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
There it is again: an appeal to authority fit to be an example in a text on common fallacies.
Let’s be real, BruceS. ‘Aboutness’ (Anglo-Heideggerianism) of mentality is fun semantic myopia! You’re a retired technician now starting to read philosophy. Contrast I was meeting last week with an international group of scholars working on this topic. Maybe you should search more, even outside of your atheist ideology? Decadent Canadians are among the most detestable kind.
To return to the OP, at least you could suggest a non-naturalistic source of ‘code,’ if you believe in one. Mung’s IDism is silly. But many non-IDists, including atheists, realise a code (‘depending’ on topic/field) needs an intelligent source. If you don’t embrace biologism, this should be easy to accept.
Oh moderators!!
Another way to interpret the “could-have” is, at the level of biological explanation, that event was random.
Perhaps if we could formulate a complete history in physics, we would see that there was no other possible outcome given the state of the universe just before the event occurred. In that case, the randomness and the could-have are epistemic, I think.
However, if we found some kind of quantum event was involved, then it might be that it was random. Or maybe other possibilities happened in other universes.
Now who is name-dropping? (and name-calling). ‘Nuff said.
With the way he used “must”, I took him to be saying that there’s a difference from (a) asserting his belief in design, and (b) asserting that there is a logically necessary conclusion of design.
BruceS,
Which names, BruceS? It’s nothing to echo what you’ve already said here in labelling yourself an atheist. Is that ‘name-calling’ to you?
No doubt KN feels welcome if others rank him as their secular ‘skeptical hero’ on this site, even if in the name of a ‘philosophy’ which most skeptic posters at TAMSZ reject anyway. BruceS has often seemed curious-infatuated to explore the philosophistic emptiness with KN. There’s yet another small-thinking dime-a-dozen disenchanted dead-end Canadian imagining he’s proud and profound, while far more good, ethical and responsible Canadians (including the outgoing and incoming PM) recognise their religiosity as ‘normal’.
BruceS is directed down a self-defeating, life-hating/avoiding pathway. Codeword: depressing.
“decadent”, “detestable”
Gregory,
I congratulate you on your attempts at achieving normalcy, Gregory. I note however, that most people, Canadian or not, are both nicer and brighter than you are. They understand that believing what most people believe doesn’t entail being correct and that nobody is likely to be bullied into believing something because they have been repeatedly insulted.
But keep at it–there’s always hope! Your day of achieving real normality may come!!
“decadent”, “detestable”, “depressing”
When it comes to “natural philosophy” you are right on.
However I would definitely be at odds with the theology of those guys
peace
Gregory,
I consider it my bounden duty to enjoy my life to the full. Even if it were not rewarding in itself, I might hope, in some small way, that doing so despite atheism might annoy Gregory. Small of me, I know.
again bingo
peace
Allan Miller,
Take it in scale Allan. You’ve got less than a speck of insignificance to celebrate and ‘maybe hope in some small way’ with your ‘enjoyment.’ The point is that Jews, Christians, Muslims, Baha’is and other theists live differently in their vertical enjoyment. Your empty worldview is not inevitable.
Is the ‘code’ of life a vertical adventure, rather than a horizontal ‘stay-at-home’ dead-end?
Right, but there’s no real distinction in that analysis between physics and biology is there? Metaphysical or epistemic randomness could arise in either (or neither) field. Same issues arise.
Frankie’s argument depends on there being a crucial difference. In Allan’s last post on this issue, he fleshes out an interesting suggestion, I think.
Gregory,
Some have great lives, some not. Same as everyone, really.
Kind of is if I don’t believe in God. But it is far from empty. I’m having a great time, ta very much.
I’ll let you know when I find out.
Mung:
You do? In that statement I report an assumed conclusion, as a parody.
As (it is my bald assumption that) selectionist causation is the natural process capable of spinning out codes in nature, and that all phenomena capable of supporting that process would be classified as biological (virtually by definition), we aren’t likely to find natural codes outside of biology.
Claim. Reponse.
If it is, it is. Amen.
I’m not sure if metaphysical randomness is a part of biological explanation.
For example, we can say genetic drift happened because certain members of a finite population just happened to die at random. But presumably, if we trace every physical interaction, we’d see that their deaths were inevitable. (ETA: We could only do so using the explanations and laws of physics, not by using the explanations of biology; I should have made this clearer)
As far as I know, there are three arguments against this type of Laplacean determinism.
1. QM has inherent randomness. Maybe. But some interpretations, eg MWI, say that there is no randomness in the big picture (ie in all universes, at the level of the overall quantum wave function). In any event, any such randomness is at the level of physics, although of course it could affect biology (maybe DNA mutation, for example). But that would still be randomness in physics as I see it, not biological explanation.
2. Unpredictability due to chaos from limited knowledge of initial conditions. But that would not apply to an all knowing Laplacean demon.
3. Insufficient resources in the whole universe to do the physical computations needed to do this prediction, at least to do it faster than just waiting to see what happens. That may very well be the case. But I’m not sure I’d call that randomness. I’m not sure if it is metaphysical or epistemic either.
Whatever happens in the future, I have been luckier and better off than 95 percent of everybody alive today.
Aside from not being rich and famous (not conducive to happiness in my experience) I can’t think of any area of life where I have not been lucky.
As for being happy, that comes from realizing how well off I am.
Gregory,
So … I just make myself believe in God? And suddenly I don’t have an empty worldview? Fantastic. I’ll get right on it.
The generalized genetic code is applied to alternative codings recently derived from studies of mitochondrial protein synthesis. It is argued that mitochondrial protein synthesis is comprised of a class of biological contexts, rather than a single biological context, and that there exist, therefore, multiple mitochondrial genetic codes. The evolutionary implications of multiple mitochondrial genetic codes are discussed.
Genetic coding theory: Multiple mitochondrial genetic codes
Multiple mitochondrial genetic codes. What’s a code denialist to do.
Mung,
Shrug. I did not just hear about this a second ago.
Once again, you seem to be thinking that finding usages of the word ‘code’ is a refutation of my argument.
Code is an incantation. It magically refutes mainstream biology.
Or something.
You are arguing with Frankie because you swore off arguing with FMM? <grin>
Gee, multiple chemical reactions that produce the same output. Multiple chemical”codes” none of which use symbolic representations or abstractions in their function and none of which required an intelligence to produce.
What’s a desperate to prove GODDIDIT IDiot to do?
It’s IDiot logic.
Some codes are designed
DNA is a code
Therefore DNA is designed.
Some mammals live in the ocean
Giraffes are mammals
Therefore giraffes live in the ocean
IDiot logic.
And I would like to see someone here say what a code is and then make the case that the genetic code is not a code. Frankly there’s a greater chance of you getting your wish than there is of me getting mine.
One thing about variant codes/’codes’ is that the variant codons are, with just one exception, STOP in at least one modern lineage. That’s 9 variant positions and 55 invariant ones.
This is supportive of an evolutionary explanation. It is easier to convert a STOP into a true codon than it is to convert one true codon into another. This is because the former will simply add a short ‘tail’ to the peptide in those proteins using that STOP, whereas the latter will cause a substitution throughout the proteome, every 32nd triplet all else being equal. From protein chemistry, that is more likely to be disruptive. Additionally, it’s easier to fill a gap – to create an assignment where none exists – than completely swap specificity in two AARSs.
It won’t happen very often, because it is still more likely to be detrimental than not. But factors favouring it will be stochastic diminution in the number of proteins using that particular STOP, and reduction of the total number of proteins – something that mitochondria and plastids will experience, because most of their genes actually reside in the nucleus.
On Design, it seems ad hoc to have one code in the mitochondrion and another in the nucleus. But then Design can accommodate any known scenario.
Mung,
Flipping heck! I thought I had. Several times.
Most definitely. Code = Goddidit. And I have an airtight argument to prove it. I would post it here but my intellectual integrity doesn’t allow that.
Heh. Get a time machine….
Allan, if so I missed it. Perhaps it got lost in the technical details you were providing of how the actual mapping from the source alphabet to the code alphabet actually takes place.
Did you think that by explaining the details of the code you were explaining away the code?
I cannot reply to the point about Allan as I am not sure what post you are referring to.
As per posts in previous thread, I have no idea what argument Frankie is making, if any.
I’m interested in discussing what philosophical argument he might be making, on some charitable reading of some of his posts.
Why does e map to • in morse?
Are all of these code words?
Here is a argument in line with the theme of this thread but which I have not seen here yet.
In the linked essay, Heller points that that the genetic code is a language which creates the machinery needed to interpret it. So it is not only a language, it is a meta-language too.
Specifically, it is a meta-language that talks about itself, in some sense. It implements self-reference.
Although Heller does not go this far, surely we could shoe horn Godel into that somehow? Could there be a protein sequence that we can see DNA could not encode, even though that could not be proven (that is, transcripted) using the meta language itself? And what would that say about the designer?
But probably Godelian incompleteness is a bit a of stretch.
(BTW, Heller also disparages a God of the Gaps argument for the genetic code at one point in the essay, FWIW).
The post of Allan’s I was referring to was the one in which he said this:
My attempt to reconstruct Frankie’s argument was the (1)-(5) biz I posted this morning. As indicated, I have no idea whether the premises (particularly 1 and 2) are any good. Allan provided some reasons why he thinks they aren’t.
Oh goodness.
Morse code is abstract and can be implemented in any number of media.
The genetic code can only be read and interpreted by chemicals.
Because dot is the shortest line between two points and e was Samuel Morse’s favorite color.
That argument, which involves representation, is different from (let’s call it) “the Frankie argument” from arbitrariness I put this morning, which does not.
OK, thanks, Allan’s point make sense as being something different from situations where variation and selection could not occur. That is what Frankie et al are missing, IMHO, regardless of what argument they are making. Or if not missing, at least not giving enough credit to.
By the way, Smolin wrote about book which included a hypothesis on variation and selection of universes using a reproductive mechanism involving black holes. So evolution shows up in that cosmological theory. Don’t think he got much support. Probably had pissed off too many string theorists by that point.
I know. It was the self-reference form of representation which I thought was new.
I understand my latest posts have nothing to do with your attempt to construct a formal argument from Frankie’s posts. Maybe I am wasting time. Maybe that does make me decadent. Oh well, that’s the life of a bourgeois retiree.
Thanks for the link. I haven’t read it yet, but John von Neumann may have been the first to explore the logic of self-replication.
By the way, von Neumann’s work also refutes code denialism. I’m sure we’ll get to it, eventually.
Why should anyone do that? It’s your stupid strawman argument. Everyone has agreed that DNA is a type of code, a process where the inputs map to the outputs. It’s just not one that uses arbitrary symbols as abstraction and therefore doesn’t require intelligence to create.
Everyone here would like to see Mung grow a spine and give us his definitions of ‘code’ and ‘real code”. But it won’t happen.
I wouldn’t spend too much time on it if I were you. I’ll try to explain what is meant as we go along. Sorry, but my time here is limited. 🙂
Perhaps this will help:
IOW, we’re just saying what other scientists have been saying all along.
I’m jealous.
Allan, would you be so kind as to direct me to where you posted the definition of a code?