What A Code Is – Code Denialism Part 3

My intent here in these recent posts on the genetic code has been to expose the absurdity of Code Denialism. The intent has not been to make the case for intelligent design based upon the existence of biological codes. I know some people find that disconcerting but that would be putting the cart before the horse. No one is going to accept a conclusion when they deny the premise. And please forgive me if I choose not to play the game of “let’s pretend it really is a code” while you continue to deny that it actually is a code.

First I’d like to thank you. It’s actually been pretty neat looking up and reading many of these resources in my attempt to see whether I could defend the thesis that the genetic code is a real code. I admit it’s also been much too much fun digging up all the reasons why code denialism is just plain silly (and irrational).

That the genetic code is a code is common usage and if “meaning is use” that alone ought to settle the matter. But this is “The Skeptical Zone” and Code Denialism is strong here. But I’m not just claiming that it’s a code because we say it’s a code in common usage. I’m claiming it is a code because it meets the definition of a code. The reason we say it is a code is because it is in fact a code.

My first two posts have been on some of the major players and how they understood they were dealing with a code and how that guided their research. I’ll have more to say on that in the future as it’s a fascinating story. But for now …

What A Code Is

: Information Theory and Coding
: Norman Abramson
: 1963
: Chapter 3

Definition. Let the set of symbols comprising a given alphabet be called S = {s1,s2,…,sq}. Then we define a code as a mapping of all possible sequences of symbols of S into sequences of symbols of some other alphabet X = {x1,x2,…,xr}. We call S the source alphabet and X the code alphabet.

Definition. A block code is a code which maps each of the symbols of the source alphabet S into a fixed sequence of symbols of the code alphabet X. These fixed sequences of the code alphabet are called code words.

“…the genetic code is a block code…” – Yockey, 1992. p. 102

For some people the word “symbol” seems to be a stumbling-block. Tt’s not quite clear why that is the case.

: Introduction to Coding Theory – Lecture Notes

Definition 1.1

Let A = {a1,…, aq} be an alphabet; we call the ai values symbols.

More on that shortly.

: Information Theory, Evolution, and the Origin of Life
: Hubert P. Yockey
: p. 6

The genetic code has many of the properties of codes in general, specifically the Morse Code, the Universal Product Bar Code, ASCII used in computer equipment, and the U.S. Postal Code. I shall explain the relation of these codes to the genetic code in the following discussion. Every code, as the term is used in this book, can be regarded as a channel with an input alphabet A and an output alphabet B. Here is the formal definition of a code.

Given a source with probability space [Ω A, pA] and a receiver with probability space [Ω B, pB], then a unique mapping of the letters of alphabet A on to the letters of alphabet B is called a code. (Perlwitz, Burks, and Waterman, 1988)

Here pA is the probability vector of the elements of alphabet A and pB is the probability vector of the elements of alphabet B.

My claim has been all along that the genetic code meets the mathematical definition of a code. This is hardly a matter of dispute.

To close out this OP I’ll leave you with the following:

Sydney Brenner remembered going to a talk Sanger gave at that time [1951] – the excitement, especially among the younger scientists, as they emerged. “At last, we knew what proteins were.” With that vanished any possibility of a general law, a physical or chemical rule, for their assembly. “With that, you absolutely needed a code,” Monod said.

119 thoughts on “What A Code Is – Code Denialism Part 3

  1. Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.

    – Hubert P. Yockey. Information Theory, Evolution, and the Origin of Life. p. 6

  2. : Norman Abramson
    : Information Theory and Coding
    : 1963
    : Chapter 3

    Note 2. One of the most interesting applications of the ideas discussed in Chapter 3 is that of genetic coding (Golomb, 1961, 1962). It has been determined that the vast amount of information necessary to specify the structure of a biological system is contained in the chromosomes of the parent system. More precisely it is the deoxyribonucleic acid (DNA) contained in the chromosomes which transmits the genetic information. In 1953 Crick and Watson showed that DNA existed in the form of a double helix. These helices may be thought of as being connected by sequences of four nucleotides which comprise the genetic message. The nucleotides, usually designated A, C, G, and T (for adenine, cytosine, guanine, and thymine), correspond to the code symbols discussed in Chapter 3. Experimental evidence therefore indicates that nature operates with a four-symbol code alphabet. These code symbols are combined in some manner to represent about twenty amino acids which must be manufactured by the new biological system. The manner in which nucleotides (A, C, G, T) are coded to represent the different amino acids is the primary problem in genetic coding.

    Messages, symbols, representations and codes. Only a problem for code denialists.

  3. They will burn their own house down to stop that foot from getting in the door, Mung. It’s pathological.

  4. Hey Mung,

    Back to UB’s dual admission:

    – It does not follow from semiotic theory that any particular class of causation – e.g. “intelligence,” “agency,” etc. is required for the origination of “semiotic systems” in biology.

    – It does not follow from semiotic theory that any class of causation, e.g. unguided natural processes, selection, etc., is excluded from the origination of “semiotic systems” in biology.

    I gather you would characterize “real” codes as symbol-bearing, and therefore semiotic, systems.

    Does it not follow from UB’s admissions that semiotic theory is silent on the origins of “semiotic systems,” and therefore the origins of symbol bearing codes, in nature?

  5. Richardthughes:
    Given your entailments, non of this helps ID?

    It’s joy enough to point out the faux skepticism of the anti-ID anti-science crowd here at TSZ. 🙂

    My reasoning is like this, if the existence of biological codes and biological semiotic systems did not in some way support the case for ID, people here would not be so adamantly opposed to those facts. But they are opposed.

    Reciprocating Bill seems to be an exception. I think that he accepts that the genetic code is a real code and that it’s not the only biological code that exists. I hope I got that right.

  6. Mung,

    Do you think the genetic code was designed by an intelligence? If you do, then why do you believe it?

  7. I’m not sure I’ve commented on codes at all. Our last meaningful ID exchange was me teaching you basic probability distributions.

  8. Mung,

    My reasoning is like this, if the existence of biological codes and biological semiotic systems did not in some way support the case for ID, people here would not be so adamantly opposed to those facts. But they are opposed.

    That’s bad reasoning.

  9. Neil Rickert:

    My claim has been all along that the genetic code meets the mathematical definition of a code.

    Well, quite obviously, it doesn’t.

    Good luck getting that fact to penetrate the fog. 🙁

  10. Gatlin describes a code as a way of mapping a domain on to a counterdomain. If several elements in the domain code for (map onto) the same element in the counterdomain, a degenerate relation exists. This is the case in the genetic system, where several codons can code for the same amino acid. … This formal requirement for a code should be kept in mind.

    – Susan Oyama. The Ontogeny of Information. p. 81.

  11. William J. Murray: They will burn their own house down to stop that foot from getting in the door, Mung.

    What foot? You’ve never read the bible so it can’t be that god?

    I’m guessing that you just want to submit to something, anything William, anything to take the responsibility away.

  12. Mung,

    And please forgive me if I choose not to play the game of “let’s pretend it really is a code” while you continue to deny that it actually is a code.

    Who is this *you* you speak of?

    I think the time has come to name names and have an actual back and forth debate with those people, rather then just post quotes that seem to support your argument in new OP’s.

  13. William J. Murray,

    They will burn their own house down to stop that foot from getting in the door, Mung. It’s pathological.

    So the insistence that a triplet is not a symbol is ‘burning down the house’? A tad hyperbolic, I feel.

    ID is tripe regardless whether the Genetic Code is a ‘real code’ or not. What makes you think it is unevolvable, beyond the drumbeat insistence “it’s a code, I tells ya, and code don’t evolve!”? Or if you agree that it is evolvable, why all the hoo-hah about whether someone thinks it’s a code or not?

    There’s certainly some pathology going on somewhere. 4 threads here, plus endless snickering at UD, all because I made the teasing statement to Mung “You know I don’t think the genetic code is really a code, don’t you?” Were I a troll, I’d be rubbing my hands with glee at the fun I’ve caused.

    I notice you have not addressed the case as to whether the triplet can genuinely be said to symbolise the acid that is attached to a growing peptide. I know you think ‘yes it does’, but do you have a more substantive reason? Or are we just trading semantic opinions (which is certainly what I think we’re doing)?

  14. Neil Rickert,

    : My claim has been all along that the genetic code meets the mathematical definition of a code.

    Well, quite obviously, it doesn’t.

    Unless you write it down!

  15. Chortle!

    Would this be a code? (Tried this before, but no-one reads what Code Denialists write, because it’s such a preposterous position it’s not worth the effort 🙂 ).

    You have a set of paint brushes with 3 different ends. 3 different paint-loading machines can only handle one of the brushes each, based on the shape of its bottom end. You end up with a consistently-inked set of brushes, with correlation between shape and colour.

    Does the shape of the bottom end represent the colour?

    Now you have a set of holes which are complementary to the brush-end shapes, such that they neatly dock within them. The brush-ends are attracted by magnets to sit within their complementary shape. The sequence of the holes dictates the sequence of colours at the other end. Wipe against a sheet of paper and you get a consistent pattern on the paper.

    Does the complementary shape of a given hole represent the colour consistently associated with it? Does the sequence of holes represent the sequence of colours? I’d say not. That’s all. Hang me for my impertinence!

  16. My reasoning is like this, if the existence of biological codes and biological semiotic systems did not in some way support the case for ID, people here would not be so adamantly opposed to those facts. But they are opposed.

    Yeah, ‘cos everything is about ID. It colours my every thought. How to defeat it? I know! I’ll become a Code Denialist! Game, Set and Match, I think. That’ll show ’em.

  17. William J. Murray:
    They will burn their own house down to stop that foot from getting in the door, Mung. It’s pathological.

    Mung has presented a convincing case. I now believe the genetic code is a code.

    Thank you Mung.

    Will there be a part 4?

  18. Mung: Reciprocating Bill seems to be an exception. I think that he accepts that the genetic code is a real code and that it’s not the only biological code that exists. I hope I got that right.

    I’m granting “real” codes arguendo as groundwork for this question regarding UB’s dual admissions:

    – It does not follow from semiotic theory that any particular class of causation – e.g. “intelligence,” “agency,” etc. is required for the origination of “semiotic systems” in biology.

    – It does not follow from semiotic theory that any class of causation, e.g. unguided natural processes, selection, etc., is excluded from the origination of “semiotic systems” in biology.

    I gather you would characterize “real” codes as symbol-bearing, and therefore semiotic, systems.

    Does it not follow from UB’s admissions that semiotic theory is silent on the origins of “semiotic systems,” and therefore the origins of symbol bearing codes, in nature?

  19. Allan Miller:
    Would this be a code?

    It is not a code although it could be the realization of a code.

    If there are separate rules about what constitutes correct mapping of symbol to reference (for language) or of input string to output string (for math codes), then that would make a code.

    As I understand your physical instantiation, the shapes of the paint brushes are the input instantiation and the colors are the output instantiation.

    I suspect the rules for the code were in your head when you designed the machine which implements it.

    In the other thread, Mung says codes can have material causes. So I take this as agreeing that your arguments about how DNA transcription could have arisen could very well be correct.

    But I may be misreading him. I doubt that I will ever know, one way of the other. There are too many threads to be created to take the time to answer questions in old ones.

  20. Rumraket,

    Will there be a part 4?

    Looks like:

    I’ll have more to say on that in the future as it’s a fascinating story.

    And indeed it is. One I’ve known for 40 years. You’d think I’d have realised it was a ‘real code’ by now.

  21. BruceS,

    I suspect the rules for the code were in your head when you designed the machine which implements it.

    I nicked them from nature! It’s a reasonable analogue of the translation system. DNA triplets are holes, anticodons the complementary shape on the brush end, and amino acids the colours.

    One can use it as a code, by writing down the mapping. Then, ‘hexagonal hole’ would map to ‘blue’ and so on. But it is not itself a code. An actual, physical hexagonal hole causes blue to appear in a specific place by a purely physical, non-symbolic, set of links. It’s only when we abstract it into symbolic representation that it becomes a code.

  22. BruceS,

    As I understand your physical instantiation, the shapes of the paint brushes are the input instantiation and the colors are the output instantiation.

    Strictly, it’s the shape of the holes the brushes slot into which forms the ‘input’. This is the equivalent to saying an RNA triplet ‘represents’ an amino acid. Although of course RNA is copied from DNA, so DNA triplets have the same profile as anticodons. The amino acid is variously ‘represented’ either by part or counterpart, depending where you start.

  23. hotshoe_: Good luck getting that fact to penetrate the fog.

    I do wonder why Mung is so obsessed with this.

    Allan Miller: Unless you write it down!

    Yes, that makes a difference.

    The important point here is that what makes something a mathematical object is human intentions, rather than its physical properties.

  24. BruceS: If there are separate rules about what constitutes correct mapping of symbol to reference (for language) or of input string to output string (for math codes), then that would make a code.

    The problem in biology is not chemical mapping, but effect mapping.

    When I started my thread about “What is a Code” I was referring to the problem of mapping sequences to effects. By effects I mean somatic effects.

    Let UPB or Mung try mapping sequences to effects.

    Isn’t that what we are talking about when we speak of design?

  25. Is complementary pairing a code? You can create a mapping, but does A represent T, C represent G, and vice versa? Let’s add sequence – does AAAGC represent GCTTT, TTTCG, or neither?

    The relationship is the same as codon-amino acid, albeit a smaller matrix and a less convoluted causal chain.

  26. petrushka: The problem in biology is not chemical mapping, but effect mapping.

    Isn’t that what we are talking about when we speak of design?

    I don’t understand what you mean by “effect mapping”.

    When I speak of a “designER” as I understand some of the ID people to be using the term, I mean the fact that they claim that some intelligent agent must be chosen the rules for the right mapping.

    OTOH, I understand Walto’s version of the ID argument to say that some agent must have made the essentially arbitrary (random?) decision on what the mapping will be, since no scientific law can make such arbitrary (random) choices.

  27. Allan Miller: One can use it as a code, by writing down the mapping. Then, ‘hexagonal hole’ would map to ‘blue’ and so on. But it is not itself a code. An actual, physical hexagonal hole causes blue to appear in a specific place by a purely physical, non-symbolic, set of links. It’s only when we abstract it into symbolic representation that it becomes a code.

    As you’ve said elsewhere, there’s no sense denying it’s a code, since codes can be defined not to require symbolic representation. I think that tack makes more sense, myself. You define ‘code1’ and ‘code2’ where one of them requires repesentation and the other doesn’t. Both kinds are REAL. But only one of them is useful for making a case for design, and that’s where the evidence/argument is needed.

    Without sticking with carefully defined terms, this discussion is a waste of life, consisting of nothing but question-begging, equivocations, and snide remarks about who’s denying the obvious.

  28. BruceS: I don’t understand what you mean by “effect mapping”.

    I mean, IDists need to demonstrate that it is — in principle — possible to design biology. They need to demonstrate that there is some property of chemistry that makes it possible to anticipate the effects of sequences and changes to sequences.

    Design means anticipating the effects of novel combinations of materials.

    My take is that biology is an emergent phenomenon. The properties of novel arrangements and novel structures cannot be anticipated. Without foresight, there is no design.

    There can, however, be evolution.

  29. Allan Miller,

    You have a set of paint brushes with 3 different ends. 3 different paint-loading machines can only handle one of the brushes each, based on the shape of its bottom end. You end up with a consistently-inked set of brushes, with correlation between shape and colour.

    Does the shape of the bottom end represent the colour?

    Now you have a set of holes which are complementary to the brush-end shapes, such that they neatly dock within them. The brush-ends are attracted by magnets to sit within their complementary shape. The sequence of the holes dictates the sequence of colours at the other end. Wipe against a sheet of paper and you get a consistent pattern on the paper.

    Does the complementary shape of a given hole represent the colour consistently associated with it? Does the sequence of holes represent the sequence of colours? I’d say not.

    Do you have the graphic skills to put this in a diagram (I certainly don’t)? That would allow the discussion to focus on the actual biochemistry instead of equivocations on the word “code”.

  30. walto: Without sticking with carefully defined terms, this discussion is a waste of life, consisting of nothing but question-begging, equivocations, and snide remarks about who’s denying the obvious.

    The shame is that the biochemistry is truly fascinating. Semantics and linguistics are (or can be) interesting too. Political agendas, not so much.

  31. Again, if anybody actually wants to write something sensible on this subject–and I here mean not only mung, UB, FMM, Frankie, etc., but also those here who think they’re wrong–you need to define any of these that you use: ‘code’ ‘map ‘symbol’ ‘arbitrary’ etc. And then you must stick religiously to the terms AS defined. Otherwise, as I said above, you might as well be yelling into your shoes.

  32. Patrick,

    Do you have the graphic skills to put this in a diagram (I certainly don’t)? That would allow the discussion to focus on the actual biochemistry instead of equivocations on the word “code”.

    Sadly no. I barely have the linguistic skills! Still, I do think it helpful to think of complementary shapes rather than symbols. This isn’t just a matter of ‘denying ID’; it’s better biochemistry to avoid misrepresenting the system.

    The 64 triplets can be divided into 2 sets of 32 by putting one triplet in one and its complement in the other. Each element in one set has its exact antiparallel complement, a snug fit of optimal binding on shape and charge. You can make 32 triplet pairings from these sets. Because either one of a pair can take the role of codon and anticodon respectively, you get 64 possible tRNAs (61/62 actual). They aren’t Scrabble tiles, and people genuinely interested in the science would be better stopping thinking of them as such. They bind, and whatever is on the other end gets bound at the same time.

  33. walto,

    I think I have defined my terms, and followed those definitions consistently. I am simply told I am wrong to define things thus!

  34. Neil Rickert: I do wonder why Mung is so obsessed with this.

    Probably because dealing with the evidence is so unproductive. I mean, they never do, other than cut and pastes to show that it’s a code, then they pretend that indicates intelligent design. No, the trick would be to show that intelligent design made the genetic code and life, then they could conclude that (all known) codes require intelligent design. Do it backward, though, and you may look to the rubes like you have a case, when one can’t possibly do it forward, that is, right.

    Glen Davidson

  35. Allan Miller:
    walto,

    I think I have defined my terms, and followed those definitions consistently. I am simply told I am wrong to define things thus!

    I think you have been pretty good about this. But while the last post of yours I excerpted denied that the genetic connections are a code (because they don’t evidence representativeness), you earlier said you had no problem calling those connections codes. I get that that’s because you are simply noting that people can define terms as they like, but, as indicated it’s better not to have fifteen different meanings of “code” floating around–all of them in use. It’s simply impossible to tell who is disagreeing with whom (or what) because everyone is (or at least might be) just talking past each other.

    That’s what I mean by a waste of life.

  36. Richardthughes:
    Indeed. By that ‘reasoning’ we should all be design denialists.

    LOL! Brave Sir Mung is back with latest installment of IDiot Strawmen on Parade.

    Mung likes to think of himself as the smartest guy in the IDiot room. He has his strawman talking point just like Joe G has “Stonehenge” and KF has his fishing reel. Exactly like them he’ll repeat the stupidity ad nauseum until people get tired of answering. Then he’ll scurry back to UD and declare victory.

    Of course Brave Sir Mung will never provide his definitions of “code” and “real code”. That would be too much like honest discussion.

  37. walto,

    I think we all agree (?) that a code is a mapping of symbols. My case is that a physical triplet is not a symbol mapping to (translating to, being converted to, referencing) a physical amino acid in a peptide chain. You can write the relationship down, using symbols. That’s a code, the relationship isn’t.

    I know it’s a bit dull and repetitiously expressed.

  38. Allan Miller:
    walto,

    I think we all agree (?) that a code is a mapping of symbols.

    I wouldn’t think so. It’s mapping, but why “symbols”? Just because that’s what human-made codes use? That’s what I’ve never liked about denial of the genetic code as code, the assumption that a code must be just like a human code, rather than to simply work “like a code” in the sense of one thing mapping to another.

    My case is that a physical triplet is not a symbol mapping to (translating to, being converted to, referencing) a physical amino acid in a peptide chain.

    Why define a code as having to be made by symbol-using intelligence? Stick with mapping, forget the symbols, and we’ve got a code. Is the lens of the eye not a lens because no one ever thought up the eye lens (or did so only after its discovery)? To me it just doesn’t make sense to define things in terms of human thought processes, thereby categorizing evolved systems differently from intelligently concieved ones.

    You can write the relationship down, using symbols. That’s a code, the relationship isn’t.

    Yet they follow the same mapping, if done right, the symbolic representation and the chemical/biologic transcription/translation. We symbolize what actually happens, and I can’t see why one mapping is “code” just because it truly involves symbols, and the other is not “code” because it isn’t symbolic, merely functional.

    Glen Davidson

    I know it’s a bit dull and repetitiously expressed.

  39. Allan Miller: You can write the relationship down, using symbols. That’s a code, the relationship isn’t.

    Are you saying that codes do not exist without someone to write them down using symbols? What makes it a code is in the writing of it? And of course, what the writing represents is the relationship, but it’s not the relationship that is the code?

    ETA: Agree with Glen. Look at that.

  40. Patrick: That would allow the discussion to focus on the actual biochemistry instead of equivocations on the word “code”.

    If this is aimed at me, saying I’m equivocating over the use of the word code, please read the OP.

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