411956 Here is a fact:

    Unfortunately for an educated person of his/her caliber, Dr Rec is reduced to these repeated off-hand comments because he has to actually ignore the contents on this site. The fact that recorded information requires an IC system of physical representations and transfer protocols is one of those observations to be ignored. It is not a data point anywhere in materialist biology, yet is is observably true on empirical grounds, and stands unrefuted.

    http://www.uncommondescent.com/intelligent-design/silly-arguments-against-god-by-very-clever-writers/#comment-416722
    An “IC system”? Perhaps that can be examined? And it does seem that his claim is that the (any) system cannot evolve:

    Recorded information requires abstract representations and transfer protocols; two material objects that must be coordinated even though they do not interact, and each must both be present in order for information transfer to take place. By definiton, such systems are beyond “step by step” configuration.

    So it seems ID is baked in by definition. http://www.uncommondescent.com/intelligent-design/once-upon-a-time-before-dna-or-rna-there-was-tna-if-it-ever-existed-in-life-forms/#comment-416519 He does give a way to falsify his claim:

    Aternatively, you can show that informational control is not required for the complex systems under question, or that information transfer does not require representations and protocols.

    And on and on and on.

  68. I wonder what the difference between ”genuine recorded information” and “recorded information” is….

  69. I think the analogy with language fails at the most elementary level.

    UPB observes that one string maps to another through “translation,”  but that is equivalent to saying that “jwqojdfrtoi3″ can be mapped to “pknvknjsdei” by a translation algorithm.

    What is lacking in the analogy is mapping symbols to meaning. 

    Mapping DNA strings to proteins is not mapping symbols to meaning, because biological meaning can only be assigned by selection. Proteins are not functional except as selected. 

    Even more remote is the possibility of mapping symbol strings to regulatory functions.  While it is possible in principle to map coding strings to proteins, it is not possible to anticipate the actions of regulatory networks. You simply can’t build a dictionary.

    This ties to my longstanding claim that biological design is impossible except through evolution. 

  70. I am not saying it is impossible, I am saying that no one can even provide a plausible conceptual pathway for making the jump to genuine recorded information, particularly one based upon the (entirely speculative) direct templating of relatively simple organic compounds.

    So we have a god of the gaps. 

  71. Just for the record, my posts are coming out wrong because the WYSIWYG editor is removing all my formatting, making it impossible to distinguish quotes from my comments.

  72. If you are going to define DNA as a symbolic language you have to ask whoo or what is reading or interpreting the language.

    It is not the biochemical translation system, because that is just doing chemistry. It doesn’t know anything about meaning.

    It is just as happy making a creature with three heads or Tay Sachs disease as it is making an individual for survival and reproduction.

    The interpreter of meaning is the process of differential reproductive success. 

  73. Upright Biped on UD said:

    If the theory of material origins is actually true, then the idea itself predicts that the information in the genome is not semiotic – to borrow Dr Moran’s term – it is only ‘analogous’ to the kind of information transfer we as sentient beings use. One is symbolic and the other is chemical. Indeed, that position is argued by materialists (one way or another) ever day on this forum. The information transfer in the genome is said to be no more than a cascade of physical reactions, but of course, all information transfer is a cascade of physical reactions, so that is no answer, and it never has been.

    Well, an important point is missing here, although ultimately it is irrelevant, I think.  But what Upright Biped is missing is that when an intelligent agent sends information (let’s say a message) to another intelligent agent, using a shared semiotic system (a shared system of symbols), the actual material substrate of those symbols is irrelevant.  A morse message can be sent by beeps, pixels, even knotted string.  The message will be the same, no matter what the physical carrier – what matters is that sender and receiver both know what to do with the pattern, no matter what kind of molecules or events actually make up the pattern.  However, in a cascade of chemical processes, the actual molecules are critical.  You couldn’t just write the sequence of the nucleotides on microscopic piece of paper, insert it into a cell, and expect the cell to “know” how to make the protein from the sequence of symbols on the paper. 

    That is not to say that the processes by which we intelligent agents decode morse is not, at bottom, physical.  I’d say it is (being a materialist and all).  But human intelligence is such that we devise shared symbol systems in which the symbols we use are independent of their physical substrate – and so the words I hope Upright BiPed is reading now will make no more or less sense in pixels than they would if he printed my comments out on a printer, and read them in ink, just as a paleolithic hunter who scratches an arrow shape on a tree can be as well understood by his colleagues as when, lacking a scratching tool to hand, he has the novel idea of making an arrow-shaped pattern of stones on the path instead.

    However, I am willing to accept, for the purposes of this argument, that we can regard DNA codons and codon sequences as “symbolic” by a somewhat stretched definition.  I have been saying so for some time.  So let’s move on:

    But why does the truth of materialism predict this (chemical-only transfer) anyway?

    I don’t see that it does, any relevant sense, but let’s grant it for now:

    Because the representations and protocols involved in semiosis would have only appeared on the map after billions of years of evolutionary advancement in organisms. 

    If we define “semiosis” in the sense I have suggested above, as being to do with symbol systems in which the information conveyed by the symbols is quite independent of their physical substrate, yes.  But not if we use your UBP’s definition.

    An imaginative materialists may see a chemically non-complex origin of inheritable Life in his or her mind’s eye, but that image blows up if that heredity is accomplished by using representations and protocols.

    Yess!!!!!!  I think we found the key to the problem here.

    Interestingly, this is a good example of what I have been asking for for some time.  When Upright BiPed has talked about “information transfer” in the past, he has mostly referred to the “genetic code” and, in particular, protein synthesis.  Here we are not talking about information transfer in protein synthesis, but information transfer from parent to daughter.

    So instead of the information transfer going from, in effect, DNA molecule (sender) to the rest of the cell (receiver), so that the cell makes the protein corresponding to the “instructions” sent by the DNA, we are talking about information transfer between parent (sender) to daughter (receiver).  And if we compare parent to daughter we can confirm that the message has been received with fairly high fidelity (because the pattern present in the parent is repeated in the daughter, more or less).

    Now we know that some molecules self-reproduce – in other words, they transfer the information embodied in themselves to a daughter molecule, who in turn becomes a parent, etc, and, indeed, we can track the lines of inheritance in such transfers.  It even happens in inorganic crystals, so it’s not confined to organic molecules. 

    But while Upright BiPed while appears to class the DNA -> cell process as  “semiotic”, when the result of the transfer is the production of a protein, by means of transcription and translation, does he also class parent -> daughter information as “semiotic”?

    Probably, yes, in the case of a cell.  But this raises the sixty-four-thousand-dollar question: how simple does self-reproduction have to be before it ceases to be “semiotic” for Upright BiPed?

    I have given a number of examples in the past, including the example of my round deck table in Vancouver, which had a hole in the middle for the umbrella.  One very snowy day, the table acquired about 1 meter depth of snow, and each layer had  dimple in the middle “representing” the hole was.  By the time my mother arrived at the breakfast table, their was maybe 1 foot of snow.  She asked why the snow had a dimple in the middle.  We explained that the table had a hole in it.  So information from the table was being regularly conveyed through each layer of snow, resulting in not-entirely illegible information being available to my mother, long after the hole itself had vanished from sight.

    Upright BiPed, IIRC, rejected this process as being “semiotic”.

    So my question to him now is: how complicated does self-reproduction have to be before you would class it as “semiotic”?

    And, as a follow up: why couldn’t the very earliest life forms have been a-semiotic (like my snow-table), with the semiotic stuff kicking in later?

    Ask a materialists “what came first on the great time-line of Life: a) molecular inheritance by genetics, or b) representations and protocols?” Typically confusions ensues, and the embattled assumptions of materialism are pushed to the very front of the defense.

    The confusion, I suggest, Upright BiPed, is on your side.  Either “molecular inheritance” need not involve “representations and protocols”, as I think you rejected in my snow-table, or something as simple as my snow-table should count as your “representations and protocols”, and there isn’t a problem for materialistic origins of “representations and protocols” (they can clearly emerge spontaneously within physical non-intelligent systems).

    If a double-stranded polymer consisting of a string of paired bases regularly split to form two single strands which each then bonded to free bases to form two copies of the original double-stranded polymer, would you say that was was a system of “representations and protocols”?  

    If so, we seem to have a system of inheritance without them.

    If not, why not?

     

  74. If you don’t like the wysiwyg editor, click on the HTML button and use regular HTML editor. 

    Most of the allowable tags are on the button bar, but if you want to use, say latex tags, you can use the HTML editor just for that, then, if you like, close the HTML and do the rest in the wysiwyg editor.

    I’ve made the number of allowable tags as large as I easily could.  I’d like to add image tags, but I haven’t figured that out yet (wp assumes we don’t want to risk spam images).

  75. petrushka on May 16, 2012 at 4:11 pmsaid:Edit

     

    This ties to my longstanding claim that biological design is impossible except through evolution.

    And to my twin claims that

    • Intelligence is itself a quasi-Darwinian process (learning algorithms are essentially evolutionary algorithms, and Hebb’s Rule is essentically Darwinian)
    • If we ever achieve convincing AI robots, not only will their artificial brains use evolutionary learning algorithms, but we will probably have used evolutionary systems to achieve them.  And we probably won’t be able to figure out easily, post hoc, how they work!
  76. Off topic note:

    There’s something a bit weird here.  As I read your comment, I see an “edit” button, which looks as if it is for editing the quoted petrushka message.

  77. “However, I am willing to accept, for the purposes of this argument, that we can regard DNA codons and codon sequences as “symbolic” by a somewhat stretched definition. “

    I don’t accept that. If it were symbolic it would be possible to create a dictionary mapping symbol strings to function. All UPB has is that the observation that a symbol set can be mapped to another equivalent symbol set (DNA–>protein).

    That is a chemical/mechanistic process that is entirely dependent on the emergent properties of chemicals. You cannot abstract the process. You cannot predict what protein(if any) will map to a novel coding string.

    Nor can you predict function.  In short, you have chemistry, but nothing that is equivalent to a language.

  78. Upright BiPed,

    Upright BiPed: “What else can be said?”

    What is left is what should have been agreed upon by all of us at the beginning and that is a clear meaning of what the term semiotic leads to and that is the existence of an “interpreter”.

    petrushka: “If you are going to define DNA as a symbolic language you have to ask whoo or what is reading or interpreting the language.”

    Our definition of semiotic does not seem to agree with your, (Upright BiPed’s), use of the term.

    When you have a “code”, you need a “decoder”, BEFORE it can be used.

    In the 70′s there was a computer called the Sage that used “p-code”, not CPU native code as most systems do.

    Their apps would be able to run on any platform supporting the “interpreter” for “p-code”.

    This is a system that would run the way you, (UPB), are using the term semiotic.

    The instructions for the app were not presentable to the CPU as object code but had to be read by a piece of native code that would “interpret” what operation should be carried out and then call the appropriate native code to execute the intended operation.

    Native code systems do NOT have an interpreter and are thus NOT semiotic as far as the host CPU is concerned as the object code be used without interpretation.

    Even though we say “object code”, it is not really a “code” that is presented to the CPU in native mode, since there is no intermediate “interpretation” going on.

    That is why we are having a problem understanding you.

    What happens in the cell is “native” chemistry, not “interpreted” chemistry.

    There is no intermediate layer or operation done that looks at a molecule and says, “Add A to B”, which then presents the “native” molecules required to carry out the chemical operation “requested”.

     

  79. Science fiction has explored the potentials of AI fairly extensively, and eventually the authors in the field sort of arrived at the idea of a phase change – that good AI simply isn’t going to happen until a computer becomes sophisticated enough to start programming itself. At which point improvements in AI will become both explosive, and incomprehensible to mere humans.

    I think this same phase change happened in the biological world with the advent of the first replication-with-heritable-variation. Exponential growth soon led to resource scarcity, which led to selection, which led to explosive speciation, etc. 

  80. Some days ago, I attempted to simplify this by considering the combination of oxygen and hydrogen to make water. Where are the “symbols” for this operation? Is UPB using oxygen as the “representation” for oxygen, and then calling it symbolic? Are more complex chemical reactions qualitatively different? If so, what exactly is the symbol, who is abstracting it, how is it stored, who is decoding it, etc.

    As I recall, this was basically ignored. 

  81. It doesn’t really matter whether it is P-code or object code, for any given instance of an interpreter. For any given machine, the “ability” to read and execute scripts is simply another layer of hardware (although one that can be altered without any apparent outward change).

    What matters to UPB’s discussion is that the entire process of translation is entirely mechanistic. What matters is how the interpreter came to exist in its current configuration.

    UPB has declared the system to be irreducible, just as the chicken and egg system are irreducible. He is, of course, assuming the conclusion he claims to be proving.

    So it is fair to ask why this argument is new or different from all the other ID arguments from irreducibility.

     

  82. Flint: “If so, what exactly is the symbol, who is abstracting it, how is it stored, who is decoding it, etc.

    As I recall, this was basically ignored. “

    This is what I don’t understand about UPB and other IDists.

    They say we haven’t refuted their claims yet they don’t respond to key responses we make to them and yet anyone reading the comments can clearly see the problems we have raised for their position.

    I haven’t been involved with creationists anywhere near as long as Mike Elzinga, but I’m already depressed at our chances of doing anything but keeping them out of classrooms with legislation.

    Logic and reason don’t work.

     

     

     

  83. Well, one serious problem here is that, by observation, education does not generally cure creationism. Instead, creationists learn ways of gussying up their simple fallacies with more sophisticated misdirection and more obscure scientistical jargon.

    After all of these many posts, I think we’ve reduced UPB’s complex system of distortions, assumptions, opionions, assertions-labeled-facts, and the like down to a simple argument from incredulity, all dressed up.  He simply can’t believe chemical reactions can become that complex without Divine Guidance. His “semiotic” argument is nothing more than engineering a gap to stick his god into – a gap that doesn’t exist.

    And even THAT isn’t the core problem. The core problem is, UPB “knows” that his god did it. This is axiomatic, not subject to negotiation or even to consideration. It just IS. And without that core impenetrable conviction, much of reality wouldn’t be incredible at all. Amazing, fascinating, to be sure. But not incredible.

    So the challenge as I see it isn’t to use logic, reason, experience, observation, etc. As you say, that doesn’t work. The challenge is to simplify all the misdirection well enough that the creationist must either deny the self-evident and look foolish, or simply ignore the objections. If the responses are done well, he has no other choices.   

  84. I find both UBP and WJM excruciatingly boring; and I suspect that the reason is that there is a remarkable similarity to other crackpots who, in their attempts to validate their crackpot ideas, will latch onto scientists, or anyone else who seems sympathetic, and dog them for months at a time.

    I am struck by the fact that both UBP and WJM, just as do crackpot perpetual motion machinists, seem to be trying to get folks here to work out the details of their “theories” for them.

    When one just looks at the pages and pages of “discussion” along with the amount of time it takes to get a single coherent thought out of either of them, one begins to wonder if there is any thought process there at all.  I would suggest not.

    They have this “intuition,” built on fallacious ideas floating around in their subculture, that they have stumbled upon some form of logic or theory that trumps and overturns all of science.  So all they have to do is hone and validate their “idea” against people who understand science.

    This has at least two advantages for the crackpot; they get the attention of someone in the science community who gives them “legitimacy,” and they hone their marketing shtick for their presentations to the gullible.

    There is another frequent correlation one sees among crackpotists; they often quote scripture from the Christian bible. That is, they have some connection to the subculture of sectarianism that has an instinctive hatred and distrust of science and any other perceived “competing authority.”  Crackpostist want to BE authorities and to be viewed with awe and respect.  They don’t do “science” to learn and contribute; they do “science” to get that awe and respect (and money).

    I have had direct encounters with crackpots at least three or four times over the course of my career; and I have heard and read of the encounters that others have had with them.  The patterns of these encounters are remarkably similar; and one of the most common themes in these encounters is that they will eat up all the time in the universe if one allows it.  Crackpots never let go voluntarily; they will ride you to death.

    There was a remarkable documentary on National Public Radio about six months ago of a science instructor in some university on the east coast who took a crackpot under his wing hoping to educate him about how science is done.

    The sympathetic approach started out looking like it might work; but as soon as some partial data were collected that looked like it might support the crackpot’s notions, the crackpot immediately went public with the incomplete and unverified data while claiming his ideas were supported by real scientific research done in a university in collaboration with real scientists.

  85. UPB: “Again, I note…no one has attacked the material observations made within the argument.”

    Of course not. There is nothing wrong with the material observations. What is wrong (among many other aspects that other people here have addressed) is the unwarranted labeling of a perfectly material process as an immaterial relationship. I notice that my last reply to you in this respect stands unanswered, and you have quietly retreated from discussing this fatal flaw in your argument.

    I would like to remind you that the last exchange addressed the fact that your claim to the existence of some presumably immaterial relationship (e.g. between the letter *a* in the English alphabet and the *ahhh* sound uttered by English speakers) rested on the absurd claim that this relationship is arbitrary in relation to material processes in general. That is, as I have pointed out, not only not the case, it cannot be the case. For the one phenomenon (the letter *a*) to be a representation of the other phenomenon (the *ahhh* sound), the processes establishing (and sometimes modifying) the relationship between the two (e.g. nerve impulses on one level, cultural influences on vowel-shifts on another level) must be non-arbitrary. That all these phenomena and processes are perfectly material should go without saying. Some of the phenomena and processes involved may be more law-like, whereas others may be more stochastic, but none of them can be arbitrary with regards to the components of the relationship.

  86. UB:

    For an abstract formulation to be valid, it must demonstrate the relationships it is said to be analogous to. I’ve already highlighted the fact that Bill’s analogy (among other major flaws) could only demonstrate the relationships between two elements, because it only has A and B. This is, of course, a problem because to be valid his analogy must demonstrate the relationships he is trying to refute – which includes three elements…

    a) the transfer of recorded information

    b) the physical consequences of that transfer

    c) The term “semiotic” or “semiotic state.”

    By now you’re eager to respond to the following: What does “semiotic” or “semiotic state” entail that “transfer of recorded information” does not entail?

    If nothing, then you in fact have two terms, not three.

    If something, then what? What does “semiotic state” entail that “transfer of recorded information” does not, therefore justifying your claim that your argument includes three terms?

    UB:

    By your logic, the claim that “hominid footprints at Laetoli confirm bipedalism in the Pliocene” creates the same logical fallacy… By the way, I note that instead of responding to any criticism of your objection, you simply repeated it.

    Then I refer you back to my statements vis what can, and what cannot, be confirmed by observations, just above.

    Useful theories generate operationalizable entailments that predict observations and may therefore be tested. Empirical tests can disconfirm a theory (if that which is predicted isn’t observed), but never really confirm it as a logical necessity. I cited my “rainstorm theory of wet lawns” which includes the theoretical entailment that rainstorms always result in wet lawns. The failure to observe a wet lawn following a rainstorm can disconfirm that theory (because the theory of wet lawns entails that rainstorms always result in wet lawns), but observing a wet lawn following such a storm, while increasing confidence in the theory, never confirms it with logical force, because although A entails B, it does not follow that B entails A.

    Nevertheless, confidence in the theory has increased, because a prediction generated by the theory has been confirmed. Confidence may be further increased by specifying further entailments of the theory. For example, another entailment of the theory might be a drop in barometric pressure prior to the appearance of a wet lawn. Failure to ever observe a drop in barometric pressure may disconfirm my theory of wet lawns, and certainly weakens it. OTOH, to observe a drop in the barometric pressure further strengthens confidence my theory, but never closes the issue.

    Confidence in the theory may also be increased because competing explanations for wet lawns may also have entailments that may be subject to disconfirmation. A competing theory that the wet lawns result from a neighbor operating a sprinkler entails that I have a neighbor and he has operated a sprinkler. If, upon testing that theory (upon observation I find that I have no neighbors, or that I have a neighbor but he doesn’t own a sprinkler) indirectly strengthens my theory by testing and disconfirming a reasonable competing theory. Other competing theories (say, the temperature dropped below the dew point) also have entailments that may be tested (the “falling dew point” explanation entails a drop below a specific temperature, given the humidity.) Notice confirmation is not accomplished simply by assuming the conclusion that there are no other possible explanations – as does the “semiotic theory of ID.” 

    The above is the iterative process by means of which we “confirm” theories. Confidence is strengthened by correct predictions arising from one’s theory and the discomfirmation of entialments arising from competing theories. Ultimately, some theories (the main assertions of contemporary evolutionary theory being a good example) have passed so many such tests that they are regarded as “confirmed.” However, as you well know (I hope), all such conclusions are ultimately provisional. The examples you cite have been “confirmed” in the above sense. They have not been confirmed in the sense that “A causes B, therefore if B, then A.”

    Your argument, by contrast, has exactly that structure, and commits that error.

    UB:

    What confirms semiosis is the presence of the unique material consequences of representations and protocols within a system. Representations and protocols are instantiated in material objects, and are associated exclusively with the phenomena of transferring recorded information.

    In the word “exclusively” we catch the assumed conclusion sneaking in the back door.

  87. In the word “exclusively” we catch the assumed conclusion sneaking in the back door.

    Also with the word “unique”. I always call this the religious approach to knowledge. SAY it’s true, and it becomes true. SAY it’s unique and exclusive, and POOF it’s unique and exclusive. And as has now been pointed out by many, the information transfer involved in protein synthesis, or of reproduction, is quite thoroughly explained by evolutionary theory. UPB isn’t referring to anything that hasn’t been long since observed in great detail, or fully explained.

    There is no dispute about any of the evidence in this case. The dispute seems to revolve around the meaning of the evidence. Both evolutionary theory and poof theory fully explain this evidence. Potentially, several other theories might do the same. UPB continues to repeat that poof theory explains everything, therefore poof theory must be correct.

    I think the difficulty trying to communicate boils down to UPB simply KNOWING poof theory is correct. To him, it’s stone obvious.

  88. Upright, Yesterday I posted the following synopsis of my interpretation of your argument. You have yet to respond. Does this fairly summarize your argument? If not, please supply us with a similarly concise and explicit synopsis of the argument you are making.

    keiths on May 16, 2012 at 5:30 am said:

    As far as I can tell, this is what Upright is trying to argue:

    1. A system that transfers information by arbitrarily mapping a representation to an effect is a semiotic system.

    2. A semiotic system consists of a representation and a protocol.

    3. Remove either of these and you no longer have information transfer; therefore semiotic systems are irreducibly complex.

    4. Irreducibly complex systems can only be the result of intelligent design; therefore semiotic systems are the result of intelligent design.

    5. RNA-to-protein transcription arbitrarily maps nucleotide triplets to amino acids.

    6. Therefore, by #1, RNA-to-protein transcription is a semiotic system.

    7. By #3, RNA-to-protein transcription must be the result of intelligent design. It’s a problematic argument, to be sure, but it seems to be what UB is claiming.

  89. I wonder if Upright thinks that protein synthesis is necessary for self-reproduction i.e. heredity?

  90. RB,

    By now you’re eager to respond to the following: What does “semiotic” or “semiotic state” entail that “transfer of recorded information” does not entail?

    Eager? These terms have already been described for you. The transfer of recorded information is the process whereby a representation induces a material effect within a system by means of a material protocol. I’m certain you were aware of that. The word semiotic is a term used to describe a system that operates via representations and protocols. The reason we are having this conversation is because representations and protocols are instantiated in matter by necessity; they have material consequences and can be individually identified by those consequences operating within a system. If there is a point you want to make about this, then by all means say it.

    If nothing, then you in fact have two terms, not three.

    The claim you have been attacking has three elements: the transfer of recorded information, its material consequences, and a semiotic state.

    Then I refer you back to my statements vis what can, and what cannot, be confirmed by observations, just above.

    You asserted that a fatal logical flaw had been committed because a claim was made about the transfer of recorded information. This fatal flaw, you argued, was based on the possibility that the claim could be wrong. You then claimed that this was not just a possibility, but a logical possibility, and that its status as a logical possibility meant that no evidence need be examined since none could change the logical possibility that the claim could be wrong. It was “fatally flawed” you repeated. But this effectively eliminates the ability to make any claim, because the only viable alternative is a claim that must be correct and cannot be wrong. The only purpose of your objection was to separate the claim from the evidence, and block the conversation. You all but said exactly that, emphasizing the necessity to correct this fatal flaw before continuing. Keiths said much the same thing. And all along the way, I’m trying to reassert that it’s the evidence itself which must mediate a claim.

    But when I bring this little problem to your attention, you return to take me on a tour of how it’s only the evidence which can increase or decrease our confidence in claims. Hello?    

    The examples you cite have been “confirmed” in the above sense. They have not been confirmed in the sense that “A causes B, therefore if B, then A.”

    Then you turn right back around, and once again try to use the bogus objection to separate the claim from the evidence. The level of rhetoric is embarrassing. Our confidence in every one of the examples I gave stems directly from the evidence that supports it. And I’ve already stated several observations which support my claim – not the least of which is observing “the presence of the unique material consequences of representations and protocols within a system. Representations and protocols are instantiated in material objects, and are associated exclusively with the phenomena of transferring recorded information.”

    In the word “exclusively” we catch the assumed conclusion sneaking in the back door.

    Sneaking in the back door? It’s a simple matter of fact; there’s not a single instance of these material consequences appearing in any physical process other than the transfer of recorded information. They are not documented anywhere else. It’s also perfectly clear that no one can even conceive of a method to record and transfer information by any other means. Hardly being a gap in knowledge, it’s a matter of genuine necessity – how else to record and transfer information if not by using the material in the cosmos?  If this is sneaking in the back door, then the homeowner has a hang-up. Perhaps he/she should become acclimated to the knowledge that representations and protocols are instantiated in material by necessity, and can been identified by their material roles.  

  91. Keiths,

    Your request is not unreasonable, but I am out of time just now. And quite frankly, outlining the argument is basically what I have been doing all throughout this thread. Here is a link to the argument as it was given to Dr Moran:

    http://theskepticalzone.com/wp/?p=659&cpage=1#comment-10621

    You might want to also keep in mind that the conclusion of the argument is that protein synthesis is observably semiotic and requires a mechanism capable of creating a semiotic state. That is the conclusion which is appropriate to the evidence. 

  92. UB:

    The claim you have been attacking has three elements: the transfer of recorded information, its material consequences, and a semiotic state.

    OK. Three elements.

    Maybe now you will answer this question: What does “a semiotic state” entail that “the transfer of recorded information” does not?

  93. RB,

    Maybe now you will answer this question: What does “a semiotic state” entail that “the transfer of recorded information” does not?

    Did you not see this in my previous post?

    These terms have already been described for you. The transfer of recorded information is the process whereby a representation induces a material effect within a system by means of a material protocol. I’m certain you were aware of that. The word semiotic is a term used to describe a system that operates via representations and protocols. The reason we are having this conversation is because representations and protocols are instantiated in matter by necessity; they have material consequences and can be individually identified by those consequences operating within a system. If there is a point you want to make about this, then by all means say it.

    The transfer of recorded information entails the transfer of form in order to produce an effect. A semiotic state entails the use of represenations and protocols.  

  94. UB

    You might want to also keep in mind that the conclusion of the argument is that protein synthesis is observably semiotic and requires a mechanism capable of creating a semiotic state. That is the conclusion which is appropriate to the evidence. 

    It is observably a mechanism of repeatable transfer of sequential information from one form into another – if that is what you mean by ‘semiotic’, then yes, and it is self-evident that that state requires a mechanism of coming-into-being. Analogous states come into being by various means – from the mind of a single or several designers with a specific intent (eg EBCDIC, ASCII), or by evolutionary change from simpler precursors with no overall plan (eg human language). In the latter respect, ‘semiosis’ comes from a gradual replacement and elaboration of symbols – for example, pointing at something and gurning becomes the more specific “LION!”, then the more detailed “LION ATTACK!” or “LION FUNNY-LOOKING!” … All very interesting, but hardly a foolproof guide as to how ‘semiotic’ relationships in biological macromolecules would be expected to arise.

    It is an interesting fact that biological macromolecules are almost exclusively built upon template. DNA is template-copied and transcribed, RNA is reverse-transcribed and theoretically capable of direct copying to its complement. Never mind protein; is this is a ‘semiotic’ relationship? A means T (or U); T(or U) means A; C means G; G means C.

    In the ribosome, these relationships hold true. The tRNA anticodon follows those ‘rules’. It just so happens that the tRNA anticodons are at one end of a complex RNA that has an amino acid at the other. That amino acid could be any acid, naturally occurring or synthetic, and the ribosome will still clip it to the growing chain. So there is nothing ‘semiotic’ going on there. aaRSs are the real ‘lookup table’ in this setup – the closest approach to a ‘semiotic’ state. But that state – a set of acid-specific protein aaRSs, and a rather slack one-way linkage from codons – is entirely derivable from a non-semiotic one – an even slacker single (non-protein) aaRS analogue.

    As Elizabeth and Petrushka have wondered, and I too have noted, you conflate the origin of the code with the origin of life, without any definitive basis for doing so. Without a reliable means to accurately replicate DNA, there is no starting material for an effective mechanism of ‘specified’ protein synthesis – the best translation system in the world would fail if the underlying text were routinely corrupted. If one infers from present complexities that the whole system of protein-aided replication and protein sythesis, complete with error-correction, was cooked up ab initio by a Designer, we simply have a variant of Creationism, unsupported by anything other than the present-day absence of viable precursor systems, and a strained analogy.

    The gradualist scenario explains salient features of the code – codon groupings by acid property, binary subdivisions of the 64-element table, the inequality of significance of the three elements of the triplet, aaRS and tRNA ‘families’ based upon their structure and sequence, the centrality of RNA to the mechanism. It explains, in principle, how natural ‘semiosis’ can evolve.

  95. Upright BiPed on May 17, 2012 at 1:12 pmsaid:

     

    The transfer of recorded information entails the transfer of form in order to produce an effect. A semiotic state entails the use of represenations and protocols.  

    So can you give an example of a transfer of information (“recorded” or otherwise) that does not “entail the use of representations and protocols”?

    Or are you saying that all information transfer is semiotic?

  96. UB:

    The transfer of recorded information entails the transfer of form in order to produce an effect. A semiotic state entails the use of represenations and protocols.

    That doesn’t really answer the question, does it?

    Are you saying that a semiotic state entails the use of representations and protocols, but the transfer of recorded information does not? (I would think not, based on your previous posts).

    Are you saying that the transfer of recorded information entails the transfer form in order to produce an effect, but a semiotic state does not? (I would think not, based on your previous posts.)

    Then what? What does a “semiotic state” entail that “the transfer of recorded information” does not?

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