Uncommon Descent Serving The Intelligent Design Community

A review of Nicholas Spencer’s Magisteria: The Entangled Histories of Science and Religion

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Due May 16, 2023:

At UK Spectator:

So this is a profoundly puzzling book. Spencer knows his history of science. He recounts the set pieces of any such story – the trial of Galileo, Huxley vs Wilberforce, the Scopes monkey trial – with bravura. He has a good grasp of how science has changed over time, and he also understands that the word ‘religion’ meant very different things to Cicero, Augustine and the author of The Golden Bough. But he doesn’t seem to grasp that the pared down, purely ‘spiritual’ religion he defends has virtually nothing in common with that of Augustine, Calvin, Loyola and Newman.

What this book marks, in fact, is the quiet triumph of meta-science over faith, for faith in the Bible as history, in the great eschatological drama of redemption, has been replaced here by faith, not in a creator and redeemer God, but in the peculiar specialness of human beings. Perhaps we are special; but there’s more to religion than an insistence that, because we make our lives meaningful, the universe must have a meaning. Though Spencer finds the idea repugnant, maybe we are just peculiar machines whose functioning depends on producing, in endless succession, deepity after deepity. If there is one thing that is clear about human beings, after all, it is that we have a remark-able talent for self-deception – and what is religion but a trick we play on ourselves? – David Wootton (March 18, 2023)

Comments
UB, for the sake of argument, let's assume your claim about the evolvability of the genetic code has merit and you have convinced me. What will be your next step?Alan Fox
April 4, 2023
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the fact that RNA World is a plausible precursor still stands. RNA is still both replicator and catalyst today.
You continue to assume your conclusions while avoiding the physical detail (the science). - - - - - - - - - - - - - - - - - - - - - - This is how you lose an argument by assuming your conclusions, and then spare yourself of the reason: AF: Upright Biped! Upright Biped! Upright Biped! AF: your whole “semiosis” argument fails on the existence of RNA and its dual role as replicator and catalyst. UB: Being able to play a “dual role” (as a catalyst and as an information carrier like mRNA) implies that there are certain conditions that enable the RNA to play those two roles. AF: My challenge is to propose the steps that could have taken RNA world to DNA-protein world. AF: One! The answer to your question, Upright Biped, (now you have clarified) is one. AF: No I don’t suggest any biochemically active suite of proteins can be constructed from polymers consisting of a single amino acid. AF: RNA World does not have to explain the genetic code and protein synthesis. (thud) - - - - - - - - - - - - - - - - - …and despite having glorious funding and a hardy open door at every suitable institution on the surface of the planet for decades on end, you don’t even have an autonomous self-replicating RNA, do you.Upright BiPed
April 4, 2023
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For Upright Biped: Anyway, the fact that RNA World is a plausible precursor still stands. RNA is still both replicator and catalyst today. RNA World scenario allows evolutionary processes to add polypeptides, genetic code, aminoacyl tRNA synthetases incrementally. But no doubt you will continue to claim I have not refuted your argument. But what can you do? Nobody actually working in the field of OoL has heard of you or your “hypothesis”. Over a decade and counting with no progress. Are people cowering in fear of your mighty insight? I don’t think so. But my claim is testable. Why don’t you test it? Publish a paper where it might get noticed. Bio-Complexity should be beating a path to your door.Alan Fox
April 4, 2023
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Q, sadly yes.bornagain77
April 4, 2023
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Bornagain77, See what I mean? -QQuerius
April 4, 2023
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• 'The Church “proclaims that by the light of reason the human intellect can readily and clearly discern purpose and design in the natural world, including the world of living things.” • “Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.” ' "Christoph Cardinal Schönborn is archbishop of Vienna and general editor of the Catechism of the Catholic Church."relatd
April 4, 2023
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It’s a pity that Alan Fox won’t ever listen to this information, because he finds it ideologically incompatible with his beliefs.
Oh, physician heal thyself.Alan Fox
April 4, 2023
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Likewise, Relatd! Bornagain77 @97, What a great clip of the brilliant expert, Dr. Tour! Thank you. It's a pity that Alan Fox won't ever listen to this information, because he finds it ideologically incompatible with his beliefs. All we get is denials and vacuous unsupported assertions in reply. What a waste. But others of us appreciated it. -QQuerius
April 4, 2023
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Ba77, Your posts are much appreciated. "CHURCH: But none of us has recreated that,,. SHAPIRO: There must have been much more primitive ways of putting together. CHURCH: But prove it." My comment to these men would be: If it is so simple, why hasn't it been done in a lab?relatd
April 4, 2023
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The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm Inferring efficiency of translation initiation and elongation from ribosome profiling - 2020 Abstract Excerpt: Our method distinguishes between the elongation rate intrinsic to the ribosome’s stepping cycle and the actual elongation rate that takes into account ribosome interference. This distinction allows us to quantify the extent of ribosomal collisions along the transcript and identify individual codons where ribosomal collisions are likely. When examining ribosome profiling in yeast, we observe that translation initiation and elongation are close to their optima and traffic is minimized at the beginning of the transcript to favour ribosome recruitment. https://academic.oup.com/nar/article/48/17/9478/5895331 Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service - 2009 Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act." https://www.science.org/doi/full/10.1126/science.326_346 Armed Forces in the Cell Keep DNA Healthy - September 8, 2015 Excerpt: According to Prof. Hurt, the production of ribosomes is an extremely complex process that follows a strict blueprint with numerous quality-control checkpoints. The protein factories are made of numerous ribosomal proteins (r-proteins) and ribosomal ribonucleic acid (rRNA). More than 200 helper proteins, known as ribosome biogenesis factors, are needed in the eukaryotic cells to correctly assemble the r-proteins and the different rRNAs. Three of the total of four different rRNAs are manufactured from a large precursor RNA. They need to be "trimmed" at specific points during the manufacturing process, and the superfluous pieces are discarded. "Because these processes are irreversible, a special check is needed," explains Ed Hurt. http://www.evolutionnews.org/2015/09/armed_forces_in099121.html Ribosomes Optimized for Speed, Flexibility - August 2, 2017 Excerpt: The DNA translation machines in the cell show unexpected complexity, forcing molecular biologists to revise what they thought they knew about ribosomes. In particular, they appear optimized for speed of self-duplication and modularized for flexibility.,,, if you think of “orchestrated function” again, the sheet music won’t do any good if the stage isn’t already set up and the players aren’t in their seats.,,, The “orchestrated function of hundreds of proteins” has time limits. The conductor is pounding his foot and tapping his baton on the podium, rushing the orchestra to get in place. Imagine how much harder if each player, instrument, chair, and music stand has to make a copy of itself first for a show across town!,,, https://evolutionnews.org/2017/08/ribosomes-optimized-for-speed-flexibility/ Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013 Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within cells consisting of tightly stacked sheets of membrane studded with the molecules (ribosome machines) that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell. "The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,, ,, this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,, http://www.sciencedaily.com/releases/2013/07/130718130617.htm
Moreover, (and as if the inference to intelligent design needed any more help), the Ribosome of the cell is also found to be very similar to a CPU in an electronic computer:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf
bornagain77
April 4, 2023
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AF, "Remnants of RNA World exist now. Ribosomes are essentially ribozymes, their catalytic site consists of an RNA molecule. RNA is very versatile, performing many rôles in cellular metabolism." LOL, :)
LIFE: WHAT A CONCEPT! Excerpt: The ribosome,,,, it's the most complicated thing that is present in all organisms.,,, you find that almost the only thing that's in common across all organisms is the ribosome.,,, So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be? George Church http://www.edge.org/documents/life/church_index.html Leading Biologists Marvel at the "Irreducible Complexity" of the Ribosome, but Prefer Evolution-of-the-Gaps - Feb, 2008 Excerpt: VENTER: Below ribosomes, yes: you certainly can’t get below that. But you have to have self-replication. CHURCH: But that’s what we need to do — otherwise they’ll call it irreducible complexity. If you say you can’t get below a ribosome, we’re in trouble, right? We have to find a ribosome that can do its trick with less than 53 proteins. VENTER: In the RNA world, you didn’t need ribosomes. CHURCH: But we need to construct that. Nobody has constructed a ribosome that works well without proteins. VENTER: Yes. SHAPIRO: I can only suggest that a ribosome forming spontaneously has about the same probability as an eye forming spontaneously. CHURCH: It won’t form spontaneously; we’ll do it bit by bit. SHAPIRO: Both are obviously products of long evolution of preexisting life through the process of trial and error. CHURCH: But none of us has recreated that,,. SHAPIRO: There must have been much more primitive ways of putting together. CHURCH: But prove it. http://www.evolutionnews.org/2008/02/leading_biologists_marvel_at_t004789.html Of note, although the ribosome is present in all life, and is necessary for life, it is not uniform (i.e. conserved) across all life as is presupposed within Darwinian theory, i.e. the 'non-conserved' nature of ribosomes falsify Darwin's theory. Ribosomes Excerpt: Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth) differ in their size, sequence, structure, and the ratio of protein to RNA. https://sites.google.com/site/jjohnsonelps301/home/animal-cell-structure/ribsomes Information Processing Differences Between Bacteria and Eukarya—Implications for the Myth of Eukaryogenesis by Change Tan and Jeffrey P. Tomkins on March 25, 2015 Excerpt: In a previous report, we showed that a vast chasm exists between archaea and eukarya in regard to basic molecular machines involved in DNA replication, RNA transcription, and protein translation. The differences in information processing mechanisms and systems are even greater between bacteria and eukarya, which we elaborate upon in this report. Based on differences in lineage-specific essential gene sets and in the vital molecular machines between bacteria and eukarya, we continue to demonstrate that the same unbridgeable evolutionary chasms exist—further invalidating the myth of eukaryogenesis. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-bacteria-and-eukarya/
bornagain77
April 4, 2023
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The RNA world does not exist now, and never has existed, in the real world.
Remnants of RNA World exist now. Ribosomes are essentially ribozymes, their catalytic site consists of an RNA molecule. RNA is very versatile, performing many rôles in cellular metabolism. See this list.Alan Fox
April 4, 2023
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AF: "RNA World does not have to explain the genetic code and protein synthesis. It merely has to exist as a precursor" The RNA world does not exist now, and never has existed, in the real world. But has only ever existed in the fevered imagination of Darwinian atheists and, in a highly limited sense, in highly manipulated laboratory conditions.
Abiogenesis Hypothesis ULTRA Pack! Free Course w/ Rice University Chemist - Dr. James Tour Episode 8 - Nucleotides, DNA, and RNA - RNA self-replication - 4:49 mark https://youtu.be/WKLgQzWhO4Q?t=17378
bornagain77
April 4, 2023
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Perhaps most importantly, an RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins.
RNA World does not have to explain the genetic code and protein synthesis. It merely has to exist as a precursor, where self-sustaining self-replicators are thus subject to evolutionary processes and the various steps in incorporation of amino-acids into cellular metabolism can be added incrementally.Alan Fox
April 4, 2023
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Robert Shapiro was professor emeritus of chemistry at New York University. He is best known for his work on the origin of life, having written two books on the topic...@
I hold fond memories of professor Shapiro, with whom I had extensive email interaction in 2005 over claims his review of Darwin's Black Box amounted to peer review. It was reading his books that led me to my former position of being skeptical of RNA World. I thoroughly recommend Planetary Dreams which advocates researching other worlds for evidence of life, which would give us much insight into OoL. I now think the circumstantial evidence for RNA World has piled up since such that Shapiro would take a different view, were he alive today.Alan Fox
April 4, 2023
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Alan Fox: "the fact that RNA World is a plausible precursor still stands." Others disagree.
The RNA world hypothesis: the worst theory for the early evolution of life (except for all the others) - July 2012 Excerpt: "The RNA World scenario is bad as a scientific hypothesis" - Eugene Koonin “The RNA world hypothesis has been reduced by ritual abuse to something like a creationist mantra” - Charles Kurland "I view it as little more than a popular fantasy." - Charles Carter https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/ Putting the RNA World to the Test with "Pistol" - February 24, 2017 Excerpt: In Susan Mazur's book The Origin of Life Circus, leading origin-of-life researchers describe the utter disaster of the RNA world scenario in one-on-one interviews she recorded in person. *Lawrence Krauss tells her (p. 35): "The question is, can RNA result naturally? That's been a big stumbling block." *David Deamer tells her (p. 43) that the RNA and DNA monomers don't link up naturally: "the laws of thermodynamics do not allow them to polymerize because there is a tremendous energy barrier to getting them to form bonds." That's especially true in water, he says, which breaks down (hydrolyzes) RNA. *Sara Walker tells Mazur that researchers need to move away from the RNA World, "because most of the origin-of-life community don't think that's the definitive answer." Walker herself says, "I don't see how an RNA world with only RNA can work" (p. 68). *Loren Williams tells her the original RNA World ("all RNA, all the time, and nothing else") is unreasonable and dead. RNA can't have done everything originally claimed. "Another problem is related to the origin of RNA itself. Where did RNA come from? Where did RNA precursors come from?" (p. 96). *Steven Benner tells Mazur (p. 81), "we don't know how useful function is distributed among sequence spaces. You have 4 raised to the power of 100 different sequences of RNA 100 nucleotides long. We don't know how productive function is distributed there compared to destructive function." Chances are destructive processes are increased as much as productive processes, he adds. On page 151-152, Benner lists four major "paradoxes" of the RNA world: the tar problem, the water problem, the entropy problem and the destruction problem. *RNA-world champion Nick Hud has abandoned the idea that RNA would form on its own. He's looking for candidates of not only proto-RNA, but "pre-proto-RNA" because, as Mazur reminds him, "RNA itself falls apart" (p.87). *Stuart Kauffman tells Mazur that they "tried for 40 years to get single-stranded RNA molecules to replicate, perhaps hundreds of chemists, and they all failed. It should work. But it hasn't. And after 40 years or 50 years, you think - maybe it's the wrong idea. People really tried hard" (p. 111). *Jack Szostak ups the time estimate to 60 years that researchers have worked on this problem of non-enzymatic replication. "The problem is RNA falls apart," he says (p. 218). *Norm Packard tells Mazur, "There are issues with the RNA world approach. The main one is how do you get RNA starting to get produced in the first place" (p. 297). He envisions an enzyme doing it. This speculation, of course, leads to an obvious problem: "But how do you get that enzyme?" *Pier Luigi Luisi is merciless in his attack, calling the RNA world a "baseless fantasy." Mazur puts his criticisms in bold print on pages 362-363, where he finds it "full of conceptual flaws," including its origin, the thermodynamics, the sequencing problem, the concentration problem, and more. The story of RNA turning into ribozymes he calls "chemical non-sense" (p. 363). http://www.evolutionnews.org/2017/02/putting_the_rna103513.html Can the Origin of the Genetic Code Be Explained by Direct RNA Templating? Stephen C. Meyer, Paul A. Nelson Abstract Motivated by the RNA world hypothesis, Michael Yarus and colleagues have proposed a model for the origin of the ‘uni- versal’ genetic code, in which RNA aptamers directly template amino acids for protein assembly. Yarus et al. claim that this “direct RNA templating” (DRT) model provides a stereochemical basis for the origin of the code, as shown by the higher-than- expected frequency of cognate coding triplets in aptamer amino acid-binding sites. However, the DRT model suffers from several defects. These include the selective use of data, incorrect null models, a weak signal even from positive results, an implausible geometry for the primordial RNA template (in relation to the universally-conserved structures of modern ribo- somes), and unsupported assumptions about the pre-biotic availability of amino acids. Although Yarus et al. claim that the DRT model undermines an intelligent design explanation for the origin of the genetic code, the model’s many shortcomings in fact illustrate the insufficiency of undirected chemistry to construct the semantic system represented by the code we see today. https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.2/BIO-C.2011.2 "As a medical biochemist (aka chemical pathologist) and a biologist with training in evolutionary biology, I can’t help but comment on Jack Szostak ideas regarding the issue of the origin of the genetic code. None of what he said about the issue in the context of the RNA world idea, and none of what is presented in one of the recent paper mentionned (Radakovic 2022 PNAS) has any chemical plausibility in my opinion.,,, As usual with RNA and ribozymes, catalytic activities are very weak and molecules are unstable. This has always plagued the RNA world hypothesis and no one has ever solved this inconvenient fact. And as usual with OoL research, the probability of any of these sorts of reactions occurring in natural prebiotic conditions is indistinguishable from zero. For example, the amino acid they used, Lysine, is, as they concede, not reasonably expected to be found in prebiotic environment:,,, That this sort of wild, totally implausible, speculation is allowed to appear in a respectable journal like PNAS is embarrassing.,,, Outside living cells, we know of no other chemical reaction governed by a code, not a single one, why ? The question is thus, how can chemistry become linguistic/informatics? So far, nobody has any clue." - Jblais - July 2022 https://uncommondescent.com/intelligent-design/at-evolution-news-gunter-bechly-repudiates-professor-daves-attacks-against-id/#comment-760263 ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal - December 5, 2017 Excerpt: Some researchers who study the origins of life on Earth have hypothesized that RNA evolved before DNA or proteins. If true, RNA would have needed a way to replicate without enzymes.,,,, The errors were “definitely embarrassing,” Szostak told us: "In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments." http://retractionwatch.com/2017/12/05/definitely-embarrassing-nobel-laureate-retracts-non-reproducible-paper-nature-journal/ Life What A Concept! - Robert Shapiro – video http://www.youtube.com/watch?&v=ku9wUbbPVYg#! (The late) Professor Robert Shapiro~ quote from preceding video “I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable. I’m always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words “To be or not to be, that is the question,” that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn’t be functional until it attained a certain length and could copy itself — appearing on the Earth.” Robert Shapiro was professor emeritus of chemistry at New York University. He is best known for his work on the origin of life, having written two books on the topic: The End of the RNA World Is Near, Biochemists Argue - December 19, 2017 Excerpt: Perhaps most importantly, an RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins. Finding a set of rules robust enough to do that would take far too long with RNA alone, said Peter Wills, Carter’s co-author at the University of Auckland in New Zealand — if the RNA world could even reach that point, which he deemed highly unlikely. In Wills’ view, RNA might have been able to catalyze its own formation, making it “chemically reflexive,” but it lacked what he called “computational reflexivity.” “A system that uses information the way organisms use genetic information — to synthesize their own components — must contain reflexive information,” Wills said. He defined reflexive information as information that, “when decoded by the system, makes the components that perform exactly that particular decoding.” The RNA of the RNA world hypothesis, he added, is just chemistry because it has no means of controlling its chemistry. “The RNA world doesn’t tell you anything about genetics,” he said. https://www.quantamagazine.org/the-end-of-the-rna-world-is-near-biochemists-argue-20171219/
bornagain77
April 4, 2023
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You telling me that I “just don’t understand” that the RNA World didn’t have or need all that stuff is nothing more than hand-waiving (sic) under the big bright lights.
Bright lights? The bulbs are getting a bit dim here at UD. Anyway, the fact that RNA World is a plausible precursor still stands. RNA is still both replicator and catalyst today. RNA World scenario allows evolutionary processes to add polypeptides, genetic code, aminoacyl tRNA synthetases incrementally. But no doubt you will continue to claim I have not refuted your argument. But what can you do? Nobody actually working in the field of OoL has heard of you or your "hypothesis". Over a decade and counting with no progress. Are people cowering in fear of your mighty insight? I don't think so. But my claim is testable. Why don't you test it? Publish a paper where it might get noticed. Bio-Complexity should be beating a path to your door. What's the alternative?Alan Fox
April 3, 2023
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. Alan at 72. You come back at me again with the “you just don’t understand” bit? (ahem) Are you not going to tell me that I carelessly, but quite mistakenly, have some dates and experimental findings and their authors incorrect? Crick’s adapter hypothesis surely came out in 1955 at Cavendish, and it surely says what it says. And could Francis Crick have been any more clear? Could Von Neumann have been more clear? Could Brenner? Could the physicist, Pattee? I don’t think so. Are you not, then, going to tell me that my “interpretation” of the experimental history is wrong – wasn’t that your earlier claim. Is the physics wrong? Are you not going to argue that Hoagland and Zamecnik never confirmed Crick’s protein constraints and Von Neumann’s symbolic descriptions? It is hard to pull that off when there are papers upon papers making the same case in physical terms, not to mention having a Nobel Laureate – the guy who actually named the adapter hypothesis – speaking openly about it and making the exact same connection on the pages of the world’s most prestigious journal … which, by the way, was claim written 45 years after RNA was first suspected of having some catalytic properties and 30 years after it was confirmed. One might stumble upon the conclusion that Brenner (apparently like me today) didn’t understand the RNA World hypothesis when he wrote those words and conclusions in Nature, but I am betting that he did. He wrote them because the experimental history is correct. The physics is correct. Apparently, the fact that nucleic bases pair-up, and can sometimes have enzymatic activity, doesn’t change the fact that you have to have encoded descriptions in a transcribable medium to establish the gene — to physically enable the origin of specification, control, and heredity (i.e. life). For those descriptions to exist, as was predicted, it requires all the components and organization that make encoded descriptions physically possible in the first place. As a matter of the historical record, like a big cherry on top, it was the finding of all those components that confirmed the predictions. You telling me that I “just don’t understand” that the RNA World didn’t have or need all that stuff is nothing more than hand-waiving under the big bright lights. Its pitiable, Alan. The case has been made. Neither your dismissal nor your dogma is going to make it go away. CheersUpright BiPed
April 3, 2023
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Bornagain77 @88,
The ‘near perfect’ finding for ATP synthase, (and for other molecular systems), is far more problematic for dogmatic Darwinists, such as AF, than they will ever honestly admit to the public.
Of course. For them, abiogenesis has just GOTTA be true despite all evidence to the contrary. Similarly, in spite of the experiments of Redi, Spallanzani, and Pasteur, their own opponents never admitted they were wrong either.
Félix-Archimède Pouchet, (born Aug. 26, 1800, Rouen, Fr.—died Dec. 6, 1872, Rouen), French naturalist who was a leading advocate of the idea of the spontaneous generation of life from nonliving matter. Pouchet was director of the Rouen Museum of Natural History and the Rouen Jardin des Plantes (1828) and later a professor at the School of Medicine at Rouen (1838). In his major work, Hétérogénie (1859), he detailed the conditions under which living organisms supposedly were produced by chemical processes such as fermentation and putrefaction. His supporters were primarily among those whose religious or philosophical beliefs required the concept of spontaneous generation. Pouchet’s theory was discredited when Louis Pasteur proved the existence of microorganisms in the air. Today Pouchet’s elaborate arguments are mere curiosities. - Britannica
Louis Pasteur falsified abiogenesis using swan-necked flasks together with his germ theory and corresponded with Pouchet. Nevertheless, Pouchet defiantly published his book on abiogenesis later that same year. Similarly, the vacuous arguments and fatuous noise from the detractors here, who consistently avoid the scientific challenge from James Tour and others, will eventually become mere curiosities of history, and their desperate struggle against mounting scientific evidence will be forgotten as well. -QQuerius
April 3, 2023
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Assauber writes:
“why does there have to be a “why?” FP, You in grade school?
Nice mature response. Now, do you want to try to address the concept that “why” is not the question that science is designed to answer? The point of science is to try to answer “how.” Asking “why” instills an inherent bias to the research. It assumes an intention when an intention may not be a factor. We can hope that science can help us figure out how the universe formed, or how humans came to exist. But science can never be used to infer/imply/conclude “why” they did.Ford Prefect
April 3, 2023
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Ba77, I think this sums it up: "... an unfalsifiable religion for atheists." It would explain a necessary - for some - defense of this idea regardless of evidence against it.relatd
April 3, 2023
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AF now claims, "I don’t and never have subscribed to strict determinism. I, from first-person experience, am convinced I am able to choose among viable and constrained possible actions. They use “near-perfect” in the title and throughout the paper:" Yet previously AF claimed that his 'niche', not AF himself, was responsible for what he was writing in his posts
BA77: “So AF holds that the ‘niche”, not AF himself, is responsible for the information that he himself is writing in his posts?” Alan Fox: “Yes, sort of, though I don’t know,,,,”
So I guess AF now wants a 'do over' from this previous comment? :)
"I think I need a do over" https://media.tenor.com/SvVMlwxdZpYAAAAd/i-think-i-need-a-do-over-bad-day.gif
:) Of further note to ATP synthase in particular, David Coppedge just posted this over at ENV:
Denton’s “Puzzle of Perfection,” Then and Now David Coppedge - April 3, 2023 Excerpt: They use “near-perfect” in the title and throughout the paper: "ATP synthase produces most of the ATP in respiratory and photosynthetic cells. It is a rotary motor enzyme and its catalytic portion F1-ATPase hydrolyzes ATP to drive rotation of the central ? subunit. Efficiency of chemomechanical energy conversion by this motor is always near-perfect under different ATP hydrolysis energy (?GATP) conditions." Any deviation from perfection, however, could be due to experimental error. In their graph, the error bars transverse the slope for 100 percent efficiency (that is, for conversion of chemical energy to mechanical work). It may well be as close to perfect as is physically possible. What’s even more striking is that this “near-perfect” level of efficiency is maintained throughout a “broad range” of operation conditions.,,, https://evolutionnews.org/2023/04/dentons-puzzle-of-perfection-now-and-then/
The 'near perfect' finding for ATP synthase, (and for other molecular systems), is far more problematic for dogmatic Darwinists, such as AF, than they will ever honestly admit to the public. As William Bialek found, "Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark,,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants."
William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them the superb efficiency with which bacterial cells will close in on a food source; the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head; and the way a shark can find its prey by measuring micro-fluxes of electricity in the water a tremulous millionth of a volt strong — which, as Douglas Fields observed in Scientific American, is like detecting an electrical field generated by a standard AA battery “with one pole dipped in the Long Island Sound and the other pole in waters of Jacksonville, Fla.” In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.html
And as William Bialek further noted, "While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks."
William Bialek Excerpt: A central theme in my research is an appreciation for how well things ‘work’ in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks. https://www.princeton.edu/~wbialek/wbialek.html William Bialek is the John Archibald Wheeler/Battelle Professor in Physics, and a member of the multidisciplinary Lewis-Sigler Institute for Integrative Genomics, at Princeton University.
In fact, 'adaptation' itself is found to be 'perfect' As the following article states, “There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.”,,, Moreover, the "amazing and surprising" outcome of the study is applicable to any living organism or biochemical network of any size.,,,”
Math sheds light on how living cells 'think' - May 2, 2018 Excerpt: "Proteins form unfathomably complex networks of chemical reactions that allow cells to communicate and to 'think' --,,, "We could never hope to measure the full complexity of cellular networks -- the networks are simply too large and interconnected and their component proteins are too variable. "But mathematics provides a tool that allows us to explore how these networks might be constructed in order to perform as they do.,,, Dr Araujo's work has focused on the widely observed function called perfect adaptation -- the ability of a network to reset itself after it has been exposed to a new stimulus. "An example of perfect adaptation is our sense of smell," she said. "When exposed to an odour we will smell it initially but after a while it seems to us that the odour has disappeared, even though the chemical, the stimulus, is still present. "Our sense of smell has exhibited perfect adaptation. This process allows it to remain sensitive to further changes in our environment so that we can detect both very faint and very strong odours. "This kind of adaptation is essentially what takes place inside living cells all the time. Cells are exposed to signals -- hormones, growth factors, and other chemicals -- and their proteins will tend to react and respond initially, but then settle down to pre-stimulus levels of activity even though the stimulus is still there. "I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.,,, Professor Lance Liotta, said the "amazing and surprising" outcome of Dr Araujo's study is applicable to any living organism or biochemical network of any size.,,, https://www.sciencedaily.com/releases/2018/05/180502094636.htm
To break this down for you AF, these empirical findings are NOT good news for Darwinists, and should count as yet another falsification of Darwin's theory. And these findings would count as an empirical falsification of Darwin's theory if Darwin's theory were a normal science that was subject to empirical testing instead of being, basically, an unfalsifiable religion for atheists.
1 Thessalonians 5:21 but test all things. Hold fast to what is good.
Of supplemental note to this finding of 'perfect adaptation', Lewontin himself stated in an article entitled 'Adaptation" that, "It was the marvelous fit of organisms to the environment,,, that was the chief evidence of a Supreme Designer.,,,"
Adaptation - by Richard C. Lewontin - 1978 Excerpt: Organisms fit remarkably well into the external world in which they live. They have morphologies, physiologies and behaviors that appear to have been carefully and artfully designed to enable each or­ganism to appropriate the world around it for its own life. It was the marvelous fit of organisms to the environment, much more than the great diversity of forms, that was the chief evidence of a Supreme Designer.,,, https://dynamics.org/~altenber/LIBRARY/REPRINTS/Lewontin_Adaptation.1978.pdf
bornagain77
April 3, 2023
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Tonight o the Alan Fox Show. Alan sings The Niche. You definitely want to miss it. :)relatd
April 3, 2023
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Besides being out of touch with reality regarding OOL research, and as Alan Fox himself gives witness to, Alan Fox is also out of touch with reality regarding his own actions in the universe. Specifically, Alan Fox, via his denial of free will, denies that he himself is responsible for writing his own sentences.
Here's one straw-man. I don't and never have subscribed to strict determinism. I, from first-person experience, am convinced I am able to choose among viable and constrained possible actions.Alan Fox
April 3, 2023
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Alan Fox @84,
Whether or not the straw-men he has flailed at have been demolished, they don’t represent my views.
Seems to me that Upright BiPed did an excellent job. Maybe you should try addressing his points if you can.
I’d write more but UD keeps freezing up when I try to comment.
I wouldn't say that UD is "freezing up" in your case. I think it's simply cringing. :D -QQuerius
April 3, 2023
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Ba77 has thoroughly debunked your claims.
Well, not really. Whether or not the straw-men he has flailed at have been demolished, they don't represent my views. I'd write more but UD keeps freezing up when I try to comment.Alan Fox
April 3, 2023
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Bornagain77 @74, Thank you! Looks like Rowan Williams and Anthony Kenny demolished Richard Dawkin's speculations about consciousness. And I was astonished at Dawkins' quasi-religious description in one gigantic run-on sentence blown out in a single breath that fantasizes . . .
. . . I think that um it is a thing most wonderful almost too wonderful to be that at least on this planet and possibly on billions of other planets but certainly on this one the laws of physics have conspired to make the collisions of atoms get together to produce nothing that any physicist would have dreamed of but to produce things like us to produce plants, trees, kangaroos, uh insects, and us to produce collections of matter collections of atoms that don't just obey Newton's laws in a passive way they don't obviously disobey them but not in a passive way but which move and jump and spring and hunt and flee and mate, and think at least in our case which is a quite astonishing thing to have happened and we know since 1859 how it happened and it's almost too wonderful to believe but we have to believe it because we now know it's true it's almost too wonderful to believe that um the laws of physics working through this very remarkable process that Darwin called natural selection has produced these gigantic collections of apparently purposeful beings which look overwhelmingly as though they had been designed they carry a a terrific illusion of design which fooled humanity until the middle of the 19th century um now I think that Darwin's achievement in doing that was not only a magnificent achievement in itself but it was a triumph of science which can be generalized to science generally because once Darwin had solved the problem of how you can get big complicated purposeful and apparently designed things out of very simple beginnings once Darwin has solved that problem, it then gives courage to the rest of science that the same thing can be done in general and that we shall end up understanding literally everything as springing from almost nothing or according to some modern physicists even literally nothing and I think that that is a truly wonderful thought when i say almost too wonderful to be it's a thought that is extremely hard to comprehend and believe and many people have great difficulty in believing it and resort to uh what in my view is is an unsatisfactory uh resolution to the problem which is to say an intelligence did it that seems to me to be an invasion of the question an invasion of the scientific responsibility to understand how things come about how complicated things come about in terms of of simple things . . .
Later, Dawkins wonders whether consciousness is an illusion, and (after hundreds of more words) how babies meld such illusions into a unified identity that somehow explains consciousness. Pure, hilarious entertainment! -QQuerius
April 3, 2023
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AF at 76, Ba77 has thoroughly debunked your claims.relatd
April 3, 2023
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Q, I had problems connecting to UD Thursday evening and over the weekend. Andrewasauber
April 3, 2023
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Asauber @79, But WHY does there have to be a "Why does there have to be a why?" Rinse and repeat. LOL -Q P.S. I'm having a hard time accessing UD. Yesterday was impossible. It always seems to be timing out. Anyone else have that problem?Querius
April 3, 2023
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