…the noyau, an animal society held together by mutual animosity rather than co-operation
Robert Ardrey, The Territorial Imperative.
The Skeptical Zone
"I beseech you, in the bowels of Christ, think it possible that you may be mistaken."
…the noyau, an animal society held together by mutual animosity rather than co-operation
Robert Ardrey, The Territorial Imperative.
Frankie,
Since he was not even discussing the article, and you don’t supply anything other than a reference to his name and an assertion that he thought differently, that hardly increases the force of any argument you were trying to make!
Cheers! Will do!
The symbolic relationship in the genetic code is between the mRNA codons and the amino acids.
My bad for assuming the people here were knowledgeable.
You said that we do not call Braille a code, except that we do.
Carry on…
Frankie,
The connection is multi-stepped but real. tRNAs compete for binding in the ribosome with the mRNA codon. The energy of this actually helps drive the reaction. Those tRNAs are charged with amino acids – again, this activation helps drive the peptidyl transferase reaction forward. It’s a physicochemical thang. The involvement of tRNA activation and binding make peptidyl transferase thermodynamically favourable.
Of course, the AARSs that charge those tRNAs are specific, at two sites (usually): anticodon and amino acid. One could see this as the ‘coding’ part, but it remains a physical relationship between moleucules, not symbols thereof. A physical structure with one charge pattern at one end gets something stuck on the other. The thing on one end does not ‘represent’ that on the other, any more than its complement (the codon) does. A particular AARS will only attach its specific amino acid to from 1 to 6 different anticodon-bearing tRNAs. But again, this is mediated by physical between potential substrates – differential binding energies. Binding at both sites is mediated by chemistry, not symbology. But the whole thing is purely mechanical. There is no lookup process, just physical substrates with varying affinities. Now, of course the ‘code’ might be seen as arbitrary. There is no ‘law-like’ linkage between a particular acid and a particular set of tRNAs. But weak binding can be tuned to become strong binding. Evolutionary processes can ‘capture’ and tune a particular assignment, which would not be possible with a purely symbolic assignment. I realise this is all just ‘yadda yadda yadda’ to you, but there might be onlookers more prepared to put in some effort to comprehend what I am saying.
So friggin’ what?
But we are happy to say some ‘intelligence’ magically did it cuz we weren’t watchin’? You really don’t get how inconsistent your position is, do you?
I am familiar with both, and the ribosome is nothing like a compiler. Analogies can be seriously misleading.
Frankie,
Good grief. I did not say that no-one ever called Braille a code. That word is almost invariably uttered immediately after ‘Morse’, but much more rarely associated with ‘Braille’, which typically stands alone.
1- Compiler- source code in translated to object code. Ribosome- source code in translated to object code. Both abort on errors
2- It is a stretch to say there is a physiochemical connection between mRNA and the amino acid due to a temporary bond between mRNA and tRNA.
The point is mRNAs do not become amino acids via some physiochemical process. Without that we are left with mRNAs being symbols for amino acids.
Bringing up the AARS just further solidifies the design inference. I would love to see someone model undirected processes producing all of the necessary components- and don’t forget the ribosomes! It’s ID all the way down.
3.1 million dollars, Allan. Don’t be shy…
It’s amusing when people who don’t know anything about compilers talk about compilers “aborting on error”.
If the Ribosome is a compiler then where is the Backus Normal Form specified? If you can’t say, in what sense are those people defining “error”?
All known coats (cloth or fur) have intelligent designers and Science 101 tells us that it could not be otherwise: coats require intelligent designers.
I have observed someone wearing a “coat” (put in quotes so as not to beg the question one way or another) that people couldn’t have produced, because the item is older than the human race.
May I then infer that this “coat” must have been produced by some other intelligent designer? If I resist making this inference will I be taken as saying that “mother nature magically produced it” when we weren’t looking?
Note that the only difference here is that in your argument you don’t resist begging the question at issue and just insist that transmission of “genetic information” is via a code (no quotes).
The point is that one can insist that the “genetic code” or “natural coat” is a real code or coat (by definition!). But if one does that, the definitions of these items can’t require designers without begging the question, so you will be greeted with “Fine, then this is an unusual code/coat.” If one insists that it is part of the definition of “code” and/or “coat” that these items have intelligent designers, then you will not get agreement that the “genetic code” or “natural coat” are actually examples of a real code or real coat.
The moral is that argumentation by assuming what one wants to prove is not terribly effective if one’s audience is paying attention.
Which is why ID remains popular amongst those people who don’t actually pay attention as those people just want reassurance their chosen deity is real and scientific support for that is no necessary as long as the right “it sounds like science” noises are made.
So compilers continue to run when they encounter an error? Or are you just a spewer?
Every compiler I have ever used aborts when I get the coding wrong.
Umm, walto, you can always step up and demonstrate that undirected processes can produce a code. There is a 3.1 million dollar award if you can.
That is the point- designers do codes and no one even has a clue as to how mother nature would go about it.
First there’d have to be an agreement on what “a code” is, no? And there seems to me to be considerable disagreement on that point. (I guess there’s now a thread on this here.) Anyhow, until y’all have sorted that out, I think it makes sense to hold off on “stepping up”–no matter how big the putative reward may be.
In case anyone is wondering about the “3.1 million dollar award”, a bit of Googling turned up this: http://cosmicfingerprints.com/solve/ I especially like the vagueness about other “investors” and this part of the rules: “The discoverer will retain a small percentage of ongoing ownership of the technology.”
The author of that web page may be known to many of you under a different nom de plume, if writing style is anything to go by.
And this is why your opinion on the matter is as worthless as Allan’s.
You’re a mathematician. There’s a mathematical definition of a code. You should know better.
Grow up.
They are knowledgeable. Which is why they ought to know better. In fact, it’s reasonable to believe that they do know better. So what’s the point of attempting to debate people who you believe are not posting in good faith?
Like when you claim the genome “produces” repair enzymes. Noted.
Well, I’m not a mathematician and I’m not particularly knowledgeable, so, what is the mathematical definition of a code?
LOL! Mung the Magnificent who is neither scientist nor mathematician lecturing others who know orders of magnitude more about the subject than he does.
Don’t ever grow up Mung. You and Frankie/Virgil/JoeG keep everyone amused for hours. 😀
I’m not a mathematician either, but I did find this from people who seem to know something about it. Can’t say much except that they discuss these matters, and it’s somewhat interesting.
Glen Davidson
Mung,
That’s not an analogy, merely a simple linguistic convention. Do clouds produce rain? Does a program produce its output? I’d say yes, in most conversational settings. You?
Like I say, It’s amusing when people who don’t know anything about compilers talk about compilers “aborting on error”.
If the Ribosome is a compiler then where is the Backus Normal Form specified? If you can’t say, in what sense are those people defining “error”?
I don’t think “code” is a term used much in mathematics, at least the mathematics I can remember from a long time ago in a galaxy far away (well, 40 years and Waterloo).
But I think people here are using the word “code” to mean what a mathematician would call a “mapping” or a “binary relation”.
The genetic code is a mapping of three letter sequences to proteins. Is this mapping relation describable as a semantic reference? If you accept that it is, then you can repackage the issue as original intentionality versus derived intentionality. If the genetic code is a language, then it has intentionality, but that intentionality must be derived from somewhere. Hence we need a designer to provide the original intentionality.
Thanks, Glen and Bruce.
Bruce’s definition seems to me to shift the question from what a code is to what a map is. That is, if a code exists every time a one-one relationship exists, it’s obvious that one can’t derive the existence of intentionality or a designer from the existence of a code. But if we say that not all one-one functions are codes, only those where one of the items is “mapped” to the other, then it may be possible to derive intentionality from the existence of “mapping.” But…..was this mapping a naturally occurring thing?
As I said before, the danger here is in begging the question. So the terms all have to be carefully defined. And once they are, we move to empirical science and leave the apriori arguments (There are codes in the world, so there must be a God!) behind.
The sad moral is, IMHO, that when philosophy seems to be producing mind-blowing or life-altering answers, you’ve probably made a mistake somewhere.
Mung,
OK, here’s an extended version of my worthless opinion for your contempt and summary dismissal.
One of the problems here is that we lack a linguistic toolkit that perfectly addresses what goes on in the repeatedly-replicated genotype-phenotype system. Because it is unique. So it is inevitable that someone may take exception to a particular way of describing it. Conceptual self-replicators exist, but we only have one real one. Of course the genome forms part of a self-replicating system. A single instance of it is not strictly a self-replicator. We don’t begin with a genome instance which then makes enzymes which then copy that genome instance. The enzymes which copy (or repair) a particular instance of a genome may not have been produced by that copy. Nonetheless, their specifications exist somewhere within it. They are ‘copying themselves’ – along with everything else. When new copies of any enzyme are generated, they are generated from an instance of this indefinitely-copied string. The ‘message’ persists beyind any particular instance of the medium. It is this somewhat more abstract version of the concept that is the ‘self-replicator’, and which ‘produces’ everything that we collectively call phenotype.
Within a GA, strings do not replicate themselves. They are replicated by something – the program, which in turn relies on the operating system. In real organisms, by contrast, copying and its fidelity are specified by ‘real’ stretches of DNA. But one could conceptualise the core copying functions as an immutable virtual string of no particular length, to which the ‘actual’ strings are bolted. The evolutionary competition is between the variable parts of these conceptual entities, which can indeed have length zero, because they are the extra string on which evaluation is performed following evolutionary processing.
So, what ‘produces’ a repair or copy enzyme? Strictly, a system involving tRNA, rRNA, mRNA, numerous AARSs, cofactors, initiation complexes, spliceosomes, editing, etc etc. Fair enough, as far as it goes. But what ‘produces’ any of those components? An instance of the genome. Ultimately, their specification resides within the genome – an iteratively template-copied sequence of nucleotides. A given instance of a given repair enzyme may or may not have come from the instance of the genome it repairs. But it has nonetheless come ‘from the genome’. ‘The genome’ – which is a more abstract concept than a particular instance of the polymer – has ‘produced’ everything it takes to support and replicate itself, including the system within which each component is embedded.
Yes, that is what I was referring to in my reply to KN about Grice’s natural versus non-natural information.
It comes down to whether the genetic code mapping, which happens to be implemented in DNA, can be considered a non-natural language. Or is just a natural correlation, like tree rings and tree age.
I suspect an supporter of calling DNA sequence a language would point out that DNA to protein has a purpose for the organism, whereas there is no purposeful relation for the tree in the rings being mapped to age.
That brings one back to whether etiological explanations from evolution are acceptable to explain that purpose.
But it can produce good questions.
Allan Miller,
Again, very helpful. Thanks.
Yes indeedy. And thanks to you too for your interesting post.
BTW, on a philosophy board I’ve frequented for years there used to hang a guy named Speranza who was as into Grice as I am into Hall (maybe more). Wrote a book on him. But he didn’t enjoy several of the internetty (i.e., pissy) argumentation styles and left. {It wasn’t me!! He left about a month before I came!} I’m sorry I never got to know him.
And I know Grice only from a couple of his classic papers (the one on synonymy and the one on occlusion).
What’s your point Patty? Does this mean you won’t even try to support any of the claims made by your position? Typical
Why is that a requirement? Please be specific. Note that I never said the ribosome is exactly like computer compilers in every way.
And thank you for ignoring all the other points. It proves that you are not interested in an honest and open discussion
Like I say, It’s amusing when people who don’t know anything about compilers talk about compilers “aborting on error”.
If the Ribosome is a compiler then where is the Backus Normal Form specified? If you can’t say, in what sense are those people defining “error”?
OMagain,
Compilers do abort when they detect an error. Are you really that ignorant?
I think that site adds something to Shannon info which is not part of the concept.
Specifically, I don’t think that Shannon information involves the concept of translation from one coding scheme to another. Encoding/decoding in his paper, as I understand it, is meant to represent whatever happens to take messages from sender’s input format to whatever the channel physically can carry and then to invert the process for the receiver. That coding is not about the mapping involved in genetic code transcription. Certainly, the sender and receiver could agree to include such a mapping, but that is outside the scope of the theory.
The theory is about quantifying the redundancy in a symbol set and its associated probability distribution when used to form messages. Coding arises in several ways from that usage. The redundancy can be used to quantify the maximum compression of a coding scheme used to transmit information on a noiseless channel. Or the redundancy can be used to create error-correcting schemes to deal with noisy channels.
Coding in the mapping sense is about semantic reference. So imposing that on Shannon information is to commit the error of confusing colloquial definitions of information as involving meaning with Shannon’s technical definition, which does not involve meaning.
If the Ribosome is a compiler then where is the Backus Normal Form specified? If you can’t say, in what sense you defining “error”?
I am defining “error” as the biologists define it. The Ribosome: Perfectionist Protein-maker Trashes Errors
Shannon didn’t care about meaning because he was interested in the transmission, reception and storage of information. This involves equipment which could care less about meaning.
That seems right to me.
Glen Davidson gave a reference that mentioned finite state machines. Mathematicians define a finite state machine as an abstract machine that operates based on input symbols (abstract symbols). A physical device (such as, say, a combination lock) is a mechanical implementation (or physical implementation) but is not itself an abstract machine.
Danger?
Begging the question is the underlying principle on which ID argumentation depends.
LoL! Neil, if you could find some support for an alternative to ID people will listen. Attacking ID with your ignorance means nothing.
For some meanings of abort.
Most compilers try to continue as best they can, so that they can report additional errors that they find.
Someone linked to ‘The Ribosome: Perfectionist Protein-maker Trashes Errors’ and I found it an interesting article, but I looked for a definition of “error” and could not find one. I was expecting to, from some of the comments made on this thread, but I could not.
Agreed. So adding meaning to his theory is adding something.
If you consider the genetic code as a code with meaning in the semantic sense (that is, as involving reference beyond simple causal correlation which must hence (?) be added by a designer), then you are adding something to the theory.
Buy a dictionary. Do you think that scientists have a special definition for the word “error”? Is that your “argument”?
BWAAAAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHA
Looking at that link, I see:
What makes a bee waggle information, is that we choose to interpret it as information. Information is not a natural kind. It exists only on account of our interpretations.
Neil Rickert,
The bees seem to interpret it as information, too.
It seems that evos are trying to find ways to wiggle out of the challenge. Very telling, that…
Right, it is adding the reality of information. Information isn’t information without meaning.
Someone said that error was defined in that article. It was not. Yet someone said that was the definition of error they were using. Someone was mistaken it seems.
Like I keep saying, It’s amusing when people who don’t know anything about compilers talk about compilers “aborting on error”.
If the Ribosome is a compiler then where is the Backus Normal Form specified? If you can’t say, in what sense are those people defining “error”?
Someone is a complete moron by not being able to use a dictionary. And that someone thinks its ignorance is an actual argument.
Like I keep saying you have to be a moron on an agenda to not understand that both ribosomes and compilers translate one language to another and abort on errors- compilers to not output an object code when they detect an error and ribosomes do not output a polypeptide when they detect an error.