Bob Marks Knocks it Out of the Park on AI

_{Barry Arrington

February 26, 2023

Intelligent Design}

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This is a great discussion about whether AI (1) is currently sentient and (2) can, in principle, be sentient. All three panelists agree that it not currently sentient. It is 2 to 1 on whether it can, in principle, be sentient. As you might expect, how the materialists reach their conclusion follows more from metaphysical commitments than evidence. Max and Melanie (the materialists) see no reason why, in principle, computers cannot in the future be conscious. Why not? they ask, we are all just material stuff. And if you agree with their metaphysical premises, that is an unanswerable question. Max, especially is committed to this view and thinks we should be more humble. He is so blinkered by his commitment to materialism that it does not seem to occur to him that there can be any possible reason to think machines cannot be conscious other than arrogance.

Bob is a dualist and reaches the opposite conclusion, and he gives some excellent reasons to question materialist premises. I commend this excellent discussion to you.

BTW, Bob Marks really knows his stuff, and he presents his arguments in a very winsome fashion. We should all follow his example.

Comments

To save folks having to hunt for the link to Nick Lane's video, here it is again: https://youtu.be/NxGZzcx4GF4 Eta, for the time-challenged, skip to 45 minutes in to learn about his latest experiments and the biochemistry behind them.Alan Fox_{March 13, 2023
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It’s a mystery...
Indeed. There are many questions with no answer. ...but see [link] Well, I'm comfortable with accepting we don't have answers. So we must agree to disagree whether any of the current religious explanations have merit.Alan Fox_{March 13, 2023
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At what point does the unnatural or supernatural interpose? By what method?
It’s a mystery but see https://uncommondescent.com/intelligent-design/is-there-a-center-of-the-universe/#comment-777596
Do the laws of the Universe remain intact?
Obviously true. For these laws to change, would be highly suspicious. Aside: I maintain uncertainty is a design feature. Without it existence would be meaningless. So one cannot point to it as a reason for certain types of conclusions. The basis for all ID conclusions is the fine tuning of the universe and our solar system.jerry_{March 13, 2023
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KF, your 378 continues to ignore my point that things can change in four billion years.Alan Fox_{March 13, 2023
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Jerry
Both logic and evidence point to natural means as an extremely unlikely to impossible explanation.
(Assuming for the moment that default to ID wins over an unexplained phenomenon) then where is the interface? At what point does the unnatural or supernatural interpose? By what method? Do the laws of the Universe remain intact?Alan Fox_{March 13, 2023
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AF, projection and doubling down. You have yet to properly acknowledge the force of the Nature article excerpted at 297. Next, anyone may speculate on earlier stages, unobserved and without proper empirical basis. This is plain. Protein synthesis is observably a complex cellular process, involving DNA, RNA and proteins (including enzymes). Ribosomes, as NC machines, use codes in mRNA with appropriately loaded tRNAs to build protein chains. All of this process involves proteins, and the ribosome is a blended RNA-protein structure, so recognised as like this across the kingdoms of life. Given especially complex codes and algorithms using the codes, as recognised generally, we have excellent reason to infer design with adaptation to particular purpose and setting. Your continued refusal to recognise the consensus that code is involved, is a back handed admission of its force. KFkairosfocus_{March 13, 2023
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The point you keep avoiding is things change. Everything that is is not as it has always been
To some extent true but one has no idea of how much has changed and then more importantly how the change happened. Anyone who says they know “how much” and “how” is obviously wrong. There is the fossil record to indicate new life appearances. One has to use logic and evidence to support their beliefs. Both logic and evidence point to natural means as an extremely unlikely to impossible explanation. Until evidence and logic appear, these are just assertions.jerry_{March 13, 2023
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...it is the loading of tRNA that is the point of actual encoding...
Yes, that is not in dispute by me. I may have already said that how things are is not how things have always been.Alan Fox_{March 13, 2023
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...involves proteins.
It does now, though not centrally. The point you keep avoiding is things change. Everything that is is not as it has always been.Alan Fox_{March 13, 2023
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AF, irrelevant and I am sure you know the evidentiary force of admission by one who disagrees. Yockey's adaptation of the Shannon t/com system diagram clearly shows that he understood that it is the loading of tRNA that is the point of actual encoding. An in common CCA tool tip is loaded with the particular aa, based on a loading enzyme recognising the conformation of the tRNA; the CCA chain is in common. KF PS, Kindly see https://uncommondescent.com/darwinist-debaterhetorical-tactics/protein-synthesis-what-frequent-objector-af-cannot-acknowledge/kairosfocus_{March 13, 2023
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In humans, the 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code.
I already mentioned the interesting point that aas can have up to six codons attributed to them. How can one aaaRS assign the same aa to up to six tRNAs? It must involve recognition of the physical correspondence between aaRS and tRNA other than the codons. Explanation?Alan Fox_{March 13, 2023
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AF, the just so tale continues. The whole protein synthesis process from Ribosome structure to how elongation is assisted to how tRNAs are loaded, involves proteins. Thus, that is what is actually empirically warranted, various just so stories notwithstanding. Meanwhile, the studious ignoring of warranted correction from 297 continues to be side stepped. The rhetorical pattern tells us all we need to know. KFkairosfocus_{March 13, 2023
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...pointed out by Yockey...
Hubert Yockey was no ID proponent.Alan Fox_{March 13, 2023
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PPPS, Wikipedia continues its confessions, here on tRNA:
While the specific nucleotide sequence of an mRNA specifies which amino acids are incorporated into the protein product of the gene from which the mRNA is transcribed, the role of tRNA is to specify which sequence from the genetic code corresponds to which amino acid.[4] The mRNA encodes a protein as a series of contiguous codons [--> i.e. coded, algorithmic, string structure, with start, elongate and stop codons . . . and this last word is itself a clue], each of which is recognized by a particular tRNA. One end of the tRNA matches the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three complementary base pairs with a codon in mRNA during protein biosynthesis. [--> the end that couples to the mRNA base triplet, with the opposite end having been loaded in its common CCA tool tip with an appropriate aa, see the diagram there on secondary, cloverleaf structure https://en.wikipedia.org/wiki/Transfer_RNA#/media/File:TRNA-Phe_yeast_en.svg ] On the other end of the tRNA [--> so, not determined by the anticodon, it is a common CCA tool tip, loaded separately by an enzyme, a protein, cf following] is a covalent attachment to the amino acid that corresponds to the anticodon sequence. Each type of tRNA molecule can be attached to only one type of amino acid [--> not, determined chemically, it is set by how it is loaded, CCA is a common tool tip], so each organism has many types of tRNA. Because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing different anticodons which carry the same amino acid. [--> another sign of the contingency involved in a code process] The covalent attachment to the tRNA 3’ end is catalysed by enzymes called aminoacyl tRNA synthetases. [--> the loading enzymes, cf following, of course, a protein, and the ribosome itself contains proteins as part of its structure] During protein synthesis, tRNAs with attached amino acids are delivered to the ribosome by proteins called elongation factors [--> so, a post-protein process], which aid in association of the tRNA with the ribosome, synthesis of the new polypeptide, and translocation (movement) of the ribosome along the mRNA. If the tRNA's anticodon matches the mRNA, another tRNA already bound to the ribosome transfers the growing polypeptide chain from its 3’ end to the amino acid attached to the 3’ end of the newly delivered tRNA, a reaction catalysed by the ribosome.
Now, for loading, pointed out by Yockey as the point of actual encoding, as can also be seen from the common CCA tool tip used on the other end of the tRNA from the anticodon. Wiki's further confessions:
An aminoacyl-tRNA synthetase (aaRS or ARS) [--> notice, the aaRS abbreviation that appears above, e.g. with UB], also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its corresponding tRNA [--> the actual encoding step, notice, the common CCA tool tip is in play for attachment]. It does so by catalyzing the transesterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA [--> loaded tRNA]. In humans, the 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code. [--> given AF's rhetorical agenda, notice, CODE] This is sometimes called "charging" or "loading" the tRNA with an amino acid. [--> for fairly obvious reasons] Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing peptide, according to the genetic code. Aminoacyl tRNA therefore plays an important role in RNA translation, the expression of genes to create proteins.
If there had not been a zero concession rhetorical strategy used by AF, this would not be necessary. Sadly, it is. We have to recognise the negative credibility involved on the part of this objector.kairosfocus_{March 13, 2023
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@ KF For your information: Ribosomal RNAAlan Fox_{March 13, 2023
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A ribosome is an intercellular [sic] structure made of both RNA and protein...
You see ? ;) The active site is an RNA catalyst, a ribozyme. The protein chaperones are evolved additions.Alan Fox_{March 13, 2023
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@KF You make the same mistake that UB is locked into. You read popular accounts of cellular systems and metabolism, undeniably fascinating in their intricacy, and assume how things are is how they have always been. Your personal incredulity is likely an impossible barrier for you to overcome but I nevertheless suggest you have a glance at the video of Nick Lane's lecture I linked to upthread. It may give you an idea of the current state of research into origin of life and its early development.Alan Fox_{March 13, 2023
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PPS, note this, updated today: https://www.genome.gov/genetics-glossary/Ribosome
A ribosome is an intercellular [sic] structure made of both RNA and protein, and it is the site of protein synthesis in the cell. The ribosome reads the messenger RNA (mRNA) sequence and translates that genetic code into a specified string of amino acids, which grow into long chains that fold to form proteins.
kairosfocus_{March 13, 2023
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AF, question begging. The Ribosome is what it is, a cellular protein assembling machine, part of a protein synthesis process using ribosomes and proteins (including enzymes, esp. those that load tRNAs), it is not -- absent good empirical warrant (which your stretch to point to ribosomes tells us you do not have) -- itself evidence of a prior prior origin of life world based on RNA. "Imagine" is still a tell, pointing to yet another just-so story. Meanwhile, it is obvious that you are dodging away from the direct statement of a Nobel laureate as cited in 297 above, published in Nature as "Life's code script," on the presence of [complex!] coded information in the cell, in D/RNA. Of course, this echoes Lehninger and heirs, Crick and others, indeed the clear consensus. This is why you are now of negative credibility. KF PS, let us note Wikipedia's confessions:
The sequence of DNA that encodes the sequence of the amino acids in a protein [--> direct confession] is transcribed into a messenger RNA chain. Ribosomes bind to messenger RNAs and use their sequences for determining the correct sequence of amino acids to generate a given protein. Amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules [--> which are loaded on their common CCA tool tip, by loading enzymes, i.e. proteins, chicken and egg loops begin], which enter the ribosome and bind to the messenger RNA chain via an anti-codon stem loop. For each coding triplet (codon) in the messenger RNA, there is a unique transfer RNA that must have the exact anti-codon match, and carries the correct amino acid for incorporating into a growing polypeptide chain. [--> as loaded on its CCA tool tip] Once the protein is produced, it can then fold to produce a functional three-dimensional structure. A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein complex. [--> so, it is a post protein structure] Each ribosome is composed of small (30S) and large (50S) components, called subunits, which are bound to each other: (30S) has mainly a decoding function and is also bound to the mRNA (50S) has mainly a catalytic function and is also bound to the aminoacylated tRNAs. The synthesis of proteins from their building blocks takes place in four phases: initiation, elongation, termination [--> algorithmic, code using process], and recycling. The start codon in all mRNA molecules has the sequence AUG. The stop codon is one of UAA, UAG, or UGA; since there are no tRNA molecules that recognize these codons, the ribosome recognizes that translation is complete.[4] When a ribosome finishes reading an mRNA molecule, the two subunits separate and are usually broken up but can be re-used. Ribosomes are ribozymes, because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA.[5] Ribosomes are often associated with the intracellular membranes that make up the rough endoplasmic reticulum. Ribosomes from bacteria, archaea and eukaryotes in the three-domain system resemble each other to a remarkable degree, evidence of a common origin. [--> intended to be viewed as by materialistic evolution, but common design apart from ideological imposition is obviously possible, especially given algorithmic code, design with adaptation to task] They differ in their size, sequence, structure, and the ratio of protein to RNA. The differences in structure allow some antibiotics to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes unaffected. In all species, more than one ribosome may move along a single mRNA chain at one time (as a polysome), each "reading" a specific sequence and producing a corresponding protein molecule. The mitochondrial ribosomes of eukaryotic cells functionally resemble many features of those in bacteria, reflecting the likely evolutionary origin of mitochondria.[6][7] [--> notice, the ideological inference]
kairosfocus_{March 13, 2023
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@ UB Twelve years ago, I thought your point that the genetic code could not precede the protein synthesis metabolism and vice versa was problematic for evolutionary theory. Your preamble re Pattee and von Neumann was unnecessary to the salient point. But at the time Robert Shapiro had persuaded me to be skeptical of RNA World. Now, having re-evaluated and accepted RNA World as a plausible precursor, the idea of the genetic code and protein-synthesis system evolving subsequent to and as an adjunct to a ribozyme metabolism is at least logically possible, your argument does not apply.Alan Fox_{March 13, 2023
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UB: ,
1) The amino acids specified by the system are not determined by the physical properties of the RNA, they are determined by the physical properties of the protein aaRS.
Nick Lane has something to say about the specificity of aaRSs towards the end of the video I linked to above. He makes the point that high specificity can evolve from an earlier promiscuity both in precursor RNA World and as proteins become incorporated in metabolism. The arbitrariness of tRNA to the charged protein and the redundancy between 20 canonical amino-acids and 64 codons allows up to 6 alternative codons for some aa's. Yet one aaRS can recognize more than one tRNA with alternative codons for the same acid. How is this possible? Because punched tape and memory are not involved. It's templating. The physical shape of alternative tRNAs is what is relevant. Lane mentions too the way aas group by physical properties, how the codon grouping mirrors aa properties. He talks about the aliphatic sidechain grouping for example. The last ten minutes at least of his video are worth watching.Alan Fox_{March 13, 2023
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AF, you invite us to “Imagine,” patently as you cannot show.
Ribosomes are ribozymes. In that respect, RNA World is still with us. This is known.Alan Fox_{March 12, 2023
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AF, you invite us to "Imagine," patently as you cannot show. Meanwhile, you refuse to acknowledge what is well demonstrated. Telling. KFkairosfocus_{March 12, 2023
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F/N: Wiki confesses, on strings:
In computer programming, a string is traditionally a sequence of characters, either as a literal constant or as some kind of variable. The latter may allow its elements to be mutated and the length changed, or it may be fixed (after creation). A string is generally considered as a data type and is often implemented as an array data structure of bytes (or words) that stores a sequence of elements, typically characters, using some character encoding. String may also denote more general arrays or other sequence (or list) data types and structures. Depending on the programming language and precise data type used, a variable declared to be a string may either cause storage in memory to be statically allocated for a predetermined maximum length or employ dynamic allocation to allow it to hold a variable number of elements. When a string appears literally in source code, it is known as a string literal or an anonymous string.[1] In formal languages, which are used in mathematical logic and theoretical computer science, a string is a finite sequence of symbols that are chosen from a set called an alphabet.
This is in the end familiar as we routinely use ascii coded text. KFkairosfocus_{March 12, 2023
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KF, imagine RNA World as a precursor to what we see today. The crucial difference, no codons. I know you can't grasp this but there we are.Alan Fox_{March 12, 2023
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AF, you obviously -- and sadly, predictably -- failed to recognise the substantial points as cited for the benefits of those not able.willing to see and acknowledge that DNA acts as a string of four state elements
| x0 | x1 | x2 | . . . | xn | where, each xj = A/G/C/T, ie four contingent possibilities that may be chained in any order.
As was pointed out months ago, DNA has in fact been used to store arbitrary information, now including "In June 2019, scientists reported that all 16 GB of text from Wikipedia’s English-language version had been encoded into synthetic DNA." It is actually now being proposed, "DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency." Notwithstanding, it is obvious that you have refused, not only to engage the direct evidence but also the substantial remarks on the table from eminent sources, as has again happened above. The net effect of such denialism, is that you have made yourself of negative credibility, one who can be used as an index of truth by looking for what they hotly deny or reluctantly concede. A sad state. KF PS, to exemplify: https://www.cnet.com/tech/computing/startup-packs-all-16gb-wikipedia-onto-dna-strands-demonstrate-new-storage-tech/
the next storage technology might use an approach as old as life on earth: DNA. Startup Catalog announced Friday it's crammed all of the text of Wikipedia's English-language version onto the same genetic molecules our own bodies use. It accomplished the feat with its first DNA writer, a machine that would fit easily in your house if you first got rid of your refrigerator, oven and some counter space. And although it's not likely to push aside your phone's flash memory chips anytime soon, the company believes it's useful already to some customers who need to archive data. DNA strands are tiny and tricky to manage, but the biological molecules can store other data than the genes that govern how a cell becomes a pea plant or chimpanzee. Catalog uses prefabricated synthetic DNA strands that are shorter than human DNA, but uses a lot more of them so it can store much more data. Relying on DNA instead of the latest high-tech miniaturization might sound like a step backward. But DNA is compact, chemically stable -- and given that it's the foundation of the Earth's biology, it's arguably not as likely to become as obsolete as the spinning magnetized platters of hard drives or CDs that are disappearing today . . .
Of course, they re-interpreted the patterns of the strings from the genetic code framework to another scheme. But that is the point of a storage architecture, elements and patterns of elements are arbitrarily assignable on a convention, leading to codes, record, algorithms as encoded etc. The family of naturally occurring dialects [I gather there are about two dozen variants, most notably the mitochondrial code] of the genetic code, shows that arbitrariness. Similarly, the string structure is obvious and chained instructions, START (load methionine), load aa2, load aa3, . . . STOP, exhibit algorithms used by ribosomes to create AA chains for proteins. None of this is particularly controversial, save to certain of UD's penumbra of objectors, utterly unwilling to acknowledge well founded facts because they know the significance of finding and recognising complex digital information processing in life, i.e. language in action using deep knowledge of polymer chemistry. Namely, a blatant sign of design. So, we are seeing a gaslighting effort. Sad, sadly telling. Indeed, a backhanded negative credibility admission.kairosfocus_{March 12, 2023
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Now, FYI, punched paper tape, punched cards, computer reel to reel tape, and DNA* are all known, established information storage devices, memory in the computational sense. KF
* my emphasis. Nope. DNA is not any of those things. It's a molecule with some amazing and very useful properties, above all the property of self-replication under the right conditions.Alan Fox_{March 12, 2023
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You wrote this sentence in an attempt to conceal what you were having to agree to.
This is particularly odd, given that agreeing to “that” isn’t onerous. Specifically, I'd suggest that this reflects an attempt to conceal a more fundamental way of characterizing biological replicators.
The amino acids specified by the system are not determined by the physical properties of the RNA, they are determined by the physical properties of the protein aaRS.
And these proteins are determined by what? 37 physical genes in human beings. For example, to date there are 56 human genetic diseases caused by mutations in aaRS genes, of various severity and heredity. Also, here’s a paper that suggests “the 20 human tRNA synthetases acquired new architectures to expand their functions during evolution.”
The new features are associated with novel, appended domains that are absent in prokaryotes and retained by their many splice variants. Alanyl-tRNA synthetase (AlaRS) is the single example that has a prototypical appended domain—C-Ala—even in prokaryotes, which is spliced out in humans. X-ray structural, small-angle X-ray scattering, and functional analysis showed that human C-Ala lost its prokaryotic tRNA functional role and instead was reshaped into a nuclear DNA-binding protein. Thus, we report another paradigm for tRNA synthetase acquisition of a novel function, namely, repurposing a preexisting domain rather than addition of a new one. […] Crystal structures of two forms of human C-Ala, and small-angle X-ray scattering of AlaRS, showed that the large sequence divergence of human C-Ala reshaped C-Ala in a way that changed the global architecture of AlaRS. This reshaping removes the role of C-Ala in prokaryotes for docking tRNA and instead repurposes it to form a dimer interface presenting a DNA-binding groove. This groove cannot form with the bacterial ortholog. Direct DNA binding by human C-Ala, but not by bacterial C-Ala, was demonstrated. Thus, instead of acquiring a novel appended domain like other human aaRSs, which engendered novel functions, a new AlaRS architecture was created by diversifying a preexisting appended domain.

2) The aaRS are the necessary constraints in the system, physically establishing the RNA as an inactive medium, and the codon as a token of memory.
Inactive in what sense? If RNA changes, protein synthesis changes. And changes in proteins results in, well, changes in the features of organisms. So, considering RNA an “inactive medium” seems rather arbitrary.
A codon of RNA serves only as an token, where the spatial arrangement of bases within the codon are used to distinguish one referent from another.
Yet, there are very specific physical tasks that must be possible, while others that must be impossible, for RNA to “be” a token.
4) The specification of an amino acid from a codon is therefore discontinuous.
It’s mediated by other knowledge laden genes. As I’ve pointed out before, this can be unified in the sense that knowledge is information that plays a causal role in being retained when embedded in a storage medium, which is scale independent.
5) And the relationship between codon and amino acid is physically established by memory, just as predicted. (Turing, Von Neumann, Crick, highlighted by Brenner).
An accurate self-reproducer consists of a “vehicle” and a replicator, and its self-reproduction occurs by copying the replicator and re-constructing the vehicle afresh. This “replicator-vehicle” logic can be reformulated in terms of a constructor theory network of physically possible and impossible constructor tasks. Constructor theory quite literally represents a generalization that ranges from simple catalysts to the quantum theory of computation. It’s more fundamental in that it underlies all physical theories including general relativity and quantum mechanics. For example, some physicists suggest biological replicators operate at such high accuracy that the design of replicators must have already existed in the laws of physics at the outset. From the paper....
In the biosphere self-reproduction is approximated to various accuracies. There are many poor approximations to self-reproducers - e.g., crude replicators such as crystals, short RNA strands and autocatalytic cycles involved in the origin of life [11]. Being so inaccurate, they do not require any further explanation under no-design laws: they do not have appearance of design, any more than simple inorganic catalysts do.(4) [...] In contrast, actual gene-replication is an impressively accurate physical transformation, albeit imperfect. 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].
This specific question is the focus of the constructor theory of life. As a new mode of explanation, constructor theory allows expressing the appearance of design, information, biological replicators, and even no-design laws of physics (laws that do not contain the design of replicators) exactly. For example, in regards to no-design laws….
Consequently I require no-design laws to satisfy these conditions: Generic resources can only perform a few tasks, only to a finite accuracy, called elementary tasks. These are physically simple and contain no design (of biological adaptations). Familiar examples are spontaneous, approximately self-correcting chemical reactions, such as molecules “snapping” into a catalysts regardless of any original small mismatch. No good approximation to a constructor for tasks that are non-elementary can ever be produced by generic resources acting on generic resources only. Under no-design laws, the generic resources and the interactions available in nature are allowed to contain only those approximate constructors that unequivocally do not have the design of those very adaptations the theory of evolution is required to explain.(7) Examples of laws that would violate these conditions are: laws including accurate constructors, such as bacteria, in the generic resources; laws with “copy-like” interactions, designed to copy the configuration of atoms of a bacterium onto generic resources; laws permitting spontaneous generation of a bacterium directly from generic resources only; laws permitting only mutations that are systematically directed to improvements in a certain environment. The exact characterization of no-design laws is a departure from the prevailing conception - which can at most characterize them as being typical, according to some measure, in the space of all laws. The latter is unsuitable for present purposes, as the choice of the measure is highly arbitrary. Moreover, it is misleading: some laws that may be untypical under some natural measure - such as the actual laws of physics, because of, say, local interactions - need not contain the design of biological adaptations, thus qualifying as no-design in this context. Furthermore, laws with the design of biological adaptations are a proper subset of those laws that in the context of anthropic fine tuning have been called “bio-friendly”: those having features - such as local interactions, or special values of the fine-structure constant, etc. - which, if slightly changed, would cause life as we know it to be impossible. These features, though necessary to life, are not specific to life: their variation would make impossible many other phenomena, non specifically related to biological adaptations.
With this defined, we can move on to characterizing accurate replicators. Which, BTW, covers the ground from the above list you seem to think needs to be accepted as, apparently, the only formulation. (Fortunately, we’re not limited to the current connection of physics, regardless of how convenient it might be to your position.)
A task T being possible means that for any given accuracy (short of perfection) the laws of physics permit an approximate constructor capable of performing the task to that accuracy.?Consider a possible, non elementary task T and an object F that can perform T to a high accuracy (8) ?. For instance, T could be the task of constructing a car from generic substrates and F a generalized car factory, including all the processes converting raw materials such as iron, etc., into a car. The approximate constructor F executes a procedure - a recipe - to perform the task T to accuracy ?. I will show that F must include a replicator and a programmable constructor; and that the recipe must have a hierarchical structure and be instantiated in the replicator. No-design laws contain no good constructor for T, such as F - neither in the elementary interactions, nor in the generic resources. Hence the recipe used by F to perform T must be decomposable into steps (not necessarily sequential) that are allowed by no-design laws. That is to say, sub-recipes - procedures to perform sub-tasks that are executed by sub-constructors contained in F. To avoid infinite regress, two conditions must be fulfilled. One is that the subtasks be non-specific to T. For instance, when T is the task of constructing a car, the subtasks are those of constructing sub-parts of the car - e.g., door handles, windows, etc. Hence, the constructor F must include two parts: One – which I call V – performs T blindly, i.e., subtask by subtask, and it is non-specific to T, because so are the subtasks. The rest of F – which I call P – is specific to T and instantiates the recipe for T: it specifies the sequence of the subtasks, thus controlling V. Hence F can be described as a programmable constructor, V , programmed with a program P having the same logic as the recipe: it has a modular structure P = (p1, p2, · · · , pN ) where each instruction pi takes values in an information variable and tells V which sub-task to perform, when, on the substrates(9). V is non-specific to T because it must also be capable of executing other programs - different combinations of the elementary units pi. For example, a car factory contains robots executing sub-recipes to construct the car’s doors. These robots contain sub-robots to construct handles, windows, etc., which could be used to construct other objects than cars. The other condition is obtained by applying the same reasoning recursively to the subtasks. If they, too, are non-elementary, they require a recipe that is decomposable into non-specific sub-recipes. The base for the recursion - for T to be performable to that particular accuracy - is provided by the elementary sub-recipes of the recipe for T being elementary tasks - which can be performed by (approximations to) constructors that are available in nature, as generic resources. Note that these elementary sub-tasks need not be specified in the recipe: they are implicit in the laws of physics. For instance, the elementary steps in the car recipe are tasks like, say, “oxidise the aluminium coating”, and occur simply by leaving the substrate exposed to air. Under no-design laws, any (approximation to a) constructor wears out after a finite time. Therefore F, to perform the task T to the accuracy ?, must undergo a process of maintenance, defined as one whereby a new instance of F - i.e., of P and V - is brought about, from generic materials, before the former one stops working. In the case of the car factory, this is achieved by replacing old subparts of the robots, assembly lines, etc. and by preserving the programs they run. To avoid an infinite regress, implementing the maintenance must not in turn require the recipe P for T. Also, the design of the recipe P cannot be in the laws of physics. Thus, the only other possibility is that the new instance of P is brought about by blind replication of the recipe P contained in the former instance - i.e., by replicating its subunits pi (that are non-specific to T). We conclude that, under no-design laws, the substrate instantiating the recipe is necessarily a modular replicator: a physical object that can be copied blindly, an elementary subunit at a time. In contrast, V - the non-specific component of F - is constructed anew from generic resources. Moreover, under no-design laws errors can occur: thus, to achieve high and improvable accuracy, the recipe must include error-correction. In the car factory, this includes, say, controlling the functionalities of the subcomponents (e.g., fine checks on the position of doors, wheels, etc.). Hence the recipe P must contain information about the task T, informing the criterion for error detection and correction. The information in the recipe is an abstract constructor that I shall call knowledge (without a knowing subject [26]). Knowledge has an exact characterization in constructor theory: it is information that can act as a constructor and cause itself to remain instantiated in physical substrates. Crucially, error-correcting the replication is necessary. Hence the subunits pi must assume values in a discrete (digital) information variable: one whose attributes are separated by non-allowed attributes. For, if all values in a continuum were allowed, error-correction would be logically impossible.
While it’s not targeted directed at intelligent design, it’s still quite relevant. Specifically, if the laws of physics do not need to contain the design of biological replicators, at the outset, its unclear why biological replicators would require their design to be present in some designer, at the outset, either.critical rationalist_{March 11, 2023
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AF, it's over, long since. Your inability to address well known facts speaks for itself. Statements such as have been cited only suffice to show just how far wrong you have been for months. Now, FYI, punched paper tape, punched cards, computer reel to reel tape, and DNA are all known, established information storage devices, memory in the computational sense. KF PS, again, Nature: https://www.nature.com/articles/s41467-021-22277-y
DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency. Previous studies have used artificially synthesized DNA to store data and automated next-generation sequencing to read it back. Here, we report digital Nucleic Acid Memory (dNAM) for applications that require a limited amount of data to have high information density, redundancy, and copy number. In dNAM, data is encoded by selecting combinations of single-stranded DNA with (1) or without (0) docking-site domains. When self-assembled with scaffold DNA, staple strands form DNA origami breadboards. Information encoded into the breadboards is read by monitoring the binding of fluorescent imager probes using DNA-PAINT super-resolution microscopy. To enhance data retention, a multi-layer error correction scheme that combines fountain and bi-level parity codes is used. As a prototype, fifteen origami encoded with ‘Data is in our DNA!\n’ are analyzed. Each origami encodes unique data-droplet, index, orientation, and error-correction information. The error-correction algorithms fully recover the message when individual docking sites, or entire origami, are missing. Unlike other approaches to DNA-based data storage, reading dNAM does not require sequencing. As such, it offers an additional path to explore the advantages and disadvantages of DNA as an emerging memory material.
Wikipedia confesses:
DNA digital data storage is the process of encoding and decoding binary data to and from synthesized strands of DNA.[1][2] While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently severely limited because of its high cost and very slow read and write times.[3] In June 2019, scientists reported that all 16 GB of text from Wikipedia's English-language version had been encoded into synthetic DNA.[4] In 2021, scientists reported that a custom DNA data writer had been developed that was capable of writing data into DNA at 18 Mbps.[5] Encoding methods Countless methods for encoding data in DNA are possible. The optimal methods are those that make economical use of DNA and protect against errors.[6] If the message DNA is intended to be stored for a long period of time, for example, 1,000 years, it is also helpful if the sequence is obviously artificial and the reading frame is easy to identify.[6]
This is a matter of repurposing DNA, as a natural storage device, DNA is pervasive in the cell. The zero concession denialism, of course, predictably, will continue.kairosfocus_{March 11, 2023
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@ UB For me the issue remains that you are attempting a version of the irreducible complexity argument for which the preamble about "memory" etc is utterly irrelevant. RNA World needs addressing. Have you confronted Nick Lane?Alan Fox_{March 11, 2023
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