Is there really information being conveyed within a cell?

[Rumraket (Mikkel R.)]

@theaz101

I think that the fact that rRNA and tRNA are post-transcriptionally modified by proteins is better explained by the hypothesis that “all parts of the system were created at the same time”.

Explain why!

[Rumraket (Mikkel R.)]

@theaz101

The Genetic code, computer code and morse code are all “1b” codes. Alternative grouping of elements (dots/dashes, etc) that produce an effect. There is no such code (involving different groupings) in tree rings. The tree ring is just an artifact of the tree’s growth for a particular year.

That would mean that if someone created a code but it was never put to use (didn’t “produce an effect”), then by your rule it wouldn’t be a code.

Clearly whether it produces an effect or not is not a sensibly criterion to judge whether it is a code. Just because someone might not actively use a code, or it doesn’t “produce an effect” doesn’t make it not a code. I could write a piece of morse code on a piece of paper and stow it away never to be read, translated, or even looked at again. It would still be a code.

For entirely the same reasons, even if humans never learned to translate tree rings it wouldn’t make them not be a code.

[Rumraket (Mikkel R.)]

@theaz101

They are set arbitrarily, not used arbitrarily.

The genetic code isn’t “set” arbitrarily either. It has demonstrable chemical and physical patterns to the “mapping” between amino acids and codons. The associations are not arbitrary or random at all.

But I would still be fine calling it a code. It’s just that using that label for the system of translation doesn’t tell us how it came to exist. Our labels do not travel back in time and force the code to come into existence in a specific way. The code came to exist regardless of how we decide to categorize it. Your argument can go nowhere at all.

[AnEvolvedPrimate]

@theaz101

I think that the fact that rRNA and tRNA are post-transcriptionally modified by proteins is better explained by the hypothesis that “all parts of the system were created at the same time”.

Created how?

[theaz101]

@Rumraket

@theaz101

I think that the fact that rRNA and tRNA are post-transcriptionally modified by proteins is better explained by the hypothesis that “all parts of the system were created at the same time”.

Explain why!

I said earlier that I believe a naturalistic origin of life has to be a “bottom-up” process vs the "all parts

If you’re going to use peptidyl transferase or other rRNA as evidence for RNA world, then you have to show how it can be produced and function without any involvement with DNA or proteins.

If you want to say that peptidyl transferase can catalyze the bond between amino acids without the help of proteins, you also have to show that it can perform that catalytic action without first being modified by proteins. Otherwise, it’s just a case of special pleading.

[Mercer (John Mercer)]

@theaz101

They are set arbitrarily, not used arbitrarily.

What evidence suggests to you that they were set arbitrarily?

@Rumraket

The genetic code isn’t “set” arbitrarily either. It has demonstrable chemical and physical patterns to the “mapping” between amino acids and codons. The associations are not arbitrary or random at all.

It’s amazing how many times @theaz101 has repeated this objectively false claim. It is, however, an obvious prediction of the hypothesis that the system was designed.

@theaz101

@Rumraket

Explain why!

I said earlier that I believe a naturalistic origin of life has to be a “bottom-up” process vs the "all parts

We know you say that, but that’s not an explanation. It’s just an ex cathedra assertion.

@theaz101

If you’re going to use peptidyl transferase or other rRNA as evidence for RNA world, then you have to show how it can be produced and function without any involvement with DNA or proteins.

No, we don’t.

@theaz101

If you want to say that peptidyl transferase can catalyze the bond between amino acids without the help of proteins, you also have to show that it can perform that catalytic action without first being modified by proteins. Otherwise, it’s just a case of special pleading.

No, we don’t have to show anything of the sort. These RNA relics were predicted by the RNA World hypothesis. Moreover, there’s been a lot of coevolution of peptidyl transferase and the proteins that frame it, so knowing about the stability of RNA, we would never expect the rRNA to be stable in the absence of framing proteins.

Note that tRNA, another relic that is not framed, is very stable.

So what would it do to your position if the RNA does have some catalytic activity by itself? Would you move the goalposts?

YOU have to explain why there are so many RNAs at the heart of translation, which you hypothesize was created all at once.

1. Why are there tRNAs when proteins are perfectly capable of binding to specific sequences?

2. Why is peptidyl transferase a ribozyme framed (a metaphor) by proteins, when ribozymes are generally poorer catalysts than proteins?

3. How do you explain the nonarbitrary nature of the genetic code, other than repeating your false claim that it is arbitrary?

And as a general recommendation, review the basics of catalysis, as you’re missing an important point that is relevant to understanding the evolution of RNA and protein catalysts:

14.7: Catalysis

The part you’re missing is covered in the first paragraph and first figure.

[Rumraket (Mikkel R.)]

@theaz101

@Rumraket

@theaz101

I think that the fact that rRNA and tRNA are post-transcriptionally modified by proteins is better explained by the hypothesis that “all parts of the system were created at the same time”.

Explain why!

I said earlier that I believe a naturalistic origin of life has to be a “bottom-up” process vs the "all parts

This isn’t an explanation for why rRNA or tRNA being post-transcriptionally modified is supposedly more expected/more likely on the hypothesis that “all parts of the system were created at the same time”, than on the hypothesis that the translation system evolved.

Evolution is in it’s most basic form a theory of descent with modification. It says that things change over time, over generations, and therefore will gradually appear more and more different from however they looked in the past. Post-transcriptional modification is neither unexpected, nor unlikely, nor unexplained on evolution. So why is it somehow a piece of data favoring your idea? What leads you to think creationistm raises our expectation of post-transcriptional modification over and above that of evolution?

It’s just blatantly obvious you’ve never truly thought all that deeply about any of this, and couldn’t defend any of these shallow, mostly-based-on-a-feel, never-truly-considered ideas you have.

@theaz101

If you’re going to use peptidyl transferase or other rRNA as evidence for RNA world, then you have to show how it can be produced and function without any involvement with DNA or proteins.

No I don’t have to show any such thing. This demand that I am required to show what might have occurred in the ancient past, in order to say that some data point is evidence favoring hypothesis A over hypothesis B, is both logically false (a data point can be evidence of a hypothesis even if I can’t show, empirically, the truth of every entailment of that hypothesis), and also fundamentally a hypocritical demand since you are entirely incapable of showing the thing you think really occurred to give rise to life, the translation system, or whatever (creation by divine fiat).

In other words you are demanding of me what you cannot do yourself, and you don’t even truly believe is required to be rationally convinced of the truth of some proposition. Because here you are believing life was divinely created and you have never seen such a thing occur. As such it simply cannot be the case that you require such a thing in order for something to be reasonably believed.

@theaz101

If you want to say that peptidyl transferase can catalyze the bond between amino acids without the help of proteins, you also have to show that it can perform that catalytic action without first being modified by proteins.

That I can show:

Landmark achievement in RNA world experiments:

So apparently researchers have succeeded in finding a highly reduced RNA-only ribosomal core capable of catalyzing multiple successive rounds of peptide bond formation, resulting in 9-mers of polylysine: Abstract Ribosomal protein synthesis is a central process of the modern biological world. Because the ribosome contains proteins itself, it is very important to understand its precursor and evolution. Small ribozymes have demonstrated the principle of “RNA world” hypothesis, but protein free peptide ligase remains elusive. In this report, we have identified two fragments in the peptidyl transfer center that can synthesize a 9-mer poly-lysine in a solution contains Mg2+. This result is deduced from isotope-shifting in high resolution MS. To our best knowledge, this is the longest peptide oligo that can be synthesized by a pure ribozyme. Via single molecule FRET experiments, we have demonstrated the ligase mechanism was probably by substrate proximity via dimerization. We prospect th…

[RonSewell (RonS)]

@theaz101

If you’re going to use peptidyl transferase or other rRNA as evidence for RNA world, then you have to show how it can be produced and function without any involvement with DNA or proteins.

If you want to say that peptidyl transferase can catalyze the bond between amino acids without the help of proteins, you also have to show that it can perform that catalytic action without first being modified by proteins.

I agree that we do not have a complete picture, but is not the RNA world hypothesis the basis of research addressing such questions? That is the heuristic value of natural explanations.

Your alternative is that “all parts of the system were created at the same time.” Can the act of creation be reenacted in the lab? Do you have an experimental control? What research program do you have other than “could not have happened so why bother looking”? - which is the ultimate special pleading and shuts down further investigation.

Are you at all curious, or is it all about apologetics?

[theaz101]

@RonSewell

@theaz101

Whatever we have learned about the Genetic code and the transcription/translation processes is knowledge gained from research. My claim is that this knowledge implies a creator.

Each to their own, but I find “transcription/translation, ergo creator” the oddest jump. It is just chemistry.

I don’t think it’s an odd jump at all.

I’m not appealing to a creator to explain how the transcription/translation machinery operates. I agree that it operates by “just chemistry” (though I do think that God created the laws of chemistry).

However, the sequence of bases, which determines what the function of a protein will be, is not simply a matter of chemistry. The laws of chemistry do not require any specific sequence of bases.

“ergo creator” is my answer to the question of “how did the bases get in the right sequences to form the transcription/translation machinery in the first place”? as well as the question of “how was the transcription/translation machinery produced without the machinery of transcription/translation in the first place”?

[theaz101]

@Dan_Eastwood

@theaz101

What we should say is that codons are symbols that arbitrarily stand for something else that is unrelated to it (amino acids). This rules out the signs that stand for something that it is related to.

This is most useful, I think, because it gets at the heart of the disagreement. On the other hand, some maintain the term “code” is being abused, hence …

@AllenWitmerMiller

There are many editions but the one I have most readily at hand says under the word code:

“a system of words, letters, numbers, or symbols that represent a message or record information secretly or in a shorter form,”

Of course, DNA doesn’t fit that primary definition of code. Yet, it doesn’t really matter, just as @Puck_Mendelssohn said—because the important question is whether there is EVIDENCE that the genetic code was designed.

Any idea why @AllenWitmerMiller chose this definition instead of the one that specifically deals with the Genetic code?

Oxford English Dictionary

II.6. Biology. A means by which information and instructions determining the nature, development, and functions of living organisms is stored within them, esp. by the structure or organization of particular biomolecules; (also) a conformation or sequence of molecular components or physiological events embodying or conveying such information;
spec. = genetic code n.

and you can see how similar that definition is to the following one.

II.7. Computing. Any system of symbols and rules for expressing information or instructions in a form usable by a computer or other digital machine for processing or transmitting information. Also: information or instructions written according to such a system.

@Dan_Eastwood

BUT I want to explore the idea that codons ARE a code, and this gives evidence of a Intelligent Designer.

The genetic code is evolvable. We can argue origins later, but it is clear that genomes change over time in response to environmental pressures. We can also consider that the code itself has evolved, with amino acids like tyrosine, tryptophan, selenocysteine and pyrrolysine being the more recent additions. (A source for this, but I should leave biochemistry to the biochemists).

The point being, if we really think codons are an Intelligently Designed code, then we already have strong evidence that Evolution is the Designer.

AND this is nothing new. This is a long standing criticism of ID; that nothing prevents evolution itself from being the Designer. ID is an apologetic for those who need that sort of thing to shore up their faith, and a big waste of time to those engaged in science and science education. ID has been tested scientifically, and it’s had its day in court, and most importantly, it has produced no useful results.

So if you really want to claim that codons are a “Designed” code, go ahead; this idea has no value beyond apologetics.

“We can argue origins later”

This also is nothing new. You want to look at whether or not the system has changed over time as if that will account for the origin of the system in the first place. And there is also the question of whether or not the code evolved (changed over time), or are they simply a few rare exceptions that were part of the system to begin with?

[theaz101]

@Faizal_Ali

Yes, excellent point. It emphasizes the fact that many creationist arguments do not falter on lack of evidence, so much as they do on poor logic.

Instead of “All codes are produced by an intelligent designer”, let’s say the premise was “All swans are white.”

Now, if one encounters what appears to be a black swan, but wishes to maintain the position “All swans are white,” there are a few ways one could respond. One could demonstrate that the bird in question is not actually a swan, but just another species that closely resembles one. Or, one could demonstrate that the bird is a white swan that has been painted black.

What the creationists do, however, is simply assert that it isn’t black at all. It’s white, because it’s a swan, and all swans are white. The fact that anyone can plainly see that it isn’t white is not allowed to intrude on their reasoning.

Speaking of poor logic…

Your analogy fails because in the comparison of, say, the Genetic code and a computer code like ASCII, both swans are white. What you are claiming is that one swan was conceived and born in the wild (the Genetic code) and one swan was conceived (artificially) and born in captivity (ASCII).

[Mercer (John Mercer)]

@theaz101

However, the sequence of bases, which determines what the function of a protein will be, is not simply a matter of chemistry.

Yet we routinely start with random sequences and evolve function in the lab.

[AllenWitmerMiller (Semi-Expired Professor & Minister.)]

@theaz101

Any idea why @AllenWitmerMiller chose this definition instead of the one that specifically deals with the Genetic code?

I thought I already made that clear.

So, yes, I will tell you why: Because it is a first-tier or primary meaning. Nobody denies that the word CODE is often used in biological contexts as you are describing. That’s not the issue.

I won’t go through the entire linguistic argument again because I don’t think that would accomplish anything. The fact that the word CODE has become a term in biology does NOT mean that it thereby takes on the denotations of the primary meaning and somehow bolsters the “intelligent design” argument based upon it—just as calling a guinea pig a pig doesn’t somehow establish its taxonomy as that of a type of pig.

I’m very busy for a few days so just passing through but I don’t think my previous posts were ambiguous on these topics.

[Dan_Eastwood]

@theaz101

And there is also the question of whether or not the code evolved (changed over time), or are they simply a few rare exceptions that were part of the system to begin with?

The point remains. If we really think codons are an Intelligently Designed code, then we already have strong evidence that Evolution is the Designer.

There is no falsifiable hypothesis for Design here, only word games.

[Puck_Mendelssohn]

@theaz101

The laws of chemistry do not require any specific sequence of bases.

I’m always a bit puzzled by these suggestions that somehow things which aren’t caused simply and directly by the mere operation of the sorts of invariable general principles we have classified as “laws” are, therefore, of mysterious origin. There are no “laws” of biology which mandate the existence of flightless waterfowl, or the non-existence of flying molluscs. Loads and loads of phenomena in the physical world can be chalked up to contingency of one kind or another. This in no way suggests design; it suggests only that nature is interesting.

[Puck_Mendelssohn]

@AllenWitmerMiller

The fact that the word CODE has become a term in biology does NOT mean that it thereby takes on the denotations of the primary meaning and somehow bolsters the “intelligent design” argument based upon it—just as calling a guinea pig a pig doesn’t somehow establish its taxonomy as that of a type of pig.

It is truly sad that this simple reality has to be stated again and again, and seemingly is never heard.

[AllenWitmerMiller (Semi-Expired Professor & Minister.)]

And while we are reiterating things which we really shouldn’t have to, I want to add this point (yet again) for the benefit of any newcomers to Peaceful Science and/or those who are curious about Intelligent Design:

This question of information being conveyed within the cell—and the general topic of Intelligent Design—should not be considered a matter all that relevant to whether one is theist or agnostic or atheist. Ultimately, ID is a question of whether one can use the scientific method to determine if an intelligent designer (a mind) must be behind what we observe. Hey, I’m a Bible-affirming Christian and if someone had actually published a compelling scientific analysis of the evidence and demonstrated that everything (especially living organisms) originated in a mind, I would be quite fascinated and drawn to it. But that simply hasn’t happened. Until it does, I’m going to continue to view intelligent design arguments as philosophical arguments which happen to intersect scientific topics. Either way, the question—and its answer—poses no threat to any of my religious positions. I don’t see why it should.

I am often fascinated by the fact that there are many Christian writers who seem to go out of their way to try and discredit science—and yet they clearly assume that it is a very reliable and powerful discipline. Or else they wouldn’t try to so hard to “prove” their theological beliefs with “scientific” discourses.

I don’t know the motivations or epistemology behind the question which launched this thread but I just wanted to make my point about ID if that is either the motivation of the poster OR some reader’s interpretation of the question. Meanwhile, readers should avoid assuming that “ID theory” simply claims that God designed everything intelligently. No, if that is what it meant, I guess I would thereby be considered an ID’er. But I’m not. I don’t believe anyone has compellingly demonstrated that the scientific method looks at the evidence and demands that a divine mind designed everything—even if my personal philosophical/theology position is that ultimately God designed everything when he created the universe and chose particular chemistry and physics for it.

[Faizal_Ali]

@theaz101

@Faizal_Ali

What the creationists do, however, is simply assert that it isn’t black at all. It’s white, because it’s a swan, and all swans are white. The fact that anyone can plainly see that it isn’t white is not allowed to intrude on their reasoning.

Speaking of poor logic…

Your analogy fails because in the comparison of, say, the Genetic code and a computer code like ASCII, both swans are white.

Hey, great. You just went and did the exact thing that I claimed creationists do. Thanks!

@theaz101

What you are claiming is that one swan was conceived and born in the wild (the Genetic code) and one swan was conceived (artificially) and born in captivity (ASCII).

Yup, that is what I am saying. Though to call it a mere “claim” is an understatement. It is an obvious fact that examples of ASCII only exist thru human action, whereas examples of the genetic code exist in nature without the involvement of humans (who are the only intelligent designers known to exist).

If you refuse to acknowledge the empirical evidence that the genetic code evolved that has been presented several times in this discussion, you still have to deal with the fallacious logic of your argument. As I have already pointed out, there is an inductive argument that mirrors yours almost perfectly:

1. Every intelligent being that can create a code requires the genetic code to exist.

2. Therefore, if the genetic code does not exist, then no intelligent being capable of creating a code can exist.

Conclusion: The genetic code could not have been created by an intelligent being.

How do you deal with that?

[Rumraket (Mikkel R.)]

@Faizal_Ali

@theaz101

@Faizal_Ali

What the creationists do, however, is simply assert that it isn’t black at all. It’s white, because it’s a swan, and all swans are white. The fact that anyone can plainly see that it isn’t white is not allowed to intrude on their reasoning.

Speaking of poor logic…

Your analogy fails because in the comparison of, say, the Genetic code and a computer code like ASCII, both swans are white.

Hey, great. You just went and did the exact thing that I claimed creationists do. Thanks!

I can’t even…

[theaz101]

@RonSewell

@theaz101

the words on this post are just “hard-wired” by the laws of electronics or physics.

They are not.

They are recognizable because and only because you and I have a prior mutual agreement as to what the physical hard-wired patterns indicate. They have zero intrinsic significance.

Not only does the physical layer not constrain the meaning, but by way of the same agreement between parties, the transmission can be realized by independent physical means. Morse code can be sent by wire, flashlight, or banging on pipes. The words are independent of physics.

And the messaging with any on these can be encrypted, where the transmitted patterns then stand for other meanings.

You are missing my point.

The words in these posts as typed as English letters, translated to binary code when stored in memory, and then displayed on the screen as English letters.

My comment is saying that even though the computer operates by the laws of electronics or physics, the laws of electronics or physics do not account for the words being encoded/decoded. The words come from an intelligent mind.

@RonSewell

Symbols, call them whatever you wish, are abstractions to communicate from one person to another based on mutual understanding. Outside of this, in respect to communication they do not exist. DNA and proteins are not persons, so there are no symbols involved.

You (and others) keep making the point that information has to be communicated person to person, which is just not true.

The computer that you are using probably came pre-loaded with an operating system. When you start the computer, the programs of the operating system are read from the hard drive and start running as the computer boots up. Those programs don’t communicate to you, they only serve to run the computer. That’s a relevant example of what we see happening in the cell. The genes don’t communicate to you, they only serve to supply the information to produce the proteins that help operate the cell