Upright Biped’s “Semiotic Theory” redux.

I have been having an exchange with Upright Biped here about his perception of how his “semiotic theory of Intelligent Design” has fared among sceptics. In the hope that he will be prepared to re-engage with us in addressing a few outstanding points, I post his argument, originally published at lawyer Barry Arrington’s Uncommon Descent blog

1.  A representation is an arrangement of matter which evokes an effect within a system (e.g. written text, spoken words, pheromones, animal gestures, codes, sensory input, intracellular messengers, nucleotide sequences, etc, etc).

 

2.  It is not logically possible to transfer information (the form of a thing; a measured aspect, quality, or preference) in a material universe without using a representation instantiated in matter.

 

3.  If that is true, and it surely must be, then several other things must logically follow. If there is now an arrangement of matter which contains a representation of form as a consequence of its own material arrangement, then that arrangement must be necessarily arbitrary to the thing it represents. In other words, if one thing is to represent another thing within a system, then it must be separate from the thing it represents. And if it is separate from it, then it cannot be anything but materially arbitrary to it (i.e. they cannot be the same thing).

 

4.  If that is true, then the presence of that representation must present a material component to the system (which is reducible to physical law), while its arrangement presents an arbitrary component to the system (which is not reducible to physical law).

 

5.  If that is true, and again it surely must be, then there has to be something else which establishes the otherwise non-existent relationship between the representation and the effect it evokes within the system. In fact, this is the material basis of Francis Crick’s famous ‘adapter hypothesis’ in DNA, which lead to a revolution in the biological sciences. In a material universe, that something else must be a second arrangement of matter; coordinated to the first arrangement as well as to the effect it evokes.

 

6.  It then also follows that this second arrangement must produce its unambiguous function, not from the mere presence of the representation, but from its arrangement.  It is the arbitrary component of the representation which produces the function.

 

7.  And if those observations are true, then in order to actually transfer recorded information, two discrete arrangements of matter are inherently required by the process; and both of these objects must necessarily have a quality that extends beyond their mere material make-up. The first is a representation and the second is a protocol (a systematic, operational rule instantiated in matter) and together they function as a formal system. They are the irreducible complex core which is fundamentally required in order to transfer recorded information.

 

8.  During protein synthesis, a selected portion of DNA is first transcribed into mRNA, then matured and transported to the site of translation within the ribosome. This transcription process facilitates the input of information (the arbitrary component of the DNA sequence) into the system. The input of this arbitrary component functions to constrain the output, producing the polypeptides which demonstrate unambiguous function.

 

9.  From a causal standpoint, the arbitrary component of DNA is transcribed to mRNA, and those mRNA are then used to order tRNA molecules within the ribosome. Each stage of this transcription process is determined by the physical forces of pair bonding. Yet, which amino acid appears at the peptide binding site is not determined by pair bonding; it is determined  by the aaRS. In other words, which amino acid appears at the binding site is only evoked by the physical structure of the nucleic triplet, but is not determined by it. Instead, it is determined (in spatial and temporal isolation) by the physical structure of the aaRS. This is the point of translation; the point where the arbitrary component of the representation is allowed to evoke a response in a physically determined system – while preserving the arbitrary nature of the representation.

 

10.  This physical event, translation by a material protocol, as well as the transcription of a material representation, is ubiquitous in the transfer of recorded information.

 

CONCLUSION:  These two physical objects (the representation and protocol) along with the required preservation of the arbitrary component of the representation, and the production of unambiguous function from that arbitrary component, confirm that the transfer of recorded information in the genome is just like any other form of recorded information. It’s an arbitrary relationship instantiated in matter.

 

My personal view is that there are a couple of basic faults with UB’s argument. It appears to address origin-of-life (OOL) theories rather than than the theory of evolution (ToE) and it is a default argument; “OOL fails, therefore Intelligent Design”. I have no training in logic, so Reciprocating Bill’s comments, later taken up by keiths, have been a bit over my head. It is a shame that UB seemed to lose interest in defending his argument before we got to the meat of the biochemistry, where I have a little knowledge, now outdated, as this is where his argument really falls apart for me. I think the attempt to link semiosis to protein synthesis just fails utterly.

I invite other critics of Upright Biped’s argument to briefly summarize, paste or link their queries or objections in the hope that Upright Biped may find the time to respond.

ETA:

Elizabeth has devoted some considerable time to considering Upright Biped’s semiotic argument as previous threads, such as this one demonstrate.

152 thoughts on “Upright Biped’s “Semiotic Theory” redux.

  1. OMTWO:

    I guess that’s your way of saying that I am the only evidence that my ancestors ever existed. But how stupid is that?

    By the way, what evidence do you have that proteins had ancestors, other than the fact that proteins exist?

  2. Stupid is as stupid does, my dear Mung.  
    Yes, you are the only evidence that your great-great-great-great-great-great-grandparents ever existed (well, you plus any other descendants, your many-times distant cousins, that they managed to leave).  We don’t have their names, their birth certificates, their photographs, their DNA on file, their gravestones, their bones … nothing.  Their existence is proven only by the fact that here you are and you had to have come from someone.

    Unless you are going to claim that you were poofed into existence without human ancestors?   

  3. Yes, hotshoe, I understand. I am the only evidence that my ancestors existed, as long as we disregard any other evidence they existed. Relevance?

  4. C’mon, Mung, don’t be more stupid than you have to.

    We’re not disregarding any other evidence that your great-great-great-great-great-great-grandparents existed.  We don’t have ANY evidence that they did exist – no bones, no DNA, no records whatsoever.  They died, rotted, and are gone forever.  Except for the proof that they must have existed because – here you are – today’s living descendants must have come from somewhere.

    Please tell me you are smart enough to understand this simple logical concept.  

     

  5. gpuccio:

    They explored the space one step distant from the functional protein. Of course they found a lot of functionality. What did you expect? And, even so close to the original protein, for 20 sites even one substitution was essentially fatal to function. And this would be an argument against the “islands of functions” model?

    You are standing on a vast chessboard. Someone tells you that the square you are on is the only square on which you can possibly exist. You are on an island so tiny … so you try a step. You immediately explode. Better not go there again (though you do, repeatedly, poor sad memoryless sap that you are)! Maybe they were right.

    Hey ho. Another move. This time … no, everything seems fine. The entire population comes with you – it has to settle somewhere. “OK”, intones the mystery voice, “maybe your island is 2 squares big. But that’s it. You can go no further.”.

    So now … you are standing on a vast chessboard. Someone tells you that the square you are on … OK, and the one you just left … are the only squares on which you can possibly exist. You are on an island so tiny … so you try a step …

    At some point, of course, the protein whose evolution we are visualising no longer catalyses the same reaction. But if it doesn’t matter, or if something else does (a duplicate, for example), you leave that on ‘functional island’, and drift merrily on waters that, it turns out, aren’t full of boiling acid. You fetch up on a strange shore …

  6. Mung,

    By the way, what evidence do you have that proteins had ancestors, other than the fact that proteins exist?

    By the way, what evidence do you have that Mung had ancestors, other than the fact that Mung exists?

  7. What is this “evidence” that you have that you can use to prove you have ancestors Mung?

    Are you like the witches out of Dune, can you recall your ancestral memories?

    If not, please do tell what evidence you have for your 25th Grandfathers existence?   

  8. So for 75 positions out of a hundred, any substitution is essentially synonymous. So out of 300 possible one-stem mutations, 225 have little effect.

    This is a vertical cliff? 

  9. OMTWO:

    By the way, what evidence do you have that Mung had ancestors, other than the fact that Mung exists?

    I had no ancestors.

    But why do you think my existence is evidence that I had ancestors?

    hotshoe:

    Please tell me you are smart enough to understand this simple logical concept. 

    You haven’t presented a logical concept.

    All living things which exist, or have ever existed, exist because they had a living ancestor. Is that the logical concept you’re talking about?

    The biogenetic law?

    But surely you believe that the first living thing did not have a living ancestor, right?

    Please tell me you are smart enough to understand this simple logical concept.

  10. Funny how you all seem to think that the only way for an organism to die is if it falls off a cliff.

  11. Noah is everyone’s common ancestor.

    Noah had a wife. Let’s assume she was not a descendant of Noah.

    Noah had three sons, who also had wives. Let’s assume the wives of Noah’s sons were not a descendant of Noah.

    Noah is not everyone’s common ancestor.

     

  12. This is too funny not to quote. Axel, at UD:

    You are voices in the wilderness, UDers, crying out for every valley of ignorance to be filled with understanding, and every mountain and hill of nonsense to be be brought low; and the crooked to be made straight, and the rough ways to be made smooth and erudite;…

  13. And no one is saying each ‘island of function’ is only one amino acid in width.

    No, of course they aren’t, and the fact that you think that we think people think that makes me wonder if you still haven’t ‘got’ what a fitness landscape represents. 

    A point in a fitness landscape is simply a genotype. It could be anything from the entire genome of an individual, down to a single base at a particular position. The whole space consists of every possible permutation of strings of that length. However big or small you make your segment of interest, there are other points in the space of all strings-of-that-length that will be either ‘closer’ or ‘further away’, based upon the amount of amendment you have to do. You could make it an amino-acid in size, or even smaller, because you are talking of a particular locus in a wider genome. But you don’t have to. However big or small, it will have a fitness landscape, in the space of of all possible genotypes at that position.

    Among a set of close-together points, there will be some that are more fit, and some that are less. At the extreme, the less-fit will be lethal. And GP points to this as some kind of evidence in favour of islanding. By single-acid amendment within the longer amino acid sequence, they find that a percentage of the local neighbourhood is lethal – the fitness slope from a funtional point to these is vertical: a cliff. GP leaps on this and say “see – an island!” Despite the fact that everywhere else is not directly blocked by such a vertical drop. Confirmation bias!

  14. I don’t think the word incorrect means what you think it means. Gpuccio asserts that there are missing intermediates because there cannot be. He is wrong about this.

  15. Mung: Noah had a wife. Let’s assume she was not a descendant of Noah.

    Noah had three sons, who also had wives. Let’s assume the wives of Noah’s sons were not a descendant of Noah.

    Noah is not everyone’s common ancestor.

    But Noah’s sons have Noah as a common ancestor.

    Am I missing something?

     

  16. But Noah’s sons have Noah as a common ancestor.

    Knowledge of sex seems to be missing among biblical literalists. I noticed this when I pointed out that all men should have the same X chromosome.

  17. Perhaps, again, it would be illuminating if Mung explained who was and who was not on Noah’s ark and where the wives of Noah’s sons came from. 

    Let’s assume the wives of Noah’s sons were not a descendant of Noah.

    Is poor wordplay all you’ve got?
    No, the wives were not Noah’s descendants (although in those days…) but it’s quite true to say: Noah is everyone’s common ancestor as for everyone living that’s true (if your story is true of course). 

    To keep Mung happy you should have said: “Noah is not everyone’s common ancestor, as his son’s wives were not decended from him but apart from those couple of people Noah is for everybody else from the time of teh fludde on”

    as we all know how demanding Mung is re: accuracy. 

  18. It’s not wordplay. Mung simply doesn’t understand how sex works. It is not possible for the story of Noah to be true and Noah not be the ancestor of every living human and his X chromosome not the X chromosome of every living male.

  19. I have suspected for a very long time now that ID/creationists really believe that by not ever looking at real science and never cracking open a real science textbook – even at the most basic level – they never have to take science or scientific evidence into consideration.

    Therefore, any arguments against them that are derived from scientific evidence and common scientific knowledge can simply be brushed aside, allowing the ID/creationist to go on claiming no one has refuted his assertions and “arguments.”

    It’s like the little kid standing in the middle of the room with his eyes closed thinking that he is invisible.  Deny reality; therefore reality doesn’t exist or count for anything.

    Actually, maybe they are more like the Ravenous Bugblatter Beast of Traal that is so stupid it thinks that if you can’t see it, it can’t see you.  Hence all the ID/creationist razzle-dazzle tap dancing around, spamming up threads, and avoiding any accountability for anything.

    This Mung character fits both profiles pretty closely.  He eats up threads saying nothing.

  20. Maybe here is where the “worldview” wordgame makes sense. In the science world, reality makes all the final decisions. Eventually, scientists everywhere converge on the same explanation, for the simple reason that the explanation is pretty damn nearly correct. And so we constantly see people from the science world taking it for granted that evidence matters, that observations mean something, that a single correct explanation exists and it can be understood with some effort.

    Over in the religious world, there is no reality on which all claims must ultimately rest. There are only opinions which can’t be supported, and can only be asserted. “Knowledge” in the religous world means others agreeing with you, so the battle isn’t against a reality reluctant to reveal its details, but rather against those fighting to win hearts and minds to an inferior cause. And when the scientific types demand evidence, the religious response is one of frustration. They SAID it, over and over. How much more evidential can any assertion GET?

    So the goal in science is to increase understanding of reality, and the goal in religion is to increase the number of converts to one’s opinion.  And these are appropriate goals, given that in science there ARE answers and in religion there aren’t any, but there IS power.

    The difficulty happens when religious folks make scientific claims, but utterly lack the tools to evaluate them — the main tool being the ability to recognize what IS a scientific claim. It is quintessentially religious that the answer to whether the sun revolves around the earth or the earth around the sun depends solely on who has the power to punish those of the other opinion.

    And it’s equally religious to decide potentially scientific questions by controlling access to comments. We flatter ourselves that the UD people don’t much come here because their idiotic claims are unprotected here from the slings and arrows of outrageous reality. But in truth, they see little reason to join a congregation whose faith conflicts with their own. The “cult of evidence” seems determined to deny what they’ve always known to be true.     

  21. As best I can tell, Mung, nobody hereabouts thinks this ‘semiosis’ thingie isn’t real. The point on which Upright Biped differs with his critics, is whether or not ‘semiosis’ renders unguided evolution impossible, which I would hope you recognize is a different question than whether or not ‘semiosis’ is real.

  22. Things a bit slow over at UD, you thought you’d come and shake the tree? 🙂

    I hate to dive into Merriam-Webster like some Creationist hack indulging a passion for argument by definition, but it says here:

    Semiosis

    a process in which something functions as a sign to an organism

    New Latin, from Greek sēmeiōsis observation of signs, from sēmeioun to observe signs, from sēmeion

    Soooo … yes, semiosis is real. Consider it dealt with. Organisms make and receive ‘signs’. But no-one outside Biped and his coat-holders at UD takes seriously the argument that protein translation is such a communication methodology (despite the common use of words such as ‘translation’ or ‘represent’). And whatever words you use to describe them, none of its features are intrinsically unevolvable.

  23. OMTWO:

    Semiosis is real. Therefore ID. Wow, your argument is persuasive.

    That’s not my argument, so I don’t care whether you find it persuasive or not.

     

  24. Mung, at UD (see BA’s post:

    Materialist OOA Research is Obviously Silly. What Does That Say About Materialist OOL Research? 🙂 )

    That’s what I love about Upright BiPed’s argument. It makes them focus on the material requirements.

    And when the see the implications, they run like hell.

    Talk about intellectual dishonesty.

    How many threads was it? Three, four here, several there? Thousands of posts, tens of thousands of words, all (according to Mung) the sound of ‘anti-UB’ argumenters ‘running like hell’.

  25. All their victories, yet where are the fruits?

    They came, they saw, they conquered.

    They think. 

  26. What then was 
    Semiosis is real. Deal with it.
    Supposed to mean? What’s the relation to ID? 

  27. Sorry to resurrect this thread, but it seems to be a recurring theme among the UD people. 

    Alan Fox posted this component of Upright Biped’s formulation of the UB semiotic theory:

    “3.  If that is true, and it surely must be, then several other things must logically follow. If there is now an arrangement of matter which contains a representation of form as a consequence of its own material arrangement, then that arrangement must be necessarily arbitrary to the thing it represents. In other words, if one thing is to represent another thing within a system, then it must be separate from the thing it represents. And if it is separate from it, then it cannot be anything but materially arbitrary to it (i.e. they cannot be the same thing).”

    I am too weary to verify that Alan’s representation matches UB’s published version, but I assume it does.

    After so many comments, it appears that “arbitrary” should be taken to mean “not governed by a causal law of the behaviour of natural materials”. In particular, he seems to focus on the arbitrariness of the relationship between the nucleotide structure of codons and their corresponding amino acids. In other words, any nucleotide sequence (or evidently, any number of sequences made up from the UAGT letters), could have been “chosen” to represent a particular amino acid.

     I have two questions:

    1. How does he account for the experimentally observable fact that there is  correlation between the physical/chemical characteristics of a particular codon and the amino acid to which it matches (or more accurately between the codon’s characteristics, the matching RNA that mediates the protein assembly, and the amino acids that are assembled)?

    2. Why are UD proponents so keen on asserting the primacy of “information” in explaining biological processes? Is it simply a transliteration of “In the beginning, there was the Word”?

    In relation to 1: without any prior knowledge about the mechanics of the DNA > RNA > protein chain, I would hypothesise that there is some law-like relationship between the physical and/or chemical attributes of a codon and those of the amino acid that it codes for (via corresponding characteristics of its RNA, of course). If it were not so, how would proteins ever reliably assemble?

    And it appears to be so: on the talk page for the Wikipedia entry on “genetic code”, there are a number of entries pointing to papers that show a forward and reverse correlation between the hydrophilic or electrophilic characteristics of particular codons and the corresponding characteristics of the coded amino acid. Surely, this is saying that the codon > amino acid translation is not arbitrary, but is naturally law-like.

    In relation to 2: I would assume that the simple existence of a sequence of code translations (meaning translations in recording form that preserve the coded content) can tell you absolutely nothing about how the coding systems arose. In particular, there is nothing in a current series of coding forms that can tell you whether the sequence always existed, or whether it arose from some other arrangement via change and feedback. So why prioritise the current form of the code?

  28. timothya,

    In regard to your point 1, there is some apparent correlation, but I’m inclined to be dubious about its significance for code evolution. It is not at all necessary that the association be ‘law-like’ in any way before natural processes can account for it.

    The most essential part of the system is chemical: the activation of carriers, locking energy in the bond holding the acid to the acceptor stem, and the serial daubing of these activated carriers to the growing end of a peptide chain by the ribosome’s peptidyl transferase activity. No code is necessary for this, and reduced tRNAs, a few nucleotides in length, with no anticodon at all, will perform peptide synthesis. Such peptides are not ‘specified’ – there is no means of determining the sequence of acids – but that does not mean that their products would be nonfunctional – there are more roles for protein in the cell than highly-specified catalysis.

    UB is obsessed with the notion that you can’t make protein without protein. But very short RNA ribozymes have been discovered that will aminoacylate, and peptidyl transferase is an RNA function even today. There is no reason to consider protein essential for its own manufacture.

    The codon has a physical role in docking the tRNAs, which assists the formation of the bond as well as providing for sequence specificity, and the STOP codon has a physical role in causing the peptide to terminate. STOP does not ‘mean’ terminate, it actually has the physical effect of causing termination, due to the absence of tRNAs.

    So the early code may have been simple, with the triplet matrix divided in some proportion between STOP and just a single nucleotide-tRNA association – perhaps all xUx codons bound tRNA and all other codons caused STOP. This is a physical link in both cases, not a semantic one. You either bind a tRNA or you cause termination.

    It’s not hard to see how such a simply-partitioned triplet matrix could become increasingly subdivided, in days when protein was not so embedded in metabolism as it later became. ‘Law-like’ properties would constrain changes to tend towards substituting chemically similar acids in given triplet neighbourhoods, but would not force any particular codon-acid link – that would be down to a combination of history and the ‘accident’ of current codon usage permitting a nonlethal subdivision on 1st or 3rd position discrimination. This may go down to the specific base or to purine vs pyrimidine level.

  29. Allan Miller posted:

    “In regard to your point 1, there is some apparent correlation, but I’m inclined to be dubious about its significance for code evolution. It is not at all necessary that the association be ‘law-like’ in any way before natural processes can account for it.” 

    Agreed that the correlation between the codons’ current physical/chemical relationship to their amino acids tells us nothing about how that relationship came to be (its code evolution).

    But. We can demonstrate (through tests like Lenski’s) that pre-existing systems of “code to function” (code to protein) can develop new functions under the influence of environmental selection.

    If those new biological functions are not a product of permissible law-like physical/chemical protein structures, then how do you propose we explain the novel protein structure and its novel function?

  30. Allan Miller posted:

    “So the early code may have been simple, with the triplet matrix divided in some proportion between STOP and just a single nucleotide-tRNA association – perhaps all xUx codons bound tRNA and all other codons caused STOP. This is a physical link in both cases, not a semantic one. You either bind a tRNA or you cause termination.”

    I think this may worth focus. The evolution of the STOP codon must be fundamental. Without a physical delimiter, a “gene” makes no sense (without a reliable STOP (or START) instruction, the RNA transcription process would just rip through the entire length of the chromosome).

    Can we see when the STOP codon evolved? 

  31. I was referring to the code, rather than things made with it. The ‘law-like’ reference is to the ‘naive chemistry’ of certain denizens of UD who think that natural mechanisms can only account for chemical interactions where the interactors are directly transformed, or some other physical constraint drives things in a particular direction. Selection is of course such a constraint, but there is a significant role in evolution for the ‘truly’ random. 

    I’m not saying that the various steps in code evolution did not have adaptive significance, but that it is likely many other pathways could have occurred which (had they occurred) may have had equal adaptive significance. Many different codes are possible, but that arbitrariness is not evidence that it had to be designed. So in refutng UB it isn’t necessary (not fundamentally, anyway) to point to particular chemical correlations in the current code and infer adaptative, or evolutionary, significance to them. The codon does not have to have any of the properties of the acid.

    Where law does come into it is in the role of energy in the interaction. The amino acid is activated with a phosphorylated intermediate, and (in modern organisms) the peptide bond energy comes both from this activated intermediate and the alignment from docking against mRNA triplets. Why triplets rather than doublets or quadruplets is open for discussion, but in a ‘primitive’ triplet code there still need only be two states, dock/non-dock. Non-dockable triplets are STOPs; dockable triplets do so by ‘law’ – a tRNA is attracted towards them. Variation in the strength of this binding can lead to discrimination among a growing family of differently-charged tRNAs during evolution, provided the substitutions are not excessively disruptive to existing proteins.

  32. I’d say the STOP is there all along. But we’d need to know what primitive genes looked like, and the primitive library of available amino acids, to ascertain the proportions of STOP/non-STOP on the matrix.

    It could be that all codons were initially STOP except one, and genes were highly mutation-susceptible repeats of this triplet, making poly-something (I favour polyglycine).

    More likely, the matrix may have been initially subdivided by a 2nd-base purine/pyrimidine distinction alone. xRx binds the (sole) tRNA, xYx does not, or vice versa. Subsequent refinement would bring other bases into play, and more tRNAs bearing more and more acids, reducing the number of STOP codons to 2 or 3 (which probably is adaptive – STOP mutations and errors are likely more disruptive than any individual acid-for-acid swap, so reducing the set renders you less prone to this). 

  33. Alan Miller writes:

    Many different codes are possible, but that arbitrariness is not evidence that it had to be designed. So in refutng UB it isn’t necessary (not fundamentally, anyway) to point to particular chemical correlations in the current code and infer adaptative, or evolutionary, significance to them. The codon does not have to have any of the properties of the acid.

    I admit to not following the discussion once Upright BiPed scuttled back to UD, but was his issue really with the arbitrariness of the mapping between codons and amino acids?  That would indeed be foolish, since any mapping could be used as evidence for ID by that logic.

    I thought, based on his original discussion with Elizabeth when I was still reading UD, that he was basically making an argument from incredulity based on the fact that he couldn’t imagine how something like a ribosome could evolve.  Is that not still his schtick?

  34. Patrick,  your argument from plausibility is hardly a superior alternative to what UB offers.

    Your ‘I don’t see how such and such could not evolve given …..etc etc’ hardly makes for a convincing argument. 

  35. Yet, all we can expect to see from Miller is a promissary note for the actual demonstration of how it can/did evolve.

    Arguments from plausibility are promotional give-aways; cheaper by the dozen.

    It is ID that demonstrates intelligence as the only known method of creating the system.  That is the default observation that needs to be proven wrong.

    So until a demonstration from your side is forthcoming, ID is the logical, rational conclusion.

    Alan Miller: “Soooo … yes, semiosis is real. Consider it dealt with. Organisms make and receive ‘signs’. But no-one outside Biped and his coat-holders at UD takes seriously the argument that protein translation is such a communication methodology (despite the common use of words such as ‘translation’ or ‘represent’). And whatever words you use to describe them, none of its features are intrinsically unevolvable.”

  36. Patrick,

    Arbitrariness is not the whole of the argument, but it is a point that arises repeatedly in discussions. It is a cousin of gpuccio’s ‘necessity mechanisms’ accounting for sequential information – if something could take many forms, and the one it does take is useful, then they infer agency.  

    But generalisations such as ‘arbitrary’ are not in any case particularly useful in something as complex as the genetic code, in an evolutionary scenario. If a particular 4-codon group is taken by a given amino acid, and those codons are used in proteins, then subdivision of that group is constrained depending upon codon usage and the chemical properties of the substituted acid. If the new acid is ‘sufficiently similar’, and the codons affected occur in ‘sufficiently non-critical’ positions, then substitution may occur and not be overly detrimental.

    The result appears designed – the codon neighbourhood is divided between two acids of similar chemical properties, meaning that accidental misreads result in chemically similar substitutions at single sites – fault tolerance. But the origin of that apparent single-site tolerance (in the above scenario) is that genome-wide substitution of that codon favours chemical similarity.

  37. So until a demonstration from your side is forthcoming, ID is the logical, rational conclusion.

    Scientifically speaking, that is nonsense. All there is with ID is the conclusion. There is no testable hypothesis that attempts to explain anything at all. There are things we don’t know and things we maybe are incapable of ever knowing but we can observe, experiment and hypothesize. You are making the same default assumption that Upright Biped uses to arrive at his “an agency did it”. There is no more reason to default to “ID” (though it is unclear what you have in mind as “ID”) than space aliens, God or the flying spaghetti monster. They are all equally imaginary.

  38. Steve,

    You speak in stock ID jargon. ‘Promissory notes …?’. I’m promising nothing. The origin of the genetic code is an historic fact which neither of us could ‘prove’ by doing it afresh. All I am doing – all anyone can do – is to examine the only information we have – the molecular biology of modern organisms – and attempt to infer constraints and possible historic pathways that could account for the undeniable patterns. There is no attempt to deny reality here – scientific hypotheses must take account of the facts and properties of matter, not simply waft them away when they prove inconvenient. Arguments from plausibility are certainly to be preferred to arguments from implausibility. 

    UB’s argument is essentially a philosophical one. “Based on these material observations, is there a way other than Design … ?” Yes, there is. Try understanding it. He takes ‘material observations’ and attempts to determine ‘best explanation’ for those. It rather hinges upon an opinion as to what is the best explanation. With a rather limited understanding of biochemistry, many of you feel that ‘best explanation’ is a cobbling together of the pieces by a designer. And of course so does Behe. But I don’t consider that to be the case at all. Where does that leave us?

    It is ID that demonstrates intelligence as the only known method of creating the system.  That is the default observation that needs to be proven wrong.

    Not even slightly. How could anyone ‘prove wrong’ the involvement of agency in an unwitnessed historic event, even if one managed to do something similar by another means?

    Intelligence is the only known method of making the things that we make. Biological entities are not currently among them. This idea that ID should be the null hypothesis (how come KF goes into paroxysms when we suggest that ID sees itself that way?) is a fantasy that has yet to find its way into science and (if I may make a prediction) never will.

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