The Nirenberg and Matthaei experiment was a scientific experiment performed on May 15, 1961, by Marshall W. Nirenberg and his post doctoral fellow, Heinrich J. Matthaei. The experiment cracked the genetic code by using nucleic acid homopolymers to translate specific amino acids.
The Nirenberg and Leder experiment was a scientific experiment performed in 1964 by Marshall W. Nirenberg and Philip Leder. The experiment elucidated the triplet nature of the genetic code and allowed the remaining ambiguous codons in the genetic code to be deciphered.
The Marshall W. Nirenberg Papers Public Reactions to the Genetic Code, 1961-1968
Nevertheless, the problem of the genetic code at least in the restricted one-dimensional sense (the linear correlation of the nucleotide sequence of polynucleotides with that of the amino acid sequence of polypeptides) would appear to have been solved.
In the years after 1953, scientists scrambled to be the first to decipher the genetic code. In an attempt to make the race interesting, theoretical physicist and astronomer George Gamow came up with a plan. He organized an exclusive club, the “RNA Tie Club,” in which each member would put forward ideas as to how the nucleotide bases were translated into proteins in the body’s cells. His club had twenty hand-picked members, one for each amino acid, and each wore a tie marked with the symbol of that amino acid. The group—which did not include Marshall Nirenberg—met several times during the 1950s but did not manage to be the first to break the code.
Genetic memory resides in specific molecules of nucleic acid. The information is encoded in the form of a linear sequence of bases of 4 varieties that corresponds to sequences of 20 varieties of amino acids in protein. The translation from nucleic acid to protein proceeds in a sequential fashion according to a systematic code with relatively simple rules. Each unit of nucleic acid defines the species of molecule to be selected, its position relative to the previous molecule selected, and the time of the event relative to the previous event. The nucleic acid therefore functions both as a template for other molecules and as a biological clock. The information is encoded and decoded in the form of a one-dimensional string. The polypeptide translation product then folds upon itself in a specific manner predetermined by the amino acid sequence, forming a complex, three-dimensional protein.
Scads of scientists. Two Nobel Prizes. Isn’t consensus science grand?
“…the fact is that present life requires semiotic control by coded gene strings.”
– Howard H. Pattee
For a donation of a mere $5…
Alan Miller,
You know, you just hate god.
walto,
I think it’s a mistake to equate “arbitrary” with “random” here. When Upright Biped argues that certain features of the genetic code are arbitrary, he doesn’t mean that they’re random — after all, he thinks they were chosen by an Intelligent Being who had specific goals in mind. By “arbitrary”, he merely means that the codon-to-AA assignment scheme isn’t dictated by the laws of physics themselves. Other codon-to-AA assignments are physically possible.
His error is in assuming that if more than one option is physically possible, then intelligence must have been involved in picking the one that prevailed.
Note also that “arbitrariness”, in UB’s sense, is compatible with a wholly deterministic universe. The codon-to-AA assignments could be arbitrary with respect to the laws of physics yet still be determined by the combination of the laws of physics and the boundary conditions of the system.
Arbitrary is pretty much the opposite of random. There are three categories “random”, “dictated by law” and “Arbitrary”. Notice the connection to the design filter.
The problem is we can never from a position inside the universe determine if a non determined phenomena is truly random or merely arbitrary.
This is the point where we will hit a wall. From our position inside the universe we can never discover if the boundary conditions were a fixed necessity or if they were arbitrarily chosen.
IOW did God have a choice in the matter?
Like I said it all boils down to the problem of other minds.
peace
I can’t “get at” whether you are a conscious agent or just a complex animatron. I choose to believe I am talking to a real boy.
peace
Back from the opera.
Essentially the reply I had in mind as Tannhäuser’s salvation was restored and the pope’s staff sprouted leaves. It would not follow from the fact that a mapping is arbitrary in the sense of multiply realizable that the mapping that happened to obtain was not determined nor scientifically predictable (modulo quantum randomness, chaotic behavior and the contingencies of history). Other combinations of causal precursors and selectionist contingencies could determine alternative mappings that are adaptively equivalent. The contingencies of selection determined the mapping that actually obtained, not the laws of physics, which may be neutral to any given mapping.
If not a result of physical laws and pre-existing conditions or some mind of ‘spontaneous choice’, what’s left besides randomness?
Same question.
To the extent that I understand this post, I don’t agree with much of it–particularly the equation of arbitrary and intended. Much mire common to equate arbitrary and random.
Did you miss the actual definition of arbitrary?
quote:
arbitrary: subject to individual will or judgment without restriction; contingent solely upon one’s discretion:
end quote:
sounds like intended to me
peace
Hi Allan,
Would you agree that if we have symbols we have representations?
“There are no symbols” isn’t going to fare any better than “it’s not a code.”
The same people who figured out they were dealing with a code knew this meant they were dealing with symbols. I was just reading Francois Jacob today and he uses that term.
People are happy to call it a code because it is a code. Except here at TSZ. Odd that.
That it is a code was decided as a matter of logic. It’s specific properties were discovered, not bestowed. Science at it’s finest.
Heads we win tails you lose. 😉
If we’re talking information then we’re talking about symbols and representations.
So does Allan deny that what we have in the genome is information, and if not, what is it information about? The DNA contains information about how to construct the organism, a description. A symbolic description.
I don’t know. What are you talking about? Semioticians are more than happy to look for material causes.
Because if it were not then people could argue that it’s not really a code and actually have a basis for thinking so.
Someone alert me when Brave Sir Mung gets done with the same boring and dishonest equivocations over “code’ and ‘information” the IDiots have been flailing and failing with for years.
Why do IDiots think repeating the same failed semantic arguments over and over for years will win them converts? Do they think the dishonesty and stupidity gets better with age?
Most people would think Mung is lying since he’s seen numerous people at TSZ say the exact opposite of his claims. But the rules require we assume he’s just terminally stupid and/or confused.
LOL! Brave Sir Mung is back at UD
lyingbeing very confused and bragging about how he humiliated all the Darwinists at TSZ and showed God did it with his “code” devastating argument. 😀Brave Sir Mung gets confused very easily it seems.
fifthmonarchyman,
And I choose to believe that the roulette wheel is being guided by angels. Nonetheless, I can’t get at their methodology, so I treat the behaviour as ‘random’ (a word that has multiple senses, so let me substitute ‘stochastic’).
fifthmonarchyman,
Looks like we got us another argumentum ad dictionarium. Nothing or everything in nature is arbitrary if we restrict ourelves thus. If God is Calvinist, all is his personal whim. If there is no God, there is no whim.
Mung,
I am not compelled to agree with any of the pioneers in this field as to how to most accurately represent what they were uncovering. Jacob thought they were symbols, Crick thought it was a ‘real code’ … so what? Fact remains, the relationship between a codon in DNA and an amino acid added to a peptide on an mRNA that includes the complement of that codon is not symbolic. Or, if it is, the relationship between a stretch of promoter and any molecule that binds to it is also symbolic. Or that between penis and vagina. It’s fundamentally about physical complementarity and attachment. Penises generally have men attached to them. The vagina does not ‘represent’ that man.
Save your breath or line them all up as you prefer. I don’t really care who you think ‘agrees with you’, I do not. It simply boils down to whether one thinks a triplet is itself a symbol, or a set of tRNAs a code.
‘Code’ was a perfectly reasonable word to use; better than a neologism. I’ve explained why I don’t agree that it is a ‘code’ in the pre-existing senses. You haven’t really explained why you do, just (like Frankie and Torley) called in supposed expert witnesses, but they aren’t linguistic authorities. It’s semantics; there is no absolute right answer. Unless you’re a Calvinist.
Mung,
It was called a code before the implementation was known – they were looking to build up the matrix of assignments, which is a code when you write it down. You have a consistent input and can correlate it on the matrix with a consistent output from a ‘black box’.
But the implementation (to my mind) makes the appellation ‘code’ less strictly applicable. What they were doing was building up the matrix on a notional white board. Then they could look up UUU and read across to phenylalanine. They could use it as a code. They could read the map. And IDists are going blue in the face trying to insist it is the territory.
If they had said ‘UUU’ into a loudspeaker and the system always replied ‘phenylalanine’, that would have been a code! If internally, this was implemented by an actual biological mechanism converting the phrase ‘UUU’ into a physical DNA triplet, transcribing and translating it, reading along to the appropriate amino acid then converting it into the vocalisation ‘phenylalanine’ – that would be using the ‘genetic code’ as a code! In that model the physical UUU triplet is being used to represent the initial phrase ‘UUU’. But it does not represent the downstream output. It causes it.
Mung,
What do those symbols represent? You seem to be compounding levels now. If a triplet is argued to represent an amino acid in a peptide, what does a sequence that becomes part of a tRNA or promoter represent? You can’t do anything with a symbol. It just sits there, all symbolic. But you can do something with DNA. If you transcribe a tRNA (whose sequence happens to precisely match that on the antisense strand), all you have done is copy the sequence information into a very similar form. But it folds and then you can do something biologically useful with it. The antisense version of this exact same transcribed sequence does not fold, because of the physical presence of upstream, downstream and complementary strand. Even if it could fold it would not work because of 2′ -OH and methylated uridine. But it’s the same ‘symbol’. Biology is about physical stuff. Over-egging informatics is a load of old symbolics.
Didn’t you read my question? I’m talking about UB’s dual admission:
– It does not follow from his 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 his 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.
My question to you therefore is: does it not follow from UB’s admissions that semiotic theory is silent on the origination of “semiotic systems,” and therefore symbol bearing codes, in nature?
Do you mean that your two threads have not been about making an implicit argument for ID?
Or are some material causes, like those described by Allan M, immaterial, in a manner of speaking.
Coincidently, Upright Biped has just posted on arbitrariness here.
He has also finally opened his website for business here.
I didn’t “miss” that definition. I simply thought it was very bad. While it’s consistent with “uncaused,” that use of “arbitrary” actually connotes “without reason” or “capricious.” So, while it give you the spontaneity you’re looking for, it doesn’t rule out randomness.
In any case, I’d pick a better definition, one that comports with most people’s actual usage.
Yep it’s simply the problem of other minds. When confronted with a universe that passes the Turing test we can always appeal to the Chinese room defense.
The results of the roulette wheel and possible mappings will form normal a probability distribution.
When it comes to the Genetic code we have only one point of reference and it’s far out on the left tail. If it weren’t for that single unlikely arbitrary point we would not be here to contemplate our good fortune.
It’s as if a stranger arrived put all his chips on a single spin of the wheel and broke the bank. You could treat the outcome as a random accident or you could assume that something more was at work.
As always it will come down to your choice
peace
I think it’s unfortunate for design backers that the “Frankie argument” I put, which only analogizes with languages because of the arbitrary assignment of symbol to referents, gets all tied up with representation nonsense on the sites you linked. I completely agree with Adapa, you and Allan that those arguments are completely confused. Furthermore, when I pressed Frankie to support the claim that the genetic code was actually symbolic, s/he (angrily of course) relied on an argument from arbitrariness. So to avoid a circle here, it’s necessary to put the latter argument in a form not relying on anything being symbolic.
The “Frankie argument” may also not be any good, but I don’t think it obviously confuses maps with territories the way arguments relying on representativeness do. It’s not as obviously question-begging, IMO.
The other thing I wanted to ask was, Is Frankie this Upright Biped person? If so, s/he did a better job here than on those sites, I think (or could have, with a little time in an anger management class).
No, the other minds issue is a red herring. It’s just slopping together a bunch of stuff that appeals to you.
Or, if you like it best, you should understand that it’s an entirely separate argument and that should be put with it’s OWN premises and conclusions. If it’s half-way decent–say, similar the the one Plantinga puts together in his first book–Bruce can add it to his taxony of basic design arguments (which I wish he would update, BTW). But shoveling up all of this stuff together doesn’t do anybody any good; it ends up being nothing more than argument by obfuscation.
fifthmonarchyman,
How do you know that? We have a single data point. We have spun the wheel once. Oh hang on – revelation. I should have known.
fifthmonarchyman,
And indeed I do. I do not treat the outcome as a ‘random accident’ (I suspect we need to use a better word than ‘random’ here. I can see clear as day what you think its antithesis is).
walto,
Good Heavens, no! Visit ‘Intelligent Reasoning’ for a sample of Frankie’s unfettered approach. UB is more an intellectual superiority kind of guy.
Aha, thanks. And wow is that guy/gal angry! I thought it was just being around us, but the blog is the same pile of vitriol. What a way to live. FWIW, I don’t see much solace having been gained from his/her theism.
ETA: I noticed at Uncommon Descent UB being congratulated by (I think) kairofocus for refuting the claims that ID is not providing empirical support. But I didn’t find any empirical support for anything on the new site, just really bad philosophy.
walto,
Yep, it’s a funny kind of empiricism that insists one accept a particular category into which an observed process must fall.
And while I’m talking about UD (if that’s allowed here), I will say that I was a little disappointed to see Mung put forward those “mathematical definitions” of “code” there as if anything followed from them. I think the discussion here that they show nothing relevant and that their use in proofs of design are generally question-begging was dispositive, and, in any case, Mung made no response to those arguments here, IIRC.
As I say, I was kind of disappointed by that. I get liking a bunch of praise among the faithful for ostensibly coming here and pounding everyone into submission, but…well…that’s not exactly accurate. The if codes, therefore code makers argument is entirely question-begging.
There may be good arguments for Design for all I know, but that is basically rubbish. And it doesn’t matter how many pages it takes up, how many authorities are quoted, or how in how many internet sites it finds a home. Anyone who takes the trouble to strip it down to its essentials can easily see that it requires confusion of ratio essendi and ratio cognoscendi.
Anyhow, I found those remarks disappointing.
{ETA: I see that I said I was disappointed three times above. I guess that settles it.}
One possibility is multiverses plus anthropic reasoning.
Also, you find a necessary set of physical laws that predict multiverses.
I admit, that necessary part might be a bit tricky. I suppose you could try a necessary Being instead.
Or pull a Tegmark and say all possible, computable laws must exist in some universe or other.
walto,
Yes, I can see how associations that do not rely specifically on the respective properties of the things being associated is a different argument. In the case before us, the association also relies on properties of the things in between – though none of the associations is wholly ‘necessary’, in some non-circumstantial sense. In Frankie world, if you eliminate ‘chance’ and ‘necessity’, there is only one thing left. But it’s not ‘pure chance’ either, whatever that may really mean.
I have to say, I don’t actually understand those alternatives (which, of course, doesn’t mean they aren’t real).
Maybe keiths will have some responses to my questions a bit more on my level when he makes it back here….
{In the meantime, maybe I’ll just go somewhere and, as you suggest, pull a Tegmark 😉 }
walto,
One learns to live with such disappointments! Numerous approaches were tried by Mung, including the classic ‘why should I listen to anything a Code Denialist might say’ (!). I doubt that many would trouble to find their way over and wade through the threads, so bite-size reportage is sufficient to confirm their prejudices re: arguments made here.
On the ‘mathematical definition of code’, I would note that there is also a mathematical definition of ‘random’ which does not equate with the senses in which the word is often used colloquially. It means subject to a probability distribution, not ‘equiprobable’, ‘unplanned’, ‘aimless’ etc. I don’t think there is any particular reason to let maths have the final word on anything, but I have come, somewhat reluctantly, towards that usage in relation to evolution. It is random in the mathematical sense, even when selection is in play.
Let me be a bit more specific.
1. Multiverse theory says that many physical universes exist with varying laws and varying initial conditions..
2. Anthropic reasoning says that the universe we live in seems special only because we would not exist without a universe that has physical laws and initial conditions that make our type of life possible. So to get the physical laws and the initial conditions that happened to lead to the particular genetic code requires we find the right universe.
It may take some time given there are an infinite number of them, of course.
Further, in some other universe, perhaps a different code came into being. In fact, given there are an infinite number of universes, any possible code (under the laws of that universe!) is represented.
3. Now the problem is this: Where did the laws that created multiverses come from? (the current favorite for those laws involves eternal inflation).
I don’t think science can answer that question. So you have to find a philosophical argument to show those laws are necessary. We probably would not be able to do that until we found the laws. But if you did not want to wait, you could make a theological argument instead that they were mandated by a Deist God.
It’s a hypothesis. We know that the mapping is fortuitous for producing folks like us because it did. We test the idea that other mappings are not as good by looking for mappings everywhere else and by trying to come up with our own.
It’s possible we will discover a better alternative mapping on titan or someplace else or that big pharm we will develop one . Till then the hypothesis stands
Such is science.
I have not noticed you to explicitly answer this question, Allan:
Is that randomness a result of limits on our ability to know or is it inherent in the world?
That is, could some Laplacean demon who had full knowledge of the initial state of the inverse and of its physical laws predict the specific code we have?
Please ignore possible QM randomness and assume the demon’s computing abilities are unaffected by chaos or by limits on physical computation.
Walto, vis the Frankie argument:
A minimum, I don’t see that this follows from the “arbitrariness” exhibited in the mapping of codon to amino acid.
Keiths and I have tried to articulate this distinction above:
Keiths:
RB:
So I don’t think characterizing codon to acid mapping as “arbitrary” gets us to the second Frankie premise.
Aprops no one in particular:
“Never wrestle with a pig. You only get dirty, and the pig likes it.”
What do you mean by “find the right universe”? Presumably we’re in it, no? Wouldn’t just waving our arm around and saying “this one” constitute finding it?
fifthmonarchyman,
It’s a hypothesis that a single datum point is in the tail of the distribution? I think you are trying to dress assertion up in scientific garb.
I don’t think so.
We have a case of the universe acting like a person and making “arbitrary” choices that turn out to be providential in retrospect. IOW passing the Turing test
We can in turn choose to assume either that the universe is not acting or that one of Bruce’s suggestions are at play.
That in the end is what this always boils down to
peace
I’m still not completely following this. Obviously no laws (which are general) result in any specific events on their own. To do anything at all, they require pre-existing conditions to act upon. I’m not sure if that’s what keiths meant by “boundary conditions” but, if so, I don’t see how that affects claims of the truth of (1) or (2). I’m likely missing something, though.