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

Still no specific example of a “quantum storage medium”? Are you about to tell me that you’re actually referring to a different “quantum storage medium” – different than the one where they encode the input and interpret the output?Upright BiPed_{December 10, 2017
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@UB I've referenced just such a paper that explains this in detail. Multiple times. You haven't. Does this mean you don't have a physical theory of information? from the paper....
Much of Shannon’s theory is about unreliable transmission and measurement, and inefficient representations, and how to compose them into more reliable and efficient ones. But here we are concerned with the fundamental issues that remain even in the limiting case when all error rates have been reduced to their physically possible minima and there is no redundancy in the message being transmitted. In that limit, receiving the message only means distinguishing it from all the other possible messages. And in that regard, Shannon’s theory is inadequate in two ways. The first is that it cannot describe information in quantum physics, because certain prohibitions that quantum theory imposes – such as the impossibility of cloning – violate the kind of interoperability that is assumed in Shannon’s theory. Consequently the type of information studied by Shannon is now called classical information. The second is that Shannon’s theory is about information represented in distinguishable states, but does not specify what distinguishing consists of physically. So, consider the non-perturbing measurement that distinguishes two possible messages x and y. It has the following effects in those two cases: message receiver message receiver [diagram] where x0 is a receptive state of some medium capable of instantiating the outcome x or y. But this does not in fact distinguish message x from message y unless the receiver states x and y are themselves distinguishable. Therefore (1), considered as a definition of distinguishability, would be circular. Indeed, no existing theory of information provides a non-circular account of what it means for a set of physical states to be mutually distinguishable. The theory that we shall present here does. Likewise quantum information theory, as it stands, never gets round to specifying what it is referring to as ‘quantum information’, nor its relation to classical information. It is not, despite the name, a theory of a new type of information, but only a collection of quantum phenomena that violate the laws of classical information. A new theory of information is needed, within physics but at a deeper level than both quantum theory and Shannon’s theory. In this paper we provide that, via constructor theory (Deutsch 2013). [Skipped details on the algebra used to describe tasks and types of networks in constructor theory, used below] 3 Computation Our theory of information rests on first understanding computation in constructor-theoretic terms. This will allow us to express information in terms of computation; not vice-versa as is usually done. This is the key to avoiding the circularity at the foundations of information theory that we described in Section 1. A reversible computation C? (S) is the task of performing a permutation ? over some set S of at least two possible attributes of some substrate: [ diagram ] For example, swapping two pure quantum states constitutes a reversible computation, and may be a possible task even if they are not orthogonal. It is then natural to define a computation variable as a set S of two or more possible attributes for which C?? for all permutations ? over S, and a computation medium as a substrate with at least one computation variable. (Since side-effects are allowed in the performance of C? , this definition does not require physical processes to be reversible.) Note again that in this paper we are not taking computation to be an a priori concept and seeking necessary and sufficient conditions for a physical process to instantiate it (cf. Horseman et al. 2014). We are conjecturing laws of physics: objective regularities in nature. These happen to be conveniently expressed in terms of the tasks we have called ‘computations’ and the property that we shall call ‘information’. We think that these correspond reasonably closely to the intuitive concepts with those names, but our claims in no way depend on that being so. 4 Information As we mentioned in Section 1 the intuitive concept of information is associated with that of copying. We shall express this association exactly and without circularity, in terms of computations as defined in Section 3. We first consider computations involving two instances of the same substrate S. The cloning task for a set S of possible attributes of S is the task [ diagram ] on S?S, where x0 is some attribute with which it is possible to prepare S from generic, naturally occurring resources (Section 6 below). This is a generalization of the usual notion of cloning, which is (3) with S as the set of all attributes of S. A set S is clonable if RS(x0)? for some such x0 . An information variable is a clonable computation variable. It is then natural to define an information attribute as one that is a member of an information variable, and an information medium as a substrate that has at least one information variable. Also, a substrate S instantiates classical information if some information variable S of S is sharp, and if giving it any of the other attributes in S was possible. And the classical information capacity of S is the logarithm of the cardinality of its largest information variable. The principle of locality II implies the convenient property that the combined classical information capacity of disjoint substrates is the sum of their capacities. Thus we have provided the purely constructor-theoretic notion of classical information that we promised. But we have emancipated it from its dependence on classical physics, and cured its circularity.
Of note is that, in the process of bringing information into fundamental physics, by developing a unifying single theory that scales to both classical and quantum physics, there was no reference to observers, knowing subjects, etc.critical rationalist_{December 10, 2017
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KF @70: Well done. Another episode in the important discussion on fundamental concepts and associated issues. Thanks.Dionisio_{December 10, 2017
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I have headlined 62: https://uncommondescent.com/atheism/cr-and-the-question-of-knowledge-with-his-championed-constructor-theory-in-play/ KFkairosfocus_{December 10, 2017
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The papers referenced @63-68 were published this year. The below referenced paper by the same authors was published around 8 years ago: "Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?,” that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology." Origin and evolution of the genetic code: The universal enigma Eugene V. Koonin, Artem S. Novozhilov DOI: 10.1002/iub.146 Volume 61, Issue 2 Pages 99–111 In those 8 years much has been discovered in biology. However, the pseudoscientific speculative hypotheses remain imprecise and incoherent. The known -not the unknown- clearly points to complex functionally specified informational complexity.Dionisio_{December 10, 2017
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"The standard genetic code (SGC) is virtually universal among extant life forms." "The structure of the SGC is nonrandom and ensures high robustness of the code to mutational and translational errors." Origin and Evolution of the Universal Genetic Code. Koonin EV, Novozhilov AS Annu Rev Genet. 51:45-62. doi: 10.1146/annurev-genet-120116-024713. Did somebody say 'nonrandom'?Dionisio_{December 10, 2017
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"[...] none of the three major theories of the code evolution has been fully successful in providing a definitive explanation although each has highlighted important features of the code." Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code Eugene V. Koonin Life (Basel). 7(2): 22. doi: 10.3390/life7020022Dionisio_{December 10, 2017
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“It is almost impossible to discuss the origin of the code without discussing the origin of the actual biochemical mechanisms of protein synthesis” - Francis CrickDionisio_{December 10, 2017
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The known -not the unknown- clearly points to complex functionally specified informational complexity.Dionisio_{December 10, 2017
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"The origin and evolution of the translation system is a forbiddingly difficult problem, and therefore, in many studies on the code evolution, it is formally treated as a separate issue and approached almost like a mathematical puzzle [...]" Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code Eugene V. Koonin Life (Basel). 7(2): 22. doi: 10.3390/life7020022Dionisio_{December 10, 2017
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"The genetic code that defines the rules of translation from the 4-letter nucleic acid alphabet to the 20-letter alphabet of proteins is arguably the single central informational invariant of all life forms [...]" "[...] the code is universal among modern life forms because any change in codon assignment would be highly deleterious." "[...] 49 years of code studies have elucidated notable features of the standard code, such as high robustness to errors, but failed to develop a compelling explanation for codon assignments." "In particular, stereochemical affinity between amino acids and the cognate codons or anticodons does not seem to account for the origin and evolution of the code." "The 64 triplet codons are neatly organized in sets of four or two, with the third base of a codon typically being synonymous. The assignment of codons to amino acids across the code table is clearly non-random [...]" Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code Eugene V. Koonin Life (Basel). 7(2): 22. doi: 10.3390/life7020022Dionisio_{December 10, 2017
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CR:
constructor theory formalizes the view that, in science, justification isn’t possible or even desirable and brings emergent phenomena, such as information, into fundamental physics
First, no-one has discussed justification as a component for knowledge, as post Gettier, to be justified in holding a belief that turns out to be true is understood for cause as not equal to knowledge. The matter of warrant has long since been brought to your attention repeatedly but insistently ignored. Thus, you have shamelessly played the strawman tactic. And, as the discussion of knowledge has played out on other threads, I simply note that scientific knowledge claims fall under a weak, fallibilist, inductively grounded sense of knowledge, warranted, credibly true (and empirically reliable) belief. I add: note, the very name, "Science," is derived from a Latin word denoting knowledge. Dictionaries are useful points of reference:
sci·ence (s???ns) n. 1. a. The observation, identification, description, experimental investigation, and theoretical explanation of phenomena: new advances in science and technology. b. Such activities restricted to a class of natural phenomena: the science of astronomy. 2. A systematic method or body of knowledge in a given area: the science of marketing. 3. Archaic Knowledge, especially that gained through experience. [Middle English, knowledge, learning, from Old French, from Latin scientia, from sci?ns, scient-, present participle of sc?re, to know; see skei- in Indo-European roots.] American Heritage® Dictionary of the English Language, Fifth Edition. Copyright © 2016 by Houghton Mifflin Harcourt Publishing Company. Published by Houghton Mifflin Harcourt Publishing Company. All rights reserved. science (?sa??ns) n 1. the systematic study of the nature and behaviour of the material and physical universe, based on observation, experiment, and measurement, and the formulation of laws to describe these facts in general terms 2. the knowledge so obtained or the practice of obtaining it 3. any particular branch of this knowledge: the pure and applied sciences. 4. any body of knowledge organized in a systematic manner 5. skill or technique 6. archaic knowledge [C14: via Old French from Latin scientia knowledge, from sc?re to know] Collins English Dictionary – Complete and Unabridged, 12th Edition 2014 © HarperCollins Publishers 1991, 1994, 1998, 2000, 2003, 2006, 2007, 2009, 2011, 2014
Thus, we need to reckon with the provisional, incremental, inductive sense of knowledge so derived. A point well understood since Newton, here, I clip Opticks, Query 31:
As in Mathematicks, so in Natural Philosophy, the Investigation of difficult Things by the Method of Analysis, ought ever to precede the Method of Composition. This Analysis consists in making Experiments and Observations, and in drawing general Conclusions from them by Induction, and admitting of no Objections against the Conclusions, but such as are taken from Experiments, or other certain Truths. For Hypotheses are not to be regarded in experimental Philosophy. And although the arguing from Experiments and Observations by Induction be no Demonstration of general Conclusions; yet it is the best way of arguing which the Nature of Things admits of, and may be looked upon as so much the stronger, by how much the Induction is more general. And if no Exception occur from Phaenomena, the Conclusion may be pronounced generally. But if at any time afterwards any Exception shall occur from Experiments, it may then begin to be pronounced with such Exceptions as occur. By this way of Analysis we may proceed from Compounds to Ingredients, and from Motions to the Forces producing them; and in general, from Effects to their Causes, and from particular Causes to more general ones, till the Argument end in the most general. This is the Method of Analysis: And the Synthesis consists in assuming the Causes discover'd, and establish'd as Principles, and by them explaining the Phaenomena proceeding from them, and proving the Explanations.
Of course, our understanding of inductive reasoning has been updated to denote arguments where premises (often, empirically derived) provide support for the credible truth of conclusions, as opposed to entailing them. Where, a key aspect of this is that if something has a stable distinct identity, it can be expected to behave in a consistent, reasonably predictable pattern. Kusha bushes produce thorns reliably (so that a donkey I heard of would deliberately brush its rider against these bushes, if it was displeased with him). Manchineel trees produce sweet tasting but caustic, toxic beach or death apples. Mango trees produce thousands of varieties of that luscious fruit. Unsupported objects near earth tend to fall under a force of 9.8 N/kg or thereabouts. The earth, due to angular momentum being conserved, rotates once every 23 hrs 56 minutes relative to the "fixed" stars. And so forth. So, there are good common-sense grounds to expect orderly, coherent patterns in the world. But common sense can be a suspect commodity when there is a dominant ideology to the contrary. But, we must go on. Knowledge, itself, is from a Greek term, gnosis, so let's use Wikipedia on that term as a handy reference:
Gnosis Gnosis is a feminine Greek noun which means "knowledge".[4] It is often used for personal knowledge compared with intellectual knowledge (?????? eídein), as with the French connaitre compared with savoir, the Spanish conocer compared with saber, or the German kennen rather than wissen.[5] Latin dropped the initial g (which was preserved in Greek) so gno- becomes no- as in nosc? meaning "I know", noscentia meaning "knowledge" and notus meaning "known". The g remains in the Latin co-gni-tio meaning "knowledge" and i-gno-tus and i-gna-rus meaning "unknown" and from which comes the word i-gno-rant, and a-gno-stic which means "not knowing" and once again this reflects the Sanskrit jna which means "to know", "to perceive" or "to understand".[citation needed] Gnostikos A related term is the adjective gnostikos, "cognitive",[6] a reasonably common adjective in Classical Greek.[7] Plato uses the plural adjective ????????? – gnostikoi and the singular feminine adjective ???????? ???????? – gnostike episteme in his Politikos where Gnostike episteme was also used to indicate one's aptitude.[citation needed] The terms do not appear to indicate any mystic, esoteric or hidden meaning in the works of Plato, but instead expressed a sort of higher intelligence and ability analogous to talent.[8] Plato The Statesman 258e —?Stranger: In this way, then, divide all science into two arts, calling the one practical (praktikos), and the other purely intellectual (gnostikos). Younger Socrates: Let us assume that all science is one and that these are its two forms.[9] In the Hellenistic era the term became associated with the mystery cults. Gnosis is used throughout Greek philosophy as a technical term for experience knowledge (see gnosiology) in contrast to theoretical knowledge or epistemology.[citation needed] The term is also related to the study of knowledge retention or memory (see also cognition), in relation to ontic or ontological, which is how something actually is rather than how something is captured (abstraction) and stored (memory) in the mind.[citation needed] Gnosticism Irenaeus used the phrase "knowledge falsely so-called" (pseudonymos gnosis, from 1 Timothy 6:20)[10] for the title of his book On the Detection and Overthrow of False Knowledge, that contains the adjective gnostikos, which is the source for the 17th-century English term "Gnosticism".
Such words refer to a common, important phenomenon, which we have to reckon with in philosophising about it, i.e. in epistemology. First, without a knowing subject willing to accept and act on a claim, we are not dealing with knowing or knowledge. Without reasonable and responsible grounds, one is not warranted to accept a claim or perception etc as credibly true (and reliable), but that warrant needs not be wholly held by a given subject; we all routinely accept warrant per credible authority and/or perhaps simplified explanation or examples. Likewise, warrant chains as A as B, B as C etc. Thus, there is a regress, where infinite chain is impossible, question-begging circularity is futile, so we face finitely remote first plausibles taken as a credible start-point or foundation or root of one's worldview. Yes, there is a positive hatred for the suggestions that we have a finitely remote foundation involving trust in first plausibles but that is actually patent. And, worldviews need not be question-begging once held i/l/o comparative difficulties across factual adequacy, coherence and balanced explanatory power (elegantly simple not simplistic or an ad hoc patchwork). In such, key self-evident elements starting with the point that distinct identity (A vs ~ A) leads directly to the triple first principles of right reason, LOI, LNC, LEM as well as to the set of natural numbers thence the logic of structure and quantity, AKA Mathematics. Self-evident truths are examples, in turn, of strong-form knowledge, warranted as certainly true and thus accepted as undeniable on pain of absurdity on the attempted denial. Thus, warrant is an integral component of knowledge, which is a function of knowing subjects. And, science is a weak form, with facts of observation being far better warranted than integrative theoretical constructs, which are best understood as explanatory, abductively warranted models which are possibly true as opposed to credibly true. Thus, while information can and does play a role in fundamental physics -- e.g. the position-momentum and energy-time versions of the Heisenberg-Einstein uncertainty principle -- that is not where it is primarily founded. Information theory is an extension of physics indeed, but that in the end is about distinct identity leading to designation of entities by labels tracing to y/n chains in structured description languages, or to analogues that then face issues of storage, processing, modulation, transmission etc. Information is not knowledge but is involved in the process. And, the reality of phenomena in the world is not reducible to information without residue. That is, there is a real world. Now, let's pick up and do some inline commenting on your un-sourced text gobbet. Of course on track record you will studiously ignore or find some tangent to divert, but record is needed:
>>2.5 What is the initial state? The prevailing conception regards the initial state of the physical world as a fundamental part of its constitution, and we therefore hope and expect that state to be specified by some fundamental, elegant law of physics.>> 1 --> Cosmology, and the hoping for some super-law to lock up the initial condition simply points onward to the source of such fine-tuning to set up a world habitable by C-chem, aqueous medium, cell based life. 2 --> This materialistic focus neglects that just to do physical cosmology we need responsible, rationally free morally governed creatures accountable before truth and logic, ethics etc. 3 --> This moves us beyond physics and shows that physics is inherently not the root of a rational understanding of our world and its inhabitants. It studies an important cross-section: matter-energy, space-time and interactions thereof, in a fundamental manner involving mathematics and logic as well as observation and measurement. 4 --> Where Mathematics is NOT an empirical discipline but a logical one rooted in distinct identity, first principles of right reason and the endless set of the naturals, duly extended into other structures of interest and where possible axiomatised. Computing is an applied branch. 5 --> So, we correct in brief an impoverished, factually grossly inadequate worldview. >> But at present there are no exact theories of what the initial state was. Thermodynamics suggests that it was a ‘zero-entropy state’, but as I said, we have no exact theory of what that means. Cosmology suggests that it was homogeneous and isotropic, but whether the observed inhomogeneities (such as galaxies) could have evolved from quantum fluctuations in a homogeneous initial state is controversial.>> 6 --> Physics, including physical cosmology is incomplete. >> In the constructor-theoretic conception, the initial state is not fundamental. It is an emergent consequence of the fundamental truths that laws of physics specify, namely which tasks are or are not possible.>> 7 --> fundamentals-phobia, or more precisely, an irrational fear of recognising worldview structures, warrant chains i/l/o our finitude and proneness to error. 8 --> Fundamental, warranted credible truth is a way to describe knowledge in the relevant weak form without admitting that this is what one is doing. 9 --> Fundamental, of course is precisely the much despised metaphor of foundations in another guise, as would be basics. You can run but you cannot hide. >> For example, given a set of laws of motion, what exactly is implied about the initial state by the practical feasibility of building (good approximations to) a universal computer several billion years later may be inelegant and intractably complex to state explicitly,>> 10 --> Sneaking in by the back-door the idea that the cosmos is something like a Turing universal computational device. 11 --> Computing the states of a cosmos is so far beyond the complexity of its physical instantiation as to be implausible. Indeed, as computation is envisioned on a material substrate, we have here an emerging regress of computing the computing entity that computes the physical cosmos. 12 --> But perhaps, what is meant is, the existing cosmos is computational in the sense of obeying a coherent set of physical laws that in effect can be compressed into a description in some language and called "physics." 13 --> This then becomes little more than a pretentious way of saying that we live in an orderly, organised cosmos that unfolds across time per initial constituents, conditions and laws that can be empirically, inductively identified. 14 --> What is valid, then, is not new, and what is novel is either unnecessary or plain wrong and confusing as it obfuscates what should be plainly said. >> yet may follow logically from elegant constructor-theoretic laws about information and computation (see Sections 2.6 and 2.8 below).>> 15 --> More of the same mish-mash. >>The intuitive appeal of the prevailing conception may be nothing more than a legacy from an earlier era of philosophy: First, the idea that the initial state is fundamental corresponds to the ancient idea of divine creation happening at the beginning of time.>> 16 --> Dismissiveness towards the concept that that which begins is contingent and has a cause. 17 --> Similar dismissiveness towards the point that an initial framework that triggers onward unfolding is patently of fundamental character. >> And second, the idea that the initial state might be a logical consequence of anything deeper raises a spectre of teleological explanation, which is anathema because it resembles explanation through divine intentions.>> 18 --> Little more than anti-theism surfacing by way of reassurance to a presumed atheistical audience. 19 --> If a cosmos has a beginning and is shaped by coherent, fine tuned laws and circumstances conducive to C-Chem, aqueous medium, terrestrial planet, cell based life, that points to intelligent design at the hands of a designer of awesome power. 20 --> So, we come to motive: anti-theism, leading to unwillingness to objectively examine the evidence of cosmological fine tuning and that of a cosmos that credibly had a beginning at a finitely removed time. 21 --> Where, refusal to engage the phenomenon of physics being done by creatures who are physically embodied but responsibly and rationally free and morally governed in reasoning towards the truth about our world allows evasion of the IS-OUGHT gap and the gap between mechanical computation on blind cause-effect mechanisms and ground-consequent, consciously insightful reasoning. 22 --> Those two gaps point beyond the world of matter, energy, space and time shaped by mechanical necessity and stochastic processes to yet deeper issues tied to world-roots. 23 --> Post Hume, the only level where IS and OUGHT can be bridged coherently is the root of reality. 24 --> This points to the only serious candidate, after centuries of philosophical debates, given the nature of being:
the inherently good creator God, a necessary and maximally great being, worthy of loyalty and of the reasonable, responsible service of doing the good in accord with our evident nature.
25 --> If you doubt this, simply provide a coherent alternative: _____ . Predictably, objectors will not do so, as they will find it an insuperable task. 26 --> That mind transcends computing is also pivotal, as we have forgotten that computers of various architectures are mindless mechanical, GIGO limited products of minds, that may well mechanise aspects of reasoning to solve problems, but which are in the end not capable of insightful, responsible, reasonable inference on ground and consequent. Such machines have to be set up right to work, by those capable of reasoning. 27 --> So, the great evasion has failed on all counts. >> But neither of those (somewhat contradictory) considerations>> 28 --> Projection, not well founded. The contradictions perceived are patently little more than reflections of the inner incoherence of the scheme of thought being propounded, and likely of an underlying commitment to a priori evolutionary materialism or one of its fellow travellers that by accommodating that, pick up its incoherence. >> could be a substantive objection to a fruitful constructor theory, if one could be developed. >> 29 --> In short, there is no such established theory, just a cluster of incoherent ideas as in part corrected in this note.
For record. KFkairosfocus_{December 10, 2017
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Is this related to the discussed topic? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383835/#!po=0.641026 https://academic.oup.com/nar/article/45/3/1059/2605964Dionisio_{December 10, 2017
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.Dionisio_{December 10, 2017
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UB, That seems like an interesting paper, at least judging by the abstract. Thanks.Dionisio_{December 10, 2017
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Is this the kind of “quantum storage memory” you are talking about, CR?
http://science.sciencemag.org/content/357/6358/1392 Nanophotonic rare-earth quantum memory with optically controlled retrieval - Tian Zhong1 et al A rare-earth quantum memory The development of global quantum networks will require chip-scale optically addressable quantum memories for quantum state storage, manipulation, and state swapping. Zhong et al. fabricated a nanostructured photonic crystal cavity in a rare-earth-doped material to form a high-fidelity quantum memory (see the Perspective by Waks and Goldschmidt). The cavity enhanced the light-matter interaction, allowing quantum states to be stored and retrieved from the memory on demand. The high fidelity and small footprint of the device offer a powerful building block for a quantum information platform.
Upright BiPed_{December 9, 2017
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Still no example. I can look one up for you.Upright BiPed_{December 9, 2017
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The interchange between UB and CR is one of the most astonishing things I've seen in years. CR has failed to make the slightest dent in UB's argument; yet he continues to spill hundreds and hundreds of words into the combox, proving once again that he believes "typing" is a synonym for "arguing." By now the question is no longer about the science. The really intriguing question to me is the psychology behind CR's dissembling. No one believes his shtick, least of all him. But he persists. He is like that bunny in the battery commercial. It is truly astounding.Barry Arrington_{December 9, 2017
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@53 addendum https://www.youtube.com/embed/liFXYpdAZnQDionisio_{December 9, 2017
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@Origenes
in what sense does your theory attempt to explain the same phenomena, as pointed out by UB?
The constructor theory of information brings information into fundamental physics. Not only is this something that UB's "theory" does not do, it is something UB is opposed to, in principle. As I've said before in other threads, we're not going to get anywhere because we still don't agree on a definition of information at a fundamental physical level, or if it's even possible, in principle.critical rationalist_{December 9, 2017
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For some of us unfamiliar with the concepts and terminology used in this discussion: https://www.youtube.com/embed/DH5kn1aT76cDionisio_{December 9, 2017
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UB @51: Of course!Dionisio_{December 9, 2017
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Does this mean you don't have an example?Upright BiPed_{December 9, 2017
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But you haven’t refuted that how semantic memory works, have you? You haven’t refuted the description of genetic memory, have you?
I've referenced a theory of information that operates at a more fundamental level, which explains why symbols are possible in the first place. Constructor theory is even more fundamental than our most current fundamental physical theories: GR and QM. From this paper....
Constructor theory seeks to express all fundamental scientific theories in terms of a dichotomy between possible and impossible physical transformations – those that can be caused to happen and those that cannot. This is a departure from the prevailing conception of fundamental physics which is to predict what will happen from initial conditions and laws of motion. [...] However, the constructor theory that I shall propose in this paper is not primarily the theory of constructions or constructors, as the prevailing conception would require it to be. It is the theory of which transformations input state of substrates -> output state of substrates (2) can be caused and which cannot, and why. As I shall explain, the idea is that the fundamental questions of physics can all be expressed in terms of those issues, and that the answers do not depend on what the constructor is, so it can be abstracted away, leaving transformations (2) as the basic subject matter of the theory. I shall argue that we should expect such a theory to constitute a fundamental branch of physics with new, universal laws, and to provide a powerful new language for expressing other theories. I shall guess what some of those laws may be, and explore the theory’s potential for solving various problems and achieving various unifications between disparate branches of physics and beyond, and propose a notation that may be useful in developing it. [...] Explanatory theories with such counterfactual implications are more fundamental than predictions of what will happen. For example, consider the difference between saying that a purported perpetual motion machine cannot be made to work as claimed ‘because that would violate a conservation law’ and that it won’t work ‘because that axle exerts too small a torque on the wheel’. Both explanations are true, but the former rules out much more, and an inventor who understood only the latter might waste much more time trying to cause the transformation in question by modifying the machine. [..] The theory of relativity is the theory of the arena (spacetime) in which all physical processes take place. Thus, by its explanatory structure, it claims to underlie all other scientific theories, known and unknown, in that requires them to be expressible in terms of tensor fields on spacetime, and constrains what they can say about the motion of those fields. For example, any theory postulating a new particle that was unaffected by gravity (i.e. by the curvature of spacetime) would contradict the general theory of relativity. Another theory that inherently claims to underlie all others is quantum theory, which requires all observable quantities to be expressible in terms of quantum-mechanical operators obeying certain commutation laws. And so, for example, no theory claiming that some physical variable and its time derivative are simultaneously measurable with arbitrary accuracy can be consistent with quantum theory. Constructor theory would, in this sense, underlie all other theories including relativity and quantum theory. The logic of the relationship would be as follows: Other theories specify what substrates and tasks exist, and provide the multiplication tables for serial and parallel composition of tasks, and state that some of the tasks are impossible, and explain why. Constructor theory provides a unifying formalism in which other theories can do this, and its principles constrain their laws, and in particular, require certain types of task to be possible. I shall call all scientific theories other than constructor theory subsidiary theories.
In addition, in constructor theory, neither reductionist and emergent explanations are more important than another. Nor is it concerned with trying to justify theories as initial conditions are often untraceable and uninteresting in respect to solving problems, in practice.
2.5 What is the initial state? The prevailing conception regards the initial state of the physical world as a fundamental part of its constitution, and we therefore hope and expect that state to be specified by some fundamental, elegant law of physics. But at present there are no exact theories of what the initial state was. Thermodynamics suggests that it was a ‘zero-entropy state’, but as I said, we have no exact theory of what that means. Cosmology suggests that it was homogeneous and isotropic, but whether the observed inhomogeneities (such as galaxies) could have evolved from quantum fluctuations in a homogeneous initial state is controversial. In the constructor-theoretic conception, the initial state is not fundamental. It is an emergent consequence of the fundamental truths that laws of physics specify, namely which tasks are or are not possible. For example, given a set of laws of motion, what exactly is implied about the initial state by the practical feasibility of building (good approximations to) a universal computer several billion years later may be inelegant and intractably complex to state explicitly, yet may follow logically from elegant constructor-theoretic laws about information and computation (see Sections 2.6 and 2.8 below). The intuitive appeal of the prevailing conception may be nothing more than a legacy from an earlier era of philosophy: First, the idea that the initial state is fundamental corresponds to the ancient idea of divine creation happening at the beginning of time. And second, the idea that the initial state might be a logical consequence of anything deeper raises a spectre of teleological explanation, which is anathema because it resembles explanation through divine intentions. But neither of those (somewhat contradictory) considerations could be a substantive objection to a fruitful constructor theory, if one could be developed.
IOW, constructor theory formalizes the view that, in science, justification isn't possible or even desirable and brings emergent phenomena, such as information, into fundamental physics, though the use of exact statements about what transformations are possible, which transformations are impossible and why. IOW, the idea that we need to "ground" our theories in some initial conditions is explicitly not part of constructor theory or its subsidiary theories.critical rationalist_{December 9, 2017
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CR: We can explain information in a more fundamental way that doesn’t require a knowing subject, etc.
"More fundamental" is incoherent when you cannot explain the semiotic system on which it depends.Origenes_{December 9, 2017
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@UB. Again, what you just descried is compatible with "the literature" just as what is required to launch a rocket into space is compatible with the literature of Newtown's laws. So what? I'm saying is that what “the literature" that you seem to be appealing to doesn't scale. We can explain information in a more fundamental way that doesn’t require a knowing subject, etc. Now, If you'd like to dispute that, be my guest. However, this seems unlikely as, despite asking at least a dozen times, you have still yet to reference an actual physical theory of information. For example, when I pointed out your site links to Shannon's theory, and that doesn't scale, you seemed to imply it wasn't even relevant to the problem at hand. It’s unclear how you could depute the status of a theory you refuse to disclose. So, where is the literature for your physical theory of information? Put your money where your mouth is. Here's a hint. Merely saying parts of the genome / translation system could be interpreted as symbols isn't a formal physical theory of information. For example, it doesn’t address, in a more fundamental way, what tasks are necessary for people to exploit the laws of physics that make symbols possible. Nor does it address what tasks must be physically possible to copy information from one medium to another. After all, that’s what ID claims, right? A designer copied information from one physical source medium external to the cell to a second physical destination medium internal to the cell. Or did I get it wrong?critical rationalist_{December 9, 2017
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CR, When you say you are referring to "quantum storage memory" in your comments here, why don't you give us an example of this system? Give us a specific example.Upright BiPed_{December 9, 2017
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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.
But you haven't refuted that how semantic memory works, have you? You haven't refuted the description of genetic memory, have you? What you've done (in an effort to plaster over the failure of your claims in the OP) is to claim that the observations of semantic memory in the gene system do not scale to quantum memory. But you have two problems that you fail to address: #1) the cell describes itself in a system of semantic memory, not quantum memory; and #2, this ...
Question #5 When you avoid the genetic information system by dissembling about quantum information, you say “I am referring to quantum storage mediums”. Okay. If a researcher uses quantum memory to store a simulation for, say a cure for cancer, he or she will (depending on the system) use various techniques to set the superposition state of the medium (i.e. the nuclei of a particular atom, for instance), thus encoding the qubits of memory. Is the state of a qubit of memory a cure for cancer, or is it about a cure for cancer, and thus, has to be interpreted?
Upright BiPed_{December 9, 2017
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CR Newton held that gravity is a force and GR informs us that it is something that arises from the curvature of space and time. What we see here is that both theories make an effort to explain the same thing: gravity. GR could not replace Newton’s theory of gravity if it were differently, because it would have no replacement to offer. This brings us to your discussion with UB. The question is: in what sense does your theory attempt to explain the same phenomena, as pointed out by UB?Origenes_{December 9, 2017
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CR your cite (alternate pathway) does not answer the question posed, so I'll try again: 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?Upright BiPed_{December 9, 2017
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