(2017-12-02, 03:08 PM)Paul C. Anagnostopoulos Wrote: [ -> ]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.
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.
Of course there are exceptions.
http://medicine.jrank.org/pages/2292/Gen...-Code.html
There you go.
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?
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.
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
I'd say that the periodic table is simultaneously a code and not a code depending on context.
In the human context, tables of all sorts are a kind of extension of written language enabling concepts to be more easily grasped, or data interrelationships to be conveniently presented. All language is a code: it enables ideas originating in human minds to be presented in symbolic terms (spoken and/or written letters, words, sentences, grammar, syntax, tables, mathematical notation, and so on). The intention is for ideas to be coded by one mind and transmitted to another mind, where they are decoded back into ideas. Sometimes, as in what I'm doing now, they may be decoded by not only other minds, but also the same mind as a means of checking faithfulness to the original ideas.
The rules for the coding are
shared learnings about the conventions used (the above-mentioned spoken and/or written letters, words, sentences, grammar, syntax, tables, mathematical notation, and so on), which constitute the lookup table for communication. These symbols are often codified in dictionaries and explanatory texts of various kinds.
Hence in the human context,
all tables are codes: in fact
all sharable symbols are codes. So
both the periodic table and the codon table are codes in this sense. That said, the items in the two tables point to something in the so-called "real world" (I prefer "the world of perception").
In the case of the periodic table, what's pointed to are the elements and their interrelationships. None of the elements maps 1-to-1 to anything else. Sure, the periodic table is rich in information that can inform understandings about various combinations of elements found in chemical compounds, but it's not a 1-to-1 relationship.
In the case of the codon table, on the other hand, 1-to-1 relationships between codons and anticodons, and of anticodons with amino acids, are represented. The relationships are most often shown as being between codons in mRNA and anticodons in tRNAs. But actually, DNA codons specify mRNA codons, those specify tRNA anticodons, and those in turn are linked with specific amino acids:
[Image: T7.gif]
The mRNA is constructed of nucleotide sequences that match the
sense strand of DNA -- you can see this in the correspondence between DNA sense codons and mRNA codons, which are identical except that Uracil (U) is used in mRNA instead of Thymine (T) in DNA.
The
sense strand of DNA is accompanied by its
anti-sense strand, which latter is used as the template for mRNA. That is why the sequence on the mRNA matches the sense strand on DNA. Think of a simple code where alphabetic characters are encoded in reverse:
sense: A B C D E F
anti-sense: F E D C B A
Let's suppose the message is "FADE". The anti-sense message would be "AFCB". In DNA, the two complementary messages are on two separate and intertwined strands.
Next, we separate the two messages and transcribe the antisense message (AFCB) into a sense message, which is "FADE" again. This is analogous to the sense message on the mRNA which is identical to the sense message on DNA.
Then the message "FADE" on mRNA is matched by the analogue of an anticodon at one end of a tRNA that contains "AFCB". At the other end is a gizmo that interprets the message and dims a light for us. This is analogous to the translation of codes into proteins, the things that actually do stuff in cells.
Though that's a simple code, it's quite complicated how we would get the message to do its stuff in the "real world". See
here for an explanation of sense and anti-sense strands in DNA. Note that in some cases mRNA is a copy of the
anti-sense strand of DNA, but we won't go into that here.
Think about this for a moment: usually, the codons are already present on the DNA sense strand; they already specify the complementary anticodons on tRNAs, except for the Thymine-Uracil difference. This difference is actually just the absence of a methyl group in Uracil:
[Image: uracil-thymine.png]
In certain experiments, e.g.
here, synthesised single-stranded DNA has been shown to be able to code directly for anticodons, but it doesn't happen in nature. The lack of methylation in uracil, plus the differences in the sugars used by DNA and RNA, make for differences in stability of the two (DNA is the more stable -- for thousands of years, actually -- and is therefore better for storing the code).
Snipping the DNA molecule and directly using the sense strand to specify anticodons won't work because of the thymine/uracil and sugar differences with mRNA. And even if it could, there'd be the problem of re-inserting the DNA strand back in place after translation at the ribosome -- which would apply whether or not the cell possessed a nucleus (as in eukaryotes) or not (as in the archaea and bacterial prokaryotes).
I suggest that it's much easier to have the double-stranded DNA sense/antisense configuration and be able to make a copy using single-stranded mRNA, because that can be done in place by simply unzipping the DNA, which then zips back up after transcription.
You say:
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.
This is nonsense. The code is right there in the sense strand of DNA, which via its anti-sense complement specifies same-sense single-stranded mRNA. IOW, the mRNA is, usually -- apart from the Uracil difference -- a copy of the sense strand of DNA. And even where the mRNA is a copy of the anti-sense strand, the code is still copied from DNA. No DNA, no functioning code. I was simply suggesting why, in evolutionary terms, DNA couldn't have been the
direct specifier of anticodons; why there has to be an mRNA intermediary to transport the message.
What I think you may be trying to say in a roundabout way is that although DNA is a code, it doesn't use a lookup table. If so, maybe that's because you can't get past thinking of a lookup table in literal terms. But ordinary language, which is a code (or are you denying that?), apart from our constructions (dictionaries, etc) also doesn't have a literal lookup table, and certainly didn't for thousands of years before spoken language was codified in written terms (it still isn't for some languages). Nonetheless, language has, and always has had, the equivalent of a lookup table in the form of learned rules about its use.
The current theory being pursued by evolutionary biologists focuses on RNA. They think that RNA came first. They conjecture that, prior to the emergence of life, RNA existed and was able to specify simple polypeptides (like proteins, but containing much shorter amino acid sequences). Somehow, this schema complexified and worked backwards towards DNA. This is to avoid the awful implications of the way things are now and have been for at least 3.7 billion years since prokaryotes appeared in the fossil record.
What way is that? Well, DNA specifies mRNA, which specifies tRNAs, which are associated with amino acids, which at the ribosome, become sequenced into proteins. Without DNA, there can be no proteins. At the same time, without proteins, DNA can't be processed: they are present as enzymes and subcellular agglomerates we often think of as machines that do the processing.
Which came first? Proteins, or DNA? They are mutually interdependent and so some way has to be found to decide on this chicken-and-egg situation; because if it can't be resolved, a mechanistic cause-and-effect schema is highly suspect. The fact that the elements of the schema have to be present all at once for it to work, can't be explained in a deterministic way. There'd have to be something akin to intelligence in the explanatory system, and that's the most awful and threatening thing.
Incidentally, you still haven't come up with a naturally-occurring code and explained how it arose without intelligence of some kind. You just keep on asserting that codes
could arise naturally, and pushing the burden of proof in my direction. You say:
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.
Actually, I do have a principle that prevents nature from inventing a code. That principle is the lack of intelligence of "nature" in the mechanistic way you're thinking of it. I don't know exactly how intelligence plays into the game, it is true, but as I mentioned in an earlier post, it's common and uniform experience that codes have only been observed to have arisen from intelligent consciousness.
Also note that I don't deny evolution has occurred; just that it hasn't happened in a Darwinian fashion. I think evolution is explained by natural selection coupled with
non-random mutation, and I think that what has driven the process has been doing so in an "experimental" sort of way, viz. it doesn't "know" exactly how things are going to turn out. My conception of MAL isn't at all like the Abrahamic God.
As for ignoring research, get out of here. You post links, but I have my doubts whether you do much research and really understand them. I suspect you just mine them for supportive tidbits without doing any heavy lifting yourself. Your posts tend to be gnomic -- obscure enough so that you always have enough wiggle room to deny your mistakes.