(2017-12-04, 01:16 PM)Dante Wrote: [ -> ]Nice nuanced response, steve. Did you actually read his post or just see that it was Michael posting and go to your usual box of stock responses?
(2017-12-04, 01:24 PM)Michael Larkin Wrote: [ -> ]Just another gnome who wouldn't understand a nuance if it came up and punched him on the nose.
(2017-12-04, 01:16 PM)Dante Wrote: [ -> ]Nice nuanced response, steve. Did you actually read his post or just see that it was Michael posting and go to your usual box of stock responses?
Dante Wrote: Wrote:I think it's important to always remember that a lack of an alternative does not magically make issues with the primarily accepted model disappear. They are real issues. Those issues are not rendered irrelevant because people don't have a fully supported alternative, especially when little research has been conducted into any such alternative path. Additionally it seems clear that it might be difficult to scientifically uncover intelligent intent or something of the like, if such a thing exists. Regardless, evolutionary theory as it is rests on incredibly shaky reasoning that is rarely challenged at all, which probably has led to a lot of the discord surrounding the issue.
Quote:Some things I've noticed. People love science as long as it does not threaten their existential beliefs. TOE does just that. If the study of psi had the same depth of knowledge as does evolutionary theory does you'd and a few others would say psi is a bonifide science backed up by a big marching band. Tell me what really chaps your arse about TOE?
(2017-12-02, 11:36 PM)Paul C. Anagnostopoulos Wrote: [ -> ]"The formal definition of a code according to Perlwitz and Waterman (see below) is a set of symbols that uniquely map a point in space “A” to a point in space “B.” In other words there is special symbolic correspondence between a letter or word (idea) and a real physical entity. The word “coffee” represents a beverage made from cocoa beans, for example. Symbolic relationships of this kind are only created in the mental world; they by definition do not exist in the purely material world."
The first sentence says that a code maps a point in space A to a point in space B. The second sentence suddenly asserts that space A is a space of ideas. How do we resolve the apparent inconsistency between those two sentences?
If the second sentence is to be assumed, then the process of translation from RNA to DNA does not involve a code.
~~ Paul
DaveB Wrote:Linda introduced the analogy between a pheromone and the genetic code - perhaps you would agree it wasn't really helpful to our discussion!No, I wouldn't agree. We also mentioned polymorphic crystals and the periodic table. The goal is to try to pin down a definition of code that includes natural mechanisms that people think are coded and excludes ones that are not. One definition was given in post #510 that appears to exclude the genetic code.
Quote:I think the reference to random polymers in that paper related to random RNA molecules, but those could, I suppose, give rise to random strings of amino acids if the rest of the mechanism was in place - but so what? The difference between a random heap of letters and a specific code, is exactly what we are talking about!People keep asking me to describe how the genetic code evolved, as if I somehow know. One possibility is that it started with random assembly of amino acids and then evolved a simple mechanism that could distinguish between broad categories of amino acids, eventually evolving more specificity. This idea is explored in detail in this paper:
Quote:I believe that the hypothesis that life started as RNA molecules (storing the code and acting as 'enzymes') has been more or less abandoned because these molecules are too unstable.No, it hasn't been abandoned. The research focuses on how it might have evolved in the face of the instability. There are, of course, other proposals that don't start with an RNA world.
Quote:The problem is that if you propose that the code replication and reading machinery was present in life from the beginning, then it had to be created without the benefit of natural selection - a feat described well by Fred Hoyle:No one proposes that the genetic code existed "from the beginning." Check out this paper:
Quote:Alternatively, life began in an earlier form with no code, but then it isn't clear how anything could evolve - it would simply be a bit of novel chemistry.Why is a code necessary for evolution? Evolution requires heritable chemicals with variation.
stephenw Wrote:Symbolic relationships being created in a "mental world" (whar's that), which is not part and parcel of phenomenal reality --- is precisely what I am arguing against with a worldview that information and meaning are real and measurable. Informational "space" is a scientific concept. There is no inconsistency in the definition; as symbols refer to symbols and not physical targets most of the time in conversation and in data gathered from experiements. Your claim of inconsistency is a linguistic mistake. The "pointing" goes to mapping theory, about which there is a lot written. The ideas of Bayesian probability and those of Hilbert space are found to work well together.I'm having trouble understand your use of words here.
Quote:Translation - -whether in the specific sense of RNA/DNA communication or in the sense of changing one coding format to another -- IS BY DEFINITION subject to Shannon Coding Theorem. In bio-semiotics; measurable error correction takes place, as would be expected when using a noisy channel. Living things learned and used the practical aspects of information theory as much as they subconsciously learned chemistry and physics.I agree that Shannon is relevant. But if we are going to use that as a reason to call the genetic code a code, then the definition inolving idea => physical thing is too limited.
(2017-12-04, 02:08 PM)Steve001 Wrote: [ -> ]Me:
Still waiting for the answer.
The only time you have anything to say is when you say it to me. Are you me personal fanboy? It seems you are. I've never had one and don't know whether to be pleased or alarmed.
Michael Larkin Wrote: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.Fair enough. I'm happy to agree that the DNA specifies codes that interact with the translation mechanism through an intermediary, the mRNA. There is, however, no 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.
Quote: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.Note that there is not a 1-to-1 relationship between anticodons and amino acids.
Quote: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.You're right that I can't get past thinking of a "lookup table" in computer science terms. That's where the term comes from. If you insist on misuing the term for any mechanism that humans can represent as a table, then there are hundreds of natural mechanisms that use lookup tables, including the periodic table. The idea becomes useless, although it does apparently open the door for a plethora of codes.
Quote: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.I don't understand what you think the RNA world idea is avoiding.
Quote: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.You just said that simple polypeptides could be formed without DNA.
Quote: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.Yes, this is an issue that biologists are grappling with. Do I need to post the same papers yet again? Does anyone feel like doing any reading?
Quote: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 still haven't said anything except that humans produce codes and so therefore nature cannot. I guess I will post this paper yet again:
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.
Quote: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.I have read the entirety of the two papers that I keep posting. Perhaps you could find out the degree to which I understand them by actually discussing them.
(2017-12-04, 04:11 PM)Paul C. Anagnostopoulos Wrote: [ -> ]No, I wouldn't agree. We also mentioned polymorphic crystals and the periodic table. The goal is to try to pin down a definition of code that includes natural mechanisms that people think are coded and excludes ones that are not. One definition was given in post #510 that appears to exclude the genetic code.Well not necessarily because I accept there isn't a hard demarcation line, but coding for one thing is vastly different from coding for an almost infinite number of possibilities (OK there is probably an upper limit to protein chain size).
Don't you think it's important to pin down the definition?
Quote:People keep asking me to describe how the genetic code evolved, as if I somehow know. One possibility is that it started with random assembly of amino acids and then evolved a simple mechanism that could distinguish between broad categories of amino acids, eventually evolving more specificity. This idea is explored in detail in this paper:The title of this paper is "Evolution of the genetic code through progressive symmetry breaking", so my question is, how does evolution operate in the absence of a genetic code? I mean, this point is crucial, if you don't have an organism that has any means to pass its structure on to its offspring, then what does it mean to talk about evolution?
http://www.sciencedirect.com/science/art...9314000113
Quote:So the question is: At what point in this long story of the genetic code does the evolution become impossible?Define a "heritable chemical ", and then lets see if it doesn't contain an implicit code.
No, it hasn't been abandoned. The research focuses on how it might have evolved in the face of the instability. There are, of course, other proposals that don't start with an RNA world.
No one proposes that the genetic code existed "from the beginning." Check out this paper:
https://www.researchgate.net/publication...e_Ribosome
Why is a code necessary for evolution? Evolution requires heritable chemicals with variation.
~~ Paul
Quote:You're right that I can't get past thinking of a "lookup table" in computer science terms. That's where the term comes from. If you insist on misuing the term for any mechanism that humans can represent as a table, then there are hundreds of natural mechanisms that use lookup tables, including the periodic table. The idea becomes useless, although it does apparently open the door for a plethora of codes.
DaveB Wrote:Well not necessarily because I accept there isn't a hard demarcation line, but coding for one thing is vastly different from coding for an almost infinite number of possibilities (OK there is probably an upper limit to protein chain size).Wait a minute. We are talking about the evolution of the genetic code, not the evolution of proteins. The question is whether the genetic code could evolve by naturalistic means.
Quote:The title of this paper is "Evolution of the genetic code through progressive symmetry breaking", so my question is, how does evolution operate in the absence of a genetic code? I mean, this point is crucial, if you don't have an organism that has any means to pass its structure on to its offspring, then what does it mean to talk about evolution?Here is a proof that evolution happens, by Marvin Minsky:
Quote:Define a "heritable chemical ", and then lets see if it doesn't contain an implicit code.The code exists to map DNA sequences to amino acid sequences. If there is no mapping, then there doesn't need to be a code.
Quote:The real problem with this discussion is that it inevitably involves mountains of hypothetical s created in a desperate attempt to avoid the idea that something designed life. There also seems to be a desire to blur the distinction between pre-biotic life and life.Why go off the rails now? Of course there are hypotheticals. That's the way science works. What would you expect to see if science was somehow not the rig job that you appear to believe it is? No hypotheses, just some magic instant-answer?
Quote:I can't really believe you mean that! The periodic table is something humans created to help them understand chemistry, the genetic code is actually used by the chemistry of life - we only use it to understand the process of life's chemistry using it!There is no genetic code table in the cell. The table was invented by humans to help explain what is going in with the chemistry. The periodic table is also a nice table to explain what is going on with valence electrons in atoms. What exactly is the difference? I'm willing to listen to a difference, but so far everyone is just accusing me of being an uncooperative curmudgeon.