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
Gregory, stop being a worthless shit-minded stalker and either go away altogether or clean up your act to refrain from repeating any personal references (yes, even references which one commenter has voluntarily made in some other context).
You have no business here if you can’t behave as a civilized adult.
I’m ok with those revisions. The make the claim weaker/safer.
The premises are what are interesting to me here. 1 and 2 I’m really not competent to assess at all; 4 I might be able to make some progress with if I had the time and the stomach for it.
Science. Science. And more science. Plus, isn’t that the nature of a code in the first place?
Early Fixation of an Optimal Genetic Code
Mung,
What does it say? I can’t get that article without requesting it from the author.
It’s simply not possible to insult my intelligence or my education.
hotshoe_,
Oh, so ‘hotshoe’ now seeks to dictate who has business where, even though ‘intention’ is significant as in the example cited with Lizzie’s ‘intentional’ sacramental ‘confession’ of marriage in a religious tradition, as she has stated here.
It’s kinda like petrushka, singing hymns without believing a word he speaks.
And apparently, according to Alan Fox, it’s ok to call someone *anything* ‘hotshoe’ calls them, just not a ‘moron.’ 😉
Mung,
🙂
hey walto,
I know it’s available online, I was just too hurried to find the link to the pdf. iirc, they compare the existing genetic code to alternative genetic codes.
I like the reasoning, and I obviously accept the existence of codes in biology. Can you provide an example of a code that originated in nature that isn’t a biological code?
Mung,
Any news on “code” vs “real code”?
Why?
What I mean is, what will that prove to you?
Mung,
I think Freland is wrong in his supposition about how an ‘optimal’ code arose. One can accept their case that it is in top millionth-percentile of ‘random’ codes in terms of its error tolerance. But to regard that as an example of optimising selection in action (as they do) is unlikely.
The code matrix is very good at tolerating misreads because many of them still hit an amino acid with similar chemical properties, and produce a functional product. The assumption is that we started with a random collection of 20 acids and then selection gradually optimised this code by moving the assignments about.
How could this possibly work? If you have proteins utilising all 20 acids, you would have to simultaneously change 2 AARSs to take each others’ function, and do this repeatedly. In doing so, you change the assignment in every protein. And all for the comparatively weak selective benefit of producing functional proteins on misreads. It is very unlikely that the advantage of error correction on a subset of misreads – single molecules – would be strong enough to counter the negative selection against wholesale reassignment in every protein molecule produced.
In my view, this just could not work. On the other hand you would get error tolerance for free due to constraint on substitution as a limited amino acid repertoire becomes subdivided to give 20. Starting with one assignment and negotiating constraint to get to 20 would lead to a fault tolerant code by default. The same mechanism that constrains wholesale substitution will lead to clustering of property, and hence misread tolerance.
Made me laugh.
😀
Well, we have that much in common then 🙂 glad to hear it.
This has been a long and tedious route to “Code=Jesus>”
This does not explain where in the folded proteins the active sites are going to appear.
walto,
I think you are mixing two realms of explanation. If the fundamental physical laws had been different, atoms would behave differently (or not even exist) – every atom in the universe. But evolution is a matter of history. A population of replicators has an internal and external environment. It persists as a lineage through successful replication, which can involve complex strategy. It changes as a lineage due to the mutations that get thrown up. These are constrained by the genome in which they arise – you can’t go everywhere from a given point. So if (for example) the genome can synthesise alanine but not guanine, there is one possible source of contingent constraint, not derivable from Law.
Another is simply enzyme structure. Even if both molecules are present, and perhaps both potential substrates, there is likely to be a small preferential differential affinity for one over the other in my putative ‘tRNA charging’ mechanism. If substrate discrimination leads to a ‘better’ end result, it may not matter which substrate is settled upon, but the initial small asymmetry in favour of one or the other can be tuned, ultimately to the exclusion of the other.
Equally, however, the constraint may be the product. If polyalanine is biologically useful but polyguanine is not, then there is selection for tuning the alanine association. And as far as the codon set is concerned, once you have mRNA involvement you get a potential constraint on the anticodon end too, based on the codon strings that actually occur.
Each element of the system is tuned in the presence of the other
The difficulty, of course, is that we are guessing at the constraints in an unknown organism in an unknown enviroinment.
I took it as making a serious point. It did not seem particularly hilarious.
Mung,
Does it need to? If they don’t arise anywhere, the protein is nonfunctional. Still not an algorithm.
Right–what happens in this organism or this group of organisms is a matter of history. But what happens in this star or this galaxy is also a matter of history. So what I want to know is–Given the physical laws as they are–do you take there to be a type of contingency in one arena that is absent in the other?
Chemistry can’t even be reduced to physics. And biology can’t be reduced to chemistry. The entire reductionist enterprise is in shambles. But that doesn’t stop folks from making the “it’s just chemistry” gambit anytime it’s convenient.
Neil Rickert,
Calvinists are extreme on the deterministic scale of Christian theology/worldview. FMM might have appeared to make a joke, but knowing Calvinists, he is probably quite earnest in his quasi-IDist ideology, even if tipping on the slide-scale to fatalism.
This continues what I asked FMM here: http://theskepticalzone.com/wp/code-denialism-pt-2-nirenberg/comment-page-4/#comment-89151
If FMM was well-read in non-Calvinist Christian responses critical of IDism, he might realise the unusual extremism of his current position.
Given that humans are part of nature, the Morse code originated in nature.
Reduction doesn’t mean you can predict higher order organization from lower order principles. That kind of explanation is barred by emergence.
What reduction means is that higher order organization cannot violate any constraints imposed by lower order principles.
Neil Rickert:
I’ve been thinking about this too. I think it may be that if the “must” in FMM’s first remark were explained, the humor might dissipate. He may be saying that he thinks that everything is designed but that this is a contingent fact (it need not have been that way; there are possible worlds in which some things aren’t). But he may also be saying that the claim that something is designed does not imply certainty, that one could believe it without being absolutely sure that one is correct.
From what I’ve learned about FMM from his posts here, I’m guessing he meant the latter, but it may be that he meant neither of those two. Anyhow, as you say, not really that hilarious, IMHO.
If people are going to continue to insist on using the machine metaphor, then yes.
Unlike you, FMM doesn’t seem to stake so much on whether his views are mainstream or not. You want to believe what you take pretty much everybody else to believe–whether there are any decent reasons for such belief or not. Good for you.
This is where we get into map-territory territory (territory), I think. The sciences (maps) may not be reducible even if all the world requires are laws of physics to act exactly the way it acts now. (Where “laws” are not statements or deductions (maps) but real “connections” (territory)–if that makes any sense.)
Mung,
‘People’? Name ’em! Not me, surely.
I don’t actually get your point anyway – it’s not Duelling Metaphors of which there are only two. But I have steadfastly argued against all metaphor (except when I fall off the wagon occasionally and liken tRNA to a stick …).
See, walto, I told you that you were nowhere near the top of Gregory’s list. 🙂
He’s barely able to summon up the desire to be mean to you, and even throws in a little sweetener about “be healed”.
walto,
I think the fundamental difference would be the presence of a genome, iteratively copied. That dictates the evolutionary paths available from any given state, and subsets future trajectories by weeding out some at the expense of others. There is no equivalent constraint on the gravitational coalescence of a cloud of gas.
Mung,
And yet the point Bruce and I were agreeing on, the one that sparked your comment, was the opposite of that.
Quite so.
I took fmm to be saying that he is not making an inference from “it is a code” to “it is designed”. Rather, he is making an inference from his Calvinist presuppositions to “it is designed.” I see this as more honest than the pretense that ID is science.
I would like to see Mung make a sustained argument, starting with what he believes, and following through with explanations and reasons.
Stealth bombing from 30,000 feet is ineffectual. You need troops on the ground.
Is that a useful metaphor?
Yes, I think that’s correct. But he is saying that his ID conclusion comes from his theology. He is not saying that it comes from science.
He is channelling Michael Denton’s “Nature’s Destiny.”
Also Chardin’s “Phenomenon of Man.”
What kind of processes do you think make proteins fold?
This is what I mean. IDists need to embrace intention. Intention is not universal in nature. Nature is 🙂
petrushka,
Not likely, since Denton is a vitalist agnostic. And Chardin was too welcoming of evolutionary creation for most IDist’s tastes. IDists still haven’t fully faced Chardin in a credible way.
The main point to remember, which Discovery Institute IDists conveniently and intentionally forget, is that *ALL* Abrahamic theists accept lowercase ‘intelligent design’ as a pre-IDist natural theology. There’s no need to ‘scientise’ such a perception.
Well, it seems to me that FMM is both confused and anxious in his apologetics; is he doing apologetics or isn’t he?
Mung likewise, seems to think code = intelligence. But this is too simplistic and lowbrow thinking when ‘pattern recognition’ requires no probabilism. Typical of evangelical USAmerican protestants, yet not of significant global Christian scholars and scientists.
Every human being does, Lizzie, even ex-Catholic, quasi-Buddhists like you. That you’ve apparently been duped by the dyslexia and schizophrenic (cognitive science) studies you’ve done doesn’t remove that. Or are you going to try to ‘unintentionally’ write something in response? 😉
As to a nonbiological code in Nature … how ’bout spectral lines? Nature’s elemental barcodes. Of course, not a ‘true’ (representational) code either.
Right. Which is why it’s frankly foolish (jester’s cap-and-bells foolish) that fifthmonarcyman says this:
GIven his presuppositions, in his world there is literally NO difference between those two clauses.
“X must be the result of design” — because literally everything in our universe was designed by his god, and that is all as it must be.
PLUS
“[he is] believing X is designed” — because of course he believes correctly that god designed everything, as he must believe.
And of course he claims it “is designed”, because he can’t shut up, and he can’t stop himself from making truth claims about his beliefs.
It’s ridiculous for fifthmonarchyman to write as if he could dispassionately examine the potential philosophical differences between those two clauses (which might indeed have a world of difference if one were not a god-besotted Calvinist). It might have passed unnoticed with the rest of his religious blather, but he chose to immediately juxtapose the Calvinist avowal with the other statement, and that’s what makes it funny.
Self-awareness. A worthwhile goal.
Allan Miller,
In some sense, the coalescence of stars and planets out of a gas is closer to the folding of a single protein molecule – the shedding of energy by following thermodynamic gradients, which is pretty ‘law-like’ (and good thing for us too – I’d be lost without my regularly-folding proteins).
It depends what you mean by “reduction”. I was using it in the traditional philosophical sense of reducing whole sciences to “lower-level” sciences by showing how the laws of the upper level science can be deduced from the lower level science. I agree that whole science reduction cannot be done.
But reduction of a specific phenomenon can be done through mechanisms. For example, the the biological cell process of protein synthesis have been successfully reduced to a significant extent via mechanisms based on biochemistry.
Thanks, Allan. I’ll chew on that.
Exactly.
Err, how about the phenomenologists?
Although of course they disagree with Dennett on how to understand the concept.
Which philosophers of mind or language or phenomenology do not talk about intentionality in the sense of the aboutness of mentality, if only at least to try to eliminate it?
Stalking bad.
One might cite atomic number, or the combinations of quarks to form hadrons.
Mung engages in the same — incredibly dimwitted — circular logic that Dembski uses to disprove evolution.
Code implies design because code can’t originate without design.
Code can’t originate without design because…
Where was I going with this?