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. Do while Allan sticks to his guns

    Google
    Cut
    Paste

    End while

    I think I may have said I don’t care who agrees, or appears to agree, with you. I passed all my exams despite my viewpoint. Because I know what the system does.

  2. Incidentally, I don’t strictly associate codes with mental activity. I associate them with representation. That representation eventually must hit a mind to be noticed, even if it didn’t start in one. But fundamentally, codes are maps IMO, and hence can’t be territory by definition.

    As I and others have said, spectral lines constitute a valid code for an element. They represent that element; they are not the element. Or, seasonally relevant (up here anyway), consider the pattern of leaves under a tree. They represent the shape of the tree’s branches, projected in two dimensions. They are a ‘map’ of the tree; they aren’t the tree. It doesn’t require a mind to make a map.

    Do you (Mung) think a triplet represents an amino acid? Does the triplet also represent its complement (anticodon or antisense), or any RNA that may happen to bind to it? Why, in each case?

  3. A map is a way of associating unique objects to every element in a given set. So a map f:A|->B from A to B is a function f such that for every a in A, there is a unique object f(a) in B. The terms function and mapping are synonymous for map.

    http://mathworld.wolfram.com/Map.html

    The association between nucleotide sequences and amino acid sequences exists regardless of what humans think about.

  4. Mung: The association between nucleotide sequences and amino acid sequences exists regardless of what humans think about.

    The lack of symbols with abstract meanings in DNA also exists regardless of all the IDiot equivocation.

  5. Allan, your argument against the genetic code, as I understand it, involves the claim that symbols and representations do not exist in the cell. My rebuttal to that has been to show that scientists do in fact speak in precisely those terms when talking about the cell.

    However, I fail to see how my own argument about whether the genetic code is a code hangs on the issue of symbols and representations. I think those are ancillary.

    A nucleic acid sequence – an amino acid sequence – a mapping from the elements of one set to the elements of the other set. A code.

    What those elements stand for or code for or represent, in what sense then they are symbols, all seems to me superfluous to the argument.

    Your thoughts.

    ETA: The entire question of “meaning” is beside the point.

  6. …the whole theory [information theory] could be expounded without any reference to conscious communication.

    – Henry Quastler

  7. The only condition for representation is that a complete system of translation, a code, be agreed upon. The limitations are set only by the ability to discriminate information to be represented, by the ability to produce accurately a desired representation and by the range of the code.

    – Henry Quastler

  8. Do you have a point?

    Your definition game is the most tedious and pointless set of threads in the history of this site.

    At least other lame threads have consisted of some line of reasoning and not just endless quote mining.

  9. …the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code.

    – Paul Davies

  10. Mung: …the living cell is best thought of as a supercomputer

    Doesn’t matter who said it. Chemistry isn’t a supercomputer, and computers are just junk without programming.

  11. Mung: Checkmate was long ago. That was the signal to get up and leave the table.

    Yes, it’s long time that Evolutionism gave up and allowed the practice of bolding certain sections of existing papers to take over and reign supreme.

  12. Mung,

    Checkmate was long ago. That was the signal to get up and leave the table.

    So why are you calling us back? Paul Davies, you say. Is that Paul Davies of Paul Davies Kitchen Appliances?

  13. petrushka: Doesn’t matter who said it. Chemistry isn’t a supercomputer, and computers are just junk without programming.

    And life is more than mere chemistry. If it isn’t then your side has many stupid scientists.

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