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
Great. The genome is a “real code” according to ID proponents.
Now all that remains is for them to demonstrate something useful that flows from that knowledge. Or will they just defer that actual work to actual scientists, now that they have “revealed” the truth?
If nothing, then why bother with all the words saying that it is?
No,
It’s a hypothesis that the mapping is particularly optimal for producing something like us and that the many other possibilities are at least as likely but not as capable.
peace
And what work will you be doing to prove demonstrate the truth of that claim?
Oh, right, other people will be/are doing that work for you. Or you’ll twist their work to support that, at any rate.
Typical.
fmm,
Are you aware there are in fact differences in the “mapping” even now for extant biology?
yes
peace
BruceS,
I’d say it is inherent in the world, but who knows really?
Selective advantage is a random variable. Between two competing types, there will be a differential in mean offspring number which converts to the expected increase of one against the other. Differentials are fractional, but you can’t have fractional offspring. If the fitness of a type is 1.01, they will produce 0, 1, 2, 3 … offspring in different instances, averaging out at 1.01 over infinite trials. That is random. Additionally, whether this difference has causal power depends on the population size, because we don’t have infinite resource.
Now, one could say that a demon could know up front what is going to happen to every individual from any given point – if we live in a fully deterministic universe. But the progress of the allele is still ‘random’ – subject to probability distribution.
One could apply it to roulette wheel spins (preferably not involving people, to avoid any influence of ‘mind’). It is ‘inherent in the world’ that the distribution of spins will follow a probability distribution, even if every spin has an inevitable result given starting conditions, which a demon might predict – it is also inevitable that there will be a distribution, which will approach the theoretical with increasing trials. Which any demon worth its salt would know.
How is the work of putting my tool/game on a web page going?
peace
The collapse of that probability distribution into a single observed outcome is just what people and demons (and the universe) do.
Peace
fifthmonarchyman,
So you plan to test your hypothesis how? If you could seed 1 trillion planets with this code and count how many produced people, would you do it?
It is adequate, if not definitively ‘particularly optimal’, for producing everything on this planet.
fifthmonarchyman,
Probability distributions don’t ‘collapse’ into single observed outcomes! Yeesh. Something you half-read in QM, I think.
I see what you’re saying, and it’s interesting, but do you really think there is a lot of similarity between someone sensibly answering a question you’ve asked and evolutionary descent? That seems like a stretch to me. In any case it will certainly be greeted with skepticism by most people.
I think the goal in these sorts of controversies should always be to find arguments that will seem plausible to–if not everyone–at least everyone with an open mind.
That should read:
It’s a hypothesis that we are very well adapted to the part of the universe where we find ourselves.
Incidentally, the theory of evolution provides an excellent explanation for this.
That seems like the gambler’s fallacy to me. Randomness is a difficult concept (for me, anyhow). Yes, physical forces and pre-existing conditions are ENTIRELY responsible for the roulette ball falling into a particular slot. Nevertheless that it would fall into 00 was, in a sense, random. And, in addition, it had a precise probability of X (is it 1/37? I can’t remember) of falling into that slot.
It’s hard to talk sensibly about any of this stuff without first defining our terms. E.g., FMM means something by ‘arbitrary’ that is inconsistent with randomness.
BTW, speaking of the difficulties of randomness, I have a story. I’ve been involved with insurance rate hearings for a long time, and many years ago an actuary who was an expert witness for the State Rating Bureau was conferring with an SRB attorney before giving his direct testimony. He indicated, quite clearly, that he did not want to talk about randomness.
“You got that?” he demanded.
“Sure, sure, no problem. Nothing about randomness. Got it.”
So, naturally, when he gets on the stand, the first question his lawyer asks him is to define “randomness.” About an hour later, when there was a break in the proceedings, the actuary threw an unopened Coke can at the lawyer’s head.
I’ve got real work to do. You are at the back of the queue.
However if I were to be going round hypothesizing this or that then I’d damm well make the time to follow up and support those claims. We seem to differ in that regard.
In theory, you can predict it exactly if you knew everything about the toss and the dynamics of the wheel.
In practice, you CAN do that well enough to beat the house at the roulette wheel. This book describes people doing exactly that.
So I don’t see it the way Allan M does for the Laplacean demon, given my magic calculating powers for the demon and ignoring QM.
I’m not sure why you mention the gamblers fallacy, which has to do with not understanding what independent trials means.
I have not read FMMs linked post, but his quote sounds like a mangling the Copenhagen interpretation of QM (although the “universe collapsing” bit may be how he understands decoherence). ETA: I see Allan makes the same point.
ETA: I would bet that a key aspect of Keith’s take on arbitrariness is the initial conditions of the universe, which could vary and so affect the evolution of deterministic physical laws and the resulting genetic code.
Care to take that bet? What odds will you give me?
Well, yes, but I was considering the view from nowhere which I assume you would need in order to contemplate the vast panorama of the universes in the multiverse.
In other words, it was just a lame setup line for the “joke” in the following paragraph (about needing a long time to do so).
Random=unmodeled
I understand I’m very busy as well. I’m sure that is what is going on with the little 2 week hack that Patrick needs to do in order to falsify my hypothesis.
I need to get back to work at some point as well.
It’s not like nothing is happening with this hypothesis . It is tested every time we look for extraterrestrial life every time we look at evolutionary adaptation every time we find a new fossil and every time folks like Craig Venter explore synthetic genomics.
peace
Are you saying that we should be able to model the actions of an intelligent agent? Since agents don’t act in a random way.
peace
No we are talking about the genetic code not how well we are adapted to our environment
Evolution and design are not mutually exclusive concepts.
peace
walto,
Think of it this way: probability, like possibility, can be metaphysical or merely epistemic.
Suppose you spin the roulette wheel and the ball falls into the 00 slot. If the universe is truly deterministic, then the metaphysical probability of that event is (and always was) one. A Laplacean demon could have told you that it was going to happen. Once the boundary conditions of the universe were defined, there was no other possible outcome.
To you, by contrast, the ball’s eventual resting place is anything but certain. There are many epistemic possibilities, and that remains true even if you know ahead of time that the universe is deterministic and that there is only one metaphysical possibility.
Ah, that gambit. How’s that working out for you, you parasite?
And so what? Neither is design-by-elves. Or unicorns.
Nobody denies that it’s perfectly possible that something that seems to have evolved could have been designed!
The problem for ID is that you need it to be the other way around, you need to point at something that could only have been designed and not evolved. And so far that’s not happened, not in a way that people outside of the ID circle-jerk are convinced by anyway.
So while it’s true that evolution and design are not mutually exclusive concepts that does nothing whatsoever to support ID or your cause.
Unless if course you can point to a specific design event in the history of life and explain why that could only have been design?
Of course you can’t, but that won’t stop you from making such statements will it?
OMagain,
(Innocently raises hand) Er – would the genetic code count?
This will never happen you can relax.
It boils down to the problem of other minds.
You can point at the behavior of any agent even humans and say definitively that this behavior could not be the result mindless processes and random chance
There is no way to prove that other minds exist but we know they do. Wanna guess how we know?
peace
No, not really.
Wanna know why?
We assume another mind exists which tells us minds exist?
We don’t assume other minds exist we know they do, or we no nothing at all.
peace
you only know because you assume they exist in the first place
But God has made him infallible, at least on these matters.
Now please discuss science as based upon FMM’s infallible statements, for it inevitably is.
Glen Davidson
I know,I just wish God had given him a more interesting argument
Right, I agree with all that. So just consider the metaphysical, rather than epistemic conditions. Leaving aside quantum weirdness, given some event, we would seem to have complete determination of it, randomness or indeterminateness producing its existence , or some sort of “spontaneous choice.”
Do you think there are other alternatives? And how do you classify the genetic connections? Do you think that our inability to predict pairing is simply a function of ignorance (i.e., epistemic shortcomings)?
walto,
Actually, quantum effects seem to be the only source of metaphysical randomness, with other random phenomena being only epistemically random. So I would break it down this way:
1. If the physical universe is causally closed, then every event is a function of at most a) the laws of physics, b) the boundary conditions, and c) any nondeterministic quantum events that occur within that event’s light cone.
2. If the physical universe is causally open, then events can also be affected by nonphysical influences, which for Upright Biped and like-minded folks would include actions initiated by d) God or by another nonphysical intelligence.
When Upright says that the codon-to-AA assignment is “arbitrary”, he simply means that it is not determined by (a), the laws of physics. He then jumps to the conclusion that it must have been determined by (d), an intelligence, completely neglecting the possible contributions of (b) and (c).
If you mean by “boundary conditions” those pre-existing conditions on which the physical laws operate, I don’t see how they make anything arbitrary. Once they’re specified, everything happens like Laplacean clockwork. That would just leave quantum effects to supply real (metaphysical) randomness (since, I take it) only FMM considers the “spontaneous choice” alternative a kind of “arbitrariness.” OTOH, if you mean something else by “boundary conditions,” I don’t know what it is and hope you’ll explain.
ETA: Not sure it’s clear what I meant by “once they’re specified.” The idea is that at time t, every element in the universe is in a particular place–including segments of DNA chains. Now the physical laws act upon those conditions. They either determine every element of the next state of the universe or they don’t. If they don’t, then it seems it must be a matter of quantum irregularities or “spontaneous choice”–I don’t see any other alternative (like “boundary conditions”). I admit, though, that I’ve not been able to completely follow some of Allan’s posts on this. He sometimes seems to suggest there’s something “in between” determined and not determined when it comes to biological processes.
Exactly. That’s because all the arbitrary lawless stuff get’s stuck under “boundary conditions.” That’s what allows the physical laws to be universal and unchanging.
It’s a put up job 🙂
walto,
That’s basically what I mean, though “boundary conditions” can also refer to post-existing conditions since the fundamental laws of physics are time-reversible.
They don’t — it’s the other way around. The codon-to-AA mappings are arbitrary with respect to the laws of physics, meaning that other mappings are compatible with those laws. Add the boundary conditions, however, and those other mappings are ruled out, assuming that the universe is deterministic. The boundary conditions eliminate the arbitrariness.
The argument is similar for a non-deterministic universe, except that other factors besides the boundary conditions may be involved in determining the mappings.
Either way, Upright’s error is to think that if the laws of physics don’t determine the mapping, then intelligence must be involved. That’s obviously false, because other factors (including boundary conditions and metaphysical randomness) must be considered.
To prove that the mapping was chosen by an intelligence, Upright would have to rule out all of the possible determining factors except for intelligence. He can’t do it.
I’m still not entirely following this, I don’t think. Take a non-biological event, like a coin toss. There, physical laws are consistent with either a heads or a tails, but in conjunction with prior conditions can only produce a particular one (ignoring quantum weirdness). Are you saying that precisely the same thing is true of the DNA mappings? If so, that seems to me to contradict about a hundred posts by Allan. He (and a number of others here) have conceded repeatedly that the DNA pairings are not like the coin situation, that the prior existing conditions and the laws of physics do not determine a particular result in the biological case. As I understand it, that difference is why design backers don’t claim that the relevant “arbitrariness” is involved in a coin toss case.
I just happened on this article it goes into some detail about where the term code came from with reference to the genome.
http://discovermagazine.com/2015/sept/17-genes-before-dna
interesting stuff I’m sure you all knew already.
peace
Hi fifth, thanks.
Cobb is the author of:
Life’s Greatest Secret: The Race to Crack the Genetic Code
walto,
Yes. They’re both physical phenomena governed by the laws of physics. If we eliminate quantum effects then we have removed the only source of metaphysical randomness. What’s left in that case is a deterministic universe, and in such a universe all events are determined, including the outcome of every coin toss and the outcome of every evolutionary process, including the evolution of the genetic code that predominates on earth.
I think perhaps you’ve misunderstood him. Let’s take a look at a couple of his comments.
Here he defines ‘random’ as ‘subject to a probability distribution’:
And here he affirms that by that definition, there is randomness even in a fully deterministic universe:
He’s saying that the outcome of every spin is determined, but the outcomes taken collectively conform approximately to a probability distribution. They aren’t metaphysically random, but they’re still random by his criterion of conformance to a distribution. The same reasoning applies to the evolution of genetic codes.
He is not saying that “that the prior existing conditions and the laws of physics do not determine a particular result in the biological case”, as you put it.
walto,
Splutter! People keep rattling my cage! 🙂
walto,
I think it’s just equivocating on ‘determined’. If a particular acid-triplet association is more chemically favoured than another, that is a different form of determination than the philosophical idea that everything that happens was determined from the outset. When I say a codon-triplet assignment is arbitrary, I mean completely interchangeable at the chemical level.
But another level of ‘determined’ comes in with contingency. There could be no chemical favouring of one acid over another, but simply an excess of one, or some other biological circumstance, means that this is the first acid used. It’s not a random pick from a pool if there’s only one thing in the pool.
The mention of probabilities is a red herring, I think. The point here, is that if keith’s taxonomy is correct and we ignore quantum spookiness, there isn’t any difference between a roulette ball coming up 00 and a particular protein being “chosen.” There is epistemic uncertainty in both cases, but no actual chance of anything happening other than what does happen. The biological case is exactly identical in this respect to the non-biological case.
I believe you have tried to distinguish them in any number of posts by indicating that predictability may be impossible even with unlimited knowledge in the biological case where it is not in the non-biological case.
Again, there are probability distributions (if we consider a bunch of similar cases) in both the roulette and DNA arenas, but that’s irrelevant: it just sneaks in epistemic issues. The design-backer is making a claim about metaphysical arbitrariness.
walto,
No, that’s not what I’ve been arguing. In that kind of Laplacean schema the biological is in no way privileged.
For what it’s worth this is my understanding of arbitrary as well. It is different from “random” and “determined by law” in that it is seen as optimal/near optimal in retrospect.
peace
OK, thanks for clarifying your view on that.
But I want to hold you to it by having you consider what it entails (because I don’t think you’ve been completely clear on this matter to date.)
The design argument from arbitrariness is not about human ignorance. It requires that there be something special in the case of DNA sequencing that is not epistemic, because our limitations are just as apparent in the case of roulette predictions. That argument requires that in certain biological cases only there be arbitrariness ‘all the way down.’
There have been a number of posts here, not only by you, about the consistency of, e.g., both guanine and cytosine results of a common prior condition (and how it mirrors sentence continuations with a common set of words, blah blah). But if the bio case is no different from the casino case, and so-called ‘arbitrariness’ is just a matter of our ignorance of the relevant conditions, then one could just as well make a design argument regarding not knowing precisely where a stone will fall if it’s windy out. Nobody does that.
There’s nothing special about DNA sequencing on keiths’ theory. I want it to be completely clear that this follows from the deterministic position without more (again excluding quantum effects, which might also infect both biological and non-biological cases). That’s not a criticism of keiths’ position, which seems to me entirely coherent (except maybe for its suggestion that the ‘boundary condition’ issue isn’t itself just another way of indicating our epistemic limitations).
In sum, if the position you now say you hold is right, there’s been mostly irrelevant blather coming from both sides of the ‘arbitrariness’ fence. A veritable school of red herrings. Premise (2) of the Frankie argument simply confuses ignorance with arbitrariness and is false for that reason. Period. The rest is just bio-babble.
walto,
I’m not entirely following. Maybe because I speak bio-babble better than I speak philoso-babble, I dunno 😉
When I (and, I think, Frankie) say that a codon-amino acid association is arbitrary, I mean only that there is nothing about that association that makes it more likely to fall out than any other. Arbitrary in this sense is something like ‘equiprobable’. If you have 20 As and 64 Bs, and a means of joining them up via an intermediary molecule, there is nothing in the chemical properties of either As or Bs that makes a particular pairing more likely than any other. (Though note in the early days, although we know there were 64 B’s, we don’t know there were 20 A’s).
Once you’ve taken one B out of the set, you may have a constraint on the next association which was not there at the start. But no matter, still chemically arbitrary.
The discussion of philosophical determinism is somewhat further from my comfort zone. I don’t think it capable of resolution, especially in the artifical condition of ‘ignoring QM’. Not that I think QM relevant to biomolecules – I don’t think mutations are subject to quantum indeterminacy, though I could be wrong.
One thing to be aware of that I think is pretty much unique to nucleic acid systems is the capacity of a tiny change involving one or a few atoms to amplify and resonate across the globe, due to exponential replication. If one sees Life as more than just a pretty green carpet with things crawling in it, that is pretty interesting. Given that those key changes could have gone another way, many things about present forms would be different but for that local fluctuation (is that fmm I hear clearing his throat?). Of course there would be something else instead, and also much in ecology that would be familiar due to the convergence on limitations on different ways of operating.
So, biology does have a privileged place in the world of causality beyond simple Physical Law vs Anything Goes, due to exponential replication and its several consequences. But equally, the Laplacean Demon would have all this additional chaos in its all-seeing eye too.
Whether that addresses your point, I’m not so sure!
If we are part of a cellular automaton, neither we no any finite entity present at creation can predict how the unrolling will proceed.
We are in the interesting position of creating expectations about the future based on regularities discovered in the past, but we cannot ever know enough about how things work to predict the future.
See, this is the communication problem we’re having. That equiprobability you mention is only epistemic, given your acceptance of keiths’ propositions. By that I mean that it goes no farther than saying, based on what we know, we have no basis for predicting result A over result B or vice versa. That sort of ignorance-equiprobability is no different from the equiprobability of a heads or tails given a fair coin flip. (There’s nothing in the physical properties of either heads or tails that makes a particular result more likely than the other.) There’s nothing intrinsically arbitrary about either case, we simply don’t know enough to make a good prediction in both of them.
This particular (“Frankie”) design argument DOES require there be an intrinsic difference between the two situations based on the biological aspects.of one of them.
The biological processes are either different from a coin toss (or a leaf falling in the wind) or they aren’t. But it’s clear that we’re equally ignorant in both cases and if you and keiths are correct, then (ignoring quantum effects) there’s no intrinsic arbitrariness in either of them also. The biological details can make no difference here.
To discuss these arguments sensibly, we have to be vigilant about whether we’re talking about human ignorance or metaphysical indeterminism. The Frankie argument–and I’d think likely several other Design arguments as well–require metaphysical indeterminism. And none of the arguments I’ve seen or can imagine (code-coder, obvious purposefulness, etc.) involve human ignorance/difficulty in making predictions because of what we don’t know at present. It’s whether it would be impossible to know the outcomes because there’s simply no fact of the matter that’s important here.