I’ve been pointing out that what was predicted by the RNA World hypothesis turns out to involve proteins (DNA World) all throughout the process, beginning with post-transcription modification of rRNA (before the rRNA is incorporated into the Ribosome) and tRNA.
What I’ve seen is that papers are offered to support a claim, but when you look at the paper, it says otherwise.
For example, the paper that @Rumraket cited to support this claim actually says the following:
9 amino acids is the maximum that the PTC fragments can achieve.
the ribozymes used charged tRNA, not free amino acids. Charging a tRNA with an amino acid is done by a protein (aminoacyl trna synthetase). The paper doesn’t show that a ribozyme can ligate free amino acids.
On top of that, simply stringing amino acids together ultimately doesn’t get you anywhere because any “lucky” functional string would be a dead end. You don’t have the means to replicate it, unlike today’s system where DNA is the storage medium.
Maybe you are confusing “digital” with “binary”? A digital code does not have to be binary. The base is irrelevant (not a requirement) to the code being digital. That the Genetic code is digital is certainly not irrelevant.
We certainly do not agree and you certainly not did not use the same definition of code that I did. Tree rings are not a digital code.
Of course I’m appealing to the supernatural at the time of creation (that should be obvious), but not in how living things operate today, which is what I think you’re accusing me of.
Pushing back against being taken out of context is not “moving the goalposts”.
Nothing that I’ve seen deals with how the sequence of DNA nucleotides to code for the translation system came to be, much less how it was expressed without the existence of the translation machinery in the first place.
So, to answer your question, no.
No. The digital Genetic code itself is similar to computer code, but the functions of the cell itself, like transcription/translation/replication is infinitely beyond human designed systems.
No it doesn’t. The claim of yours I was answering with that paper is that there is a ribozyme that can string amino acids together in the absence of proteins. The paper doesn’t say otherwise.
First of all this doesn’t contract anything I’ve said. It is in fact stringing amino acids together in an uncoded fashion.
Second, the paper doesn’t actually claim this is the maximum the ribozyme can produce, just that this was the only one detected. There’s quite a bit of difference between saying “we detected X product in the reaction” versus “X is the maximum the ribozyme can make.”
It’s also not clear why it would need to be able to create longer polymers, at least initially, since this is supposed to be the the beginning stages of the evolution of protein biosynthesis. The whole idea is the system gradually became more capable over time. So if this proto-ribosome can produce small peptides, and these small peptides in turn can interact with the ribosome (or other proto-translation components) and enhance it’s capability, we have the basis for a positive feedback loop where increased functional capabilities can evolve.
Irrelevant. Nobody here has claimed there was ever a stage in which free amino acids were polymerized by the ribosome, and it’s not clear why that would be necessary.
Also irrelevant since we know of ribozymes that can aminoacylate RNA. Heck, we even know of ribozymes that can self-aminoacylate.
It also isn’t required to, nor has anyone claimed it can so that is irrelevant too.
How do you know it would not go anywhere?
If a fraction of randomly synthesized polymers have useful functions, it is possible to get a feedback loop where mutations in the active ribozymes result in small biases in the synthesis of these more or less random polymers that make sequences with certain functions increasingly likely (suppose 1% of sequences produced have useful functions, and mutations in proto-translation components can raise this to 5%, which in turn makes those components even more capable). This is basically the principle that underlies the emergence of coded translation. Reduction in chemical noise, for lack of a better term.
Ribozymes (or enzymes for that matter) do not have perfectly equal substrate preferences (are not equally active on all amino acid substrates), and their substrate preferences respond to mutations. That’s usually how enzymatic specificity evolves, by mutations increasingly biasing the substrate preferences of certain enzymes.
I think this puts the burden of proof on you to explain why something like this couldn’t happen.
Total fabrication. That isn’t “what was predicted.” Not even close.
I offered to send you a paper that explained the basic prediction, but you ignored my offer. Again, every move you make suggests a fear of learning more.
You haven’t been looking carefully. Again, you literally reject the scientific method. It’s about testing hypotheses, not supporting claims.
The prediction was that the current peptidyl transferase would have an RNA core. The demonstration that the current naked RNA has activity is just gravy on top.
what evidence led you to conclude that homopolymers cannot have any function? Your sequence fetish is preventing your understanding of the basics.
If you really believed that, you would learn more about it.
Is that enzyme a catalyst? Are enzymes magical? What can’t catalysts do?
A chemical reaction that would, in the absence of any catalyst, do what?
Why did you claim that “Charging a tRNA with an amino acid is done by a protein,” and why do you appear to be avoiding the fact that said protein is an enzyme, a catalyst? What is the catalyst doing? What is it not doing?
When I pointed out that you don’t understand the fundamentals of catalysis, I referred you to a web page that pointed out the aspect you were missing. It had nothing to do with sequences of anything.
I’d think that someone with solid faith in his conclusions wouldn’t need to resort to making false claims about the evidence itself, but it happens time and time again.
When one starts from a premise that one believes must be true, but which is contradicted by the evidence, the options are limited. Either accept that the premise is not true or say a bunch of dishonest and stupid stuff. You would think the correct choice would be obvious, but I guess not.
So why is “digital” so important? You act as if it were some magical property, WHY? There is nothing about Information being in a digital format. It is no different from any other sort of Information.
Why aren’t tree rings a digital code, using your definition? (and please state your definition again, just to be clear). How would I look at a probability distribution (the source of information) and know if it is digital of not? That can’t be done using my definition, and I doubt your definition, whatever that may be, allows for it either.
Thank you. You might have saved a lot of time by stating that up front.
Nice try, but that was not the question. We have evidence that some codons were recruited to the genetic code later than others. The code itself has changed through a process of evolution, AFTER it was initially came to be (by whatever means).
We also have evidence of a precursor to the genetic code, existing before DNA “came to be”.
Either way, for any known human code we might choose, changing the code breaks the communication between sender and receiver. We can come up with a new version of a code and tell everyone to stop using the old code and switch to the new. This is clearly a different situation; no one is running around nature updating the software for a new genetic code. There is no human (intelligently designed) code that changes itself.
It is useful to think about DNA as a sort of code, but thinking about codon sequences as coded information does not change what they are. It does not make it become “intelligently designed” any more that tree rings become “intelligently designed” when we observe them. *If it looks like computer code to you, that is Pareidolia. It is a pattern found in nature; calling it “digital” is just slapping a human label on what already existed, nothing changes.
No it doesn’t. The claim of yours I was answering with that paper is that there is a ribozyme that can string amino acids together in the absence of proteins. The paper doesn’t say otherwise.
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My earlier claim wasn’t “in the absence of proteins”, it was “without being post-transcriptionally modified by proteins”.
First of all this doesn’t contract anything I’ve said. It is in fact stringing amino acids together in an uncoded fashion.
Second, the paper doesn’t actually claim this is the maximum the ribozyme can produce, just that this was the only one detected. There’s quite a bit of difference between saying “we detected X product in the reaction” versus “X is the maximum the ribozyme can make.”
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From the paper:
To our best knowledge, this is the longest peptide oligo that can be synthesized by a pure ribozyme.
Everyone loves a good story.
Isn’t that the implication of “It is in fact stringing amino acids together in an uncoded fashion.”?
Natural ribozymes, or ones designed in a lab?
Without a means to replicate it, a lucky, functional polymer can’t undergo any sort of Darwinian evolution. It would be a dead end.
I don’t recall it and I wouldn’t have turned down a paper if I had seen the offer.
Feel free to provide a link.
You haven’t been looking carefully. Again, you literally reject the scientific method. It’s about testing hypotheses, not supporting claims.
The prediction was that the current peptidyl transferase would have an RNA core. The demonstration that the current naked RNA has activity is just gravy on top.
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For me to accept any RNA functionality as evidence for the RNA World hypothesis, it has to occur without any involvement by proteins, and that includes modification of some of the bases into non-standard bases.
The prediction is meaningless (as evidence of RNA World) if it doesn’t exclude any and all involvement of proteins.
You read the paper. What function did they report?
I’m learning as much as I can.
What’s the point of this question? Just to be argumentative?
The paper was offered as evidence for RNA World. I’m pointing out the involvement of proteins, which argues against RNA World.
What it is doing is arguing for DNA World, not RNA World.
EXACTLY! (I think this is some sort of a breakthrough).
While the function of the enzyme is actually carried out by natural chemical processes, the function of an enzyme is determined by the sequence of DNA bases (once transcribed and spliced into mature mRNA) which code for the sequence of the amino acids in the protein.
That’s been my point from the beginning.
Your answer was typically “catalysis” as if catalysis explained the sequence of the DNA bases in the first place.
Glad to see that you finally admit that catalysis can’t explain sequence.
Why play this guessing game? (can you guess what my point is?). It’s just like “don’t you know what catalysis can do?”
Just put out the evidence and be done with it. Just make sure that you understand what @appsandorgs means (or at least, what I think they mean).
Then you don’t appear to understand what your own words mean. You wrote originally:
PT is the Peptidyl Transferase center of the ribosome. The ribozyme in the active site. Raw would imply it has no assisting proteins decorating the ribozyme. And you are asking whether it would be able to function even if “raw”, without being somehow modified by or assisted by proteins. Since the PT was not, in fact, modified or assisted by proteins in the paper, I did in fact answer your demand.
Then again later you wrote:
Since the PT is not, in fact, modified by proteins in the experiments detailed in the paper, I have met your challenge.
The key words there are “to the best of our knowledge” which implies a comparison to ribozymes used by other researchers (as in “this is the longest we have seen yet in any experiment”), not a claim that their experiment has shown this to be the maximum this particular ribozyme can achieve.
Yes it’s a story, but the idea with the story is to show that there is actually no logical difficulty with the process of coded translation evolving gradually. You are the one claiming that:
“simply stringing amino acids together ultimately doesn’t get you anywhere because any “lucky” functional string would be a dead end.”
The fact that my “story” is a logical possibility means your claim here is a faulty inference.
But on the topic of stories, you mean like this one?:
Don’t talk to me about stories.
No. It just isn’t. That they are not encoded implies simply that there is no reliable or systematic association between a codon and the next amino acid to be included in the growing peptide chain. It says nothing about whether those amino acids are freely floating around in solution prior to being linked up.
A ribozyme functions just as well regardless of whether it first evolved, or was designed. The point is to show that RNA can do the reaction (hence logically solves the question of what could have come before a protein enzyme catalyzing the reaction). The RNA doesn’t care whether it was created in a test tube (nor that the test-tube is located in a laboratory), as opposed to if it was transcribed from DNA by RNA polymerase.
You didn’t understand what I wrote. Try again. Until you understand it. Just one small hint: In the scenario I proposed initial codon to amino acid assignments are highly stochastic, but since this assignment is ultimately due to chemical promiscuity in the activity of ribozymes that aminoacylate tRNA, mutations that reduce promiscuity and increase specificity, in those ribozymes, will ultimately be responsible for creating the genetic code. This is just one of many possible ways of envisioning the code’s initial evolution.
More importantly, these hypotheses both make testable predictions, and make sense of the evidence (phylogenetic, bioinformatic, biochemical). Your literal story doesn’t. It explains none of the facts, is completely ad-hoc and makes no predictions, and is unestable.
Click the up arrow in the upper right corner of this box. Seems pretty clear to me. You seem to be ignoring every point that you are unable to address.
To illustrate your fundamental lack of understanding of catalysis. It’s less than a high-school AP understanding. It’s less than a Wikipedia understanding. This aspect you are missing is why you can’t see the only way in which enzymatic catalysis could have evolved.
What are all catalysts (enzymes are catalysts) incapable of doing?
It doesn’t, and as @Rumraket pointed out, the naked RNA has catalytic activity, to which you responded by moving the goalposts.
The question is not about what it is or isn’t arguing for. Besides, only people can make arguments and evidence can only support or not support them. Science is about testing the empirical predictions of mechanistic hypotheses, an approach to learning that you are completely, utterly rejecting here.
You lack the faith in your assertion to use the scientific method. Your desperate attempts at shorthand are amusing.
When a tRNA is charged with an amino acid and that reaction is catalyzed by an enzyme, what can we say about the reaction in the absence of the enzyme?
To repeat the question you keep ignoring in a different way:
A chemical reaction that would, in the absence of any catalyst, do what?
No, you’re still stuck defending an assertion you clearly have no faith in. That’s why you repeatedly ignore relevant evidence and move goalposts.
Explaining sequence isn’t the point.
To illustrate your complete lack of faith.
Well, no. An indication of the shallowness of your engagement is that you wrote “can.” The question is what it can’t do. You don’t want to learn anything that puts your assertion at risk.
Then you’ll just move the goalposts again. You lack sufficient faith to advance a hypothesis that makes predictions.
Again, one can use the scientific method to learn. You aren’t willing to.
I do. What do YOU think it means? Your assertion is that it is impossible for the machinery of translation to have evolved from a simpler system because you cannot see how it could exist in any form except the current one.
I think he’s doing his best to not understand what either of us write.
Hints don’t seem to be working.
I’m skeptical that someone who won’t think about what catalysts can’t do can understand “stochastic” or “specificity” in this context.
He’s digging in his feet on asserting that even modern specificity is absolute and that somehow enzymes are magical entities personally designed by God. If that hypothesis is correct, there can be zero modern plasticity in the system, as @appsandorgs already asserted–again misrepresenting a prediction as fact.
I understand what I wrote just fine. You, however, are cherry-picking my words in order to take me out of context.
Here’s what I wrote:
You ignored the bolded text where I define “raw” as being processed post-transcription by proteins. This happens before the rRNA is assembled into the ribosome.
My usage of “raw” does not mean “without the proteins of the ribosome”.
How does "this is the longest “peptide oligo that can be synthesized” not equal “maximum”?
“longest that can be synthesized” does not mean “longest that we have seen yet”.
Until you explain how replication would happen, then your story is not logical.
When you say “codon”, you’re not suggesting that the PT fragments are somehow reading a strand of mRNA, are you?
I agree that the ribozyme doesn’t care if it was designed or not. The point is that these ribozymes don’t exist in nature (as far as we know).
Does the designed ribozyme recognize the anti-codon of the tRNA and attach the correct amino-acid the way the aminoacyl tRNA synthetase does?
I’m guessing that the answer is no.
The bolded section is invoking Darwinian evolution, which is why I’m saying that you need replication.
How does replication occur in your story?
And, again, you’re using the word “codon”. Do you have a paper that shows the PT fragments reading mRNA? Or one that shows that the designed ribozyme can recognize the anticodon of the tRNA?
Also, you have to explain how your story of:
those ribozymes, will ultimately be responsible for creating the genetic code.
resulted in the DNA sequences that code for the set of aminoacyl tRNA synthetase proteins and the other machinery of the translation system.
If creation is true, as I believe, then it is the explanation even though it isn’t a scientific explanation (it doesn’t explain how God’s supernatural processes work).
As far as predictions go, one fundamental prediction is that there wasn’t a naturalistic origin of life and therefore, OOL research will ultimately be futile.
Another one is that the deeper we research the operation of the cell, more examples of the cell using information will be found.
A fundamental flaw here (from the science perspective). It’s not possible to prove a negative.
Another one is that the deeper we research the operation of the cell, more examples of the cell using information will be found.
You still haven’t explained why “digital” information is so magical/special that it can only be Designed.
I predict that nothing useful will ever come from such speculation. And really, this is not your failure, but the failure of ID as a scientific endeavor. It has no useful results, nor any indication that it can achieve useful results.
Here is another prediction; if a natural origin of life is not possible, then there should come a point where no further scientific results can be found. A few years back that point would have been the origin of DNA, but now we have evidence of a precursor. This is what science does, expanding the frontiers of knowledge towards a more complete understanding. If life is Design, then scientific knowledge must eventually grind to a halt.
There is nothing about the scientific search for the origin of life which indicates the question is unanswerable.
This is a bs excuse and you know it. The second quote of your words (which you have now curiously completely ignored) makes it very clear you doubt the capacity of PT to catalyze the bond between amino acids without the help of proteins. It is that aspect of your question I am answering:
In the way I explained. The authors are not claiming this is the maximum, because their experiment is not designed to determine what the limitations (if any) on the length of synthesized polymers is. It is only designed to detect whether polymers are synthesized, with zero work being done to determine whether those detected have hit some sort of limit of what the ribozyme is capable of.
No single experiment can actually show what the limit is, as that would require testing a substantial range of conditions (including changing incubation times, changing concentrations of all relevant substrates, buffers, etc.) to see how each of these factors affect product length and how long they take to be synthesized. From this some relationship between the experimental conditions and product characteristics can be worked out, and then a putative limit can be estimated by this relationship. None of this work was done. So all they’re saying is that they have detected a polymer longer than previously achieved in experiments done by others.
Your interpretation of that one sentence is typical of people who don’t have clue about real experimental biochemistry, the state of the field, or the context in which certain claims are made and therefore how they are to be understood.
That’s E X A C T L Y what it means because it can mean nothing else than that due to the limitations of the experiment they did.
I see you’ve pulled the nuh-uh card, what a penetrating and insightful rebuttal. Good luck with that.
The PT does not read mRNA even in the modern ribosome. I suggest you stop arguing about this topic entirely and acquaint yourself with some knowledge of how translation even occurs in the extant translation system. Quick hint: Nothing “reads” mRNA. There is nothing like a “codon sequence reading”-like process occuring anywhere in the ribosome.Yes you read that right. mRNA isn’t “read” by anything. The ribosome does not read mRNA. mRNA is translocated (moved) across the ribosome, interacts primarily with the small ribosomal subunit and tRNA, and it is tRNA translocation by the large and small ribosomal subunits that drags mRNA along with it.
Exactly. In the scenario I detailed, the answer is no, which is the whole point. At first the association between tRNA precursors and amino acids, is primarily determined by the interplay between the concentrations of the different available amino acids, and the reaction kinetics of the ribozyme that catalyses the charging of tRNA. Early recognition of tRNA by these ribozymes was based on interactions between the ribozyme and the acceptor stem of tRNA, not the anticodon loop which evidence suggests evolved later.
This scenario is completely agnostic with respect to how replication of RNA is achieved, and it’s just moving the goalposts to yet another and yet another and yet another thing every time I answer one of your questions. This pathetic whack-a-mole with a person who couldn’t give a rats ass about evidence in the first place is getting rather stale I have to say.
Why would I need to show that? Have you ever actually spent any time reading about and trying to understand the different models proposed for the beginnings of translation and the genetic code? You clearly have zero comprehension of what is going on here.
It doesn’t explain anything at all. An explanation is something that provides reasons why things are the way they are. But you are not explaining why anything is the way it is as opposed to being different in some way. No matter what we find you can rationalize it as “what a designer wanted”, but since anything can potentially be what a designer wants, you’re not explaining why it is THIS way as opposed to another. It is therefore not an explanation at all.
This prediction is a straightworward non-sequitur. Even if there was no naturalistic origin of life, it doesn’t follow that there is no natural process by which life could originate. Strictly speaking it remains a logical possibility that God wanted to create life on Earth, but that he also wanted there to be some natural process by which it could originate on it’s own if the right conditions were satisfied (perhaps here, or on other planets too).
Another non-sequitur. There is nothing about the proposition that life originated supernaturally that gives any expectations about to what degree cells should be “using information”. It’s not a prediction at all.
You don’t know what evidence is, you don’t know what explanations are, and you don’t know what predictions are. Were you homeschooled?
But you clearly don’t believe it–in either the religious or secular sense. If you did, you’d be supremely confident that learning more about biology would only support your belief.
As it’s merely wishful thinking, you constantly move the goalposts and try to avoid learning more. Prime example: I offered to provide the paper describing the very clear prediction of the RNA World hypothesis. You ignored the offer and deliberately misrepresented the prediction as something else.
Your (never clearly stated) premise is that translation is too complex in its current state to have evolved, that every component of the system must be present to support life, no?
Why do you dance around this? It’s very testable.
Yet it continues to be very fruitful, which is why the hearsay (all you’ve apparently read) produced by IDcreationists simply lies about OOL research, including the hypotheses, their predictions, and even the evidence itself.
And that’s not an empirical prediction, so it isn’t science. Your lack of real belief means that you have to set easily moveable semantic goalposts for when you are challenged, in this case “futile.” You are utterly predictable.
Why are you using the first-person pronoun when your own understanding is far shallower than that of Wikipedia?
Also, “using information” has nothing to do with your hypothesis. It is, however, a tacit admission that your pseudoscientific argument is circular.
And a few decades ago, the goalposts were set at DNA replication.
And this is why IDcreationists deal in nothing but rhetoric.
The simple question “Why does life work the way it does?” has led to a lot of exciting OOL research, particularly in metabolism, that IDcreationists pretend doesn’t exist.
quote=“Rumraket, post:605, topic:16951, full:true”]