Code Denialism Pt. 1 – Crick

There are a lot of great resources available on the internet for countering Code Denialism. I’ve gathered a few of them for your convenience. I envision a multi-part series on this topic because the evidence against Code Denialism is so extensive and Code Denialism seems to be surging in popularity here at TSZ.

The 1961 paper by Crick et al. is an outstanding example of the use of thought and logic to solve basic biological problems. In my opinion, it is a superb paper to assign to students in courses because it illustrates how combining knowledge and wisdom can provide answers to important scientific questions.

Establishing the Triplet Nature of the Genetic Code

They demonstrated that three bases of DNA code for one amino acid in the genetic code. The experiment elucidated the nature of gene expression and frame-shift mutations.

…the mutant strains could be made functional again by using proflavin to insert or delete a total of three nucleotides. This proved that the genetic code uses a codon of three DNA bases that corresponds to an amino acid.

Crick, Brenner et al. experiment

“This concept of a phase shift, or a ‘frameshift’ [in the genetic code of an rII gene] as we later called it, was so foreign to people in genetics that we had endless problems trying to explain this work.”

Seems like they still have work to do.

The famous paper:

THERE is now a mass of indirect evidence which suggests that the amino-acid sequence along the polypeptids chain of a protein is determined by the sequence of the bases along some particular part of the nucleic acid of the genetic material. Since there are twenty common amino-acids found throughout Nature, but only four common bases, it has often been surmised that the sequence of the four bases is in some way a code for the sequence of the amino-acids. In this article we report genetic experiments which, together with the work of others, suggest that
the genetic code is of the following general type:

(a) A group of three bases (or, less likely, a multiple of three bases) codes one amino-acid.

(b) The code is not of the overlapping type.

(c) The sequence of the bases is read from a fixed starting point. This determines how the long sequences of bases are to be correctly read off as triplets. There are no special `commas’ to show how to select the right triplets. If the starting point is displaced by one base, then the reading into triplets is displaced, and thus becomes incorrect.

(d) The code is probably `degenerate’; that is, in general, one particular ammo-acid can be coded by one of several triplets of bases.

Is the Code Degenerate?

… the code is probably `degenerate’, that is, in general more than one triplet codes for each amino-acid. It is well known that if this were so, one could also account for the major dilemma of the coding problem, namely, that while the bese composition of the DNA can be very different in different micro-organisms, the amino-acid composition of their proteins only changes by a moderate amount.

General Nature of the Genetic Code for Proteins

The Nobel Lecture:

I shall discuss here the present state of a related problem in information transfer in living material – that of the genetic code – which has long interested me, and on which my colleagues and I, among many others, have recently been doing some experimental work.

…It is convenient to have a word for a set of bases which codes one amino acid and I shall use the word “codon” for this.

…There is nothing in the backbone of the nucleic acid, which is perfectly regular, to show us how to group the bases into codons. If, for example, all the codons are triplets, then in addition to the correct reading of the message, there are two incorrect readings which we shall obtain if we do not start the grouping into sets of three at the right place.

In spite of the uncertainty of much of the experimental data there are certain codes which have been suggested in the past which we can now reject with some degree of confidence.

Francis Crick – Nobel Lecture On the Genetic Code

Message, messenger, or genetic message appears 12 times. Other codes were proposed and rejected.

The genetic code is a code.

The evidence against Code Denialism is overwhelming.

There’s really nothing to discuss. But if you insist…

222 thoughts on “Code Denialism Pt. 1 – Crick

  1. Neil Rickert: Clearly this is a very important post, and completely settles the issue of what is a code.

    Yeah, it’s pathetic. There’s always some excuse why IDers won’t step up to the plate and it’s never their fault. It’s the system oppressing them, man.

  2. Message, messenger, or genetic message appears 12 times.

    I know! messenger RNA! It speaks fluent Codon.

  3. I’ve been away at a wedding, just back.

    Mung, I’ve looked through this thread, and I can’t see anywhere where you clearly state what it is you think that “code denialists” are denying.

    Can you explain?

  4. Mung: Sure. Let’s pretend that Code Denialism isn’t popular here at “The Skeptical Zone.”Let’s pretend that Code Denialism doesn’t exist at all here at “The Skeptical Zone.”

    Let’s observe that Mung has set up a particularly dumb strawman and is burping out the usual IDiot arguments while refusing all requests to provide his definitions of “code” and “real code”.

  5. Mung,

    I envision a multi-part series on this topic because the evidence against Code Denialism is so extensive and Code Denialism seems to be surging in popularity here at TSZ.

    I’m sure that could be avoided if you just answered a few of the questions that have already been asked in the thread.

    Here’s a few more:

    Are codes things that can only be created by intelligent designers?
    What designer created the genetic code? How do you know?
    Did that designer create anything else? How do you know?
    At the origin of life, was DNA and the cell exactly the same as it is now?
    What did the designer do at OOL with relation to the genetic code? How do you know.

  6. As I see it, the question is whether the concept of a “code” is a helpful way of understanding how genes regulate cellular metabolism.

    Quite frankly, I can see a case being made either way. I can see why some theoretical biologists use dynamical systems theory to criticize what they call the “genocentrism” of mid-20th-century biology. According to these people, there is so much circular, reciprocal causality at different spatial and temporal scales within the cell that it doesn’t make sense to give DNA any privileged status.

    Although gene activation, transcription and translation play an important role in regulating cellular metabolism — the argument goes — these processes are themselves strongly constrained by the whole context of cellular metabolism.

    What makes an organism (whether unicellular or multicellular) a self-organizing, self-constructing dynamic unity is not explained in terms of the genetic code, as if DNA were the top-most level of some hierarchy, but in terms of how DNA, mRNA, tRNA, rRNA, peptides all function together as an integrated whole.

    At the same time, it doesn’t seem objectionable to me to think of genes as coding for peptide chains. (It is highly problematic to think of genes as coding for traits, of course!).

    There’s something here like the debate over “representations” in embodied-embedded cognitive science. Some philosophers (Thompson, Chemero, Hutto) prepared to reject the concept of representation altogether and others (Wheeler, Clark) are willing to revise the concept in light of embodied-embedded cognitive science. I wonder if debates about the role of genes in cellular metabolism are similar.

  7. The problem is that while DNA codes for RNA, it does not code for function.

    Function happens or not, as a result of chemistry and of the environment.

    When IDists use the word “code”, they are implying something like a language or a blueprint. Something that would enable designers to speak life-ese. To design.

    But DNA does not enable foresightful design.

  8. petrushka,

    The problem is that while DNA codes for RNA, it does not code for function.

    Well that’s another level of code again. Really, RNA and DNA are simply different ‘fonts’. And they are interchangeable – the sequence of RNA can be faithfully transcribed to DNA and vice versa.

    Often forgotten are the many RNAs that are not ‘messengers’ – that bind to promoters and repressors, or mop up other RNA, splice out introns or function as ribozymes or tRNA. They are ‘encoded’ in DNA, though this it is even less code-like. There is a notional reversible mapping of A to T and C to G. But more important is their physical affinity. That’s what’s ‘really’ going on – as is also the case in triplet docking in protein synthesis.

  9. Uh oh!

    I note a commenter at Uncommon Descent calling himself Virgil Cain has asked Larry Moran

    Do you think the genetic code is a real code (like Morse Code is a real code)?

    and Larry Moran responds:

    Yes. That’s how I describe it in my textbook.

    I wonder if we are due a visit from Frankie?

  10. Alan Fox: note a commenter at Uncommon Descent calling himself Virgil Cain has asked Larry Moran

    Do you think the genetic code is a real code (like Morse Code is a real code)?

    and Larry Moran responds:

    Yes. That’s how I describe it in my textbook.

    I wonder if we are due a visit from Frankie?

    Bet ya 10 dollars ya can’t guess what Virgil’s next comment is.
    .
    .
    .
    .
    .
    How about this:

    Thank you, Larry @ 79. Thank you very much.

    Did you realize the genetic code is evidence for Intelligent Design?

    Why Larry Moran is willing to give those eejits the time of day, I’ll never understand. 🙁

  11. design is to designer as code is to ???

    a) evolutionary processes
    b) ham sandwich
    c) coder

    peace

  12. fifth,

    Design is to designer as rust is to ruster. Good thing we have a theory of intelligent rusting, isn’t it?

  13. keiths: Design is to designer as rust is to ruster.

    Unlike designer and coder a quick google search for “ruster” returned no definitions.

    What exactly is a “ruster”?
    Is water a “ruster”?

    Design is to designer as rust is to ????

    a) water?
    b) The atmosphere?
    c) Age and neglect?

    Are all three answers equally valid?
    peace

  14. keiths: Use your formidable analogical skills to figure it out.

    Figure what out?

    How to substitute a vague ad hoc made up term for a well defined term in common use?

    peace

  15. fifthmonarchyman:
    design is to designer as code is to ???

    a) evolutionary processes
    b) ham sandwich
    c) coder

    There are more than one definitions of code. Which one do you mean?

  16. fifthmonarchyman:
    design is to designer as code is to ???

    a) evolutionary processes
    b) ham sandwich
    c) coder

    peace

    Design is to designer as word game is to ???

    a) Open-minded disputant
    b) IDist
    c) Word gamer

    Gee, you can load many things into such a simplistic and leading question.

    Design is designer as lose is to ???

    a) Winner
    b) Word gamer
    c) Loser

    Proves…what?

    Oh, nothing, except what a pathetic gambit FMM’s is.

    Glen Davidson

  17. Adapa: There are more than one definitions of code. Which one do you mean?

    According to Larry Moran we mean the one that is “like Morse code”.

    regardless

    A coder is a person or thing that codes.
    Does that change if we are using an alternative definition of “code”?

    peace

  18. GlenDavidson,

    The answer is “c” in both cases

    GlenDavidson: Proves…what?

    Proves nothing except that critics are afraid of common definitional usage and are willing to jump through all kinds of hoops to avoid it

    Peace

  19. fifthmonarchyman: According to Larry Moran we mean the one that is “like Morse code”.

    Like in what way? Please be specific.

    A coder is a person or thing that codes.
    Does that change if we are using an alternative definition of “code”?

    Yes, What kind of thing? Please be specific.

  20. fifthmonarchyman:
    GlenDavidson,

    The answer is “c” in both cases

    Proves nothing except that critics are afraid of common definitional usage and are willing to jump through all kinds of hoops to avoid it

    Peace

    Proves that we’re not satisfied with cut-and-dried tripe based on nothing but how words have been used in the past.

    Commendable, versus your unquestioning belief in word-absolutes.

    Glen Davidson

  21. Adapa: If you are indeed talking about the genetic code as Larry Moran was then the answer is “a”.

    ?????
    a) Open-minded disputant
    a) Winner

    If we are talking about a genetic code then lose is to “winner”

    How odd.

    peace

  22. fifthmonarchyman: ?????

    If we are talking about a genetic code then lose is to “winner”

    You forgot to list the similarities and differences between the genetic code and Morse code.

    Don’t you know them?

  23. ..-. .. ..-. – …. — — -. .- .-. -.-. …. -.– — .- -. / .. … – / . .. -. / -.. ..- — -… -.- — .–. ..-.

    Everyone can read and understand that, possibly with a bit of help.

    There is, however, no cheat sheet that will enable you to generate a novel, functional DNA string.

    It makes no difference whether DNA is a code. It is a read only code. You cannot make new statements except by evolving them.

  24. Mung will be along to define ‘code’, to allow us to say whether the AARS matrix is a ‘real code’ or not, any minute now I expect. Maybe what makes the genetic code a ‘real code’ by definition is hidden in here somewhere:

    Full Definition of CODE
    1: a systematic statement of a body of law; especially : one given statutory force
    2: a system of principles or rules
    3a : a system of signals or symbols for communication b : a system of symbols (as letters or numbers) used to represent assigned and often secret meanings
    4: genetic code
    5: a set of instructions for a computer

  25. fifthmonarchyman: Proves nothing except that critics are afraid of common definitional usage and are willing to jump through all kinds of hoops to avoid it

    Very well. You are a “coder” and the genome is a “code”.

    Please code me some genome code that will allow citrate to be used as an energy source for humans.

    Oh, what’s that, you can’t? I guess there must be something wrong with your “code/coder” idea. Can you think what it is fmm?

  26. OMagain: Very well. You are a “coder” and the genome is a “code”.

    actually I’m not much of a coder.
    Coding is hard work but I’m learning

    OMagain: Oh, what’s that, you can’t? I guess there must be something wrong with your “code/coder” idea. Can you think what it is fmm?

    1) I don’t have a “code/coder” idea.
    2) If my limited introduction to coding has taught me anything it’s that the coding process is very constrained by the language and starting conditions and you just can’t magically do stuff by writing code.

    peace

  27. Hey, I want to play!

    Hmmm–there’s no Earth–Earther or Heaven–Heavener….But I think I’ve got it!!

    Flat earth–Flat earther
    Dumb–Dumber

    Wait, why is there no “universer” or “peopler” or “humaner”? And how come “lifer” means someone who has to spend his life in prison?

    Did I just disprove theism?? To whom do I give the address to send my 3.1 million dollars?

    (And to show what a fair and generous guy I am, I’m going to turn over that last $100K to Erik since he is the one who taught me how to do this kind of philological proof.)

  28. Coding is hard work in the same sense as speaking or writing is hard work. But fluency is possible.

    But no one becomes fluent in DNA coding.

  29. fifthmonarchyman: 1) I don’t have a “code/coder” idea.

    I guess I imagined this then:

    fifthmonarchyman: design is to designer as code is to ???

    a) evolutionary processes
    b) ham sandwich
    c) coder

    fifthmonarchyman: If my limited introduction to coding has taught me anything it’s that the coding process is very constrained by the language and starting conditions and you just can’t magically do stuff by writing code.

    So I guess you take back what you said about the genome being a code and how codes require coders?

    Now imagine all you don’t know about biology too! Imagine how wrong your current conclusions are because of all that missing knowledge.

  30. OMagain: So I guess you take back what you said about the genome being a code and how codes require coders?

    1) I did not say anything about the genome being a code. That was Crick
    2) I did not say anything about codes requiring a coder. That was your imagination

    OMagain: Imagine how wrong your current conclusions are because of all that missing knowledge.

    What conclusions are you referring to?

    I except that I have lots of wrong conclusions and some correct ones. That goes for most things not just the genome

    peace

    peace

  31. fifthmonarchyman: I except that I have lots of wrong conclusions and some correct ones. That goes for most things not just the genome

    Was the genome designed by an intelligent designer, or god?

  32. Richardthughes: Mung is so proud of his work he is touting it over at UD. bless

    That’s the Brave Sir Mung we all know and love!

    To the IDiots, interacting with scientifically knowledgeable folks must be like “counting coup” was to native Americans. If you run up and touch your enemy in battle you’re a great warrior and earn the tribe’s respect.

    No disrespect to native Americans intended by mentioning them in the same sentence as IDiots.

  33. While we wait for Mung to show up, here is a hint at his argument (in classic Mungian boilerplate: “xxxxxxx”. Pathetic.”)

    Meanwhile, over at “The Skeptical Zone,” Neil knows what a “code” is but claims to not know what a “real code” is.

    Code Denialism (link)

    Pathetic.

    Mung is the one making the claim that the genetic code is a ‘real code’. I certainly know what the genetic code is, and what (say) Morse Code is. I know a bit about programming, comms and formal/informal rules of conduct too. I’m also always up for a bit of linguistic pedantry. It can’t be a code in all those senses, surely? So what is the essential feature of ‘real’ codes? Invoking mathematics does not help here, in part because the physical implementation of the GC is not a mapping, but a set of physical interactions. It can be represented as a mapping in Larry Moran’s biochemistry textbook. But that’s a pedagological tool, and LM is not in any case pursuing the semantic case, nor likely very interested in it.

    But even if we accept that it’s ‘pathetic’ to deny it, what extra insight do we gain by calling the GC a real code? It would be question-begging to argue that it is a code because codes are uniquely a product of intelligence – that that is what makes it a real code.

  34. Larry @UD

    I understand your position. You, personally, can’t see any rational and reasonable naturalistic explanation for the existence of the genetic code therefore you conclude that an intelligent designer exists who could make species and insert into them the necessary genes and proteins for interpreting the genetic code.

    I say that you are basing your conclusion on attacking and rejecting evolutionary explanations rather than on presenting positive evidence that such an intelligent designer actually exists and is capable of doing what you claim.

    For some reason you disagree. Why? Your position isn’t that the mere existence of the genetic code proves intelligent design because surely you agree that there could, in theory, be a naturalistic explanation. Your position has to be based on the idea that such a naturalistic explanation is impossible or highly improbable to you.

    From there you leap to the idea of an intelligent designer who can create species. That’s not a logical leap unless you already believe in the existence of such a designer based on entirely different “evidence.”

    The vast majority of scientists who are knowledgeable about this topic do not see it the way you do. We do not think that a naturalistic explanation can be ruled out based on our knowledge of biochemistry and molecular biology. Therefore, we do not feel compelled to invent a story about a supernatural intelligent designer.

    Why do you think you have a better insight than these experts? It’s possible that you have studied biochemistry and molecular biology and that you know more than we do. It wouldn’t be the first time that experts have been proven wrong by better experts. What what I’ve seen over the past few days I’m confident that you are not very knowledgeable about this topic.

    Another possibility is that you actually don’t know a lot about the genetic code and molecular biology but you do know a lot about how people think. You conclude that the vast majority of experts must be wrong because they have a materialistic bias that prevents them from seeing the explanation you prefer.

    I suspect that this is your main rationalization. That’s fine but you need to be honest enough to admit it when you are advancing your case.

    In conclusion, your “evidence” for the existence of an intelligent designer is based on your pre-existing, non-scientific, belief that such a being exists plus your rejection of any naturalistic explanation. Your rejection is probably not based on expert knowledge and you almost certainly realize that the traditional experts don’t agree with you. Thus, an important part of your logic relies on discrediting the experts, probably by claiming that they have a materialistic bias that prevents them from seeing alternative explanations involving gods.

    But that position, anti-materialism, is itself based on a prior commitment to a belief in supernatural beings.

    I conclude that in spite of what you say you are not providing evidence for the existence of gods based just on the existence of a genetic code.

    We been over this ground many time in discussions about irreducible complexity. That argument has two parts just like the the existence of the genetic code. The first part is whether irreducibly complex things exist. They do. The second part is whether they can be explained by unguided evolution. Some of them can. It’s the second part that’s important.

    You’re asking me to “demonstrate that such a system can come about by natural processes.” On the surface this looks like a perfectly reasonable request from someone who really wants to learn about biochemistry. But that not the case here. You have already made up your mind that the existence of the genetic code is evidence of an intelligent designer and that MUST mean that you have already rejected the possibility of any naturalistic explanation.

    Since your rejection is not based on knowledge of the topic, it must be based on your distrust of scientists. Many of your comments confirm that you won’t ever believe anything a scientist says. I conclude that no answer from a scientist will ever satisfy you.

    fmm, that comment might as well have been addressed to you.

  35. Allan Miller:

    fifthmonarchyman,

    design is to designer as code is to ???

    As badge is to badger.

    Allan wins all.

    I know some of our cohorts-in-crime have a PotW sticker, so consider this to be the invisible PotW sticker:
    .
    .
    .
    .
    .
    🙂 🙂 🙂

  36. fifthmonarchyman: you just can’t magically do stuff by writing code.

    Holy shit. Fifthmonarchyman just dismantled the entire basis of all ID claims in nine words.

    Game’s over, kids. ID has been wiped off the board.

  37. Design is to designer as anteat is to anteater.
    Design is to designer as moth is to mother.
    Design is to designer as fat is to fatter.
    Design is to designer as fur is to furrier.
    Design is to designer as butch is to butcher.
    Design is to designer as mast is to master.

    Well, if we’re going to base science on word endings, this broadens our possibilities.

    Glen Davidson

  38. OMagain: Was the genome designed by an intelligent designer, or god?

    Yes but you already knew that

    OMagain: So you don’t think it’s a code then?

    No,
    I know it’s a code.
    I know that because people like Crick did the research that determined this was the case.

    OMagain: fmm, that comment might as well have been addressed to you.

    Why,

    I never once claimed that an existence of a code in the genome proves that God exists. I really have no use for human efforts to prove God’s existence. God has already done that conclusively.

    On the other hand acknowledging that the genome is a code could lead to all sorts of useful scientific advances and denying that fact in order to avoid the implications is just silly and anti science.

    peace

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