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Michael Larkin Wrote:The thing about codes is that to be codes, they necessarily have to have a lookup table or its equivalent.
Sure, given a broad definition of "equivalent."

Quote:You claim there is no lookup table for tRNAs. I beg to differ. At one end, tRNAs contain anticodons (the name, which I didn't originate, should be a clue that they're something to do with codes)  that match codons on MRNA; and those are are specified by DNA. Hence DNA ultimately contains the lookup table for tRNAs. If you deny that tRNAs are specified by triplets in DNA, then you're denying that DNA is a code, and if so, you're challenging entirely conventional biological opinion.
Yes, you've defined "equivalent" broadly enough to include patterns for building components that then operate nothing like a table. This is like saying that the instructions to build an old-fashioned coin sorter means that the coin sorter operates by a lookup table.

https://www.google.com/search?q=old+fash...q5bmuzUbhM:

Quote:As to your assertion that codes can arise through "natural process", first off you're going to have to come up with an example that is not DNA, because you've already, effectively, denied that DNA is a code. Please, snowflake me no snowflakes. Name me one code that has arisen through natural process without the help of any intelligence external to it. Explain to me how it arose, why it is a code, and what form its lookup table assumes.
I'm perfectly happy to say that codons constitute a code. I was arguing that the ribosome does not work by table lookup. And the genes coding tRNAs don't operate by table lookup, either. The only way to involve tables is to say that all of our DNA is a giant table, which is a rather pointless analogy.

I don't need to come up with an example, since I am not the one making the claim. If you believe that a code-like mechanism cannot arise naturalistically, then you must have some sort of proof in mind. Otherwise, what stops evolution from doing it, given enough time? What is special about a code-like mechanism, other than the observation that humans design codes?


~~ Paul
(2017-12-01, 03:32 PM)Paul C. Anagnostopoulos Wrote: [ -> ]I don't need to come up with an example, since I am not the one making the claim. If you believe that a code-like mechanism cannot arise naturalistically, then you must have some sort of proof in mind. Otherwise, what stops evolution from doing it, given enough time? What is special about a code-like mechanism, other than the observation that humans design codes?


~~ Paul

So, you accept that it is a code but you want to shift the burden of proof. Could you at least describe how you think evolution did it? And how much time was required? I've read the Wikipedia page - in particular, the section on its origin - and am no wiser. What I see there is a lot of scratching around for a hypothesis that might go some way to an explanation but nothing substantive. Of course, I don't understand the science so you are welcome to point to the part I may have missed which provides the evidence of how the code evolved. A bit of further searching and reading led me to a paper by Koonin and Novozhilov and, in particular, their conclusions (I didn't read the whole paper because, for the most part, it is way over my head).

The paper is titled: Origin and Evolution of the Genetic Code: The Universal Enigma

Quote:Nevertheless, this proposal, even if quite plausible, is only one facet of a much more general and difficult problem, perhaps, the most formidable problem of all evolutionary biology. Indeed, it stands to reason that any scenario of the code origin and evolution will remain vacuous if not combined with understanding of the origin of the coding principle itself and the translation system that embodies it. At the heart of this problem is a dreary vicious circle: what would be the selective force behind the evolution of the extremely complex translation system before there were functional proteins? And, of course, there could be no proteins without a sufficiently effective translation system. A variety of hypotheses have been proposed in attempts to break the circle (see (Noller 2004; Penny 2005; Noller 2006; Wolf and Koonin 2007) and references therein) but so far none of these seems to be sufficiently coherent or enjoys sufficient support to claim the status of a real theory.
Kamarling Wrote:So, you accept that it is a code but you want to shift the burden of proof.
I don't have a burden of proof because I don't think a code is anything special. You must have something in mind that makes a code impossible/supremely difficult to evolve. I just want you to tell me what that reason is. It just seems like an argument from similarity to human codes. Why is this more interesting than, say, a kinesin protein?

Quote:Could you at least describe how you think evolution did it? And how much time was required? I've read the Wikipedia page - in particular, the section on its origin - and am no wiser. What I see there is a lot of scratching around for a hypothesis that might go some way to an explanation but nothing substantive. Of course, I don't understand the science so you are welcome to point to the part I may have missed which provides the evidence of how the code evolved. A bit of further searching and reading led me to a paper by Koonin and Novozhilov and, in particular, their conclusions (I didn't read the whole paper because, for the most part, it is way over my head).
You are right that we don't know how it evolved. But there are many papers on the subject. Many of them discuss the modular structure of tRNAs.

https://biologydirect.biomedcentral.com/...-6150-6-14

More papers:

https://www.bibliotecapleyades.net/cienc..._adn09.htm

https://www.nature.com/articles/6801086

I'm not sure why you would expect this problem to be solved, or why the lack of a solution is any sort of evidence against the evolutionary perspective. There must be a principle involved.

~~ Paul
(2017-12-01, 09:46 PM)Paul C. Anagnostopoulos Wrote: [ -> ]I don't have a burden of proof because I don't think a code is anything special. You must have something in mind that makes a code impossible/supremely difficult to evolve. I just want you to tell me what that reason is. It just seems like an argument from similarity to human codes. Why is this more interesting than, say, a kinesin protein?

You are right that we don't know how it evolved. But there are many papers on the subject. Many of them discuss the modular structure of tRNAs.

https://biologydirect.biomedcentral.com/...-6150-6-14

More papers:

https://www.bibliotecapleyades.net/cienc..._adn09.htm

https://www.nature.com/articles/6801086

I'm not sure why you would expect this problem to be solved, or why the lack of a solution is any sort of evidence against the evolutionary perspective. There must be a principle involved.

~~ Paul

First you insist that there is no problem: that there is nothing special about the code (at least you admit it is a code) and that it should not be impossible/supremely difficult to evolve such a code. Then you go on to say that we don't know how it evolved nor should we expect this problem (suddenly, it is now a problem) to be solved.

The other (Skeptiko forum) discussions I mentioned earlier in the thread were centred around the point that there are no examples of codes appearing/evolving other than the genetic code. All other known codes have been originated by some intelligent agency. So why go over the same arguments again? You are just repeating an assertion - as Michael pointed out to you above. He challenged you to give an example yet you duck his challenge. I simply don't see the point in going further until you back up your assertion.
Kamarling Wrote:First you insist that there is no problem: that there is nothing special about the code (at least you admit it is a code) and that it should not be impossible/supremely difficult to evolve such a code. Then you go on to say that we don't know how it evolved nor should we expect this problem (suddenly, it is now a problem) to be solved.
I'm not saying there is no problem. I'm saying that the problem is just like the problem of evolution of every other mechanism. But people who insist that the code is something special must have a principle in mind. Why can't anyone state the principle?

Quote:The other (Skeptiko forum) discussions I mentioned earlier in the thread were centred around the point that there are no examples of codes appearing/evolving other than the genetic code. All other known codes have been originated by some intelligent agency. So why go over the same arguments again? You are just repeating an assertion - as Michael pointed out to you above. He challenged you to give an example yet you duck his challenge. I simply don't see the point in going further until you back up your assertion.
As you'll recall, we spent a lot of time discussing what makes something a code. Why is the genetic code more of a code than other selective binding molecules, or more of a code than the valence electron patterns? There must be a principle involved. Why is it interesting that there are (supposedly) no other natural codes?

You could just as well say that there is no example of a walking kinetic molecule other than kinesin molecules. Does that make it special, too?

Until someone can state the principle, why would you assume that I could explain why it's not a principle that prevents nature from evolving a code? For example, why couldn't it start as a single-base code, evolve slowly into a 2-base code, and then evolve a third degenerate base in order to improve fidelity?


~~ Paul
(2017-12-01, 03:32 PM)Paul C. Anagnostopoulos Wrote: [ -> ]Sure, given a broad definition of "equivalent."

Yes, you've defined "equivalent" broadly enough to include patterns for building components that then operate nothing like a table. This is like saying that the instructions to build an old-fashioned coin sorter means that the coin sorter operates by a lookup table.

https://www.google.com/search?q=old+fash...q5bmuzUbhM:

I'm perfectly happy to say that codons constitute a code. I was arguing that the ribosome does not work by table lookup. And the genes coding tRNAs don't operate by table lookup, either. The only way to involve tables is to say that all of our DNA is a giant table, which is a rather pointless analogy.

I don't need to come up with an example, since I am not the one making the claim. If you believe that a code-like mechanism cannot arise naturalistically, then you must have some sort of proof in mind. Otherwise, what stops evolution from doing it, given enough time? What is special about a code-like mechanism, other than the observation that humans design codes?


~~ Paul

The reason I said "or equivalent" is that there isn't a literal table in the DNA or anywhere else in the cell. However, the table is unambiguously implied because triplets in DNA follow rules which biologists have elucidated and most conveniently represent as a table.

The video I posted showed this table -- from mRNA codons to tRNA anticodons, but one could just as easily construct a table from DNA triplets to tRNA anticodons. The mRNA is used because DNA is in the nucleus, whereas tRNAs, ribosomes and amino acids are found in the cytoplasm; and mRNA, unlike DNA, can conveniently pass through nuclear pores. Besides, snipping out bits of DNA is hardly a viable proposition; and so the code applies even in prokaryotes (archaea and bacteria), which don't have a membrane-bound nucleus.

It's a fact that in DNA, every one of the 64 triplet codons (except for the 3 stop codons) always ends up specifying the same amino acid. Biologists can always predict which amino acid that will be, just by looking at the table -- no exceptions*. Hence the table, although not literal, is demonstrably embodied in the DNA code. If you can't see that, then you 're either a dunderhead or engaging in sophistry as an attempted diversionary tactic.

*I should note here that apparently, the code isn't quite universal: there are some organisms that use somewhat different codes, but the principle employed is the same. This is mentioned in the paper that Kamarling linked to.

You say you don't need to come up with an example of a code produced by "natural process". Does this mean that you know of such a code but aren't prepared to name it? Or that you don't know one but in any case don't have to name it? Just because you previously asserted without evidence that it's a fact that codes can be produced "naturally"?

Go take a hike; that's about as scientific as asserting the moon is made of green cheese without showing a sample of moon rock that tastes of unripe Wensleydale. Where do you get off asserting things by fiat? And I'm meant to roll over before the force of your assertion? Think again -- grow a pair and give me your example or admit you can't.

The ID proposition uses a tenet that Charles Darwin himself ascribed to: that causes in operation in the present should be looked to first to explain the past (i.e. the uniformitarianism of Lyell -- who profoundly influenced Darwin): "He [Lyell] influenced Darwin so deeply that Darwin envisioned evolution as a sort of biological uniformitarianism." (see here).

All codes we know of outside cells originated in minds. For the code in DNA -- inside cells -- we're being asked to abandon the uniformitarian principle that  Darwin so admired and come up with some other kind of explanation than that of conscious input. But in the absence of concrete evidence that codes can in fact be generated through "natural process", any such appeal is baseless, just an assertion based on ideological faith in materialistic metaphysics coupled with promissory materialism.

Your claim is baseless, and you can't adduce any evidence for it, whereas the ID claim does at least have some basis, and the evidence comes from uniform common experience: that codes always originate in consciousness, and never through deterministic or stochastic processes. All you have to do to disprove this claim is to come up with a single code where you can fully explain how it arose without the need for consciousness. Stop trying to shift the burden of proof to others to save your own face. And do please stop asserting things without evidence.
Just as a minor addendum to Michael's excellent rejoinder:

(2017-12-01, 03:32 PM)Paul C. Anagnostopoulos Wrote: [ -> ]what stops evolution from doing it [i.e. producing the code which is DNA --Laird]

Oh, I don't know, perhaps the fact that evolution (in the neo-Darwinist terms which you seem to accept i.e. random mutations plus natural selection) is predicated on the existence of that code in the first place?
(2017-12-02, 09:45 AM)Laird Wrote: [ -> ]Just as a minor addendum to Michael's excellent rejoinder:


Oh, I don't know, perhaps the fact that evolution (in the neo-Darwinist terms which you seem to accept i.e. random mutations plus natural selection) is predicated on the existence of that code in the first place?

I'm missing something and maybe you can explain. What is it about neoDarwinism that ruffles feathers?
Michael Larkin Wrote:The reason I said "or equivalent" is that there isn't a literal table in the DNA or anywhere else in the cell. However, the table is unambiguously implied because triplets in DNA follow rules which biologists have elucidated and most conveniently represent as a table.
But we represent lots of things with tables. The periodic table comes to mind. My objection is to use the fact that we can represent things as tables to imply that those things are designed like humans design.

Quote:The video I posted showed this table -- from mRNA codons to tRNA anticodons, but one could just as easily construct a table from DNA triplets to tRNA anticodons. The mRNA is used because DNA is in the nucleus, whereas tRNAs, ribosomes and amino acids are found in the cytoplasm; and mRNA, unlike DNA, can conveniently pass through nuclear pores. Besides, snipping out bits of DNA is hardly a viable proposition; and so the code applies even in prokaryotes (archaea and bacteria), which don't have a membrane-bound nucleus.
Hang on. There is nothing in the DNA that we could snip out to interact with the anticodons. What's in the DNA are genes that code for RNAs and proteins that make up the ribosome, tRNA, tRNA synthetases, and so forth. There is nothing like a codon table in the DNA.

Quote:It's a fact that in DNA, every one of the 64 triplet codons (except for the 3 stop codons) always ends up specifying the same amino acid. Biologists can always predict which amino acid that will be, just by looking at the table -- no exceptions*. Hence the table, although not literal, is demonstrably embodied in the DNA code. If you can't see that, then you 're either a dunderhead or engaging in sophistry as an attempted diversionary tactic.
Of course there are exceptions.

http://medicine.jrank.org/pages/2292/Gen...-Code.html

Quote:I should note here that apparently, the code isn't quite universal: there are some organisms that use somewhat different codes, but the principle employed is the same. This is mentioned in the paper that Kamarling linked to.
There you go.

Quote:You say you don't need to come up with an example of a code produced by "natural process". Does this mean that you know of such a code but aren't prepared to name it? Or that you don't know one but in any case don't have to name it? Just because you previously asserted without evidence that it's a fact that codes can be produced "naturally"?
My assertion is there is nothing stopping a code-like mechanism from being produced naturally, given enough time. To refute my assertion, you can specify the principle that prevents such a thing. But before you do that, you need to carefully define "code." Is the periodic table a code? Are other kinds of selective binding a code?

Quote:Go take a hike; that's about as scientific as asserting the moon is made of green cheese without showing a sample of moon rock that tastes of unripe Wensleydale. Where do you get off asserting things by fiat? And I'm meant to roll over before the force of your assertion? Think again -- grow a pair and give me your example or admit you can't.
I'm not asking anyone to roll over. I'm asking for the principle that you must have in mind. Because if you don't have a principle in mind, then surely you are not going to accuse me of making unwarranted assertions without doing a double-take.

Quote:All codes we know of outside cells originated in minds. For the code in DNA -- inside cells -- we're being asked to abandon the uniformitarian principle that  Darwin so admired and come up with some other kind of explanation than that of conscious input. But in the absence of concrete evidence that codes can in fact be generated through "natural process", any such appeal is baseless, just an assertion based on ideological faith in materialistic metaphysics coupled with promissory materialism.

    Your claim is baseless, and you can't adduce any evidence for it, whereas the ID claim does at least have some basis, and the evidence comes from uniform common experience: that codes always originate in consciousness, and never through deterministic or stochastic processes. All you have to do to disprove this claim is to come up with a single code where you can fully explain how it arose without the need for consciousness. Stop trying to shift the burden of proof to others to save your own face. And do please stop asserting things without evidence.
Really, you're not doing a double-take here?

You apparently have no principle that prevents nature from inventing a code via evolution. You just assume it can't because humans can. And in the process, you ignore all the research on the evolution of the genetic code.

~~ Paul
(2017-12-02, 09:45 AM)Laird Wrote: [ -> ]Just as a minor addendum to Michael's excellent rejoinder:


Oh, I don't know, perhaps the fact that evolution (in the neo-Darwinist terms which you seem to accept i.e. random mutations plus natural selection) is predicated on the existence of that code in the first place?

So you don't think it could have started as, say, a single base code? Then slowly evolved to use two bases? Then evolved to use three in a degenerate manner (the third codon in highly degenerate).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

Why do people keep imagining the evolution of life on Earth as an "all of it, all at once" sort of process?

Here's a particularly interesting paper:

https://www.sciencedirect.com/science/ar...9314000113

~~ Paul