Upright Biped’s summary on information systems in cell based life

_{kairosfocus

December 4, 2017

Design inference, Food for thought, ID Foundations, Origin Of Life, rhetoric, Selective Hyperskepticism, specified complexity}

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UD participant Upright Biped (of ~~Complexity Cafe~~ U/D: Biosemiosis) has commented recently in the what is knowledge thread, replying to frequent objector CR by summarising key aspects of the role of information systems in observed cell based life. His remarks are well worth headlining:

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UB, 195: >>We can start by summarizing the core physical requirements of the system we are trying to explain: an autonomous self-replicator with open-ended potential (i.e. it can describe itself or any variation of itself).

The system requires:

1) a sequence of representations in a medium of information.

2) a set of physical constraints to establish what is being represented.

3) a system of discontinuous association between representations and referents, based on spatial orientation (i.e. a reading-frame code)

4) functional coordination (semantic closure) between two sets of sequences; the first set establishes the constraints that are necessary to interpret the representations, and the second set establishes a system whereby the representations and their constraints are brought together in the specify way required to produce a functioning end product – an autonomous self-replicator. Coordination is required because changes to the first set affect the second set.

Did you follow all that? You have to have a medium of information, representations, constraints, discontinuous association, a reading-frame code, and semantic closure in order to create a material system capable of Darwinian evolution. Each interdependent piece has a physical manifestation, and each brings a critical capacity to the system.

So … when you remove the translation machinery in order to simplify the system (to meet your ideological requirements), you remove the capacity of the system to specify objects among alternatives. You remove the physical capacities that are enabled only by having a medium of information organized within a system (i.e. RNA, for instance, is only a medium of information when it is organized as such, otherwise it’s just another molecule with its particular characteristics, determined by energy). In other words, you remove the very system that enables Darwinian evolution to exist, not to mention removing the very thing that enables biological organization in the first place.

Thus, what are you then left with? You are left with a system that can only organize itself based upon the energy of the individual and collective components in the system (i.e. your “no-design laws”). But, magnetism does not establish a medium of information. Thermodynamics does not create a reading-frame code. Dissipative processes do not coordinate semantic closure among unrelated sequences of symbols. In other words, you have nothing but your prior assumptions.

So now that we have a lay of the land, we can take a look at your claims:

Claim #1: Darwinian evolution is the source of the translation apparatus.

This claim is dead on arrival. The only way to resuscitate this claim is through a) massive equivocation of terms, and b) abject denial of molecular science. In other words, it’s right up your alley.

Claim #2: Only high fidelity replication requires translation.

You need to get your head straight. The simpler system you are talking about is not a semiotic system that merely operates with poor fidelity, it is a non-semiotic system that operates by pure dynamics. It doesn’t establish a medium of information; it cannot specify objects among alternatives, and it obviously cannot achieve semantic closure. In an effort to save your theory, you can certainly start to equivocate on terms like “specify” and “medium of information”, but at the end of the day, the only thing that such an entity can lead to (be the source of) will be determined solely by dynamics. Thus, I asked you the clarifying question: Does the non-semiotic system you assume preceded and created the semiotic system have to specify the semiotic system that follows it? If so, then how does it do that?

You have no response to that question that doesn’t also include repeating your claim and assuming its true.

The bottom line is that there is no conceivable environment at the origin of life on Earth that inanimate matter operating under physical law (your “no-design laws” for crying out loud) where purely dynamic properties such as electromagnetism, hydrophobicity, etc., will push and pull and cajole molecules and constituents into simultaneously creating a sequence of symbolic representations, interpretive constraints, a system of discontinuous association, a reading frame code, and semantic closure. In short, the issues surrounding the origin of a semiosis in the cell are not about “fidelity”, they are about organization instead.>>

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Again, food for thought. END

PS: As debate points have been raised, here is a summary of protein synthesis, from Wiki:

This should be seen i/l/o this more complete overview of the whole synthesis:

Here is Yockey’s info-system view:

Yockey’s analysis of protein synthesis as a code-based communication process

And, here is a summary of the wider metabolism set:

Comments

UB: Does the system require what is listed and operate as it is described in the literature, or does it not?
Is a system required to launch a rocket into space not compatible with the literature of Newton's laws of motion? Of course it is. However, Newton's have become untenable as an expiation for how gravity works as it has been refuted by general relativity. It's an approximation.critical rationalist_{December 9, 2017
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@UB #35 From this paper...
A common misconception is that the genome of almost every organism contains a complete set of 20 AARS, each being individually responsible for coding the enzyme that charges a cognate tRNA with one of the 20 naturally occurring aa. With the ever-increasing availability of complete genome sequences, it is becoming evident that gene duplication, horizontal gene transfer, and gene loss are much more frequent events among the AARSs than originally thought. The absence of an AARS-encoding gene from a genome is possible because it does not necessarily correlate with the absence of the corresponding essential biochemical function. For example, the absence of glutaminyl-tRNA synthetase (GlnRS) is rescued by a non-discriminating glutamyl-tRNA synthetase (ND-GluRS) that can mis-acylate Glu to a tRNAGln, which is then modified to Gln-tRNAGln by a tRNA-dependent amidotransferase (3). Enzymatic modification of a mischarged aminoacyl-tRNA (aa-tRNA) is documented for Asn, Gln, Cys, selenocysteine and formylmethionine (4–8). Therefore, cataloguing all those cases where classical AARS genes are missing is a necessary first step in identifying known alternative pathways that enable cognate charging of the tRNA species for which the cognate AARS is missing. Genetic code decoding is a much more variable step than originally thought and needs to be quantified (9). There are numerous reports of genomes with more than one gene for the same AARS enzyme or even paralogous fragments consisting of free-standing domains of AARSs (e.g. catalytic-, anticodon-binding- and editing domains). These paralogs and paralog fragments have been the focus of intense interest since their gene products exhibit diverse functions outside translation. These range from tRNA-dependent aa synthesis, tRNA posttranscriptional modification, editing of misactivated aa and antibiotic resistance in bacteria, to molecular hubs within essential signaling pathways that regulate tumorigenesis in humans (10–16). Evolutionary analyses have highlighted the importance of horizontal gene transfer (HGT) in the evolution of the AARS family (17) and it has been found that this is often linked to antibiotic resistance, especially in microbes (11,18–21). The fact that bacterial AARSs do not often (22) participate in complex protein-protein interactions and that they are frequently compatible with tRNAs from phylogenetically distant organisms suggests that they are frequently functional (and hence selectable) following HGT.
critical rationalist_{December 9, 2017
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CR, dumping energy into a system tends to INCREASE entropy, as the Clausius heat transfer model used to derive his 2nd law statement highlights. It requires carefully channelled coupling to partly convert input energy into shaft, constructive work, with exhaustion of waste degraded energy (typically, heat). The oh the earth is open to the sun rhetoric utterly fails to account for the rise of functionally specific complex organisation of metabolising entities joined to a von Neumann kinematic self replication facility using alphabetically coded information (which implies language . . . a strong sign of intelligence). And that is what needs to be accounted for. KF PS: FSCO/I is NOT a synonym for irreducible complexity. It is speaking to complex, coherent functional organisation beyond a threshold of 500 - 1,000 bits. Debates on whether removal or disabling of any one of several core parts instantly cripples function are irrelevant to this. Though, it is common that only very limited perturbation is tolerable, without functional collapse -- even, allowing for redundancies and the like.kairosfocus_{December 9, 2017
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KF, Thanks for adding graphic illustration. This subject discussed by UB here is fundamental.Dionisio_{December 9, 2017
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UB, The more I read your discussion with your politely dissenting interlocutor, the more I’m convinced that you’re a strong candidate for the “most patience” award. Normally that recognition is given to KF and GP, but this time it seems like you’re the man. My friend, I don’t even understand what your interlocutor means in his comments, but my reading comprehension is rather poor.Dionisio_{December 9, 2017
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F/N: I have added some diagrams of protein synthesis in context, including Yockey's mapping to the classic communication system model. KFkairosfocus_{December 9, 2017
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UB: Does the system require what is listed and operate as it is described in the literature, or does it not? CR: Do you make a habit of quote mining?
Answer the question.Upright BiPed_{December 9, 2017
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Good grief. Does the system require what is listed and operate as it is described in the literature, or does it not?
Do you make a habit of quote mining?
UB: you are an observer, and you do not get to decide how the cell describes itself.

CR: And, as an observer, we do not get to decide how to launch a rocket into space. That did not change one bit, despite the fact that [we] now conclude something completely different is happening there, in reality, when Newton’s laws were superseded by general relativity.
Are you saying that, since Newton's laws were refuted, we do not think something completely different is happening there in reality, and that is of completely no consequence? Of course, not. Specifically, we have to know under what conditions Newton's laws would be insufficient to result in a successful rocket launch, such as the presence of objects that has a significantly larger mass or is moving at a very high velocity, etc. Needing to know when Newton's laws will work, and when they will not, is a consequence of those laws having been refuted. We have to take that into account because we think something different is happening there, in reality. General relativity, on the other hand, doesn't require making those specific exceptions. Our explanation for how gravity works, in reality, scales to very high velocity or a very high mass, with the exception of, say the center of a black hole, in which it breaks down. So, there are only specific conditions when we can pretend those laws had not been refuted. I'm suggesting the same thing with how the cell describes itself. Since your theory of information does not scale, the idea that it works like you think it does, in reality, is untenable. A more fundamentally theory is needed, which explains both classical and quantum information in a way that assumes something completely different is happening there, in reality. And that conflicts with information theory specific claims, such as all information needs to be interpreted, etc. As I understand it, this is what would separate your argument from merely claiming "how the cell describes itself" is irreducibly complex. Again, you seem to have two choices. Either... A. You think the ability to pretend a refuted theory is true, under specific conditions, is a problem for the theory that refuted it B. You think there is some yet to be expressed problem the with constructor theory of information, in that you think it does not provide a more fundamental explanation for information, at both the classical and quantum physics - in the same sense that general relativity is a more fundamental explanation for gravity. Otherwise, your argument can be boiled down to merely, the way the cell describes itself is irreducibly complex. Are you denying that you do not think the way the cell describes itself is irreducibly complex? if that's not the argument your making, then what is it?critical rationalist_{December 9, 2017
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CR, when the cell synthesizes a protein, the anticodon-to-amino acid association (establishing the constraints in the system, i.e. the code) is spatially and temporally isolated from the codon-to-anticodon association (which occurs when the medium is being read). Is that true or false? This architecture establishes a physical discontinuity in the operation of the system, where the lawful process of constructing a protein includes a variable and that variable is determined outside the process of the construction. The variable is determined independently by the organization of the constraints. Is that true or false?Upright BiPed_{December 9, 2017
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CR, "When a ribosome pairs a "CGC" tRNA with "GCG" codon, it expects to find an alanine carried by the tRNA. It has no way of checking; each tRNA is matched with its amino acid long before it reaches the ribosome. The match is made by a collection of remarkable enzymes, the aminoacyl-tRNA synthetases. These enzymes charge each tRNA with the proper amino acid, thus allowing each tRNA to make the proper translation from the genetic code... " -- Research Collaboratory for Structural Bioinformatics; PDB - Protein Databank When a specific codon is presented to the ribosome, a specific amino acid is added to the protein being constructed. Does the codon determine which amino acid is added?Upright BiPed_{December 9, 2017
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UB: you are an observer, and you do not get to decide how the cell describes itself. CR: And, as an observer, we do not get to decide how to launch a rocket into space.
Good grief. Does the system require what is listed and operate as it is described in the literature, or does it not?Upright BiPed_{December 9, 2017
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You need to get this through your head: you are an observer, and you do not get to decide how the cell describes itself.
And, as an observer, we do not get to decide how to launch a rocket into space. That did not change one bit, despite the fact that now conclude something completely different is happening there, in reality, when Newton's laws were superseded by general relativity. The ability to pretend that Newton's laws were not refuted, in the specific case of launching rockets, doesn't mean we actually thing gravity works like Newton's laws, in reality, in the specific case of launching rockets into space. It's an approximation. So is your 'theory" of information in regards to how the cell describes itself. The ability to pretend your theory of information works like you think it does, in the specific case of how a cell describes itself, does't mean we should actually think information works the way you think it does, in reality, when when considering your argument. So, at best, it's irreducible complexity in sheeps clothing.critical rationalist_{December 9, 2017
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CR [to UB]: You’re just merely trying to pass of the tired claim off “irreducibly complexity” as a theory of information.
To my knowledge UB has never done such a thing, nor has anyone else. Frankly, I have no idea what it would look like to have irreducibly complexity as a theory of information. CR, instead of making incoherent unsupported claims about the position of others, it would help if you provide quotes in support.Origenes_{December 9, 2017
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We do not pretend that the translation system requires the establishment of a medium of information, and representations within that medium. The question to you: Does it? We do not pretend that the translation system requires the as set of physical constraints to establish what is being represented. The question to you: Does it? We do not pretend that the translation system requires a system of discontinuous association and a reading frame code. The question to you: Does it? We do not pretend that the translation system requires semantic closure. The question to you: Does it?Upright BiPed_{December 9, 2017
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@UB It doesn't? So, you're basally claiming that the translation system in cells we can observe are irreducibly complex, irrespective of a working theory of information. Again, without a theory of information that actually scales, it's unclear why we should pretended that information actually works like you think, in reality. As such, information has nothing to do with it. You're just merely trying to pass of the tired claim off "irreducibly complexity" as a theory of information.critical rationalist_{December 9, 2017
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CR, I’m not confused by this situation at all CR. You need to pack on as many words as possible in order to give your participation here the gloss that you are still in the conversation, dealing with important concepts. Yet, you still haven’t actually engaged any of the requirements of the genetic translation system (as I have listed them) and shown them to be unnecessary or factually dubious in any way. You’ve merely squirreled and dissembled yourself into a ridiculous position where you hope to sell the idea that you don’t have to address the physical evidence because ‘Newton doesn’t scale to general relativity’ – which has absolutely nothing to do with the issues at hand. You need to get this through your head: you are an observer, and you do not get to decide how the cell describes itself.Upright BiPed_{December 9, 2017
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Why don’t you answer this really simple question CR? Why not tell us what the first step is from a non-semiotic system to a semiotic system? Do we get a translation system first and then the code, or vice versa?
What was the first step in the Arabic number system? Tallies. Or how about the previous step before universal Turing machines (UTM)? Each of these things represented leaps to universality that were disproportionate to the underlying change that occurred. Nor is their explanation found at the level of atoms, etc. Furthermore, we stumbled upon them. For example, some number systems would have been universal but they had rules that actually prevented it. In each case, this universality is an emergent property of cogs, transistors, vacuum tubes, etc. The desire to reduce errors and make it faster to reconfigure a dedicated computer to perform different tasks resulted in UTMs that can run any algorithm that any other UTM can run. Making them universal was a unintended but extremely useful side effect. People only originally cared if they could represent numbers of the scale that they actually had to detail with on a daily basis. An attempt to bump up the capacity in the favor of reduced notation ended up making a leap to represent any possible number (universality.) So, as like all aspects of Neo-Darwnism, the theory is that aspects of the cell that performed some other function was up also being useful in that ended up producing that leap to universality as well. I’ve already pointed out an example of that in a previous thread, in that multiple molecules can take the place of single molecules in the translation system that were though to be always present across all cells.
You often speak of “unreliable replication”. What does that look like? Where can we find it now in nature?
Constructor theory is the theory that all scientific theories can be expressed as which tasks are physical possible, which tasks are physically impossible and why. This includes the theory of evolution. As such, what current cells look like, in addition to what more primitive cells would look like would “look like”, how they both replicate, etc. is described in that form in the referenced paper. Constructor theory is the ultimate generalization of the idea of catalysis. From the paper....
This can be seen by modeling the logic of natural selection as an approximate construction, whose substrates are populations of replicators and whose (highly approximate) constructor is the environment. This occurs over a much longer time-scale than that of self- reproduction, whereby replicators – constructors on the shorter scale – become now substrates.
For example, the cells in your body are modeled as approximate replicators. They heavily rely on error correction, which can be modeled separately. The appearance of design is also expressed in constructor theoretic terms as well. In addition to in what sense our current claws of physics do not contain the design of high-fidelity replicators, already present. Nor do we think more primitive cells are like current day cells, just with the translation system removed. That would be a straw man.
And why would it be on a course towards more organization instead of what the Second Law [ED: i.e. of thermodynamics] prescribes?
You’ve head of this thing called the sun, right?critical rationalist_{December 9, 2017
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Now, it seems to me that if you still have some objection, you have two choices. A, You think that the ability to launch rockets into space by pretending gravity works like Newton's laws, in reality, is somehow a problem for General relativity. or B. You do think there is some yet to be expressed problem the with constructor theory of information, in which it does not provide a more fundamental explanation for information, at both the classical and quantum physics, in the same sense that general relativity is a more fundamental explanation for gravity. Or perhaps, you’ve merely tried to pass off a claim of irreducible complexity as some kind of theory of information? But, 'information is complex” is just another version of the same flawed argument. Of course, if I'm mistaken, then please elaborate.critical rationalist_{December 9, 2017
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@UB
If a critic of Newtonian mechanics suggested that it was not necessary to overcome gravity in order to launch a rocket, then yes, that would be a problem. And that is exactly what you are doing here.
No, it’s not. You still seem to be confused. What I'm referring to is a definition of what information is, what is physically required for it, etc. which is information theory. This is contrast to suggesting information isn't needed. Just like my analogy, which is based on our current theory of gravity, not that gravity doesn't need to be overcome. Returning to an analogy of gravity analogy. It's as if you're saying since our explanation for gravity is that it works like X (Newton’s laws), in reality, and since gravity is key process in Q then Q must be designed. But X has been superseded by a theory that explains everything that X did and even more, in a different, more fundamental way: Z (space-time of general relativity), and suggests something completely different is happening there, in reality. This is because gravity working like X, in reality, cannot also explain P (GPS). As such, the more fundamental explanation that gravity works like Z, in reality, explains both P and Q, while X does not. X is an approximation because if we assume it is true, in reality, the conclusion it implies do not hold at very high mass or velocity. The fact that we can pretend that gravity works like X, in reality, to launch rockets into space does not change the fact that we actually think gravity works like Z, in reality, not X. Nor does the fact that we can pose a problem for Z. We can conceive of the very same physical, empirical aspects of launching rockets into space in a more fundamental way. Furthermore, just like there were observations that were problematic to theory X, and caused us to create theory Z to resolve them. There are observations that are problematic to Z. Namely that we do not have a theory of quantum gravity (R). So, at least quantum mechanics, general relativity (Z) or both are actually approximations as well. This may result in us creating yet another explanation (Y) for how gravity works that suggests that completely different is happening there, in reality, instead of what was thought to be happening there, in reality, by theories X and Z. Should that be the case, our ability to pretend that gravity works like Z, in reality, while building GPS satellites, and that gravity works like X, in reality, while launching rockets into space, would not a problem for theory Y. It would be a more fundamental theory than X and Z, and it would also be our actual explanation for gravity in not only the case of R and P, but Q as well. Both Z and X would be approximations of Y. Most importantly, the argument that Q is designed because we think gravity works like X, in reality, simply no longer follows. We wouldn’t pretend gravity works like X, when evaluating arguments, because we no longer actually think that is the case, in reality. With that out of the way, let’s return to the theory of information you’ve presented (X), if we can call it that. You’re claiming that since information works like X, in reality, and since information is key in self replicating cells, then self replicating cells (Q) must be designed. However, like Newton’s laws, your theory (X) doesn’t scale. Furthermore, there is a theory that explains everything that X did and even more, in a different, more fundamental way: Z (The constructor theory of information), which suggests something completely different is happening there, in reality. This is because information working like X, in reality, cannot also explain P (quantum information). Nor does it even scale to all classical systems. As such, the more fundamental explanation that information works like Z, in reality, explains both P and Q, while X does not. X is an approximation because if we assume it is true, in reality, the conclusion it implies does not hold in quantum systems. The fact that we can pretend that information works like X, in reality, in some classical systems does not change the fact a far better theory indicates information works like Z, in reality, not X. Nor does the fact that we can pose a problem for Z. We can conceive of the very same physical, empirical aspects of information in a more fundamental way that does not require anthropomorphic aspects like interpretation, etc. This theory is outlined briefly in this paper as a primer for application in the constructor theory of life, and is expanded on in significantly more detail in this paper, in which it is the main topic. So the argument that cells are designed because information works like X, in reality, no longer follows. We need not pretend that information works like X, in reality, while evaluating arguments because X is no longer tenable as an explanation for it. Now, perhaps you’ve retreated here or merely tried to pass off a claim of irreducible complexity as some kind of theory of information. But, either way, 'information is complex” is just another version of the same flawed argument.critical rationalist_{December 9, 2017
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Some people worship randomness, they should stop that "It appears to be a quite general principle that, whenever there is a randomized way of doing something, then there is a nonrandomized way that delivers better performance but requires more thought." E. T. JaynesEugen_{December 7, 2017
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CR
UB: I have a question for you, CR. Does the non-semiotic system you assume preceded and created the semiotic system have to specify the semiotic system that follows it? If so, then how does it do that? How does it organize semantic closure?
Why don’t you answer this really simple question CR? Why not tell us what the first step is from a non-semiotic system to a semiotic system? Do we get a translation system first and then the code, or vice versa? You often speak of “unreliable replication”. What does that look like? Where can we find it now in nature? And why would it be on a course towards more organization instead of what the Second Law [ED: i.e. of thermodynamics] prescribes?Origenes_{December 7, 2017
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More rhetoric. All rhetoric. If a critic of Newtonian mechanics suggested that it was not necessary to overcome gravity in order to launch a rocket, then yes, that would be a problem. And that is exactly what you are doing here. You need to remove barriers to Darwinian evolution (Von Neumann's threshold of complexity) so that you can convince yourself that the system was "crude enough that it could have arisen by chance and requires no explanation". This is the sole purpose of this utterly ridiculous line of attack. Unfortunately for you, the simultaneous requirements of a medium, representations, constraints, discontinuous association, spatial orientation and semantic closure are not subject to erasure (or any other contrivance) on the part of the observer, no more than gravity can be ignored when you launch a rocket. Thus, you are left with an unavoidable need to create these convoluted scenarios and then lament the fact that they don't interest anyone -- everyone keeps spitting out the hook. Apparently, that's still better than having to address the gene system and its requirements.Upright BiPed_{December 7, 2017
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Allow me to translate from CR-speak into plain English: “Critical rationalists such as myself do not need a theory that is in any way connected to observations or inferences from observations, because we can pull just so stories out of our asses. Who needs evidence when you can do that?”
Except, that’s not what I said. That’s would be like saying “General Realativistists do not need a theory that is connected to observations or inferences from those observations, because they can just put so stories out of their asses.” I’ll ask yet again.
CR: ...someone could give four brief requirements for launching a rocket into space. Would someone criticizing Newton’s laws [in favor of general relativity] need to refute those requirements?
Are those observations a “problem” for general relativity? Do they have to be refuted? Yes or No? Does anyone criticizing Newton’s laws in favor of general relativity need to suggest the ability to launch a rocket using newton’s laws was not “connected to reality or observations”? Yes or no? It's really simple question. Can't anyone here answer it?critical rationalist_{December 7, 2017
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if some designer copied knowledge into a cell, what are ramifications of that based on the requirements of what is physically required to copy information? UB simply doesn’t say anything about that. At. All.
This is more dishonest rhetoric. How do I know this? Because you’ve quoted me directly from an article on my website where I explain this in detail. You have yet to challenge those details. I suspect this is because none of them is even controversial. I have a question for you, CR. Does the non-semiotic system you assume preceded and created the semiotic system have to specify the semiotic system that follows it? If so, then how does it do that? How does it organize semantic closure?Upright BiPed_{December 7, 2017
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the requirements UB listed are approximations can be more fundamentally explained as a series of tasks with subtasks and other subtask that eventually end up with non-replication specific subtasks in the environment. UB has no response to this other than to keep repeating the same requirements.
I’ve offered no additional response to this because, to whatever extent it makes any sense at all, it is still incoherent. You have this grand conception in your head that if you can reduce the gene system down to physical “tasks” that are not specific to the gene system, then you can say that the gene system is explained by a set of generic tasks that are “possible under no-design laws” and therefore “require no explanation”. It truly would be hard to imagine a more useless (and illogical) explanation of origins.Upright BiPed_{December 7, 2017
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First, it’s unclear how those requirements actual get UB to ID, even at face value.
This is dishonest rhetoric. You know exactly how this “gets me” to intelligence. Prediction, logic, experimental result, and the scientific literature demonstrate that the physics of the gene system can only be identified elsewhere in written language and mathematics – two unambiguous correlates of intelligence. You know this explicitly, yet you just wrote that you didn’t know. It's pure rhetoric.Upright BiPed_{December 6, 2017
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Critical Rationalist @15:
. . . we can model replication via constructor theory as constructors with a spectrum of various degrees of accuracy – with replication being performed initially by the environment and then transitioning to both the environment and self replication.
Allow me to translate from CR-speak into plain English: "Critical rationalists such as myself do not need a theory that is in any way connected to observations or inferences from observations, because we can pull just so stories out of our asses. Who needs evidence when you can do that?" Critical Rationalist @ 16:
The thing is, I don’t need to refute those requirements.
Again, I will translate: "I don't need to address UB's argument no matter how compelling it may seem to be. Why? Because critical rationalists such as myself can pull just so stories out of our asses. Who needs to address counter arguments based on logic and evidence when you can do that?"Barry Arrington_{December 6, 2017
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I gave CR four brief requirements of an autonomous self-replicator capable of Darwinian evolution. He responded with a 3,000+ word punt. Not in one word of it did he actually refute anything I said. At this point, it is not obvious that he is even aware of this fact, or that he would allow himself to be.
The thing is, I don't need to refute those requirements. First, it's unclear how those requirements actual get UB to ID, even at face value. UB would need to add something to them which has yet to be explicitly disclosed. After what seems like putting teeth, the best I can get is that "There are abstractions in nature", intelligent agents use abstractions, so some intelligent agent(s) put it there. But that's simply inductivism in that the distant past resembles the past. Even *if* abstraction was the only way to information could exist in a cell, what other options would there be? If knowledge was genuinely created by variation and selection, what how else would the result be stored? Observations of people exploiting the laws of physics for their own purpose doesn't mean that the laws of physics can only be explored by people. IOW, this is like saying, since people use sprinklers, rain must be designed. What other options would nature have? Furthermore, none of the papers referenced actually reach that conclusion. And at least on one of them explicitly said ID is not a conclusion. So, apparently, UB has some personal theory that he has yet to disclose. Second, someone could give four brief requirements for launching a rocket into space. Would someone criticizing Newton's laws need to refute those requirements? No, they just need to point out how those requirements are approximations and how we cannot use them to, say, build a GPS satellite. IOW, those same requirements can be expressed in more fundamental way via Einstein's general relativity, which suggests something completely different is going on in reality, than Newton's laws. Nor did we have to rebuild bridges or buildings after it was refuted. In the same sense, the same requirements UB listed are approximations can be more fundamentally explained as a series of tasks with subtasks and other subtask that eventually end up with non-replication specific subtasks in the environment. UB has no response to this other than to keep repeating the same requirements. This would be like someone simply repeating the fact that we can launch rocket into space as an attempt to defect criticism of Newton's laws. "But, we can launch rockets into space using it! You can't refute that!" So what? The idea that someone would need to is apparently lost on UB. To quote UB, "At this point, it is not obvious that he is even aware of this fact, or that he would allow himself to be." See my above comment for details. Note, this isn't the first time UB was mistaken about a theory "scaling". Specifically, UB claimed...
UB: There is a fundamental principle within physics sometimes referred to as the minimum total potential energy principle. This principle is related to the Second Law of Thermodynamics, and simply states that any physical object (regardless of its size or composition, as big as a planet or as small as a molecule) will distort and twist, and naturally orient itself to seek its lowest potential energy state.
But this doesn't apply at the level of quantum physics, so it doesn't actually scale to "any physical object", as I pointed out here. Furthermore, UB's "theory of information" does not scale to quantum mechanics, either. Nor does it actually connect to physics in a fundamental way, any more than Von Neumann's cellular automata does. For example, if some designer copied that knowledge into a cell, what are ramifications of that based on the requirements of what is physically required to copy information? UB simply doesn't say anything about that. At. All. Is't that odd omission for a supposed physical theory of information? Then again, I can't say I blame him for avoiding this, either, as it has implications that do not suit his purpose. As such, it's no surprise that not only was it absent initially, but it continues to be absent after having pointing it out over and over again.critical rationalist_{December 6, 2017
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Reposting from the same thread....
UB: We can start by summarizing the core physical requirements of the system we are trying to explain: an autonomous self-replicator with open-ended potential (i.e. it can describe itself or any variation of itself).
The system we are trying to explain is the relatively recent, cell, which is capable of high-fidelity replication. Namely, when a cell replicates it first makes a copy of the recipe of which transformations of raw materials (matter) are required to make copy of itself. Then it performs those transformations to make a copy of the vehicle from that same recipe. This is contrast to replication in the form of making an atom by atom copy of an entire, previously existing cell, already constructed. This is a key point as if the cell performed a copy of itself in its entity, any damage it incurred during its lifetime would be coped as well. Nor is there is no way to perform error correction by on a vehicle only cell as that requires a recipe for which to compare and correct the entire end result, which would be exponentially more difficult at that stage anyway. To allow for error correction, the recipe must also contain which transformations to perform to correct errors that occur. And the recipe must be stored in such a way that the information it contains is in digital form. This is in contrast to analog information storage (or analog computers), which is not self correcting and fidelity is subject to even slight amounts of drift. All of these things are required for high-fidelity replication. Now, on to the question of “what are the core physical requirements” for this system we are trying to explain. If only there was some problem or criticism that motivated people to actually work on this very question in detail? What about Von Neumann? While he pioneered the key concept of replicator-vehicle logic described above, his attempt to provide the design of an actual self-reproducer, in the terms of atoms and microscopic interaction was unsuccessful. However, fortunately for us there is indeed such a problem. Just as it had brought challenges to our most fundamental theories of information, some members of the scientific community suggested specific aspects of quantum mechanics brought a challenge to our theory of life in that it was incompatible with self-replication. Specifically, they posited some “biotonic” laws, containing the design of organisms or some key aspect of self-replicators, must supplement quantum mechanics. Why? From section 1 of this paper…
But even more striking is that living cells can self-reproduce to high accuracy in a variety of environments, reconstructing the vehicle afresh, under the control of the genes, in all the intricate details necessary for gene replication. This is prima facie problematic under no-design laws: how can those processes be so accurate, without their design being encoded in the laws of physics? This is why some physicists – notably, Wigner and Bohm, [12], [13] – have even claimed that accurate self-reproduction of an organism with the appearance of design requires the laws of motion to be “tailored” for the purpose – i.e., they must contain its design [12]. These claims, stemming from the tradition of incredulity that living entities can be scientifically explained, [14], highlight a problem. The theory of evolution must be supplemented by a theory that those physical processes upon which it relies are provably compatible with no-design laws of physics. No such theory has been proposed; and those claims have not been properly refuted.
Note that the term “no-design laws” refers a set of “core physical requirements” (our current laws of physics, including quantum mechanics). It’s not a new set of laws. Rather, it’s referring to existing, general purpose laws and resources, that are not design-specific. In fact it’s the absence of a new set of yet to be proposed laws that somehow contain the design of self replicating cells, already present. While this was not specifically directed at ID or UB’s claims (there are no alternative theories to Neo-darwinism, including ID, because there has yet to be proposed a critical test for which ID can explain the same phenomena at least as well, let alone any critical difference indicated in any yet to be proposed critical test. Nor does merely pointing out a problem in Neo-darwinism result in creating a new theory. [see #175]), it is still relevant to the question at hand. This because this criticism results in asking the question: which physical laws (“core physical requirements”) are compatible with high-fidelity replication. (This more fundamental question is key because, even if we could go back in time and watch life appear and evolve into the biosphere we see today, one could always retreat to the claim that the design of critical aspects of self replicating cells, or even all organisms, was already preset in the laws of physics, at the outset. This would be like the claim of “front loading” but at the laws of physics, rather than the genome.) So, why had no theory yet to have been presented to supplement neo-Darwinism, properly refuting those claims?
Indeed, the central problem here – i.e., whether and under what circumstances accurate self-reproduction and replication are compatible with no-design laws – is awkward to formulate in the prevailing conception of fundamental physics, which expresses everything in terms of predictions given some initial conditions and laws of motion. This mode of explanation can only approximately express emergent notions such as the appearance of design, no-design laws, etc.
This is why Von Neumann was unsuccessful and is yet another reason why the paper doesn’t merely attempt to predict anything specific, such as the appearance of a goat, is true or probably true, given some initial conditions and the laws of motion. ?What we need is a way to express the “core physical requirements” of the system, along with concepts such as the appearance of design, information, no-design laws, etc, in exact terms, as apposed to approximations.
The prevailing conception also forces a misleading formulation of the problem, as: what initial conditions and laws of motion must (or must probably) produce accurate replicators and self-reproducers (with some probability)? But what is disputed is whether such entities are possible under no-design laws. More generally, it cannot express the very explanation provided by evolutionary theory – that living organisms can have come about without intentionally being designed. It would have aimed at proving that they must occur, given certain initial conditions and dynamical laws. To overcome these problems I resort to a newly proposed theory of physics, constructor theory. [16, 17, 18]. It provides a new mode of explanation, expressing all laws as statements about which transformations are possible, which are impossible and why. This brings counterfactual statements into fundamental physics, which is key to the solution. The explanation provided by the theory of evolution is already constructor-theoretic: it is possible that the appearance of design has been brought about without intentionally being designed; so is our problem: are the physical processes essential to the theory of evolution – i.e., self- reproduction, replication and natural selection – possible under no-design laws?
Our motivation to answer the very question UB asked, which “core physical requirements are necessary”, is where constructor theory comes into play.
Constructor Theory’s mode of explanation also delivers an exact physical expression of the notions of the appearance of design, no-design laws, and of the logic of self-reproduction and natural selection.(5)?
However, it seems that UB isn’t really serious about finding out what those “core physical requirements” are as he appears to be willing to settle for incomplete approximations. This would be like settling for Newton’s laws of motion with is much more of an approximation than Einstein’s more fundamental general relativity. Example? UB wrote….
1) a sequence of representations in a medium of information. 2) a set of physical constraints to establish what is being represented. 3) a system of discontinuous association between representations and referents, based on spatial orientation (i.e. a reading-frame code) 4) functional coordination (semantic closure) between two sets of sequences; the first set establishes the constraints that are necessary to interpret the representations, and the second set establishes a system whereby the representations and their constraints are brought together in the specify way required to produce a functioning end product – an autonomous self-replicator. Coordination is required because changes to the first set affect the second set.
The first problem is that UB’s theory of information, if we can call it that, is an approximation. We cannot use it at the level of quantum physics any more than you can use Newton’s laws to build a GPS satellite. It simply doesn’t scale. Furthermore, he appeals to these approximations as if they somehow support “his theory”, as someone might might try to appeal to the ability to launch rockets into space somehow presets a problem to Einstein’s general relativity. It doesn’t. Again, this was addressed in #175. Second, UB’s theory does not address key aspects of the system, such as copying information, error correction, distinguishability, digital information, as opposed to analog, etc. These key aspects are what make high-fidelity replication possible. Furthermore, if some designer put the information of which genes will result in the right proteins which will result in the right features, into the cell as ID claims that too would reflect the same process that occurs when the same information is copied during replication. Right? Or does ID suggest that information spontaneously appeared there because the designer wanted it to? None of UB’s “information theory” addresses “the core physical requirements” for these key aspects of the system. So, it’s not that I “do not follow” what UB presented. It’s very much the opposite. I follow them well enough to recognize what he presented is expressible as more fundamental, exact statements in constructor theoretic terms. Specifically, a network of tasks with subtasks of subtasks, etc. which eventually reaches a subtask that is not specific to replication. IOW, we can exactly model cells as constructors in constructor theory. This is outlined in detail in section 3.1 of the referenced paper. IOW, the paper answers the question of what these “the core physical requirements” are. Yet, apparently, he has some yet to be disclosed objection. This is like UB objecting to pointing out launching rockets into space can be explained more accurately and at a more fundamental level by using Einstein’s GR, than by using Newton’s laws. The very aspects of the physical objects that play the roles UB describes in the translation system themselves represents information. Example? Some one in a lab could apply transformations to move stop codons from their naturally occurring locations to test a theory of protein expression. Those transformations represent information need to setup up a repeatable experiment. If all information needs to be interpreted, then you either have a circular definition of distinguishability or an infinite regress. Again, this is outlined in the constructor theory of information which defines information based on a set of physically possible tasks. This includes what tasks must be possible to copy information, which is a key aspect of replication. Again, UB’s theory says nothing about this.
So … when you remove the translation machinery in order to simplify the system (to meet your ideological requirements), you remove the capacity of the system to specify objects among alternatives.
First, no one suggests any point in cellular development consisted of cells with the current level of high-fidelity replication (and necessary aspects described above to enable them) but with the translation machinery removed. That’s simply false. Is there no one willing to actually address the arguments actually being presented, as opposed to a straw man? Second, you have confused the universal theory that knowledge grows via some form of variation and criticism with an “ideological requirement”. Theories are tested by observations, not derived from them. As such, so would any theory that suggests cells were always capable of high-fidelity replication. That idea isn’t out there for anyone to observe any more than any other. Third, as the paper points out, we can model replication via constructor theory as constructors with a spectrum of various degrees of accuracy – with replication being performed initially by the environment and then transitioning to both the environment and self replication. Again, this represents the very question UB asked: “what are the core physical requirements” for this system.
However, one must also address the question: can accurate self-reproducers arise from generic resources only, under such laws??Note that what the prevailing conception would aim to prove is that the emergence of accurate self-reproducers follows (with some probability) given certain initial conditions and laws of motion. This approach, informing the search for viable models for the origin of life, [25], is suitable to solve scientific problems such as predicting the existence of life elsewhere in the uni- verse – e.g., by providing bounds to how probable the emergence of those self-reproducers is on an earth-like planet. Here I am addressing a differ- ent problem: whether accurate self-reproducers are possible under no-design laws. This is a theoretical (indeed, constructor-theoretic) question and can be addressed without resorting to predictions. Indeed, the theory of evolution provides a positive answer to that question, provided that two further points are established. I shall argue for them in what follows.?The first point is that the logic of evolution by natural selection is compatible with no-design laws because – in short – selection and variation are non-specific to its end products. This can be seen by modeling the logic of natural selection as an approximate construction, whose substrates are populations of replicators and whose (highly approximate) constructor is the environment. This occurs over a much longer time-scale than that of self- reproduction, whereby replicators – constructors on the shorter scale – become now substrates.?Evolution relies upon populations being changed by variation and selection over the time-scale spanning many generations. Crucially, the mutations in the replicators, caused by the environment, are non-specific, (as in section 3.1), to the “end product” of evolution (as Dawkins put it, not “systematically directed to improvement” [27]). This constructor-theoretic characterisation of mutations replaces the less precise locution “random mutations” (as opposed to non-random selection, [5]). These mutations are all transmitted to the successfully created individuals of the next generation, by heredity – irrespective of their being harmful, neutral or beneficial in that particular environment.?Selection emerges from the interaction between the replicators and the environment with finite resources. It may lead to equilibrium, given enough time and energy. If so, the surviving replicators are near a local maximum of effectiveness at being replicated in that environment.?Thus, the environment is passive and blind in this selection process. Since it retains its ability to cause non-specific variation and passive selection again, it qualifies as a naturally-occuring approximation to a constructor. Crucially, it is a crude approximation to a constructor: crude enough that it could have arisen by chance and requires no explanation. Its actions – variations and selection – require no design in laws of physics, as they proceed by non- specific, elementary steps. So the logic of evolution by natural selection is compatible with no-design laws of physics.
This is a natural transition because such a transition already exists when self-replication specific recipe subtasks eventually rely on generic, elementary tasks that are not specific to replication and are found in the environment.
Note, however, that the recipe is in one sense incomplete: as remarked in section 3.1, the recipe is not required to include instructions for the elementary tasks, which occur spontaneously in nature. These are indeed relied upon during actual cell development – they constitute epigenetics and environ- mental context. As remarked by George C. Williams, “Organisms, wherever possible, delegate jobs to useful spontaneous processes, much as a builder may temporarily let gravity hold things in place and let the wind disperse paint fumes”, [29].
Note that constructor theory allows us to exactly define what is mean by the appearance of design, which is crucial to indicating what kinds of constructions exhibit it and therefore require different levels of accuracy, resources, storage types, etc.
3.1.1 Appearance of design Something with the appearance of design is often described as “improbable” [27, 28]. This is misleading because probability measures are multiplicative; so that would mean that two independent objects with the appearance of design would have much more of that appearance than they do separately. But that is not the case when the two objects have unrelated functionalities (such as, say, internal organs of different organisms). In contrast, two organs in the context of the same organism, coordinating to the effect of gene propagation, do have a greater appearance of design than either separately. This can be expressed naturally in constructor-theoretic terms for programmable constructors. Consider a recipe R for a possible task T. A sub-recipe R? for the task T? is fine-tuned to perform T if almost any slight change in T? would cause T to be performed to a much lower accuracy. (For instance, changing the mechanism of insulin production in the pancreas even slightly, would impair the overall task the organism performs.) A programmable constructor V whose repertoire includes T has the appearance of design if it can execute a recipe for T with a hierarchical structure including several, different sub- recipes, fine-tuned to perform T. Each fine-tuned sub-recipe is performed by a sub-constructor contained in V : the number of fine-tuned sub-recipes performable by V is a measure of V ’s appearance of design. This constructor- theoretic definition is non-multiplicative, as desired.
So, to summarize. Neo-Darwinism cannot explain the appearance of life under the current conception of physics. This is because the current conception doesn’t allow defining key aspects of the problem in exact terms. However this is possible though using a new mode of explanation: constructor theory, which does allow defining those key aspects in more fundamental and exact ways.critical rationalist_{December 6, 2017
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WJM & Axel, this is the crooked yardstick standard for straightness and accuracy in action. If you are induced to make a crooked yardstick your standard, then what is actually straight ("true") or upright or accurate will never conform to the crooked standard. Thus, we come to the agit-prop strategist's dream: people are induced to "instinctively" reject and lock out what would ordinarily correct crookedness because crookedness is their standard. And if they identify with crookedness at deep worldview level, being passionately caught up in its world-narrative, they will put good for evil and evil for good, light for darkness and darkness for light. This will lead to marches of angry, ruinous folly. Only what is patently naturally straight and upright: plumbline, self-evident truths and similarly patent realities or facts, will suffice to correct. Sadly, some will not even be corrected by such, until it is too late, the cliff's edge has crumbled underfoot and we have broken our backs. Mass folly has serious consequences. KF PS: Jesus' words (seen as a response to ideas like the Parable of Plato's Cave [which would have been current in the Dekapolis town of Sepphoris, 5 mi from Nazareth and where the construction jobs were]) in the Sermon on the Mount are apt:
Mt 6:22 “The eye is the lamp of the body; so if your eye is clear [spiritually perceptive], your whole body will be full of light [benefiting from God’s precepts]. 23 But if your eye is bad [spiritually blind], your whole body will be full of darkness [devoid of God’s precepts]. So if the [very] light inside you [your inner self, your heart, your conscience] is darkness, how great and terrible is that darkness! [AMP]
kairosfocus_{December 4, 2017
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