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How Some Materialists are Blinded by Their Faith Commitments

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Every once in a while we get one of those “aha moments” when everything comes together.  Phillip Johnson helped me to one of those moments over 20 years ago when I read this passage from an article in First Things (when that journal still permitted dissenting voices to be heard):

For scientific materialists the materialism comes first; the science comes thereafter.  We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence.  That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

Aha!  If Darwinism or something like it must be true as a matter of deduction from materialism, then evidence takes a back seat.  Dawkins once said he would prefer Darwinism even if there were no evidence to support it.  That is hard to understand until one understands Johnson’s point.

I thought about this today when a friend reminded me of this quote from Nobel laureate Jacques Monod:

“We call these [mutations] accidental; we say that they are random occurrences. And since they constitute the only possible source of modifications in the genetic text, itself the sole repository of the organisms’ hereditary structure, it necessarily follows that chance alone is at the source of every innovation of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis.”

Seriously?  No other explanation is even “conceivable”?  I can understand how someone could consider the evidence and reject ID.  I would believe they are mistaken, but not everyone is going to come to the same conclusion as I do.  I get that.  But to say that ID is not even “conceivable”?  Well, that’s just plain stupid.  Why would Monod, obviously not a stupid man, say something so dumb?  His faith commitments blinded him and stunted his imagination.  A dogmatic commitment to materialist metaphysics makes even very smart people literally blind to alternatives.  And it makes them say stupid things.

Another example:  Paraphrasing Hawking:  Because there is something, the universe can create itself from nothing.

Comments
Another concept Bob seems to refuse or accept was pointed out by Gpuccio @132 of Functional Information that is in specific order. This is not just a concept, but a condition that must be met for life to work at all. Gpuccio @132 states,
Bits in order in a soruce code are functional information. And functional information is not just something that we use to “summarise” things. If there is not the right sequence in our source code, our program cannot work. If there is not the right sequence in our genes, our porteins cannot work.
Correcto mundo, agree with Gpuccio. Functional specificity is crucial. Without specificity, chaos breaks out. If random mutations were allowed to generate profusely in the genome, proteins are not built. Regulatory systems do not regulate, Editors do not edit and Correction Systems do not correct. And it's not just any order. And it's not just any information. It is Prescribed, Ordered Information. This goes back to ability to recognize differences in: Three Subsets of Sequence Complexity and their Relevance to Biopolymeric Information Abstract
Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: Random Sequence Complexity(RSC) Ordered Sequence Complexity(OSC) Functional Sequence Complexity(FSC) FSC alone provides algorithmic instruction. Random and Ordered Sequence Complexities lie at opposite ends of the same bi-directional sequence complexity vector. Randomness in sequence space is defined by a lack of Kolmogorov algorithmic compressibility. A sequence is compressible because it contains redundant order and patterns. Law-like cause-and-effect determinism produces highly compressible order. Such forced ordering precludes both information retention and freedom of selection so critical to algorithmic programming and control. Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string. Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).
FSC is aperiodic, but organized structure code in a very specific order - so that as Gpuccio stated Proteins can be built - to specific function. And it might be said, Functional Sequence Complexity invariably manifest Organizational structure if unrolled in the right environment.DATCG
April 5, 2018
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Bob @126, A little late to this discussion but was surprised at Bob's assertions. Hope Bob sees this and look forward to his response. A partial repost from comment I made on Gpuccio's Ubiquitin System Functional Complexity and Semiosis post. Bob states,
There is no information in the cell, only DNA with bases in order.
Leading to reductio ad absurdum, there is no information in Bob's cells, therefore no Information exist in the brain cells in Bob's head. Conclusion: Bob cannot make a logical conclusion because he has no active information encoded in his brain cells to compare or make statements with. His brain is just a bag of chemicals with no containment of active, accurate, retrievable and functional information. ----------- Yet, facts are scientist have done work on active information storage and retrieval in reprogramming brain cells of long-term memory. There is evidence information exist in brain cells in Bob's head and all of our brain cells. How else would Bob get home? Go to work? Get any place at all in his life without specific, active information in his brain cells? If Bob cannot store specific, active information in his brain cells, how can he communicate with us? Bob may not understand how specific information is encoded in his Carbon-based brain cells yet, but it is. None of us may have specific enough details yet. But a recent study on Long-Term memory shows "Place-cells" exist in our brains and can be reprogrammed. To reprogram by definition is to modify, rewrite, redirect a pre-existing program. "Summary"
Long-term memory of specific places is stored in the brain in so-called place cells. Neuroscientists have now 'reprogrammed' such place cells in free-roaming mice, by sending electrical impulses directly to individual neurons.
How to Reprogram Memory Cells in the Brain
How do we know what happened to us yesterday, or last year? How do we recognize places we have been, people we have met? Our sense of past, which is always coupled with recognition of what is currently present, is probably the most important building block of our identity. Moreover, from not being late for work because we could not remember where the office was, to knowing who our friends and family are, long-term memory is what keeps us functional in our daily lives. It is therefore not surprising that our brain relies on some very stable representations to form long-term emories(sic). One example are memories of places we have seen. To each new place, our brain matches a subset of neurons in the hippocampus (a centrally located brain area crucial to memory formation): place cells. The memory of a given environment is thought to be stored as a specific combination of place-cell activity in the hippocampus: the place map. Place maps remain stable as long as we are in the same environment, but reorganize their activity patterns in different locations, creating a new place map for each environment.
Bob's is wrong. His assertions are based on materialist reductionism that leads to absurd claims if followed to their natural conclusions. To review, Bob claims no information exist in carbon-based cells. Therefore, no information exist in his own brain cells, leading to a conclusion, no information exist in Bob's brain. Q: How is Bob comprehending information and communicating with us? If there is no information in his brain? He fails to recognize specific, active information is encoded within brain cells for Long-Term memory - scientific research known since at least 2012(MIT). As research shows, location information is encoded in brain cells. It just happens that the information encoded in our brain cells is Carbon-based, not silicon based compounds. Wet not dry. But like a silicon-based compound, cell phone hardware storage medium must be a result of tightly controlled, highly regulated, protected and error-corrected systems design. Active prescribed information must exist for protein complexes to be built based upon specific functional information. Pre-programmed interfaces must exist for Wet memory storage allocation, correct relational database information to be maintained and retrieved when required. There must be informational mapping to retrieve the correct information at the correct time. Or Bob could be forever lost. There are known brain disorders for information corruption in brain cells, like Alzheimer's and other memory disorders. Yes, information in cells exist and thankfully Bob uses that information to talk to us today :-)DATCG
April 5, 2018
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It can waddle like a duck, quack like a duck, fly, paddle and look like a duck but don't call it a duck cuz that be the human word. After all the duck doesn't know. We have totally anthropomorphized the world- we have different names for everything. We named them. :roll: And don't even get me started on the French...ET
April 3, 2018
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Origenes
The “argument” from the other side seems to be the label: anthropomorphism.
Ironically, they accuse theists of anthropomorphism ;) Their anthropomorphism is manifested in the claim that reality in its entirety can be grasped by human mind. While this is true only to an extent, because universe is not everything that exists, intelligibility of the universe does not follow from their world view at all.EugeneS
April 3, 2018
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Eugene S: It is a system level, not ‘physicality’ level.
Well said. Not being at the physicality level is confirmed by the fact that 'seeing' the system is not a simple direct observation. In order to 'see'it, one has to grasp/understand the whole thing. One has to connect the dots, so to speak. Individual letters do not mean anything by themselves — one has to be able to see words and sentences to get the message.
Eugene S: Spikes of voltage in a cable do not mean anything by themselves. It is only at the application level that they make sense!
Indeed. Only if it makes sense it can be seen. The "argument" from the other side seems to be the label: anthropomorphism.Origenes
April 3, 2018
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Origenes 226 Spot on! It is a system level, not 'physicality' level. Spikes of voltage in a cable do not mean anything by themselves. It is only at the application level that they make sense!Eugene S
April 3, 2018
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GPuccio to Bob O'H "I really don’t follow you." Me neither! Bob to gpuccio: "gpuccio - I think we are actually in agreement" I do not think so, I'm afraid. There is a lot more than just terminology here. Bob, you still have to somehow explain semiosis, which is an objective phenomenon. Semiotic causality is inherently different from physical causality (as e.g. in 2H2 + 02 -> 2H2O). Semiosis assumes multiplicity of alternative (physically indistinguishable, arbitrary) states. The problem gpuccio and I are talking about is that sign processing is never observed to arise without agency. The reason, from physic's perspective, is quite simple: this kind of causality does not reduce to physics/chemistry because it is inherently about establishing the symbolic boundary conditions on the motion of matter in a semiotic system, which the 'laws of nature' cannot do. The laws of nature and boundary conditions are two absolutely different categories (thank-you, sir Isaac Newton, for clarifying that!). In semiosis, we have a formalism instantiated into physicality. Ok, I understand that you and those who are like-minded, suggest that this formalism is a direct consequence of physicality. The problem is, you have absolutely no empirical support for such a claim. This kind of causality from physicality to formalism is never ever observed in nature! Formalism never crystallizes 'on the edge of chaos' by itself, to borrow a phrase from S. Kauffman. What is observed, is: 1. physical causality (min total potential energy, for basic types of physical interaction); and 2. the inverse causality from formalism to physical instantiation of it (as in human technology). I really do not follow your reasoning. I simply think you have no case, I'm afraid. I think I have already laid out my argument and I really do not know if spending any more time on this would actually be worthwhile.Eugene S
April 3, 2018
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Bob O'H: OK, it will be our secret. :)gpuccio
April 1, 2018
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Bob, It isn't just terminology as the terminology means something. To be a code means it has specific propertiesET
April 1, 2018
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gpuccio - I think we are actually in agreement. Don't worry, I won't tell anyone. :-)Bob O'H
April 1, 2018
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Bob O'H: I really don't follow you. We call a protein a protein because it is a protein. It is a macromolecule made of aminoacids. We call a dog a dog because it is a dog. It corresponds to the abstract concept o which we attach the word "dog". So we call a code a code because it has the property of being symbolic. That's what the word "code" means. Everything is "putting labels on things", when we use words and language. But labels are important because they correspong to cancepts. So, the word code is important because it means that the system uses arbitrary connections, and therefore it is symbolic. That property is important, because it has huge consequences.gpuccio
April 1, 2018
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Gpuccio - what you describe is simply putting labels on things. If that's the only reason why it matters whether a code is arbitrary, then it is only terminology. The world natural would work the same way whether we made this distinction or not.Bob O'H
April 1, 2018
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Bob O'H: I don't understand your point, if there is one. If a virus is the cause of a disease, we call it the cause. If it is not, we say it is not the cause. Is that "nothing more than terminology"? We define what the word "code" means in our language, and then we try to understand what corresponds to our definition and what does not. It's called cognition. It's much more than terminology.gpuccio
April 1, 2018
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So, if the code were not arbitary, it would not be a code.
As, so it's nothing more than terminology. So then my guess is that the answer to my second question @222 ("what difference would it make if it was physically possible for a DNA triplet to only code for one amino acid?") would be that we simply wouldn't call it a code. Correct?Bob O'H
April 1, 2018
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Bob O'H at #222: Excuse me: a) If an interaction is direct, and the result is the consequence of physical laws, there is no code. So, an enzyme catalyzes a reaction because of its specific configuration: there is a lot of specific functional information, but not a symbolic code. b) If the interaction is indirect, and it is mediated by an intermediate which recognizes a signal and couples it arbitrarily to an ouctome, an outcome that the signal itself cannot cause, then we have a symbolic process. So, in the translation from mRNA to protein, the coupling between codon and aminoacid is made by the 20 aatRNA synthetases. Those proteins are configured so that they recognize, independently, the codon of the correct tRNA, charging it with the correct aminoacid. The codon itself cannot cause the charging of the tRNA. The codon is simply recognized by the correct aatRNA sinthetase, and the protein itself is configured so that it couples that codon to the correct aminoacid. IOWs, the 20 aatRNA synthetases are the repositosy of the code, and the true key to its translation. So, if the code were not arbitary, it would not be a code. It's very simple, and I don't understand your difficulties with the concept. A symbol is something that represents something else, but has no direct connection with what it represents. A codon represents an aminoacid, but in itself it has no power to incorporate that aminoacid into the protein. A word represents something, but it is only a symbol. So is the codon. The same thing can be represented by different words. So, indeed, the same AA can be represented by different codons, because the code is redundant. But there is more. The code itself can be artificially changed in experiments. That has been done, to a limited extent. See here: https://www.tandfonline.com/doi/full/10.4161/adna.29408 This is possible because the code is arbitrary. It is a code, and it is symbolic.gpuccio
March 31, 2018
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Bob @114
Bob: … we know the biochemistry of E. coli, for example, and as far as I know it’s all to do with chemistry. This includes DNA replication and gene expression.
We observe chemical processes. However, we also ‘see’ an organism. Seeing a cat it is not a direct observation. We observe body parts acting in harmonious subservience to a whole. From this we deduce that there is one thing. And it is only at this point that we ‘see’ the cat. The cat who controls its body parts. There is no bottom-up explanation for subservience of parts. There is no explanation from the level of the parts. These letters that make up these sentences cannot be explained by self-arrangement. Why not? Because the letters, on their own, are not interested in forming these sentences.Origenes
March 31, 2018
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I overstepped on that conclusion @ 224. Teleological inferences are not necessary in approaching observed function, but in discovering unobserved function. My bad.LocalMinimum
March 31, 2018
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What can presuming it's not a code net us? It frees us from expectations of teleology, or that we'll continue to find function. What are we going to do with that which we have yet to discover function/teleology? Continue searching for function/teleology, or reverse engineering, which will be logically framed with an expectation of such (otherwise you'll be searching like the child who can't find anything for themselves in the refrigerator). Or we can attribute it as nothing more than a "waste product" of evolutionary processes...which nets us what, again? Denial of teleology in biology is denial of the biological research methodology that has built every bit of biology we actually put to use.LocalMinimum
March 31, 2018
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All codes are arbitrary, Bob. It is the very nature of a code.ET
March 31, 2018
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EugeneS @ 218 - why does the code have to be arbitrary? if all it does is code the order of amino acids, what difference would it make if it was physically possible for a DNA triplet to only code for one amino acid?Bob O'H
March 31, 2018
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ET: There must be two camps as some say there is a code but it did not require a mind, somehow.
A strict materialist should deny the existence of anything but fermions and bosons IMO. Most of them, however, see no problem in talking about "code", "function", "organisms", "decisions", "morality" "freedom" and what not. But, from a materialistic viewpoint, this behavior doesn't make sense. Concerning code, consider e.g. this:
But there is no such physical stuff. Physics has ruled out the existence of clumps of matter of the required sort. There are just fermions and bosons and combinations of them. None of that stuff is just, all by itself, about any other stuff. There is nothing in the whole universe ... that just by its nature or composition can do this job of being about some other clump of matter. [Rosenberg]
'Being about another clump of matter' is not a property of matter. If DNA is not about proteins, then there is no code.Origenes
March 30, 2018
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The information comes from the designer of the universe. It permeates the universe. The universe couldn't exist without it. Crystals have specification but not complexity. Their information content is very limited. As I said earlier reverse engineering is our way of teasing out the information contained in objects.ET
March 30, 2018
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ET @193: Thanks for the additional comment. We're probably close to the point of diminishing returns (so long as my very specific questions remain unanswered), so I'll just share a couple of final thoughts on this nuance and then will leave you and others to valiantly deal with the monumental blunders by Bob & Company. :)
I thought I had made it clear there is a difference. That is what CSI is all about- to differentiate between the information in a crystal (not CSI) and genomes (full of CSI) – for example.
Yes, I agree that DNA has CSI and a crystal doesn't. The point I'm making is one level deeper. It isn't just that the crystal lacks complexity. It lacks information altogether. It is a physical object that forms from basic chemical interactions. That's it. There are certainly a few things we could quibble with Gitt about, but I agree with you that he generally has some good thoughts on the topic, so allow me share just a couple of his quotes to wrap up:
"[Information] is not a property of matter, so that purely material processes are fundamentally precluded as sources of information."
and
"It is impossible to set up, store, or transmit information without using a code."
Now, two things: 1. The material process (the kind of thing Gitt is referring to) that creates crystals is well understood. This process cannot produce information, per Gitt. I agree with him. (There certainly isn't any information produced as a result of the process that produced the crystal. So if we insist that information is in everything, the most we could possibly do is refer to some vague, esoteric kind of "information" that somehow is contained in the fabric of matter and energy itself -- a concept that, even if true, is utterly unhelpful to identifying the information we are interested in for purposes of intelligent design. Again, see my detailed post on that point.) 2. If we are claiming that information is somehow "contained" in a rock or a crystal, then it must be set up somehow and stored there somehow. Per Gitt, and I agree, this is not possible without a code. So, I repeat the highly fundamental questions for you to consider later at your convenience: What kind of code is present in a rock? What language or symbolic system is the "information" encoded in? What type of system can we use to transmit that information? If you carefully read through the nuances of the post I linked to, and once you think through the chain of causation, you will see that the information you think is contained in a rock floating in space, is in fact created about the rock by the intelligent observer, using the observer's mind and tools of investigation. It arises fundamentally from the observer, from an intelligent agent's mental activity -- just like all information does. This is a nuanced but deeply insightful point related to design if we will let it sink in. If we keep the terminology clear and the chain of causation in focus, I'm convinced we will do a much better job of making the case for design without confusing people in the process. Best,Eric Anderson
March 30, 2018
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Bob Transcription is different from translation. In eukaryotes, transcription is needed to transport genetic instructions from the nucleus, where DNA molecules are located, to outside so that mRNA can be later translated there. Transcription should be considered in context together with everything else that takes place in the cell. E.g. when a program is executed on a computer, parts of physical memory may be copied as prescribed by the program, which copying by itself could be accounted for by physics. However, this copying is meant to be done for a purpose, which can only be seen in the big picture. The same situation is in the eukaryotic cell regarding the duality of transcription-translation. Specific products of transcription, mRNAs, may be needed during protein synthesis later. So, the fact that transcription does reduce to chemistry does not explain the problem away, unfortunately. Translation is done, by definition, from one language to another. While transcription treats DNA as data, during translation, in contrast, mRNA is interpreted as a program, not as data. Arbitrariness is not just there happenstantially. It is absolutely essential because it ensures that there is freedom of purposeful choice between alternative energy-degenerate chemical states (configurations). This freedom is absolutely needed in order to make sure that a nucleotide sequence carries meaning i.e. specifies primary structure of specific proteins. Without arbitrariness, it is not possible to specify one physico-chemical alternative from among many. Without arbitrariness of phoneme sequences a human meaningful speech would not be a possibility. The same applies to written text as well. Nucleotide sequences are chemically arbitrary as there is very little chemical bias, hardly any at all, towards any one of the four nucleotides during polymerization. Any nucleotide can polymerize any other. And that is a key enabler of the instantiation of meaning into the physicality of nucleotide sequences. If all we had was the necessity of a natural regularity (such as the tendency towards states with min total potential energy in the system), there would be no freedom to specify semiotic relationships. These relationships can be specified provided there is a multiplicity of chemically/physically equivalent states (configurations) to actually mean specific things. Again, in chess this is clearly seen. Chess is only possible on a horizontally positioned board (assuming the material of the board and pieces is non-magnetic), the necessity of the laws of gravity, friction etc. by itself can only provide an equilibrium condition for semiotic relationships to come into action. Each configuration of pieces on the chessboard has absolutely the same chemical/physical properties. However, in the context of the game (in the context of semiotic relationships established voluntarily) each configuration carries a different meaning. As to what the laws of nature can do outside of equilibrium states, tilt the chessboard enough, and the game is no longer physically possible.EugeneS
March 30, 2018
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Bob:
“Function” is a human interpretation of what is happening in the natural world,...
It is a word that describes something happening in the natural world.ET
March 30, 2018
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GPuccio @ 213 - no, that's not my argument. That would be a different argument. Origenes @ 214 -
Given materialism, there is no code. I can agree with Bob on that one. There is only the material stuff that appears to function as a code, but in fact it’s all just chemistry.
We agree up to here.
Sure, there is the illusion of ‘function’ and ‘organism’, but these things do not exist.
But I disagree here. "Function" is a human interpretation of what is happening in the natural world, but human interpretations aren't illusions (well, not always :-)).Bob O'H
March 30, 2018
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Origenes- There must be two camps as some say there is a code but it did not require a mind, somehow.ET
March 30, 2018
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Given materialism, there is no code. I can agree with Bob on that one. There is only the material stuff that appears to function as a code, but in fact it's all just chemistry. Sure, there is the illusion of 'function' and 'organism', but these things do not exist. Obviously, the same goes for scientific research, rationality, morality, freedom and consciousness — if materialism is true, then these things do not exist. The realm of existence is exhausted by fermions and bosons.Origenes
March 30, 2018
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Bob O'H: "As long as the evolution of the code is possible within physics, I don’t see why there can’t be some level of arbitrariness." A lot of things are "possible" within physics, but never happen. To go back to a classical example, a tornado in a junkyard assembling a Boeing 747 is certainly possible within physics. So is the evolution of a symbolic code, or the emergence of Shakespeare's sonnets from the typing of monkeys. Is that your argument?gpuccio
March 30, 2018
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Bob:
if codes don’t educe to chemistry, how come DNA transcription reduces to chemistry?
Does it? Is transcription the genetic code, Bob? No. Do you know what the genetic code entails, Bob?
As long as the evolution of the code is possible within physics, I don’t see why there can’t be some level of arbitrariness.
Question-beggingET
March 30, 2018
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