L&FP, 58b: The JoHari Window and recognising limits of our knowledge

Q, spot on. Sad. KF kairosfocus

Kairosfocus @44, So true! We see 1. Denial of data 2. Refocus on trivia 3. Circular arguments based on scientific prejudice 4. Selective hyperskepticism (straining at a gnat but swallowing a camel) 5. Appeals to consensus and authority 6. Labeling dissenters as "quacks" and suggesting ulterior motives 7. Misrepresenting the results of experiments (Lenski's bacteria come to mind) NONE of these should have a place in science. And now I read about the following bill in California:

"Assembly Bill 2098 would empower the Medical Board of California to go after the licenses of physicians who disseminate “misinformation” or “disinformation” regarding Covid-19. The bill in its latest iteration defines misinformation as “false information that is contradicted by contemporary scientific consensus contrary to the standard of care.”

Forget the first Amendment. Imagine extending this to the other sciences that could be controlled by consensus agencies: "This automobile engine has zero emissions of carbon by agency consensus, and to dispute this will result in losing your job because of your disseminating "misinformation." -Q Querius

Q, actually, at this stage, refusal to acknowledge in the face of decisive evidence is the key orienting signal. It backhandedly highlights the strength of the point and its powerful import of design: coded, complex algorithmic information in the heart of the cell, so language and goal directed process, turning on deep knowledge of polymer chemistry. We see here an ideology, evolutionary materialistic scientism or fellow travellers in unacknowledged crisis, resorting to hyperskeptical denial in the face of massive warrant. Telling, on many levels including on underlying attitudes. KF kairosfocus

Hopefully, you can see what I mean by "semi-circular" reasoning. I'm sure there's already a proper term in logic for this problem. To illustrate (maybe), there's a famous old joke about two farmers bragging to each other. Farmer A: "My farm is so large that it takes me all day just to drive all the way across it! Farmer B: "Yeah, I had a car like that once." -Q Querius

I need to clarify what I meant to say by "In other words, for natural selection to appear in biological organisms, one first needs to have . . . [the means to respond to] natural selection." So, how does that means evolve? Let's look at an analogy. In the mechanistic world of automobiles, fully automated manufacture (reproduction) is nearly a reality. However, there's no means for automobiles to respond to "selection pressure" as there is for living organisms--unless there's conscious, intelligent design intervention. Certain automobile models might have frequent catastrophic failures, but random changes in manufacture will not respond to fix such issues in subsequent manufacture. For example, there's the famous case of spontaneous acceleration in Toyotas: http://www.human-resonance.org/acceleration.html Thus, the ability to respond to natural selection also needed to evolve completely and effectively for it to have any impact on biological reproduction. This would be a practical example of Behe's mousetrap argument. -Q Querius

Relatd @40, My meme is that evolution can explain everything in retrospect, but just cannot actually predict anything in advance. The coelacanth and other "living fossils," "vestigial" organs, and "junk" DNA are good examples. But getting back to the DNA as code issue that Kairosfocus is trying to get Alan Fox to consider, one first has to agree on the definition of "code" as a symbolic representation or a series of instructions. There's also the separate but concomitant factor of compression , which is far from trivial, since both had to somehow miraculously appear through random chance and natural selection. In other words, for natural selection to appear in biological organisms, one first needs to have . . . natural selection. O.o -Q Querius

Querius at 37, Excellent summary. So, this is evolution: It can do anything at any time and even circle back on itself. It can go up, down, sideways and backwards. In other words, it explains nothing. relatd

AF, the process, involving a key and complex enzyme, is anything but simple. As Wikipedia confesses:

In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the double-stranded DNA so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP not only initiates RNA transcription [–> algorithmic start, notice, transcribing is generally stepwise], it also guides the nucleotides into position, facilitates attachment and elongation [–> notice direct parallel to stepwise synthesis of AA chains for proteins, cf Lehninger 8th edn p 3346: “RNA polymerase elongates an RNA strand by adding ribonucleotide units to the 3 ?- hydroxyl end, building RNA in the 5 ? ? 3 ? direction”], has intrinsic proofreading and replacement capabilities [–> language], and termination recognition [–> algorithmic halting] capability. In eukaryotes, RNAP can build chains as long as 2.4 million nucleotides.

And of course, the more central issue you would distract attention from is documented by Lehninger's literary heirs and others:

"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function." [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

See https://uncommondesc.wpengine.com/darwinist-debaterhetorical-tactics/protein-synthesis-what-frequent-objector-af-cannot-acknowledge/ KF kairosfocus

...the similarity of its structure to that of DNA suggested that RNA could be synthesized from a DNA template... Simple physical templating. Alan Fox

Thank you for the references, Kairosfocus. Incidentally a link that Alan Fox posted had an interesting reference regarding RNA half life: Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells https://pubmed.ncbi.nlm.nih.gov/19001483/ Here's an excerpt:

However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h.

Well, the half life is a bit shorter than the half-life of DNA (for a good reason), but at least the researchers came up with an experimentally derived value. The "semicircular" logic often associated with long ages can lead to some highly unlikely explanations. For example, the coelacanth was once believed to have gone extinct 65 million years ago. However, it somehow escaped the random undirected mutational changes of 65 million years of evolution to be discovered alive and apparently unchanged off the coast of South Africa in 1939. Here are the possible evolutionary explanations: A. Coelacanths are fantastically long lived! Each generation MUSTA remained alive for 10 million years or so. Thus, there haven't been enough generations for natural selection to have a significant effect. B. Coelacanths MUSTA not been subject to selection pressures because they MUSTA survived unchanged in a protected environment, namely the southwestern Indian Ocean. C. Coelacanth DNA is highly resistant to mutation due to a not-yet-completely-understood mechanism that MIGHTA been due to their habituating cold deep-sea caves and crevices.. D. The Coelcanth DID evolve, but MUSTA made a full circle back to what it was like 65 million years ago. E. The Coelacanth DID evolve, but unlikely as it seems, the changes MUSTA been internal only. F. Just call it a "living fossil" that somehow once again proves evolution and move on. -Q Querius

OK kairosfocus

Kairosfocus/34

H’mm, I see a sippy cup for kids for porridge, yoghurt etc. Seems to be in India? KF

There's a popular yoghurt called Chobani. That's what I thought I saw when I first glanced at the title. Seversky

H'mm, I see a sippy cup for kids for porridge, yoghurt etc. Seems to be in India? KF PS, meanwhile, on the table is a model framework for creating bodies of knowledge including in the face of polarisation. kairosfocus

Sev, there is such a brand of yoghurt? KF kairosfocus

When I first glanced at the headline I thought this thread was about a brand of yoghurt. Shows how much we are unconsciously influenced by advertising. Seversky

F/N: So, with reference to the JoHari window, how do we build a body of confident knowledge, whether public or confidential, in the face of possibilities of our own error, objections, a skeptical climate, hyperskepticism and outright polarised hostility? [And surely, this is directly relevant to ID as a scientific movement based on the design inference informed by open-ended observational evidence and analysis.] Let's use steps of thought: 1: We must properly understand what knowledge is, including its subtleties, limitations and challenges. 2: This, we can see i/l/o the warranted, credibly true [so, reliable] belief approach, buttressed by the moderated insights from Dallas Willard. To wit:

To have knowledge in the dispositional sense—where you know things you are not necessarily thinking about at the time—is to be able to represent something as it is on an adequate basis of thought or experience, not to exclude communications from qualified sources (“authority”). This is the “knowledge” of ordinary life, and it is what you expect of your electrician, auto mechanic, math teacher, and physician. Knowledge is not rare, and it is not esoteric . . . no satisfactory general description of “an adequate basis of thought or experience” has ever been achieved. We are nevertheless able to determine in many specific types of cases that such a basis is or is not present [p.19] . . . . Knowledge, but not mere belief or feeling, generally confers the right to act and to direct action, or even to form and supervise policy. [p. 20] In any area of human activity, knowledge brings certain advantages. Special considerations aside, knowledge authorizes one to act, to direct action, to develop and supervise policy, and to teach. It does so because, as everyone assumes, it enables us to deal more successfully with reality: with what we can count on, have to deal with, or are apt to have bruising encounters with. Knowledge involves assured [--> warranted, credible] truth, and truth in our representations and beliefs is very like accuracy in the sighting mechanism on a gun. If the mechanism is accurately aligned—is “true,” it enables those who use it with care to hit an intended target. [p. 4, Dallas Willard & Literary Heirs, The Disappearance of Moral Knowledge, Routledge|Taylor& Francis Group, 2018. ]

3: This means, an adequate body of knowledge is ours, independent of what those who object, are skeptical, are selectively hyperskeptical or are outright polarised have to say. Known to us, unknown to others, not yet known to the world at large is still valid knowledge. 4: At the same time, we are using a commonplace, weak form sense of knowledge, which seeks truth (& may often hit it) but which recognises limitations and possibility for error. So, we need to be our own friendly critics, willing to seek criteria of adequate warrant . . . including, recognising when negative knowledge is what is established, i.e. limits of knowledge and knowing that we do not have positive knowledge. (Where feasible, this may be the framework for a research proposal and project, including pretty informal or simple cases.) 5: Similarly, we welcome responsible, reasonable, friendly "outside" critics, as they help us refine our knowledge base. (Some of these may even be willing to join the body of knowledge project and are part of the emerging school.) 6: By contrast, hyperskeptical and hostile, irresponsible or dishonest critics lock themselves out. By their tone, tactics, refusal to be reasonable and resulting rotten fruit shall ye know them. 7: Now, adequacy. In an empirical context, we follow Locke on the candle set up in us:

[Essay on Human Understanding, Intro, Sec 5:] Men have reason to be well satisfied with what God hath thought fit for them, since he hath given them (as St. Peter says [NB: i.e. 2 Pet 1:2 - 4]) pana pros zoen kaieusebeian, whatsoever is necessary for the conveniences of life and information of virtue; and has put within the reach of their discovery, the comfortable provision for this life, and the way that leads to a better. How short soever their knowledge may come of an universal or perfect comprehension of whatsoever is, it yet secures their great concernments [Prov 1: 1 - 7], that they have light enough to lead them to the knowledge of their Maker, and the sight of their own duties [cf Rom 1 - 2, Ac 17, etc, etc]. Men may find matter sufficient to busy their heads, and employ their hands with variety, delight, and satisfaction, if they will not boldly quarrel with their own constitution, and throw away the blessings their hands are filled with, because they are not big enough to grasp everything . . . It will be no excuse to an idle and untoward servant [Matt 24:42 - 51], who would not attend his business by candle light, to plead that he had not broad sunshine. The Candle that is set up in us [Prov 20:27] shines bright enough for all our purposes . . . If we will disbelieve everything, because we cannot certainly know all things, we shall do muchwhat as wisely as he who would not use his legs, but sit still and perish, because he had no wings to fly.

8: Now, much of what we do turns on inference to best current, empirically anchored explanation and associated models. That is, 9: on current observed, recorded and shared facts O1, O2, . . . On, predictions, P1, P2, .n . . Pm and trajectory of investigations I(t), we can see which of live option explanations/models E1, E2 . . . Ek account well for the O's, has a good track record in translating P's into correctly predicted O's, and of these, which is coherent and explanatorily elegant [neither ad hoc nor simplistic]. 10: Of these we may have a few short listed E's {Es} or a best one Eb, which then are focal for onward investigation. 11: In our relevant case, when an Eb emerges, we have an epistemic right to accept it on abduction/ inference to best explanation, though we remain open to adjustment and correction. 12: On either case, we have a body of knowledge, the set {Es} are our candidate alternatives, known to be the collective best, and if we have an Eb, that is saying {Es} has become a singleton. Obviously, a good rival Er, would open out the set to {Eb, Er}. 13: With this in hand, we see that the negative knowledge case of Eb, is a special case, let's call it E0. 14: We thus see how a body of knowledge can be built even in the face of objection or hostility. 15: It then confers "the right to act and to direct action, or even to form and supervise policy." FAIR COMMENT: ID has attained that state, though it faces sharp and too often irresponsible objection. A capital illustration is the point recognised by Lehninger's literary heirs:

"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function." [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

See https://uncommondesc.wpengine.com/darwinist-debaterhetorical-tactics/protein-synthesis-what-frequent-objector-af-cannot-acknowledge/ KF kairosfocus

Q, try here https://uncommondesc.wpengine.com/evolution/at-big-think-can-we-predict-evolution/#comment-765355 KF kairosfocus

F/N: On Numerical Control, NC -- more, commonplace, empirically well warranted public domain knowledge: https://www.brighthubengineering.com/manufacturing-technology/55670-what-is-numerical-control-machine/

Numerical control, popularly known as the NC is very commonly used in the machine tools. Numerical control is defined as the form of programmable automation, in which the process is controlled by the number, letters, and symbols. In case of the machine tools this programmable automation is used for the operation of the machines. In other words, the numerical control machine is defined as the machined that is controlled by the set of instructions called as the program. In numerical control method the numbers form the basic program instructions for different types of jobs; hence the name numerical control is given to this type of programming. When the type of job changes, the program instructions of the job also change. It is easier to write the new instructions for each job, hence NC provides lots of flexibility in its use.

This is of course, as AF refuses to acknowledge, precisely what happens in protein synthesis. Even Wikipedia confesses -- it is too well known to deny:

STEP 1, NC: >>Numerical control (also computer numerical control, and commonly called CNC)[1] is the automated control of machining tools (such as drills, lathes, mills, grinders, routers and 3D printers) by means of a computer. A CNC machine processes a piece of material (metal, plastic, wood, ceramic, or composite) to meet specifications by following coded programmed instructions and without a manual operator directly controlling the machining operation.>> STEP 2, Protein synthesis stage in the ribosome: >>Protein synthesis can be divided broadly into two phases - transcription and translation. During transcription, a section of DNA encoding a protein, known as a gene, is converted into a template molecule called messenger RNA (mRNA). This conversion is carried out by enzymes, known as RNA polymerases, in the nucleus of the cell.[2] In eukaryotes, this mRNA is initially produced in a premature form (pre-mRNA) which undergoes post-transcriptional modifications to produce mature mRNA. The mature mRNA is exported from the cell nucleus via nuclear pores to the cytoplasm of the cell for translation to occur. During translation, the mRNA is read by ribosomes which use the nucleotide sequence of the mRNA to determine the sequence of amino acids. The ribosomes catalyze the formation of covalent peptide bonds between the encoded amino acids to form a polypeptide chain. Following translation the polypeptide chain must fold to form a functional protein; for example, to function as an enzyme the polypeptide chain must fold correctly to produce a functional active site.>> STEP 3, tRNA action: >>Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA[1]) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes),[2] that serves as the physical link between the mRNA and the amino acid sequence of proteins. Transfer RNA (tRNA) does this by carrying an amino acid to the protein synthesizing machinery of a cell called the ribosome. [--> cf Yockey on the encoding by attaching the appropriate AA to the CCA tip] Complementation of a 3-nucleotide codon in a messenger RNA (mRNA) by a 3-nucleotide anticodon of the tRNA results in protein synthesis based on the mRNA code. As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code. >> STEP 3, assemblers: >>A molecular assembler, as defined by K. Eric Drexler, is a "proposed device able to guide chemical reactions by positioning reactive molecules with atomic precision". A molecular assembler is a kind of molecular machine. Some biological molecules such as ribosomes fit this definition. This is because they receive instructions from messenger RNA and then assemble specific sequences of amino acids to construct protein molecules. >>

I am simply citing Wikipedia confessions to document public domain known knowns rooted in a vast body of recent empirical work on the cell. On Turing machines, Wiki confesses:

A Turing machine is a mathematical model of computation describing an abstract machine[1] that manipulates symbols on a strip of tape according to a table of rules.[2] Despite the model's simplicity, it is capable of implementing any computer algorithm.[3] The machine operates on an infinite[4] memory tape divided into discrete cells,[5] each of which can hold a single symbol drawn from a finite set of symbols called the alphabet of the machine. It has a "head" that, at any point in the machine's operation, is positioned over one of these cells, and a "state" selected from a finite set of states. At each step of its operation, the head reads the symbol in its cell. Then, based on the symbol and the machine's own present state, the machine writes a symbol into the same cell, and moves the head one step to the left or the right,[6] or halts the computation. The choice of which replacement symbol to write and which direction to move is based on a finite table that specifies what to do for each combination of the current state and the symbol that is read. The Turing machine was invented in 1936 by Alan Turing,[7][8] who called it an "a-machine" (automatic machine).[9] It was Turing's Doctoral advisor, Alonzo Church, who later coined the term "Turing machine" in a review.[10] With this model, Turing was able to answer two questions in the negative: Does a machine exist that can determine whether any arbitrary machine on its tape is "circular" (e.g., freezes, or fails to continue its computational task)? Does a machine exist that can determine whether any arbitrary machine on its tape ever prints a given symbol?[11][12] Thus by providing a mathematical description of a very simple device capable of arbitrary computations, he was able to prove properties of computation in general—and in particular, the uncomputability of the Entscheidungsproblem ('decision problem').[13] Turing machines proved the existence of fundamental limitations on the power of mechanical computation.[14] While they can express arbitrary computations, their minimalist design makes them unsuitable for computation in practice: real-world computers are based on different designs that, unlike Turing machines, use random-access memory. Turing completeness is the ability for a system of instructions to simulate a Turing machine. A programming language that is Turing complete is theoretically capable of expressing all tasks accomplishable by computers; nearly all programming languages are Turing complete if the limitations of finite memory are ignored.

This was a pivotal result. In practice most of our digital computational machines follow the von Neumann or Harvard Architectures, now with emphasis on multi level cache memory. The essential focus is input, process [including logic, decision, arithmetic, storage, erasure, shifting etc], output information, which can host and control a target machine to carry out a task, such as NC or a position arm robot etc. KF kairosfocus

AF, the gaslighting continues, and now you try to suggest other information-containing entities don't. I again point to the summary in 13, where as you full well know the information is coded in sequences per the genetic code and is used algorithmically to synthesise proteins. The net effect of your evasions is to show that the force of that well established and widely acknowledged evidence is so detrimental to evolutionary materialistic scientism that you resort to extreme rhetorical twists and turns to evade it. That tells us worlds about the ideology that drives such behaviour. It's over. KF PS, here is another source,

Although the sequence of nucleotides in DNA appeared to specify the order of amino acids in proteins, it did not necessarily follow that DNA itself directs protein synthesis. Indeed, this appeared not to be the case, since DNA is located in the nucleus of eukaryotic cells, whereas protein synthesis takes place in the cytoplasm. Some other molecule was therefore needed to convey genetic information from DNA to the sites of protein synthesis (the ribosomes). RNA appeared a likely candidate for such an intermediate because the similarity of its structure to that of DNA suggested that RNA could be synthesized from a DNA template [–> notice where templating happens and from Lehninger where string data structure encoding and expression toward protein synthesis happens] . . . RNA differs from DNA in that it is single-stranded rather than double-stranded, its sugar component is ribose instead of deoxyribose, and it contains the pyrimidine base uracil (U) instead of thymine (T) . . . However, neither the change in sugar nor the substitution of U for T alters base pairing, so the synthesis of RNA can be readily directed by a DNA template. Moreover, since RNA is located primarily in the cytoplasm, it appeared a logical intermediate to convey information from DNA to the ribosomes. These characteristics of RNA suggested a pathway for the flow of genetic information that is known as the central dogma of molecular biology: DNA –> RNA –> Protein [The Cell A Molecular Approach, 8th Edn, Cooper, adds, p. 122]

PPS, I remind onlookers of your confident manner assertion at 17 in the protein thread: https://uncommondesc.wpengine.com/darwinist-debaterhetorical-tactics/protein-synthesis-what-frequent-objector-af-cannot-acknowledge/#comment-764500

Poor analogies show your ignorance of the biochemistry. This is curable, KF. There are books that are not too technical that you wouldn’t benefit from reading them.

13 above shows what an outstanding text has to say, going to the extent of comparing an Assyrian document c 700 BC. https://uncommondesc.wpengine.com/philosophy/lfp-58b-the-johari-window-and-recognising-limits-of-our-knowledge/#comment-765579 Let's clip from p. 189 in Lehninger to see just who is projecting distortion while distorting, i.e. AF is playing the agit prop tactic of turnabout projection . . . which for the aware then becomes confession by projection:

FIGURE 1-29 Two ancient scripts. (a) The Prism of Sennacherib, inscribed in about 700 BCE, describes in characters of the Assyrian language some historical events during the reign of King Sennacherib. The Prism contains about 20,000 characters, weighs about 50 kg, and has survived almost intact for about 2,700 years. (b) The single DNA molecule of the bacterium E. coli, leaking out of a disrupted cell, is hundreds of times longer than the cell itself and contains all the encoded information necessary to specify the cell’s structure and functions. The bacterial DNA contains about 4.6 million characters (nucleotides), weighs less than 10 ^ – 10 g, and has undergone only relatively minor changes during the past several million years . . .

Rhetorical stunt collapses, and we see here what we can recognise as a fairly typical expert view. Actually, the view since Crick as we know from his March 19, 1953 letter to his son, in which he first wrote that DNA is like a code then shortly after underscored his is in asserting DNA is a code. The sequence of bases, which freely has any of AGCT/U following any other per chaining chemistry, expresses the genetic code, which is widely tabulated and described in just those terms. It is common knowledge, now literally taught in primary school science, that this code is used in protein synthesis. Where, it is obvious to anyone familiar with computer architecture . . . and AF seems unfamiliar with say the significance of a Turing machine . . . that we are seeing NC in action. Something as historic and authoritative as Lehninger simply documents the widely known known consensus. AF is using selectively hyperskeptical rhetorical stunts to pretend knowledge in the public domain is not knowledge and that his superior knowledge [apparently greater than say Lehninger's literary heirs etc] allows him to establish the negative knowledge that despite that consensus, in fact code is a mere poor analogy and ignorance. The stunt fails, fails once we know that he is trying to overturn known knowns that have been commonplace since the 1950's. This, because he realises the telling significance of our discovery of text in the cell. Text that in the end traces to origin of cell based life. Text that tells us that we have language applied to goal directed stepwise processes, using molecular nanotech rooted in sophisticated polymer chemistry. In short, AF is desperate to dismiss the signature of design, the SETI wow signal that was not found coming down to our radio antennas from the wider galaxy, but instead is in the cells of our own bodies. He can belittle ID, IDers and this blog all he wants, such flailing simply inadvertently underscores the power of the point. It's over, over for any responsible person willing to heed that wow signal. That's not analogy, it is instantiation. kairosfocus

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-00949-x Alan Fox

Q, try this article: https://www.pnas.org/doi/10.1073/pnas.95.14.7933 KF kairosfocus

It is clearly a widely understood point that the D/RNA in the cell contains code.

Not really, any more than a book, a sound recording or a video tape are encoded. Information is stored in a substrate. Call it code if you want but the mechanism of storing and retrieving information in DNA relies only on physical templating. Gaslighting? Good grief! Alan Fox

For many species, large parts of the genome are not apparently under selective pressure (yes, junk) so molecular clock rules apply: mutation and drift. Alan Fox

Color me skeptical.

Well, at least you read stuff. Thanks for the link. Alan Fox

News flash: Researchers determine that DNA can be used as a molecular clock after all! In February 2021, Nature published the findings that allowed researchers to miraculously determine the evolutionary lineages between different mammoths using DNA more than one million years old! They compared the mammoth DNA to that of modern elephants and were able to determine what the the age of the mammoths MUSTA been given the known rate of evolution! Million-year-old DNA sheds light on the genomic history of mammoths https://www.nature.com/articles/s41586-021-03224-9 Here's a quote from the article:

We extracted DNA from the three molars using methods designed to recover highly degraded DNA fragments, converted the extracts into libraries and sequenced these on Illumina platforms (Supplementary Information section 2, Supplementary Table 1). We merged the reads and mapped them against the African savannah elephant (Loxodonta Africana) genome (‘LoxAfr4’) and an Asian elephant (Elephas maximus) mitochondrial genome. DNA-based age estimates To estimate specimen ages using mitogenome data, we conducted a Bayesian molecular clock analysis that was calibrated using samples with finite radiocarbon dates (tip calibration) and a log-normal prior that assumed a genomic divergence between the African savannah elephant and mammoth lineages at 5.3 Ma15 (root calibration). On the basis of this analysis, the specimens were estimated to date to 1.65 Ma (95% highest posterior density, 2.08–1.25 Ma), 1.34 Ma (1.69–1.06 Ma) and 0.87 Ma (1.07–0.68 Ma) for Krestovka, Adycha and Chukochya, respectively (Fig. 1c, e). We also used the autosomal genomic data to investigate the age of the higher-coverage Adycha (0.3×) and Chukochya (1.4×) specimens, by estimating the number of derived changes since their most recent common ancestor with the African savannah elephant (Supplementary Information section 6). We used an approach based on the accumulation of derived variants over time, assuming a constant mutation rate. This analysis suggested that the Adycha and Chukochya specimens date to 1.28 Ma (95% confidence interval, 1.64–0.92 Ma) and 0.62 Ma (95% confidence interval, 1.00–0.24 Ma), respectively (Fig. 1d). Although we caution that this analysis is based on low-coverage data and the confidence intervals are wide, these estimates are similar to those obtained from the mitochondrial data.

Color me skeptical. -Q Querius

Kairosfocus @14, I've done a bunch of searches, but I can't find the thread. The most common value that I've seen is a computed maximum of 521 years at -5ºC (2012).

Palaeogeneticists led by Morten Allentoft at the University of Copenhagen and Michael Bunce at Murdoch University in Perth, Australia, examined 158 DNA containing leg bones belonging to three species of moa, an extinct species of giant birds, The bones were between 600 and 8,000 years old, had been recovered from three sites within 5 km of each other and were in nearly identical preservation conditions.

These researchers also concluded that

DNA would cease to be readable after 1.5 million years.

This would be 2,879 half lives. At that rate, less than 1% of the DNA would be accessible in moa bones after only 7 half lives (3,647 years)--under ideal conditions. According to references provided by Alan Fox, apparently, plant matter that's been dried has a significantly longer half life. But none of these data can reliably date organic matter, but simply indicate a maximum age under ideal conditions. I also noticed that the age of insects trapped in amber was never in question. Rather, it was assumed that the DNA recovered MUSTA been due to contamination from modern sources. Thinking about it, I'm surprised that no one tried to identify these "modern" sources or mention the comparison of the DNA in the amber with those of modern related insects. If the DNA had matched up, then the dates of the amber (~25-30 million years) would come into question and we can't have that, can we? -Q Querius

AF, that is now gaslighting. I simply invite onlookers to read 13 above. It is clearly a widely understood point that the D/RNA in the cell contains code. That is what Lehninger documents, which utterly undermines your earlier attempts to dismiss that. It's over. KF kairosfocus

The quotes you tell me are from an edition of the Lehninger biochemistry textbook that you reproduce in comment 13 are fine. It is you who is stretching the analogy of template matching as "coding" beyond breaking point. It is you who are twisting the words into pretzels. ................................................................................................ Alan Fox

AF, still doubling down on slander, tells us a lot about your sad want of credibility or of basic regard for truth. You can see a little above in no. 13 the clips with wider context and no ellipses of things like, references to figures, where ellipsis is not automatically suspect, quotation is inherently selective as you know and as you further know they are normally fairly brief. The cites are DEMONSTRABLY not misquotes, they are not distorted by selection out of context or otherwise false to the sense of this well known outstanding textbook now in its 8th edn. Fail. KF kairosfocus

@Querius you write "we [you and KF, presumably] still haven’t received a proper response for my challenges as if you have achieved something. But all you have done is posted comments here in an obscure blog that Dembski long ago abandoned. If either of you honestly thought you were mounting a real challenge to mainstream science, surely you would take the battle to them. Les chiens aboient, la caravanne passe. Why not bark louder, where you can't be ignored. Alan Fox

Querius:

So what’s the experimentally measured half life of DNA extracted from animals in caves or other even more ideal environments such as permafrost? With a constant humidity and temperature, the effects of background radiation gain importance.

As I've said more than once, it has been shown that DNA fragments survive for millenia in suitable conditions. Overlapping fragments can be matched to produce longer sequences. The risks of amplification of contaminant DNA is now well understood and can be minimised.

Tiny segments of DNA do not make the grade of “DNA sequencing.”

Short sequences can be matched for overlap.

A related question is “What constitutes the minimum useful fragment length of DNA?” Certainly not one or two base pairs, right? And then there’s DNA deamination to consider as well.

Yes, I agree that a doublet of nucleotides tells us little. But a 20 - 30 base sequence tells us something when among a mix of fragments. Alan Fox

AF, slanderer...

Good grief! You are the quote-miner!

...to double down on a false dismissal of the significance of coded information in D/RNA.

Information is stored in DNA sequences, you can call it "encoded" if you like the analogy but it is misleading.

I actually gave a more complete text already.

Then why not link to it? Do you have a copy of Lehninger? Which edition? I get the impression you are cherry-picking secondary sources.

Get thee to a Library

I live in France. The availability of anglophone scientific works is somewhat limited.

and have a modicum of decency. KF

Thou Pharisee! Alan Fox

Q, I actually found and provided half life data, tying provided values at 100 and 0 degrees C. Not sure where that thread is, but it is there. KF kairosfocus

PS, just to underscore, I start with a figure, p. 189:

FIGURE 1-29 Two ancient scripts. (a) The Prism of Sennacherib, inscribed in about 700 BCE, describes in characters of the Assyrian language some historical events during the reign of King Sennacherib. The Prism contains about 20,000 characters, weighs about 50 kg, and has survived almost intact for about 2,700 years. (b) The single DNA molecule of the bacterium E. coli, leaking out of a disrupted cell, is hundreds of times longer than the cell itself and contains all the encoded information necessary to specify the cell’s structure and functions. The bacterial DNA contains about 4.6 million characters (nucleotides), weighs less than 10 ^ - 10  g, and has undergone only relatively minor changes during the past several million years . . .

Then, pp. 189/90:

The sequence of the monomeric subunits, the nucleotides (strictly, deoxyribonucleotides, as discussed below), in this linear | polymer encodes the instructions for forming all other cellular components and provides a template for the production of identical DNA molecules to be distributed to progeny when a cell divides . . . . A human sperm or egg, carrying the accumulated hereditary information of billions of years of evolution, transmits this inheritance in the form of DNA molecules, in which the linear sequence of covalently linked nucleotide subunits encodes the genetic message.

Notice, the distinction marked between the template and "this linear | polymer encodes the instructions for forming all other cellular components . . ." I have already noted how the templating follows a stepwise sequential process with halting. Notice, Lehninger's heirs continue, "the linear sequence of covalently linked nucleotide subunits encodes the genetic message." Then, p. 192:

A single page of this book contains about 5,000 characters, so the entire book contains about 5 million characters. The chromosome of E. coli also contains about 5 million characters (nucleotide pairs).

AF is doing little more than doubling down on a hyperskeptical bluff because he understands the significance of such language and does not wish to go there. As he is manifestly in the wrong about DNA encoding, we can take his rhetorical stunts and antics as a backhanded admission of the force of the point. PPS, on the already patently false accusation of quote mining, pp. 194 - 5, in more detail but highlighted:

The information in DNA is encoded in its linear (one- dimensional) sequence of deoxyribonucleotide subunits, but the expression of this information results in a three-dimensional cell. This change from one to three dimensions occurs in two phases. | A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids (Fig. 1-31). The protein folds into a particular three-dimensional shape, determined by its amino acid sequence and stabilized primarily by noncovalent interactions. Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” (see Fig. 4-28). The precise three-dimensional structure, or native conformation, of the protein is crucial to its function. [Cited, per fair academic/educational use.]

Thus, not at all misquoted or taken out of context to distort patently and even insistently intended meaning. The latest rhetorical doubling down stunt by AF backfires and ends up underscoring the significance of four state per character text or digital code in the cell, thus language, and the significance of some of that code expressing algorithms, stepwise goal directed sequences. And, noting that this is four state per digit machine code for numerical control is actually obvious to anyone familiar with computer architecture. There is a reason why one readily finds tables of the genetic code, mention of variants and discussion of recent modification and application to general data storage. Repeat, the objections and accusations are there because of the ideological "need to deny" the patent force of the design inference on coded text and so linguistic information and algorithms in the cell. As to Lehninger, this text is not on trial, AF is. And, he has failed. kairosfocus

Kairosfocus @11, And while on the subject of DNA/RNA coding sequences, we still haven't received a proper response for my challenges of experimental data regarding:

So what’s the experimentally measured half life of DNA extracted from animals in caves or other even more ideal environments such as permafrost? With a constant humidity and temperature, the effects of background radiation gain importance.

Tiny segments of DNA do not make the grade of “DNA sequencing.”

A related question is “What constitutes the minimum useful fragment length of DNA?” Certainly not one or two base pairs, right? And then there’s DNA deamination to consider as well.

In this case I'd add, how much code can be missing from DNA or RNA sequences to render sequencing unreliable: Is it 100% missing? 50% missing (after one half life)? 75% missing (after two half lives)? -Q Querius

AF, slanderer, to double down on a false dismissal of the significance of coded information in D/RNA. I actually gave a more complete text already. Get thee to a Library and have a modicum of decency. KF kairosfocus

AF, the text makes little difference, I simply compressed.

So I'm being asked to argue with Kairosfocus' quote mines of a biochemistry textbook. Pretty deceitful behaviour, KF. Alan Fox

JVL, apparently the US Intelligence community adapted it to deal with, it seems, inter alia understanding their hall of mirrors problem. In terms of knowledge at group, movement, institution or community level, what is known to us and them are in common known knowns. What is known to us but not them is secure classified information, our known knowns and what is known to others but blind to us is the mirror image of that. Not known to anyone can be known as not known or not even known to be not known -- ultimate unknown unknowns . . . see Mr Rumsfeld's remarks which were exactly on a matter of devastating intelligence failure. . Understanding one's state of knowledge and that of relevant others is vital. And so forth, there are several twists and turns in it try the second order knowledge issues on knowing that one knows, etc . . . watch the hall of mirrors emerge and say, hi there. Knowledge, is not a simple issue. KF kairosfocus

AF, the text makes little difference, I simply compressed. And you know your attempt to reject code is precisely the issue. Answered, from a standard text, with edition and page; get thee to a Library. KF kairosfocus

Too late to edit. Should be another "is". "What text there is is uncontroversial." Alan Fox

Just out of curiosity, KF, where did you get the text from that I quote from your comment #3 above: “The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function.” Why all the ellipses? Are they in the original text? What text there is uncontroversial. I would not have used "encoded" but other than that, what's the beef? Alan Fox

While I am familiar with the 'window' I didn't realise that that particular derivation came from a technique developed in psychology.

The Johari window is a technique[1] designed to help people better understand their relationship with themselves and others. It was created by psychologists Joseph Luft (1916–2014) and Harrington Ingham (1916–1995) in 1955, and is used primarily in self-help groups and corporate settings as a heuristic exercise. Luft and Ingham named their model "Johari" using a combination of their first names.

In the exercise, someone picks a number of adjectives from a list, choosing ones they feel describe their own personality. The subject's peers then get the same list, and each picks an equal number of adjectives that describe the subject. These adjectives are then inserted into a two-by-two grid of four cells. The philosopher Charles Handy calls this concept the Johari House with four rooms. Room one is the part of ourselves that we and others see. Room two contains aspects that others see but we are unaware of. Room three is the private space we know but hide from others. Room four is the unconscious part of us that neither ourselves nor others see.

Not sure how all that applies to a general theory of knowledge however. JVL

Glancing at reviews and recommendations, it seems Lehninger is considered a good choice for first year university students taking biochemistry. Fine. So why, KF, should I be concerned about a particular biochemistry student textbook? Alan Fox

AF, you know full well that Lehninger is an epochal, yardstick reference text on the state of core biochemistry, indeed it shaped the modern approach. You further know full well that it undercuts your pretence that it is not widely recognised that D/RNA uses codes, and that undergrads and others reading the said text have a right to consider themselves, on that strength, as "able to represent something as it is on an adequate basis of thought or experience, not to exclude communications from qualified sources (“authority”)." You have now tried to double down, dismissing rather than to cogently responding to:

"The information in DNA is encoded in its linear (one-dimensional) sequence of deoxyribonucleotide subunits . . . . A linear sequence of deoxyribonucleotides in DNA codes (through an intermediary, RNA) for the production of a protein with a corresponding linear sequence of amino acids . . . Although the final shape of the folded protein is dictated by its amino acid sequence, the folding of many proteins is aided by “molecular chaperones” . . . The precise three-dimensional structure, or native conformation, of the protein is crucial to its function." [Principles of Biochemistry, 8th Edn, 2021, pp 194 – 5. Now authored by Nelson, Cox et al, Lehninger having passed on in 1986. Attempts to rhetorically pretend on claimed superior knowledge of Biochemistry, that D/RNA does not contain coded information expressing algorithms using string data structures, collapse. We now have to address the implications of language, goal directed stepwise processes and underlying sophisticated polymer chemistry and molecular nanotech in the heart of cellular metabolism and replication.]

See https://uncommondesc.wpengine.com/darwinist-debaterhetorical-tactics/protein-synthesis-what-frequent-objector-af-cannot-acknowledge/ That tells us all we need to know about the sort of rhetorical stunts you are inclined to pull. Sadly telling. KF kairosfocus

So why should I be concerned about a particular biochemistry student textbook? Alan Fox

L&FP, 58b: The JoHari Window and recognising limits of our knowledge kairosfocus