Testing predictions is the gold standard of science. And before you pull out another straw man, all scientific conclusions are formally tentative. So all that stuff you praise about science is tentative too. That’s why it works so well.
Who has said otherwise? It merely means that we real scientists go on to test other predictions, something creationist pseudoscientists never do. It’s all about pretending that science is merely post-hoc explanations.
Let’s take the first evidence you’ve pointed to, which is the sequence similarity between the peptidyl transferase center of 23S ribosomal RNA and ancestral proto-tRNAs. From this, you’ve asked why this similarity if thesei two different, and functionally distinct components of the translation system did not derive from the same ancestral RNA? Well the answer is quite simple and it is that some sequence and structural motif useful for tRNA function in the context of translation is also useful for PTC function in the same context. IOW, sequence similarity can as well be explained by design constraints than by direct historical/evolutionnary connection.
What Design Constraints are those?
Can you state them as a testable hypothesis?
Why would there be design constraints?
Especially in light of @theaz101’s claim that the mechanism involved is supernatural. I’m not aware of any identified constraints that have been presented regarding alleged supernatural causes.
Sure, but the problem is you have no a priori reason to expect these two radically distinct functions in translation to have such similar sequence and structural constraints. The PTC has been experimentally shown to be able to function as basically two copies of a single RNA polymer that dimerizes, and that functions as a catalyst that promotes the formation of peptide bonds between amino acids, whereas the tRNA molecule is essentially just scaffold-like structure which has an amino acid attached to it.
It’s not at all clear why, for the tRNA molecule alone, there couldn’t be innumerable alternative possible replacements for the tRNA molecule in both structure and sequence. It seems to function as little more than a handle presenting an amino acid for the ribozyme to work on it.
There just doesn’t seem to be any of these supposed sequence or structural constraints necessary for each component. Alternative artificial ribozymes are known that catalyze peptide bond formation, and innumerable alternative structures seem possible to “hold” an amino acid in an exposed position where an enzyme or ribozyme could “work on it”.
As such their observed similarity, since the claim that it is necessary does not seem to be based on anything, is better explained as the product of evolution from a common ancestor. A posteriori it is therefore evidence favoring evolution.
To repeat…
Well, there goes the genetic code as being arbitrary symbols.
I’m not sure what is your point here. Is it that you see a contradiction between the two quotes of mine your are pointing to? If you think so, then you’re wrong.
I see an obvious one.
The genetic code is in no way arbitrary. There is a mountain of data showing that.
I think that what he (and others) is doing is using the non-arbitrariness of the translation process (decoding process) to declare that the Genetic code itself is non-arbitrary. In other words, the mapping is necessary (non-arbitrary) because translation carries out the mapping in a mechanical sense.
This is completely invalid, of course, because a code (like ASCII) is only arbitrary when it is developed. It isn’t arbitrary when it is used.
Also, they are ignoring the fact that the translation machinery itself was first produced by existing copies of the translation machinery - using the Genetic code.
I’ve been using the meaning of arbitrary that is:
1b: based on or determined by individual preference or convenience rather than by necessity or the intrinsic nature of something.
So, not random. The fact that there are chemical patterns to the mapping isn’t the same thing as those patterns requiring (necessitating) a particular mapping. I see the patterns as a result that the Genetic code was created and not random.
You’re right, of course. Our labels did not create the code. The mappings of a codon to amino acid existed and was in use long before man had the ability to discover it (and create the labels of codon and amino acid).
This is true for everything. We gave labels to the elements, but those labels didn’t force the elements to come into existence, either.
In which case the genetic code isn’t arbitrary, because it isn’t based on “individual preference or convenience.”
This is your assumption, then. Not something you have any evidence in support of.
Thanks, yes. But I hope you can then see the problem with your argument here. If you decide to define the category “codes” as something that includes the premise that it was necessarily created by intelligent designers, and then you go on to put the genetic code into your “codes” category, have you then shown it was created by an intelligent designer? Of course not, that would simply be to assume the conclusion.
As stated elsewhere, there is no chemical necessity for the mapping as shown by the example previously given. You can take some codons (not all) and simply rearrange the bases and get a different amino acid added to the peptide chain.
Chemical patterns do not necessitate the mapping and are no surprise if the mapping was chosen, not random.
It’s a premise, not an explanation.
I never said anything about framing. I said that the post-transcriptional modification includes bases being changed into non-standard bases by proteins.
That wasn’t part of the prediction.
I don’t deny that RNA has some catalytic activity. I’m saying that it hasn’t been shown that rRNA can perform it’s catalytic activity without being modified (not talking about framing) by proteins.
And, it hasn’t been shown that rRNA can translate the Genetic code by itself.
I don’t have to explain any of that. I’m not the creator.
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3) How do you explain the nonarbitrary nature of the genetic code, other than repeating your false claim that it is arbitrary?
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The decoding of a code is not arbitrary. The development of the code is what is arbitrary.
That doesn’t tell me anything that I didn’t already know.
What you haven’t even attempted to explain is why catalysis is relevant to this discussion. What statement have I made that is answered by “catalysis”?
This comment, which you have repeated in various forms throughout this thread, is a big problem for your credibility. If I’m reading the thread right, you came close to an understanding of this when you (apparently) read the old piece by Venema. You seemed to get the concept of the stereochemical hypothesis, which is in fact a view that, to at least some extent, the “patterns” arose as necessary results of intrinsic molecular (stereochemical) realities. This hypothesis is old, and it’s clear, and to repeat mantra-like the claims that you make in this thread is to either announce that you haven’t read anything on the topic (that’s my hunch) or to unmask yourself as a dishonest apologist.
I am certain that the scientists on this thread, when they repeatedly tell you that the code is not arbitrary, have read articles like this one…
…which is an extensive review of the status of our understanding as of 2017.* It seems to me that your knowledge is so shallow that you can’t resist spawning red herrings about riboswitches when discussing views of the evolution of the code that are decades old. It seems to me that you don’t know what you’re talking about, but that you are nevertheless happy to type assertions in a conversation with people who do.
You’d be a lot better off telling the truth, for lots of reasons that an adult shouldn’t have to be told. A creator worth even infinitesimally small respect would not need lies about stereochemistry on the Hadean earth to earn that respect. I will always respect faith and those who find inspiration in Iron Age deities, but I will never understand (and never understood during my 30 years as an evangelical) why it’s not enough for SO many believers to confess a god big enough to create and sustain the cosmos we actually live in.
*The article is open access as a PDF, accessible for now via the “full text” link.
So just wishful thinking. Try to understand that arbitrariness is a negative and therefore, requires a complete understanding of the evidence to maintain.
I know, but that has nothing to do with the question of arbitrariness.
The fascinating thing is that this question has been addressed in great detail by real scientists testing hypotheses, but you seem to be reluctant to dive into the evidence they have produced.
Are you going to explain your assertion that RNA switches have codons?
I have no idea what you meant by that. Since you asserted “some” and “often,” certainly you can point to multiple examples?
Another goalpost move. We’re not referring to any vague notion of “chemical patterns.”
This is reminiscent of IDcreationist dismissal of petabytes of sequence data as vague “similarity” instead of superimposable nested hierarchies.
Please try looking at the evidence before making any sweeping claims.
More word games. Can’t someone choose something randomly or nonrandomly? How can chosen and random be mutually exclusive?
Please stop with the games; we disagree on arbitrary vs. contingent. You are asserting the former (an implicitly negative claim) with zero supporting evidence. We are pointing out that the evidence you are pathologically avoiding tells us that the mapping is not arbitrary, but was chosen by a contingent, incredibly recursive process.
Evolution is constrained in a multitude of ways that no omnipotent, omniscient being ever could be. The excuse of “I’m not the creator” doesn’t cut it.
Then why would you offer it as a response to:
???
I never claimed you did.
I pointed out that the current framing (metaphorical) by ribosomal proteins would make most, possibly all, stability-enhancing structures in the ancestral rRNA unnecessary. If you know anything about the relative stabilities of RNA and protein, you’d know why that’s important.
Which I say has nothing to do with the fulfillment of empirical predictions of the RNA World hypothesis, coupled with the falsification of multiple empirical predictions of your creation hypothesis.
So, if the genetic code was arbitrarily chosen by God, do we expect any modifications?
If the attachment of amino acids to particular tRNAs, and the enzymes that catalyze it, were specifically and arbitrarily designed by God, what should happen to any organism that lacks one of those specific, completely arbitrary (as you hypothesize) aminoacyltransferases?
That would be another goalpost move, because you removed the context of the specific activity–peptidyl transferase.
I’m pointing out that you have no idea what has been shown or not shown, just word games. I think you’re afraid to look. Isn’t God speaking more through the evidence than what any IDcreationist rhetorician writes or says?
You are moving the goalposts. You are explicitly claiming that this evidence tells you that this particular system was directly designed in detail by an omnipotent, omniscient being.
Why do you keep repeating this false claim? There’s no relevant distinction served by your goalpost move from “decoding” to “development” either.
Coulda fooled me.
But I have. What is catalysis UNABLE to do? That’s what is relevant to understanding enzyme evolution, and you’ve shown no awareness of this.
And how doing so somehow serves anyone’s understanding and/or worship of the Christian God makes no sense. Doing so in service of one’s ego clearly does!
Me neither. IDcreationism is just ridiculously bad theology, even putting the pseudoscience and mendacity aspects aside. It conceptually turns God into a tiny, cheapskate tinkerer more consistent with a minor Hindu god.
Doesn’t seem like invoking a creator offers much of an explanation after all…
I don’t understand your point at all. I’m not saying that the genetic code is special (relative to other codes) because it is digital, I’m saying that it is like other digital codes, and, like other digital codes, the product of an intelligent mind.
We are really talking past each other. I
I’m not appealing to the supernatural as a cause of a chemical reaction, and I don’t think I’ve come close to suggesting that in this thread. I honestly don’t know where you got that idea.
I’m only talking about the arranging or sequencing of DNA bases at the time that life originated. The sequence of the bases determines what the function of the functional rna/protein will be, but the function is carried out according to the laws of chemistry.
I’m also saying that there is no law of chemistry or chemical necessity or chemical reaction which determines what the sequence of DNA bases must be.
You’re using your knowledge that ASCII was designed to distinguish them, not an obvious (black and white) difference between what ASCII and the Genetic code do. i.e.: alternative groupings of elements (ones and zeros or the bases of DNA) to code for something else. And that’s the only thing I’m comparing. The means of processing, organic molecules or silicon and circuits, is irrelevant. In both cases, they are processed by unguided chemical or electronic processes.
Your philosophic assumption:
Every intelligent being that can create a code requires the genetic code to exist.
is the equivalent of “all swans are white”. It isn’t a scientific statement.
The examples that I’ve been shown supposedly show evolution of the Genetic code after it had originated. Not how it originally came to be. Sort of like comparing two airplanes, one with a two blade propeller and one with a three blade propeller and saying that it was evidence that the airplane evolved.
Venema refers to a previous blog post which refers to this paper:
Which states:
The apparent probability (P ) that cognate triplets around these sites are unrelated to binding sites is ≅5.3 × 10−45 for codons overall, and P ≅ 2.1 × 10−46 for cognate anticodons. Therefore, some triplets are unequivocally localized near their present amino acids. Accordingly, there was likely a stereochemical era during evolution of the genetic code, relying on chemical interactions between amino acids and the tertiary structures of RNA binding sites.
Fine. The same sequence as the assigned codon.
Venema, specifically on p. 190, is referring to many papers published before the time he wrote it; many more relevant to your claim have been published since then. He is explicitly referring to Meyer’s (and your) objectively false claim that the mapping (a metaphor) of amino acids to codons in translation, with no reference to riboswitches, is arbitrary.
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First of all, I wouldn’t call the mapping a metaphor, that’s your term.
Secondly, what the paper is showing doesn’t come close to a chemical necessity in mapping a codon to a particular amino-acid. The mapping is determined by the sequence of the transcribed and spliced genes (mature mRNA) that code for the components of the translation system.
There is no chemical necessity for any specific sequence of DNA nucleotides. That’s why the Genetic code is arbitrary.
Before this thread joins the silent everafter … perhaps someone should just mention the way that the gene system actually functions. The genetic code is physically established inside the living cell by the sequences of DNA that specify the aminoacyl-tRNA synthetases (aaRS) … and for any of those sequences to serve that function, they must all exist in a simultaneous coordinated state.
With @theaz101, let’s approach this with the scientific method instead of the shallow rhetorical method:
You hypothesize that the genetic code was formulated arbitrarily and simultaneously.
That’s a crystal-clear empirical prediction of your hypothesis, not a fact.
If your hypothesis is correct, that must be true; more importantly, it must be true in any and all cases, as you clearly and confidently stated. IOW, a single, present-day exception is sufficient to falsify your hypothesis!
So, how much money would you bet that there are no exceptions?