(2017-12-04, 05:01 PM)DaveB Wrote: [ -> ]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!
Well put, David. But he really does mean it -- such a literalist!
On the one hand, he seems to acknowledge the existence of the genetic code -- but on the other, believes somehow it isn't really a code because (to his way of thinking) it has no lookup table.
He agrees that in computer science, codes can be created that have lookup tables that can be written down. But so too can the lookup table for the genetic code -- I posted it earlier.
The fact that the literal table can't be found anywhere in the cell stumps him, and he simply can't get past that, even though thousands of biologists routinely accept that there is a genetic code, and its lookup table has been written down and referenced for decades.
He's so adamant about mind of any kind not being involved in the invention of the DNA code -- he prefers to think that mindless evolution somehow invented it. I don't think he can see the inconsistencies in his arguments. I'm afraid he's a hopeless case.
(2017-12-04, 06:19 PM)Paul C. Anagnostopoulos Wrote: [ -> ]Note there is no mention of a genetic code. You only need inheritable chemicals that affect the organisms' fitness and also mutate. It could be bits of RNA or bits of protein or even something else.
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.
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.
~~ Paul
No different than a bee's honey-gathering dance, decoded by bees back at the hive. Symbols convey information about the environment.
The code or codes that unfold ontogentic* development most likely are self-created as artifacts of the struggle for life and experience. The communication systems that enable the bio-information needed by life are a
natural language that evolved organically.
At the organic level, the bioinformatic mapping is from a set of instructions signalling to developing organ function of a targeted healthy state.
Its not about the magic chemical DNA. DNA dialects are just one nexus in a diverse matrix of functional communication channels in biology. The endocrine system alone has its own language and multiple bio-functions with which it interacts.
The difference between a periodic chart and the natural language of DNA/RNA/Ribosome communication is that natural language is describing an in situ process in real environments. A periodic table on a powerpoint slide; in front of a group of chemists focused on its information in a real discussion might be a fairer analogy.
In my estimation the period table is a natural event done by naturally behaving animals. The intelligence is from the nature of thinking animals, whose minds obey the rules and laws of information's, storage, structured retrieval and transfer. The difference in my viewpoint from both; you Paul, and from David, is that the information is not shadowing DNA chemistry and magically creates new chemicals with the property of inheritance.
In my version; information is actualizing and riding the chemicals like little pony trains. The structured information that says go and stop, rest or high-alert, approach/avoid, are jumping on the bio-information channels and takes them forward. Forward into the willing of their enactment, as efferent signals. The meaning that is our emotions and intentions are these structured information objects.
The living cells exhibit integration and regulation that are the hallmarks of a healthy animal is one of vast amounts of intra- and inter-cellular communication.
Quote:* Ontogeny is the origination and development of an organism, usually from the time of fertilization of the egg to the organism's mature form—although the term can be used to refer to the study of the entirety of an organism's lifespan. Wikipedia
Michael Larkin Wrote:Well put, David. But he really does mean it -- such a literalist!
On the one hand, he seems to acknowledge the existence of the genetic code -- but on the other, believes somehow it isn't really a code because (to his way of thinking) it has no lookup table.
Do we have to play this game? I'm happy to acknowledge that it's a code. But if the central argument is that a code cannot evolve, doesn't it make sense first to define exactly what a code is? Apparently handwaving is sufficient.
Quote:He agrees that in computer science, codes can be created that have lookup tables that can be written down. But so too can the lookup table for the genetic code -- I posted it earlier.
The fact that the literal table can't be found anywhere in the cell stumps him, and he simply can't get past that, even though thousands of biologists routinely accept that there is a genetic code, and its lookup table has been written down and referenced for decades.
It stumps me? I was simply objecting to the claim that there is a table somewhere in biology. And if simply being able to write down a table is all that is required for a code, then the periodic table is a code.
Why don't people give a damn about what a code is while they are going on and on about its magical nature?
~~ Paul
(2017-12-04, 04:24 PM)Dante Wrote: [ -> ]I answered that at length. Not remotely surprised that is slid under your radar, or that you outright ignored it. That seems to be your go-to move
I read all your posts the first time and I read them again just now. You didn't answer this question regardless of what you think. "
What really chaps your arse about ToE?" You see the question I'm actually asking is,
What philosophy or ideology creates this normative state of mind in you that apparently ToE cannot occur by entirely natural means?
Looking over what you've written I see you've not answered this question either.
Quote:Paul beat me to it in post 487. I'll rephrase his question a bit though. What is an example problem with "Darwinian theory" ? And describe a non-Darwinian theory that will explain said problem thoroughly? This includes Modern Synthesis.
http://psiencequest.net/forums/thread-da...8#pid11748
You didn't answer this question either
http://psiencequest.net/forums/thread-da...7#pid11507
(2017-12-04, 08:48 PM)Paul C. Anagnostopoulos Wrote: [ -> ]Do we have to play this game? I'm happy to acknowledge that it's a code. But if the central argument is that a code cannot evolve, doesn't it make sense first to define exactly what a code is? Apparently handwaving is sufficient.
It stumps me? I was simply objecting to the claim that there is a table somewhere in biology. And if simply being able to write down a table is all that is required for a code, then the periodic table is a code.
Why don't people give a damn about what a code is while they are going on and on about its magical nature?
~~ Paul
Firstly, how do you define a code? Does it involve encoding and decoding? Are there rules? Can it be represented symbolically? Does it convey meaning or determine function? Is it structured (not haphazard)?
Here is something I found online:
Biosemiotics: a new understanding of life
Marcello Barbieri
Quote:The link between sign and meaning, in turn, calls attention to a third entity, i.e., to their relationship. A sign is a sign only when it stands for something that is other than itself, and this otherness implies at least some degree of independence. It means that there is no deterministic relationship between sign and meaning. Different languages, for example, give different names to the same object precisely because there is no necessary connection between names and objects. A semiotic system, therefore, is not any combination of two distinct worlds. It is a combination of two worlds between which there is no necessary link, and this has an extraordinary consequence. It implies that a bridge between the two worlds can be established only by conventional rules, i.e., by the rules of a code. This is what qualifies the semiotic systems, what makes them different from everything else: a semiotic system is a system made of two independent worlds that are connected by the conventional rules of a code. A semiotic system, in conclusion, is necessarily made of at least three distinct entities: signs, meanings, and code.
Here, at last, we have a definition where it is stated explicitly that a code is an essential component of a semiotic system. It is the rules of a code that create a correspondence between signs and meanings, and we can say, therefore, that an act of semiosis is always an act of coding, i.e., it is always a convention. More precisely, we can say that an elementary act of semiosis is a triad of ‘sign, meaning, and convention’, whereas a semiotic system is a whole set of signs and meanings that are linked together by all the various conventions that make up a code.
Signs, meanings, and conventions, however, do not come into existence of their own. There is always an ‘agent’ that produces them, and that agent can be referred to as a codemaker because it is always an act of coding that gives origin to semiosis. In the case of culture, for example, the codemaker is the human mind since it is the mind that produces the mental objects that we call signs and meanings and the conventions that link them together. We come in this way to a general conclusion that can be referred to as ‘the code model of semiosis’: a semiotic system is a triad of signs, meanings and code that are all produced by the same agent, i.e., by the same codemaker.
This conclusion is highly relevant to biology because it tells us precisely what we need to prove in order to show that the cell is a semiotic system. We need to prove that in every living cell there are four distinct entities: signs, meanings, code and codemaker.
If bringing up pheromones is unhelpful, can someone explain why? The connection between DNA and a polypeptide seems to be the same as the connection between a pheromone and a behaviour.
Has somebody offered a definition for "code" which includes DNA, but not pheromones? The mapping of ideas was brought up, but DNA isn't an idea. It's a description of which base sequences have become associated with which amino acids.
Linda
Kamarling Wrote:Firstly, how do you define a code? Does it involve encoding and decoding? Are there rules? Can it be represented symbolically? Does it convey meaning or determine function? Is it structured (not haphazard)?
All excellent questions.
"Different languages, for example, give different names to the same object precisely because there is no necessary connection between names and objects."
Here is a critical point. Is there a "necessary connection" between a particular codon and the amino acid it codes?
"Signs, meanings, and conventions, however, do not come into existence of their own. There is always an ‘agent’ that produces them, and that agent can be referred to as a codemaker because it is always an act of coding that gives origin to semiosis."
Note the scare quotes around 'agent.'
~~ Paul
(2017-12-04, 11:13 PM)Paul C. Anagnostopoulos Wrote: [ -> ]"Signs, meanings, and conventions, however, do not come into existence of their own. There is always an ‘agent’ that produces them, and that agent can be referred to as a codemaker because it is always an act of coding that gives origin to semiosis."
Note the scare quotes around 'agent.'
~~ Paul
If you read further in he document you will find he makes a distinction between mind and "organic" as agents. What he means by organic and how it differs from mind I have not been able to fathom.
Quote:[Note: these paragraphs are not necessarily contiguous in the original document]
The sequences of genes and proteins, in short, have precisely the characteristics that define signs and meanings. They are codemaker-dependent entities made of organic molecules and are, therefore, organic signs and organic meanings. All we need to keep in mind is that signs and meanings are mental entities when the codemaker is the mind, but they are organic entities when the codemaker is an organic system
Organic information and organic meaning, in short, are not intrinsic properties of the molecules that carry them, and this raises a new problem. What kind of entities are they?
We conclude that organic information has the same scientific status as the physical quantities because it is an objective and reproducible entity. But we also conclude that it does not have the status of a derived physical quantity because it cannot be expressed by anything simpler than itself. This means that organic information has the same scientific status as the fundamental physical quantities, i.e., that it is a fundamental (or irreducible) entity of Nature (a similar conclusion was also described in Küppers 1990 and 1992).
By the same token, the rule of the genetic code that a group of three nucleotides (a codon) corresponds to an amino acid is equivalent to saying that that amino acid is the organic meaning of that codon. Anywhere there is a code, be it in the mental or in the organic world, there is meaning. We can say, therefore, that meaning is an entity which is related to another entity by a code, and that organic meaning exists whenever an organic code exists (Barbieri 2003a).
Modern biology has readily accepted the concept of information but has carefully avoided the concept of meaning, and yet, organic information and organic meaning are both the result of natural processes. Just as it is an act of copying that creates organic information, so it is an act of coding that creates organic meaning. Copying and coding are the processes; copymakers and codemakers are their agents; organic information and organic meaning are their results.
1. The sequence used by a copymaker during a copying
process is organic information.
2. The sequence used by a codemaker during a coding
process is an organic sign.
3. The sequence produced by a codemaker during a
coding process is an organic meaning.
4. Organic information, organic signs, and organic meanings
are neither quantities nor qualities. They are a new
kind of natural entities, which are referred to as
nominable entities.
5. Organic information, organic signs, and organic meanings
have the same scientific status as physical
quantities because they are objective and reproducible
entities that can be defined by operative procedures.
6. Organic information, organic signs, and organic meanings
have the same scientific status as fundamental
physical quantities because they cannot be reduced to,
or derived from, simpler entities.
So, if I read him correctly, he seems to be saying that, as some might say that mind or consciousness is a fundamental, so too is organic information or meaning. I'd prefer to class them together as a single phenomenon.
(2017-12-04, 08:48 PM)Paul C. Anagnostopoulos Wrote: [ -> ]Do we have to play this game? I'm happy to acknowledge that it's a code. But if the central argument is that a code cannot evolve, doesn't it make sense first to define exactly what a code is? Apparently handwaving is sufficient.
Well let's use a closer analogy. Suppose we have a computer instruction set in which each instruction occupies the same number of bytes (say 2), and that all of the possible codes already have a meaning. Suppose that you want to develop new hardware that can access more instructions, but can still run all the existing binary software.
I hope you can see the problem - you can't extend the instruction length because then 2-byte instructions in the old software might be interpreted as a new 3-byte instruction - and crash the program. You most certainly can't solve the problem by making random changes to the hardware, looking for something that works, because whatever change you make will crash the program!
In real life, the solution might be to have two 'addressing modes', one for legacy software and one for new stuff, but that is really a dodge equivalent to stuffing two computers in one box - but how else do you evolve the genetic code in terms of the number of bases per amino acid? Sure it could evolve a little by acquiring an extra DNA base or two, but in fact life manages with just 4 bases, but the number of bases per amino acid is much harder to change.
David
DaveB Wrote:Well let's use a closer analogy. Suppose we have a computer instruction set in which each instruction occupies the same number of bytes (say 2), and that all of the possible codes already have a meaning. Suppose that you want to develop new hardware that can access more instructions, but can still run all the existing binary software.
Hence the reason no computer architect assigns all the codes! ;-)
Quote:In real life, the solution might be to have two 'addressing modes', one for legacy software and one for new stuff, but that is really a dodge equivalent to stuffing two computers in one box - but how else do you evolve the genetic code in terms of the number of bases per amino acid? Sure it could evolve a little by acquiring an extra DNA base or two, but in fact life manages with just 4 bases, but the number of bases per amino acid is much harder to change.
You have to read the literature on this. There is a lot of thought given to ways in which a 1-base code could evolve into a 2-base code, and so forth. In particular, if early life employed fewer amino acids, the trick is to keep binding the original amino acids while opening up the binding of new ones. Remember, we have all of chemistry at our disposal.
Check out the wobble hypothesis:
https://teaching.ncl.ac.uk/bms/wiki/inde...Hypothesis
Another line of evidence is that the tRNA's anticodon loop and its amino acid acceptor appear to have evolved separately. So the anticodon could evolve independently of the associated amino acid.
Another interesting paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810241/
~~ Paul