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L&FP, 66: String — yes, s-t-r-i-n-g — data structures as key information storage arrays (thus the significance of DNA and mRNA)

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One of the more peculiar objections to the design inference is the strident, often repeated claim that the genetic code is not a code, and that DNA and mRNA are not storing algorithmic, coded information used in protein synthesis. These are tied to the string (yes, s-t-r-i-n-g) data structure, a key foundational array for information storage, transfer and application. So, it seems useful to address the string as a key first principles issue, with the onward point being that strings of course can and do store coded information.

Let us begin with, what a string — yes, s-t-r-i-n-g — is (though that should already be obvious from even the headline):

Wikipedia illustrates a string data structure

Geeks for Geeks: A string is a sequence of characters, often used to represent text. In programming, strings are a common data type and are used for a variety of tasks, such as representing names, addresses, and other types of information.

Wikipedia confesses: 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 . . . . A primary purpose of strings is to store human-readable text, like words and sentences. Strings are used to communicate information from a computer program to the user of the program. A program may also accept string input from its user. Further, strings may store data expressed as characters yet not intended for human reading . . . . Example strings and their purposes . . . Alphabetical data, like “AGATGCCGT” representing nucleic acid sequences of DNA . . .

So, it should not be surprising to see that DNA and RNA can store strings of information-bearing elements:

Where, of course, the genetic code is expressed in such strings. The (standard) code, mRNA form is:

The Genetic code uses three-letter codons to specify the sequence of AA’s in proteins, specifying start/stop, and using six bits per AA

For very simple example, HT Khan Academy:

The basic algorithmic process for protein synthesis [HT Khan, fair use edu]

Of course, the above is the mRNA form, which would be transcribed and edited to cut out introns, and it leaves out onward complexities. For example, we can see how Insulin has two strands of AA’s interconnected through di-sulphide bonds, making up a 51 AA protein:

The 51 aa, double chain protein, human insulin (fair use edu)

The end-product insulin protein is put together from the preproinsulin produced stepwise in the ribosome, by way of a clever alignment that uses a third, “scaffolding,” chain C sequence:

Assembling Insulin (fair use)

Using the code one could in principle back-translate to mRNA, however, in the DNA there are intervening Introns between the Exons expressed in the ribosome, so the human genome sequence is:

The underlying DNA sequence in the human genome (fair use)

So, as usual, we see how sophisticated life is at molecular level. That said, we also see that as a key stage of protein synthesis, as ribosomes, mRNA and tRNA interact (with a complex cast of supporting molecules) AA chains are assembled with start, elongate, stop, executing a code driven algorithm. Where, AmHD defines:

[Algorithm:] A finite set of unambiguous instructions that, given some set of initial conditions, can be performed in a prescribed sequence to achieve a certain goal and that has a recognizable set of end conditions.

Illustrating:

Step by step protein synthesis in action, in the ribosome, based on the sequence of codes in the mRNA control tape (Courtesy, Wikipedia and LadyofHats)

That should be enough to show the unbiased mind that coded algorithms are in the cell, and that DNA and mRNA act as string data structures. However, there are those who have proved resistant to such commonplace summaries or to citations from the sort of panels of experts who write major textbooks in biochemistry. For record, notwithstanding, here are Lehninger and heirs:

A page capture from Lehninger and heirs, Principles of Biochemistry, (fair use)

Lehninger and heirs go on to say, pp. 194 – 5:

Augmented citation from Lehninger and heirs, on mRNA in protein synthesis (fair use)

We may also now observe a Nobel Prize Laureate, Sydney Brenner, in his article, Life’s code script . . . yes, it’s that obvious, published in 2012 in the leading Science Journal, Nature:

[Brenner:] ” . . . The most interesting connection with biology, in my view, is in Turing’s most important paper: ‘On computable numbers with an application to the Entscheidungsproblem’5, published in 1936, when Turing was just 24.

Computable numbers are defined as those whose decimals are calculable by finite means. [–> that is, effectively, by algorithms] Turing introduced what became known as the Turing machine to formalize the computation. The abstract machine is provided with a tape [–> with marks on it], which it scans one square at a time, and it can write, erase or omit symbols. The scanner may alter its mechanical state, and it can ‘remember’ previously read symbols. Essentially, the system is a set of instructions written on the tape, which describes the machine. Turing also defined a universal Turing machine, which can carry out any computation for which an instruction set can be written — this is the origin of the digital computer. [–> there is also, a more powerful oracle machine, capable of one step decisions]

Turing’s ideas were carried further in the 1940s by mathematician and engineer John von Neumann, who conceived of a ‘constructor’ machine capable of assembling another according to a description. A universal constructor with its own description would build a machine like itself. To complete the task, the universal constructor needs to copy its description and insert the copy into the offspring machine. Von Neumann noted that if the copying machine made errors, these ‘mutations’ would provide inheritable changes in the progeny.

Arguably the best examples of Turing’s and von Neumann’s machines are to be found in biology. Nowhere else are there such complicated systems, in which every organism contains an internal description of itself. The concept of the gene as a symbolic representation of the organism — a code script — is a fundamental feature of the living world and must form the kernel of biological theory. [–> note, again, author, context and publisher]

Turing died in 1954, one year after the discovery of the double-helical structure of DNA by James Watson and Francis Crick, but before biology’s subsequent revolution. Neither he nor von Neumann had any direct effect on molecular biology, but their work allows us to discipline our thoughts about machines, both natural and artificial.

Turing invented the stored-program computer, and von Neumann showed that the description is separate from the universal constructor. [–> that ‘description’ of course is encoded] This is not trivial. Physicist Erwin Schrödinger confused the program and the constructor in his 1944 book What is Life?, in which he saw chromosomes as “architect’s plan and builder’s craft in one”. This is wrong. The code script contains only a description of the executive function, not the function itself.

That’s why Yockey adapted Shannon’s architectural diagram for communication systems:

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

So, we may freely understand that DNA and associated molecules such as mRNA express string data structures, store coded biological information, that such information as used in protein synthesis expresses algorithms, and that therefore we are dealing with computation and associated computer language in the course of protein synthesis.

We may quote a Wiki confession:

[Wiki confesses:] Since 2001, 40 non-natural amino acids have been added into proteins by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins.[22][23]

H. Murakami and M. Sisido extended some codons to have four and five bases. Steven A. Benner [–>another guy] constructed a functional 65th (in vivo) codon.[24]

In 2015 N. Budisa, D. Söll and co-workers reported the full substitution of all 20,899 tryptophan residues (UGG codons) with unnatural thienopyrrole-alanine in the genetic code of the bacterium Escherichia coli.[25]

In 2016 the first stable semisynthetic organism was created. It was a (single cell) bacterium with two synthetic bases (called X and Y). The bases survived cell division.[26][27]

In 2017, researchers in South Korea reported that they had engineered a mouse with an extended genetic code that can produce proteins with unnatural amino acids.[28]

In May 2019, researchers reported the creation of a new “Syn61” strain of the bacterium Escherichia coli. This strain has a fully synthetic genome that is refactored (all overlaps expanded), recoded (removing the use of three out of 64 codons completely), and further modified to remove the now unnecessary tRNAs and release factors. It is fully viable and grows 1.6× slower than its wild-type counterpart “MDS42”

Indeed, the function of DNA as an information storage entity is so well established, that as Wiki also confesses, it has been adapted to general archival storage:

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 [–> a lot longer than most of our digital storage media will likely last], it is also helpful if the sequence is obviously artificial and the reading frame is easy to identify.[6]

CNet gives details:

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 . . .

In short, they used a different encoding and have stored Wikipedia in DNA.

At this point, we need to ask, why is it that we have seen certain objectors from the penumbra of attack sites making strident, unyielding objections to understanding DNA and mRNA as string data structure information storage entities, part of a wider information processing, protein synthesis process in the cell?

The manifest answer is simple and sad: because such things point to design, which is being ideologically locked out at all costs.

So, it is time to recognise a key first fact about DNA and mRNA and let the chips lie where they fly. END

Comments
CR, refusal to acknowledge the evident and attempts to obfuscate functionally specific complex organisation and associated information underscore the unvelcome cogency of FSCO/I. KF
I'm confused. Are you saying we cannot make sense of out those characters in the context I provided? Or are we just somehow forced to consider it as being random? It seems that you're anti-design in this case. Are people not the best explanation?critical rationalist
April 10, 2023
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CR, refusal to acknowledge the evident and attempts to obfuscate functionally specific complex organisation and associated information underscore the unvelcome cogency of FSCO/I. KFkairosfocus
April 6, 2023
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5ovhea3tzari.udz n,dagk;kj
happens to reflect hitting keys on a QWERTY keyboard pressed without hitting the shift key. Again, it seems that a person would hit those keys given time, effort, etc as some kind of example of randomness.critical rationalist
April 6, 2023
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Yes, KF. Some strings are well adapted to serve a purpose, while other are not. They can be distinguished in this fundamental way. Your point? Infinite monkeys would eventually reproduce Shakespeare because there would be an infinity of time. But this isn't applicable to ID, as evolution is only random to any particular problem to solve. And the genomes of living things do not contain explanatory concepts like love, loyalty, rivalry, refer to other intelligent agents. etc. Only people can create explanations. So, this simply is a flawed analogy.critical rationalist
April 6, 2023
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CR, you know asasasas is a repettitive pattern, comparable to the repetitive unit cell order of a crystal explicable on mechanical necessity, which is of course not random. You know that random text of significant length 5ovhea3tzari.udz n,dagk;kj etc is overwhelmingly likely to be non functional gibberish without discernible overall pattern. You know functional text organised to communicate a message is distinct from both of these. That has long been documented, and the Wikipedia summary on Infinite Monkeys further tells us much by way of admission compelled by undeniable facts. So, you know that randomness, order and organisation can properly be distinguished. KFkairosfocus
April 6, 2023
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CR, if you cannot distinguish asasasasas from this is organised text and you refuse to recognise the difference between hello world and the linux OS as a matter of scale, you have instantly lost on the merits as of fifty years ago when Orgel penned those words.
I recognize it as being a special case of being well adapted to serve a purpose. Also, asasasasa happens to fit the first two keys where we put our fingers on a keyboard when touch typing. So, this seems to be likely something a person generated to for the purpose of some kind of example. It's not random.critical rationalist
April 5, 2023
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CR, if you cannot distinguish asasasasas from this is organised text and you refuse to recognise the difference between hello world and the linux OS as a matter of scale, you have instantly lost on the merits as of fifty years ago when Orgel penned those words. And frankly, I think you are putting up a hyperskeptical rhetorical pretence not to know, we both know better. That obstructionism tells us, backhanded concession on the merits. KFkairosfocus
April 3, 2023
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‘Organized’systems are to be carefully distinguished from ‘ordered’ systems.
This still overlaps. Only organized systems are well adapted to serve a purpose. Strings that are random, in they merely have some order, are adapted, but not well adapted. If you can swap one string's content with the content of some other random string and it has no impact on how well it serves purpose of, say, being the recipe of a bacterium, then it wasn't well adapted to serve that purpose in the first place. Both strings are both equally poorly adapted at serving that purpose. Their ability to serve that purpose does not get any worse. However, if a string that is well adapted to serve the purpose of being the recipe for a bacterium, then you cannot replace it with just any other string. Right? You cannot change it without causing a significant reduction in its ability to serve that purpose. If you could, then it's unclear how the string was actually playing the role of the recipe of a bacterium in the first place. Again, a rock can be used to tell time by using it as a sun dial. But it's not well adapted to serve that purpose. You could replace it with some other rock, or even some non-rock, like a stick, tree, even a person. The knowledge of how to tell time is in us, not the rock. However, this is not the case with the watch. It is well adapted to serve the purpose of telling time. You cannot vary it significantly without a corresponding reduction in its ability to tell time. Well, you could use a broken or operational watch, if it large enough, as a sundial, to tell time. But, again, the knowledge of how to do that is, in this case, is in us, not the watch.critical rationalist
March 29, 2023
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CR, First, real world things have to intervene, just back. I see:
if we replace one string with any other string, would that have no impact on the string serving the purpose of representing that information? Or will function will vanish? The entire argument how improbable it is that we would end up with a string that is well adapted to represent that information and result in that function. Other strings would not serve that purpose nearly as well. Right?
Obviously chance replacement of complex bit strings is likely to break function based on specific organisation, as we readily know from broken down machinery. Adaptation etc does not capture the specifically informational context on the table for fifty years now. K-complexity is an index of how much information, but of course the function is a matter of what is said in the description language statement E, which is normally quite sensitive to perturbation. Where, 367:
random strings have higher information content in terms of Kolmogorov-Chaitin complexity. So, it is more or less?
If one implicitly defines a random string as a single point target in a configuration space, of course it will have K-Complexity about equal to its length in bits, along with say bits to say print this following ______ END. In effect, lottery prize number. However, feed that into a 3-DP/C and the result for any string at least 500 - 1,000 bits will be gibberish. The information carrying capacity in bits is different from the specific functionality of the string. That functionality was well expressed by Wicken, 1979:
‘Organized’systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions and/or repetitive stepwise procedures] and therefore lack complexity, organized systems must be assembled element by element according to an [ --> originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]
This is actually the context of the abbreviation, FSCO/I. The blueprint or wiring diagram here is d(E).. Now, consider a string of 500 coins, to hold d(E). The configs from 000 . . . 0 to 111 . . . 1 have in them every possibility for 500 bits. So, all expressions in a description language will be there. However as that is 3.27*10^150, that is not practically searchable at blind strategies. This is why complex functionality is typically produced by intelligently directed configuration. In trillions of observed cases at or beyond this threshold, every time. This blind walk in a large search space approach then allows us to understand why that is. We are far beyond Paley and Cicero here. Where, well adapted just does not give enough to have these insights. For example, in the follow on thread, I take d(E) as expressing the cosmological physics of a cosmos and allow a random walk perturbation process. 3-DP/C then issues in effect virtual universes, and allows us to examine what results. As the fine tuning studies show, we are at a locally isolated functional point. Try perturbing d(E) for a fishing reel, or the like and we will soon enough see why islands of fine tuned function are real issues. And as Paley saw, adding self replication drastically compounds functional complexity. So, it reproduces does not escape the point. How do we get there. And more. KFkairosfocus
March 29, 2023
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CR, adaptation to serve a purpose does not give a way to see information content
Information content is not well adapted to serve a purpose? Huh? Are you saying that information content is not well adapted? How would that work?
Then, inject random changes in d(E) and observable sensitivity to perturbation would be an index of functional specificity of organisation. As a simple case try text strings in English as d(E) and a noisy, lossy transmission medium, giving d*(E). 3-DP/C can put out text strings on d*(E) but soon enough function will vanish as d(E) becomes gibberish.
Again, if we replace one string with any other string, would that have no impact on the string serving the purpose of representing that information? Or will function will vanish? The entire argument how improbable it is that we would end up with a string that is well adapted to represent that information and result in that function. Other strings would not serve that purpose nearly as well. Right? The argument is, some designer must have "specified" them in that very specific way. So, no. You still haven't given an example of ID that falls outside Paley's criteria of being well adapted to serve a purpose.critical rationalist
March 29, 2023
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CR, adaptation to serve a purpose does not give a way to see information content thence search challenge and why FSCO/I is a useful sign of design. I suggest you look at the 3-DP/C and K-Complexity where I = L[d(E)]. KFkairosfocus
March 29, 2023
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living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . .
This is not a counter example. IOW, they are well adapted to serve a purpose. The relevance of what you started out with, what your intentions were, how you want it to be used, etc. is unclear. Either it fits in the circle / criteria of being "well adapted to serve a purpose" or it does not. Right? See #367.
On the other hand, crystals are not well adapted to serve a purpose. They form spontaneously and lack a recipe that describes it, is used to construct new instances of it, etc. Complex but random structures, by definition, need hardly be specified at all . But, again, complex, random structures have a higher Kolmogorov-Chaitin complexity. They take more instructions to represent exactly. So, what gives? On the other hand, complex, random structures are not well adapted to serve a purpose. If truly random, in that you can replace them with some other random string in respect to some purpose, then you can vary them without a corresponding significant reduction in their ability to serve that purpose, Right? This fits the example of comparing a watch and a rock. The rock is not well adapted to serve the purpose of telling time. You can vary it significantly and it will play the role of a sundial just as well. In fact, you can replace it with something that is a non-rock, such as a stick, plant, etc. The knowledge of how to use a rock to tell time is in us, not the rock. This is in contrast to the case of the watch. You cannot vary it without reducing its ability to tell time. It’s a rare instantiation of matter. All of its parts play a hard to vary role in telling time.
IOW, it seems that your objection isn't the the shoe doesn't fit, but that it's not intentioned to be worn that way. It's unclear how that's relevant.critical rationalist
March 29, 2023
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PS, Orgel:
living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . . [HT, Mung, fr. p. 190 & 196:] These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure.
[--> this is of course equivalent to the string of yes/no questions required to specify the relevant J S Wicken "wiring diagram" for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002, also cf here, -- here and -- here -- (with here on self-moved agents as designing causes).]
One can see intuitively that many instructions are needed to specify a complex structure. [--> so if the q's to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions.  [--> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes [--> Orgel had high hopes for what Chem evo and body-plan evo could do by way of info generation beyond the FSCO/I threshold, 500 - 1,000 bits.] [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196.]
Where, K-Complexity is summarised by Wikipedia, as a first level point of reference that would have been immediately accessible all along:
In algorithmic information theory (a subfield of computer science and mathematics), the Kolmogorov complexity of an object, such as a piece of text, is the length of a shortest computer program (in a predetermined programming language) that produces the object as output. It is a measure of the computational resources needed to specify the object, and is also known as algorithmic complexity, Solomonoff–Kolmogorov–Chaitin complexity, program-size complexity, descriptive complexity, or algorithmic entropy. It is named after Andrey Kolmogorov, who first published on the subject in 1963 [1][2] and is a generalization of classical information theory. The notion of Kolmogorov complexity can be used to state and prove impossibility results akin to Cantor's diagonal argument, Gödel's incompleteness theorem, and Turing's halting problem. In particular, no program P computing a lower bound for each text's Kolmogorov complexity can return a value essentially larger than P's own length (see section § Chaitin's incompleteness theorem); hence no single program can compute the exact Kolmogorov complexity for infinitely many texts.
From this, it is but a short step to imagine a universal constructor device which, fed a compact description in a suitable language, will construct and present the object. Let us call this the universal 3-D printer/constructor, 3-DP/C. Thus, in principle, reduction of an organised entity to a description in a suitably compact language is formally equivalent in information terms to the object, once 3-DP/C is present as a conceptual entity. So, WLOG, reduction to compact description in a compact language d(E) is readily seen as identifying the information content of any given entity E. For, d(E) is a program though it can simply be a functional organisational specification, as, causally in this logic-model world: d(E) + 3-DP/C + n ==> E1, E2, . . . En. Obviously, n is an auxiliary instruction setting the number of copies to be made. I write ==> to imply a constructive causal process effected by a 3-DP/C. From this we may come back to Orgel and notice his summary:
These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure.
We thus have a formal framework to reduce any entity to a description d(E), which is informational and has as metric I = length[d(E)], where chain of Y/N q[s will yield I in bits, on the Kolmogorov assumption of compactness. I use compact, to imply that we can get a good enough estimator of I by using something compact. We do not have to actually build a most compact language. Then, inject random changes in d(E) and observable sensitivity to perturbation would be an index of functional specificity of organisation. As a simple case try text strings in English as d(E) and a noisy, lossy transmission medium, giving d*(E). 3-DP/C can put out text strings on d*(E) but soon enough function will vanish as d(E) becomes gibberish. d(E) --> lossy, noisy medium --> d*(E) + 3-DP/C + 1 ==> E*1 d*(E) --> LNM --> d**(E) + 3-DP/C + 1 ==> E**1 etc. After a few generations, gibberish predictably will destroy configuration based functional organisation, starting with text in English. And so forth. I trust this will help you understand what FSCO/I is about more clearly.kairosfocus
March 29, 2023
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CR, above you tried to frame me as derivative from Paley, which would imply or at least invite that his remarks on the self replicating watch are a root source. This is not the case, period. Click on my handle [present in every comment I have made at UD] and you will see my actual root of thought, thermodynamics and related areas. Paley is a remote antecedent to modern design thought but so is Cicero [who I actually cite at the top of my online note]. What happened is in the course of debates I took time to look at Paley and was surprised to see his self replicating watch in Ch 2, and instantly connected this to von Neumann's kinematic self replicator. (In turn, note von Neumann propagated the dominant Computer Architecture a few years before, i.e. he thought in systems architecture terms.) My deeper antecedent is Hippocrates of Cos and reasoning on signs, one of the first approaches to inductive reasoning in our civilisation, antecedent to inference to the best explanation. On the wider framework, comparative difficulties analysis on factual adequacy, coherence and explanatory power is pivotal. Thaxton et al in TMLO are in fact the key antecedents to modern design theory, with key injections from Hoyle et al on the cosmological side and from Denton on the Biological side. Dembski, Behe et al came along later. As for the design inference on FSCO/I as sign, the point you find it hard to accept despite repeated correction is that Kolmogorov-Chaitin complexity is a key concept, alluded to in Orgel's corpus by 1973. A chain of Y/N q's in a compact description language can give a reasonable index of complexity, thus configuration or state space, a cut down phase space [a key statistical thermodynamics and dynamics concept] as momentum is not relevant. Combinatorial, exponential growth is thus obvious. And this is anticipated in Orgel 1973 and in Wicken 1979, then built on in Thaxton et al 1984. This is how constructions like the slander pieces at Wikipedia are utterly wrong headed, they don't even get the basic time line right. From this, take the simple observation of configurational particularity with some tolerance to achieve function, and we see fine tuned islands of function in the configuration space. The implied idea in incrementalist trial and error is that there is a grand continent of fitness forming a vast landscape, which is empirically and conceptually ill founded. The search challenge vs sol system or observed cosmos scope resources comes to bear. And in fact on trillions of cases FSCO/I is a reliable sign of intelligently directed configuration as cause. In the focal case above, we are not even inferring information from organisation, but we are dealing with string data structure, symbolic, algorithmic code for assembling the AA chains for thousands of proteins at the heart of cell based life. So, it is not just FSCO/I but coded string data structure information, a linguistic phenomenon. It is manifest, that the best explanation for such is intelligently directed configuration by language using intelligence. Where, on Venter et al, a molecular nanotech lab is an obvious reference model. That is, cell based life is credibly designed but it does not in itself require design by God as such, not directly. Paley would not have known of this, and would not have known that much more would be required to infer God is the direct author of cell based life, on observable evidence. Inference to design is not inference to designer, something too many objectors have not been able to recognise, despite its being repeatedly pointed out. They have been tilting at strawmen. Notice, a very specific disagreement with Paley. Where things get interesting is, cosmological fine tuning. We are at a tiny operating point in configuration space for cosmological physics. That Op Point sets up the most abundant elements as H, He, O, C, with N, that gets us stars, the periodic table, Water, Organic Chemistry, Fats and Sugars, Proteins. That points to design towards cell based life. By extracosmic designer. Bring in ourselves as responsible, rational, morally governed creatures and we go further. That is, the best serious candidate root of reality is a necessary being, inherently good and utterly wise creator God, further understood as maximally great. But that is far afield of the design inference on empirically observable signs. Your alleged implications, built on a strawman caricature imposed over objection, fail. Your perceived contradictions are not there, save in your strawman caricatures. In the follow up thread, we can readily see where there are serious contradictions, in Popperian thought. Phil of Science has gone on a full generation or two since then. KFkairosfocus
March 29, 2023
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CR, my discussion of the design inference is not founded on Paley or assumptions tied to him.
I’m not following you. The design inference does not fall under Paley’s perfected argument because you didn’t copy it? Or it wasn’t your intention to end up as Paley’s argument? Huh? How is that relevant? Do you think the Vienna Circle intended logical positivism to be self contradictory? Logical positivism is contradictory because, when we try to take it seriously, for the purpose of criticism, it rules itself out. Not because of what anyone intended or stated out with. Right? In the same sense, your intent or what you might have starred out with is not relevant. The design inference either reflects Paley’s argument (or an approximation of it) or it doesn’t. Right? This is why I keep asking you for that Venn diagram. Specifically, what part of the “design inference” circle would not also fit in the “well adapted to serve a purpose circle”. All you have to do is provide an example. If it’s not Paley’s argument, this should be easy-peasy, right? As for the rest, see above. Attempting to explain something being well adapted to serve a purpose with, well, being well adapted to serve a purpose is self contradictory. For example…
bearing reliable signs of intelligently directed configuration. Such is actually common sense…
If it’s reliable, then It has universal reach for anything that has, by that criterion, the appearance of design. Otherwise, why is a relatable sign of design? That you didn’t intend the design inference circle to overlap with the well adapted to serve a purpose circle is not relevant. Right? None of us can choose what our ideas imply.critical rationalist
March 29, 2023
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CR, my discussion of the design inference is not founded on Paley or assumptions tied to him. I do acknowledge that he was historically antecedent to von Neumann in Ch 2, but that is more to say he was not properly responded to. As for your further proposing a loaded redefinition, no, the acceptance of multiple signs of design is fine, thank you, especially that functionally specific, complex organisation and/or associated information beyond a threshold is a reliable sign of design. As for your attempt to define ontology of all possible designers to manufacture an infinite regress, you have already been answered repeatedly on that. You give me no reason to believe further correction will be heeded, but for record, a contingent designer is a designer and often leaves signs of intelligently directed configuration in artifacts. As archaeologists say, natural vs archaeology [thousands of cases in point, immediately]. But intelligence and knowledge or skill to direct configuration is not dependent on contingent being ontological status, you are making a strawman caricature. There is a coherent concept, necessary being designer, one that is longstanding in our civilisation and many others. So, designers can responsibly be conceived as contingent or necessary being entities. The sense in which the past of origins we did not observe would resemble our observed past is that both are stages in which designers could or did act, and in acting could provide entities bearing reliable signs of intelligently directed configuration. Such is actually common sense so the objection is contrived and hyperskeptical, not substantial. Doubtless more and more can be spun but predictably they will be just as contrived, hyperskeptical, ineffective. KFkairosfocus
March 27, 2023
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CR, this force, the base of say medical diagnosis:
TESTED, RELIABLE SIGN --> SIGNIFIED STATE OF AFFAIRS OR ENTITY e.g. under general conditions: smoke --> fire
Beyond that, there is excellent reason to reject the hyperskepticism that has been attached to empirically founded reasoning by support rather than assertion, entailment chain, conclusion. 99+ percent of practical reasoning is materially inductive and to cast a pall of hyperskeptical doubt is to try to discredit reasoning. KF PS, the design inference on reliable sign is not a contradictory claim.kairosfocus
March 27, 2023
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Q, obviously, an empirical inference on tested, reliable sign speaks with immediate force.
Immediate force of what exactly? An universal explanation? Inductivism?
However, the upshot of all of this is plain, it is clear that cells have linguistic phenomena and this points to design, even as cosmological fine tuning [that sets the stage on which we find cell based life] also points to design.
If you're referring to inductivism, no one has formulated a principle of induction we can actual use to provided guidance, in practice. The future is unlike the past in a vast number of ways. And inductive argument in the case of ID is a variation of this, in that the unobserved distant past would resemble the observed past. See <a href="https://xkcd.com/1122/"this example from xkcd regarding electoral precedent. It beings with "No one has been elected president before." and ends with "No nominee with a first name that contains a "k" has lost. Both of those things had never been observed before. For example, every designer we have observed is a highly complicated, knowledge laden entry. So, someone could just as well argue that the distant past will resemble the past. But this is not my argument. My point is, you're implicitly assuming Paley's argument would be universal in that it's also applicable to whatever would have designed us. Being explanatory, it would have reach. Otherwise, it would be an approximation that would be incomplete. So, how do we know it's applicable to what designed us? At best, you'd have to make ID's designer more concrete by defining it as non-material. But that would be an artificially narrow application of Paley's argument. IOW, I'm suggesting ID is a special case of being well adapted to serve a purpose. It doesn't scale. But, by all means, see this diagram. What fits in the second circle that doesn't fit in the first? Give a specific example. I've only asked for this, what, at least three times? What gives?critical rationalist
March 27, 2023
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ID being a contradiction does not require the lack of an end to determination.
This means exactly what I wrote. To rephrase, the ideas “Paley’s argument for design is contradictory” and “there is an end to determination” are not mutually exclusive. If you think this, then you seem to be confused about, well, how ID is contradictory. If you do not think this, it’s unclear how this is relevant to my criticism.
What rules out an ultimate designer?
Paiey’s argument. It has universal reach for anything that has the appearance of design. This is what I mean when I suggested Paley perfected the argument for design. However, in doing so, he ruled out an ultimate designer. While this is the opposite that Paley believed he had achieved, we cannot choose what our ideas imply. What do I mean by contradictory? Here's a few examples.... Empiricism is the idea that all knowledge comes to us from the senses. While this seemed like a good foundation roughly 100 years ago, when empiricism was conceived, it turns out that sense impressions are actually complex things that are themselves, well, not observed. Right? The idea that our senses relay accurate information to us depends on a long chain of hard to vary explanatory theories. IOW, this is what I mean when I say “observations are theory laden.” So, empiricism rules itself out by nature of being a contradiction. Logical positivism is the idea that only scientific statements are meaningful. It gained significant adoption until someone pointed out that logical positivism is, itself, not scientific, rending itself meaningless. Being a contradiction, this rules out Logical positivism. Now, back to Paley. From an earlier comment…
“The inference we think is inevitable, that the watch must have had a maker…There cannot be design without a designer; contrivance without a contriver; order without choice; arrangement without anything capable of arranging; subserviency and relation to a purpose without that which could intend a purpose; means suitable to an end…without the end ever having been contemplated or the means accommodated to it. Arrangement, disposition of parts, subserviency of means to an end, relation of instruments to a use imply the presence of intelligence and mind.”
However, if we substitute “ultimate designer” for “watch” in Paley’s argument, we force Paley to ‘the [inevitable] inference…that the ultimate designer must have had a maker’. As a contradiction, that argument for design rules itself out.
You wrote…
Am I supposed to conceive of the ultimate cause as a NON-being?
Knowledge grows via conjecture and criticism. So, we guess what people mean when they write x, then we attempt to correct errors in our ideas about what x means, etc. So, what you’re “supposed to do” is elaborate on how “there is an end to determination” is mutually exclusive with ID being contradictory, or explain how it’s reliant to that criticism. Are the ideas of “an ultimate cause” and “and end to determination” completely unrelated? Or perhaps you think ID isn’t based on Paley’s argument?
Where did we discuss the ultimate cause of everything?
When you referred to “an end to causation”?
Who is to say that there can be no more than one fundamental entity?
So, you meant to write “end(s) of causation” instead of “end of causation”? Given that ideas like "necessary being" seems like a solution in search of a problem, I guess this there could just as well be multiple necessary beings?critical rationalist
March 27, 2023
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Q, obviously, an empirical inference on tested, reliable sign speaks with immediate force. In this case, per OP, it is the actual, Nobel Prize winning, empirically backed consensus that the cell has in it string data structure, symbolic, coded algorithmic information used to assemble AAs towards proteins. An objector, for months, has tried to suggest that this is our ignorance, and other objectors tip-toe around. Some have raised distractions. There may be somewhat to the suggestion it is anti-theism, not evidence and logic that drives some of the objections above, certainly Lewontin suggested that long ago now. However, the upshot of all of this is plain, it is clear that cells have linguistic phenomena and this points to design, even as cosmological fine tuning [that sets the stage on which we find cell based life] also points to design. KFkairosfocus
March 26, 2023
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Origenes @432, Good points all. The problem is that “Critical Rationalist” has conflated the ID with theism, being unwilling or unable to define or distinguish the two in a mad rush to rule out an ultimate Designer. The subject of the OP is about data structures in comparison to the information stored in DNA and RNA, but CR seems to be obsessed with arguing about whether God exists or not. Personally, I wouldn't waste any more time on CR's side-track comments and obvious evasiveness. -QQuerius
March 25, 2023
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CR I stand squarely with what I say here:
Ori: At some point, CR, there is an end to determination. Not everything can be determined by something else. It is not turtles (causes) all the way down.
This is based on general reflection. I argue that It cannot be the case that there is an infinite chain of causation. In my view, an infinite chain of causes is incoherent. Now, your response to this is completely bonkers. Let's read it together:
You seem to be confused.
I am confused because I consider a beginningless infinite chain of causes to be an incoherent concept. How can that be?
ID being a contradiction does not require the lack of an end to determination.
This sentence is bonkers. ID is a contradiction? What are you talking about? "does not require the lack of an end to determination"? My God, what is wrong with you? What do these tortured words even mean?
It just rules out an ultimate designer.
What rules out an ultimate designer? What could possibly rule out an ultimate designer? Again, what are you talking about?
Apparently you cannot conceive of a case where the ultimate cause of things is not a being?
I don't know how this connects with the previous. But what are you even asking here? Am I supposed to conceive of the ultimate cause as a NON-being?
Why is it that the ultimate cause of everything is actually a person?
Where did we discuss the ultimate cause of everything? Who is to say that there can be no more than one fundamental entity?Origenes
March 25, 2023
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F/N: the evasiveness towards eminently quantifiable information is yet another back handed admission on the significance of FSCO/I as a sign of design. KFkairosfocus
March 25, 2023
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Kairosfocus @427, Irrespective of the massive blah-blah you're receiving in response, "Critical Rationalist," has not been able to produce a coherent definition of ID. Thus, all the criticisms and unsupported assertions that we have to wade through boils down to meaningless rhetoric in light of this fundamental failure. Frankly, I don't think you'll receive anything more meaningful than a smokescreen of words. I'm not going to bother with further answers in light of a complete lack of meaningful communication. I see glaring shortfalls and objections in every unsupported assertion. For example, let's say we find a stack of three rocks or a bunch of rocks spelling out "Help me!" We'll have to endure endless speculations about how we don't know the identity of the person who stacked the rocks or spelled out the message, and therefore there must be some sort of infinite regress. Or maybe the rocks were OBVIOUSLY put in place randomly by the tide and so it's likely we'll eventually see the Tower of London or "Methinks it is like a weasel" from such random rocks over billions and billions of years. What a stupid waste of time! This is why I appreciate Dr. Tour's response of, "Okay, show me." -QQuerius
March 25, 2023
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A designer is “adapted” by who? And whose purpose is fulfilled by that adaptation?
That would be ID’s designer. Who else? Apparently, this entire abstract designer thing is just for show? When we ask, where is the designer now, how does the designer work, where are the tools it used, etc. we get push back. So what’s with all the specifics now? Furthermore, this is an odd question because, according to ID, we appear to be well designed to serve multiple purposes. In fact, that’s supposedly the criteria for being designed. For example, we seem to be designed to reproduce biologically among many other things.
At some point, CR, there is an end to determination. Not everything can be determined by something else. It is not turtles (causes) all the way down.?
You seem to be confused. ID being a contradiction does not require the lack of an end to determination. It just rules out an ultimate designer. Apparently you cannot conceive of a case where the ultimate cause of things is not a being? Why is it that the ultimate cause of everything is actually a person? This question isn't new, so it's unclear why you did not incorporate it into your question.
So, I would suggest that, assuming that it is coherent to say that a designer is “adapted” and serves a “purpose”, that a designer adapts himself, and serves his own purpose by creating bacterium. IOW explanations start and end with the designer.?
We’re communicating with each other via a number of complex systems designed by human beings. Are you suggesting we’ve adapted ourselves to the purpose of designing those things on our own, completely independent of any purpose our designer would have had for us? Or, to rephrase, do you think we were not designed to design things? Somehow I don’t think this is actually your position. I know that you desperately want explanations to start & end with physical stuff, but you cannot rationally ground your intense desire. My criticism is that ID’s criteria for design is arbitrary narrow. It doesn’t scale. Being well adapted to serve a purpose does. It scales beyond the physical. From #347
…I pointed out that the means by which you might choose to represent the watch, in bits, would vary wildly depending on the particular digital format you choose to represent it. Right? For example, the very same watch could appear to have wildly more or less of the appearance of design depending on what format you happened to chose to represent it, digitally. If you store it as a 12K by 12K png, that would be vastly more bits than, say, parametric format. You’d have to somehow use the most efficient digital representation possible, and that format might not have even been invented yet. For example, someone just recently invented a way to reduce the size of a Neural Radiance Field by 100 times. As such, did a watch represented as an NRF suddenly just have much less of the appearance of design? And what about a description in a string of text? Words are shortcuts for ideas, which would represent other information in the receiver, etc. As such, it’s unclear how this could be accurately used, in practice, to identify how much a thing has the appearance of design. Being well adapted to serve a purpose does not have this problem, as it would be format independent and wouldn’t even require a digital representation at all. It simply scales in ways FSCO/I cannot.
Again, a watch is well adapted to the purpose of telling time. A rock is not, despite the fact that you can use it to tell time as a sundial. We are well adapted to use a rock to tell time, not the rock. I don’t even need to appeal to Auto CAD, etc. Perhaps this will clarify things for you? I know you desperately want Paley’s criteria for the appearance of design to start and end with physical stuff, but you cannot rationally ground you intense desire? Take memes, for example. Memes that are well adapted to replicate go viral, while other memes do not. Their content plays a causal role in whether they will be retained or not, when embedded in a storage medium. Can we replace one meme with another and get the same result, despite memes being non-material? There must be some crucial aspect of a meme that causes it to go viral. Otherwise, we could replace one meme with any other meme and get the same result. But this doesn’t seem to the case. Right? This is despite the fact that being non-material, memes are instantiated in brains, books, hard drives, etc. So what the heck is going on here? Here’s a thought experiment. Could there be some kind of non-material Internet in some non-material realm, where some non-material memes go viral, but not others, when shard by some non-material beings? How do they get copied from one non-material being to another? The very idea of sharing between them seems to be incoherent, as the copyablility of information has very specific physical requirements in respect to possible and impossible physical laws. But there are no physical laws. How could memes play a causal role in being retained in, well, what exactly, so some memes are retained but others are not? The very idea of being retained at all seems, well highly problematic. Are they retained in some non-material beings, but not others, until the ones that go viral get copied? If so, how and where? At a minimum it seems there must be some kind of non-material “laws” that must be possible for non-material memes to get copied, that plays the same role. Otherwise, it’s unclear what would prevent every non-material being from knowing about every meme when created. Or even what it means to say a meme was created by any particular non-material being. etc. Everything could be defined by fiat, but in a very specific fiat that reflected non-material “laws” playing the same roles as our physical laws. Otherwise, why would some memes go viral in this non-material realm, but others would not, just as some memes go viral in our material realm, but others would not? Again, being well adapted to serve a purpose scales.critical rationalist
March 25, 2023
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F/N: CR has already been answered as to how a compact description language can give a measure of FSCO/I in cases where it is implicit. But that is not convenient rhetorically so the now habitual doubling down is seen. KFkairosfocus
March 25, 2023
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CR, we may not know everything about a designer, especially a contingent being designer, but one thing we do know. Namely, the self moved rational creative being cannot be reduced to inherently non rational, dynamic-stochastic, GIGO driven computation on a substrate. For, just to reason, we need responsible freedom or else the self referentiality of our utterances will lead to self discredit. Rational action rests on freedom to infer and judge i/l/o sound first principles of right reason. And again, ever more tangents pulling away from the focus of the OP, that in the cell -- despite objections -- we find symbolic, algorithmic code, a key sign of design. We can take the tangential responses as backhanded concession of the decisive point, backed by utter unwillingness to go there. KF PS, how long and hard you labour to deflect the force of a conclusion driven by trillions of cases in point and high reliability, there are signs of design that let us know entities were designed.kairosfocus
March 25, 2023
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CR @
So, it’s well adapted for the purpose of designing bacterium.
A designer is "adapted" by who? And whose purpose is fulfilled by that adaptation? At some point, CR, there is an end to determination. Not everything can be determined by something else. It is not turtles (causes) all the way down. So, I would suggest that, assuming that it is coherent to say that a designer is "adapted" and serves a "purpose", that a designer adapts himself, and serves his own purpose by creating bacterium. IOW explanations start and end with the designer. I know that you desperately want explanations to start & end with physical stuff, but you cannot rationally ground your intense desire.Origenes
March 25, 2023
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Consciousness, the free rational person, the intelligent designer, cannot be explained by mindless physical stuff.
Already addressed. "We don't know all the details" seems like a reasonable response. Otherwise, we've decided to arbitrarily abandon explanations.
Truth. CR’s insistence that the designer of the watch must itself be designed by some A, which, in turn, no doubt, must be designed by a B, and so on, only stops when we arrive at matter.
First, for the sake of argument, let's assume that is true for a moment. So, the theory of ID is that all life on earth was designed by some immaterial designer? And that designer is a mind that exists in some inexplicable realm, which operates by some inexplicable means and methods and is driven by some inexplicable motives? When should I expect the supposedly scientific theory of ID to be update to match this? I won't be holding my breath. Second, information can be brought into fundamental physics via constructor theory. Specifically, we can reformulate the theory of information into constructor theoretic terms of what physical transformations must be possible, which physical transformations be impossible and why. This includes which transformations of matter are necessary for copying information, the interoperability principle of information, etc. All of these aspects have physical requirements. If that information is instanced was in a designer and was coped into bacterium, then was that information not instantiated if not in some physical system? Seems fine if you're one of the few ID proponents who think the designer was aliens. The rest, no so much. Third, let's ignore this for the moment. You still haven't address my question.
After all, human beings are conscious, and according to you, consciousness is fundamental. So, why can’t we currently be swapped out with ID’s designer and get bacterium? What is it that makes the the crucial difference in designers?
If there is a crucial difference, then ID's designer is well adapted to design organism. This is why I pointed out FSCO/I's scalability problem earlier..
... I pointed out that the means by which you might choose to represent the watch, in bits, would vary wildly depending on the particular digital format you choose to represent it. Right? For example, the very same watch could appear to have wildly more or less of the appearance of design depending on what format you happened to chose to represent it, digitally. If you store it as a 12K by 12K png, that would be vastly more bits than, say, parametric format. You’d have to somehow use the most efficient digital representation possible, and that format might not have even been invented yet. For example, someone just recently invented a way to reduce the size of a Neural Radiance Field by 100 times. As such, did a watch represented as an NRF suddenly just have much less of the appearance of design? And what about a description in a string of text? Words are shortcuts for ideas, which would represent other information in the receiver, etc. As such, it’s unclear how this could be accurately used, in practice, to identify how much a thing has the appearance of design. Being well adapted to serve a purpose does not have this problem, as it would be format independent and wouldn’t even require a digital representation at all. It simply scales in ways FSCO/I cannot. Again, a watch is well adapted to the purpose of telling time. A rock is not, despite the fact that you can use it to tell time as a sundial. We are well adapted to use a rock to tell time, not the rock. I don’t even need to appeal to Auto CAD, etc.
To say there is no crucial "difference" between designers, which plays a hard to vary difference in the outcomes, yet we would end up with radically different outcomes, consistently, appears to be a contradiction. There must be some other crucial difference, other than consciousness is fundamental, as we are all conscious. I'm conscious. So, why can't I create universes, bacterium, etc? IOW, I'm suggesting ID is using a rather arbitrarily narrow conception of Paley's criterial for the appearance of design, that doesn't scale. And that is, well, by design.critical rationalist
March 25, 2023
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CR, how you love loaded terms. By obvious definition, a successful designer is CAPABLE of carrying out said design. Reginald Mitchell, having designed a series of racers, used knowledge and experience based skills to design the Spitfire, in two bites. A first, gull winged try was unimpressive. A drastic revision, with elliptical wings, was a breakthrough. Long before, dragonflies were subtle, powerful designs. There is no need for infinite regresses, as the point is that for many designs we find empirical signs that reliably indicate design. This frees us from needing to directly observe the design and development to credibly know something was designed. Further, contingent designers design. And there is reason to take as serious candidate designers, serious candidate necessary beings. Such a designer would be ultimate. The focus is, capability. KFkairosfocus
March 25, 2023
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