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

_{Denyse O'Leary

March 19, 2023

Intelligent Design, Religion, Science}

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Due May 16, 2023:

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

And the issue with CISS is what, exactly, Phil?Alan Fox_{April 6, 2023
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AF also claims, "regarding chirality in general, the change from hetero to homochirality can be a result of fixing on one or other enantiomer. The “choice” can be arbitrary and subsequent to establishment of a biochemical reaction pathway, rather than a prerequisite." Yet that false claim was already addressed in post 135, (since I knew that AF would try to claim what he just claimed at post 136). https://uncommondescent.com/intelligent-design/a-review-of-nicholas-spencers-magisteria-the-entangled-histories-of-science-and-religion/#comment-779373bornagain77_{April 6, 2023
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Af links to a 2022 CISS paper and asks, "What does Phil regard as problematic for biomolecules and biochemistry?" This is yet another shining example of Darwinists trying to gloss over the severe challenges for naturalistic OOL scenarios. Trying to gloss over homochirality in this instance. From the abstract of AF's very own referenced paper we read, "its physical origin remains elusive, and no theoretical description can quantitatively describe it."
Spinterface chirality-induced spin selectivity effect in bio-molecules Abstract The chirality-induced spin selectivity (CISS) effect, namely the dependence of current through a chiral molecule on spin of the electron, was discovered over two decades ago, and has been suggested for various spin- and chirality-related applications. Yet, quite surprisingly, its physical origin remains elusive, and no theoretical description can quantitatively describe it. Here, we propose a theory for the CISS effect in bio-molecular junctions, based on the interplay between spin–orbit coupling in the electrodes, molecular chirality and spin-transfer torque across the electrode-molecule interface. This theory leads to the first ever quantitative analysis of experimental data, and provides insights into the origin of the CISS effect. The theory presented here can be used to analyze past experiments and to design new experiments, which may lead to deeper understanding of what is considered one of the outstanding problems in molecular electronics and nano-scale transport. https://pubs.rsc.org/en/content/articlelanding/2022/sc/d2sc02565e#fn1
And from. the summary and discussion,
Summary and discussion To summarize, here we presented a theoretical model for the CISS effect in long bio-molecules, including the role of dephasing. We find that while dephasing tends to reduce the CISS, the polarization is rather insensitive to the molecular length. In order to explain this, a surprising and simple connection between the magnitude of the CISS effect and the differential conductance was established. This connection allowed us to clarify the behavior of the polarization as a function of dephasing and molecular length. We again stress that the length-independence of the spinterface mechanism does not mean that the CISS polarization measurements will be length-independent, because the polarization depends on the transport properties and the molecular spin polarizability, which indeed may show length-dependence. Disentangling the length-dependence of the transport properties from the CISS effect can be done by finding a molecular system with length-independent transport properties; our results predict that in such a system the CISS effect will also be length-independent. Using the theoretical model, we then proceeded to analyze the data from the paper of Xie et al.. First, the connection between the CISS magnitude and the differential conductance was demonstrated with the experimental data. Then, using a simplified model for the current through bio-molecules (motivated by the microscopic theory), we were able to reproduce the experimental data of the CISS effect with remarkable agreement, keeping the parameters of the CISS effect (namely the metal electrode SOC and the spin-torque coupling) molecule-independent, as expected. To our knowledge, this is the first theoretical formulation of the CISS effect which can quantitatively fit experimental raw data (i.e. the magnetization-dependent currents). Indeed, recent studies aiming to fit data with theory53 show a factor of two difference in polarization between theory and data, and show a qualitative experiment-theory difference in the I–V curves (which are the real experimental signal, and the polarization is only a quantity extracted from the currents); while in experiments currents increase as a function of temperature, the calculated currents decrease with temperature (compare Fig. 1(c) with Fig. S1 in ref. 53). The methodology presented here opens a route for a deeper understanding of the CISS effect in bio-molecules, as past and future experiments (some suggested in ref. 35) can now be analyzed using a microscopic theory and fitted quantitatively. Future studies will be aimed at extracting the dependence of the CISS effect on other experimental parameters, especially temperature (which is not accounted in the model presented here directly).
This paper has no answer to how CISS, i.e. homochirality, came about, but only discusses how CISS is happening at the molecular level. i.e. how they can "quantitatively describe it",, as they state in their summary, "The methodology presented here opens a route for a deeper understanding of the CISS effect in bio-molecules", and their paper DOES NOT address how homochiraility came about in the first place. In short, AF's very own referenced paper only further confirms what Dr. Tour has highlighted concerning the huge problem that homochirality presents to naturalistic OOL scenarios.bornagain77_{April 6, 2023
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Here's a recent (2022) paper on measuring CISS in biomolecules. What does Phil regard as problematic for biomolecules and biochemistry? Regarding chirality in general, the change from hetero to homochirality can be a result of fixing on one or other enantiomer. The "choice" can be arbitrary and subsequent to establishment of a biochemical reaction pathway, rather than a prerequisite.Alan Fox_{April 6, 2023
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Further notes to homochirality:
"People thought we didn't have to control the handedness of the molecule, the molecular shape. The handedness (of) whether the (molecule was) left hand or right hand. (People thought) that those (handedness of molecules) evolved later on as life got more proficient. (Yet) we now know, because of work coming out of the Weissman Institute by Ron Naaman's group, that you had to have near perfect enantiopure materials at the start of life. How that ever happened we have no idea. You can't even get life going because if you don't have an enantiopure materials. Everything burns up. The chemistry generates too much heat for the cell to ever survive because you get backscattering of electrons. These are spin valves. This is how nature, how natural systems, operate. So we can't even get it going. We can't start Evolution. So why even really discuss much about it (evolution if) we can't even start it till we have the first cell? We can't even make the first cell." - James Tour - 27:30 minute mark Origin of Life: Controversial Chemist (James Tour) Shakes up Scientific Community | Problems with Primordial Soup https://youtu.be/ZugOrSD7YL4?t=1654
In fact, Dr. Tour visited Ron Naaman personally,
The Importance of CISS - James Tour - 2017 I first became aware of chiral induced spin selectivity (CISS) in 2014 when visiting Ron Naaman at the Weizmann Institute in Rehovot, Israel. As he was describing his recent experimental results, I recall thinking that the implications of CISS are enormous, and especially in biological systems. My mind was racing as I began to wonder whether this was the reason that long-range information transfer could be effective in a cell, whereas in human-made devices we have never been able to accomplish such efficiencies. I looked at Ron and said something like, “This is amazing. You’re gonna win a Nobel Prize for this!” Yes, CISS is that profound. Yet it remains unknown, or certainly unappreciated, by most scientists, and it is almost never mentioned by biologists. So when a scientific review article on CISS appeared in 2016,1 I immediately wrote an essay for Inference which described the effect while underscoring the implications for living systems.2 In this new essay, Naaman and his long-time colleague in the study of CISS, David Waldeck, both physical chemists, provide a general background on CISS, then they specifically address the consequences of this effect in biology. The authors begin by defining terms for the reader, noting, for example, that the spin of an electron is either spin-up or spin-down, while underscoring the importance of these quantities in electron transfer processes. Electron transfer is at the heart of most biological transformation, including the ubiquitous electron shuttles that take place in the membrane of the mitochondria—the powerhouse organelle of the cell and the core of cellular respiration. This is needed for the conversion of raw nutrients into energy to drive all biochemical processes. Alarmingly, few biochemists take into account electron spin in their calculations and the interpretation of experimental data. This would be akin to working on a 2017 car engine while being familiar only with 1950s automotive technology. Nobody knew about electronic ignition, fuel injection, microprocessors, sensors, or actuators during the 1950s. Sure, the basics of combustion are the same, but there would be so much missing. Such is our knowledge of biochemistry; even the so-called experts neglect key aspects of importance to the biochemical system. CISS is revealing a new world of biological device complexity. And these are not subtle effects that are buried in the noise of a much grander biological framework. Not at all. CISS is the source of the high chemical- and enantio-selectivities in biological reactions. CISS points the way to a solution of the mystery behind an insect’s ability to synthesize organic molecules with far more efficiency and much higher yields and optical purities than the world’s top synthetic organic chemists can achieve. In the insect, chemical reactions are selected with matched electron spin, traveling down matched chiralities in molecules, to afford energy profiles that strongly favor the desired product. The insect’s reaction chemistry controls electron spin while the synthetic chemist does not. Other effects, such as steric hand-and-glove models or dipolar interactions within the enzymatic clefts, are often addressed, but an electron’s spin and its coupling with the host molecule has never before been considered. CISS is likely the dominant property in biochemistry to which kinetics and thermodynamics must pay homage. Biology is exquisite in its precision, capitalizing upon electron-spin dominated information that is read by the homochiral molecules. Thus DNA and RNA are not the only information storage systems in a cell. The chiral molecules are the readers and conduits of that information, while electrons of specific spin are the information carriers. The authors write: "Charge polarization in chiral molecules, the experiment indicated, is accompanied by spin polarization. The spin polarization imposes a symmetry constraint from the Pauli exclusion principle that affects the electron cloud overlap. As two chiral molecules interact, they induce a charge redistribution and a spin polarization in their electronic clouds which change the interaction energy. Who knew? Almost no one. And all of these electron cloud permutations, which are virtual photon interactions, are occurring at near the speed of light." Naaman and Waldeck gently peel back the layers of complexity, revealing aspects that were formerly obscured. The neglect of CISS can and has caused data misinterpretation and collective cluelessness regarding the manner by which biological systems respire, synthesize, process, and transfer information. Herein lies the problem. For one to accurately appreciate the complexity of biochemistry, it is essential to be well-versed in quantum mechanics. While Naaman and Waldeck suggest that CISS is often ignored, my only criticism of their article is that the authors are not sufficiently explicit. A higher banner must be raised. The educators of biological phenomena are themselves hamstrung in their interpretations due to their lack of knowledge of quantum mechanics. Biology is far more sophisticated than we had imagined. Such is the state of most modern science. We appreciate little. We know even less. https://inference-review.com/letter/the-importance-of-ciss
As to: "The educators of biological phenomena are themselves hamstrung in their interpretations due to their lack of knowledge of quantum mechanics." And indeed, Darwinists, because of their materialistic framework, don't even have the proper theoretical framework in which to properly understand quantum biology in the first place. As Jim Al-Khalili states at the 2:30 minute mark of the following video,,
",, Physicists and Chemists have had a long time to try and get use to it (Quantum Mechanics). Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can't build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn't really require much in the way of quantum mechanics in the way to explain it." - Jim Al-Khalili – Quantum biology – video https://www.youtube.com/watch?v=zOzCkeTPR3Q
At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state:
“To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”. - Jim Al-Khalili – Quantum biology – video https://www.youtube.com/watch?v=zOzCkeTPR3Q
In fact, materialism, in and of itself, is simply incompatible with quantum mechanics.
Quantum Physics Debunks Materialism (v2) https://www.youtube.com/watch?v=wM0IKLv7KrE
Moreover, the implications of this quantum biology, (which Darwinists are apparently blissfully unaware of), are profound.
since Darwinian Atheists, as a foundational presupposition of their materialistic philosophy, (and not from any compelling scientific evidence mind you), deny the existence of souls/minds, (and since the materialist’s denial of souls/minds, (and God), has led (via atheistic tyrants) to so much catastrophic disaster on human societies in the 20th century), then it is VERY important to ‘scientifically’ establish the existence of these ‘souls’ that are of incalculable worth, and that are equal, before God. https://uncommondescent.com/off-topic/what-must-we-do-when-the-foundations-are-being-destroyed/#comment-768496
Specifically, quantum biology provides empirical evidence for a transcendent component to our being, a eternal soul, that is capable of living beyond the death of our material, temporal, bodies. As Stuart Hameroff states in the following article, “the quantum information,,, isn’t destroyed. It can’t be destroyed.,,, it’s possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.”
Leading Scientists Say Consciousness Cannot Die It Goes Back To The Universe – Oct. 19, 2017 – Spiritual Excerpt: “Let’s say the heart stops beating. The blood stops flowing. The microtubules lose their quantum state. But the quantum information, which is in the microtubules, isn’t destroyed. It can’t be destroyed. It just distributes and dissipates to the universe at large. If a patient is resuscitated, revived, this quantum information can go back into the microtubules and the patient says, “I had a near death experience. I saw a white light. I saw a tunnel. I saw my dead relatives.,,” Now if they’re not revived and the patient dies, then it’s possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.” – Stuart Hameroff – Quantum Entangled Consciousness – Life After Death – video (5:00 minute mark) (of note, this video is no longer available for public viewing) https://radaronline.com/exclusives/2012/10/life-after-death-soul-science-morgan-freeman/
Personally, I consider these recent findings from quantum mechanics and quantum biology to rival all other scientific discoveries over the past century. Surpassing even the discovery of a beginning of the universe, via Big Bang cosmology, in terms of scientific, theological, and even personal, significance. As Jesus once asked his disciples along with a crowd of followers, “Is anything worth more than your soul?”
Mark 8:37 Is anything worth more than your soul?
bornagain77_{April 6, 2023
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AF: "Quick glance at that Tour video. He claims very little work has been done since Miller and Urey, which is far from true, as a quick google check shows." Yet the point that Dr. Tour is making is that, "Origins of life (OOL) research has, to be sure, become progressively more sophisticated, but its goal—to explain the origins of life—remains as distant today as it was in 1952."
Time Out - James Tour - 2019 Excerpt: In 1952, Stanley Miller and Harold Urey derived a number of racemic amino acids from a handful of small molecules. These were electrifying results because they suggested that the methods of synthetic chemistry might finally explain the origins of life. The excitement was justified, but premature.1 Origins of life (OOL) research has, to be sure, become progressively more sophisticated, but its goal—to explain the origins of life—remains as distant today as it was in 1952. This is not surprising. The protocols in use have remained unchanged: buy highly purified chemicals; mix them together in high concentrations and in a specific order under carefully devised laboratory conditions; derive a mixture of compounds; and publish a paper making bold claims about OOL. These protocols are as unrealistic as they are unimproved.,,, https://inference-review.com/article/time-out
In fact, truth be told, the more we learn about just how complex a 'simple' cell actually is, the worse the OOL "problem" gets for Darwinists. As Dr. Tour observes in the following interview, "we are more befuddled now than we were in 1952"
"Every year we understand more about the complexity. So we are more befuddled now than we were in 1952" - James Tour: The Origin of Life Has Not Been Explained - Science Uprising Expert Interview https://youtu.be/r4sP1E1Jd_Y?t=1102
AF goes on, "He (Dr. Tour) also mentions stereochemistry of amino-acids. I invite him to check on the stereochemistry of glycine." AF wants to act as if Dr. Tour is unaware that glycine is not chiral. Yet, Dr. Tour is well aware that glycine is not chiral.
Chiral Induced Spin Selectivity - James Tour - 2016 Chirality is ubiquitous in biological molecules. Aside from water, glycine, and acetic acid (among others), the majority of such molecules are chiral. The polymers of chiral molecules, such as the polysaccharides, polypeptides, and polynucleotides, are composed of chiral molecules. Such structures take on new shapes, including helices and spiral clefts, that are themselves chiral.,,, https://inference-review.com/article/chiral-induced-spin-selectivity
And that comment from AF on glycine is yet another shining example of Darwinists glossing over these huge problems with current OOL research as if they are no big deal. Despite AF trying to hand-wave off homochirality as if it is no big deal for OOL research, and as Dr. Tour reveals in this following lecture on homochirality, homochirality is a huge problem for OOL research that remains unresolved.
Dr. James Tour - (Problems with) Abiogenesis Theory - Homochirality https://youtu.be/tqbpd3CmBgE
Of supplemental note:
The Riddle Of Life's Beginnings feat. Biochemist James Tour (Science Uprising - episode 05) https://www.youtube.com/watch?v=Ymjlrw6GmKU
bornagain77_{April 6, 2023
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Quick glance at that Tour video. He claims very little work has been done since Miller and Urey, which is far from true, as a quick google check shows. He also mentions stereochemistry of amino-acids. I invite him to check on the stereochemistry of glycine.Alan Fox_{April 5, 2023
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Bornagain77 @131, Thanks, but the silence on Dr. Tour's analysis by the skeptics here and their sock puppets tells us that they're not open to new information. A pity. -QQuerius_{April 5, 2023
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In the following interview from 3 weeks ago, and starting around the 16 minute mark, Dr. Tour briefly goes over huge problems with current origin of life research. Huge problems that Darwinists simply gloss over as if they are no big deal.
Origin of Life: Controversial Chemist Shakes up Scientific Community | Problems with Primordial Soup https://youtu.be/ZugOrSD7YL4?t=968
bornagain77_{April 5, 2023
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Ba77, It is obvious that there are two sides here. Both sides can't be right. For Unguided Evolution: It happened, somehow. Yet repeated requests for empirical evidence have gone unanswered. Only conjecture, along the lines of Richard Dawkins' "climbing mount improbable," where evolution is given goals, direction and intelligence. Or, various complex things reached a certain level of complexity and went on to become more complex, without explanation.relatd_{April 5, 2023
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BA77, let's add, just to help recognise just how speculative this is, observe the following buried lead: https://www.ncbi.nlm.nih.gov/books/NBK26876/
Molecular Biology of the Cell. 4th edition. The RNA World and the Origins of Life . . . A Pre-RNA World Probably Predates the RNA World Although RNA seems well suited to form the basis for a self-replicating set of biochemical catalysts, it is unlikely that RNA was the first kind of molecule to do so. From a purely chemical standpoint, it is difficult to imagine how long RNA molecules could be formed initially by purely nonenzymatic means [--> enzymes are proteins]. For one thing, the precursors of RNA, the ribonucleotides, are difficult to form nonenzymatically. Moreover, the formation of RNA requires that a long series of 3? to 5? phosphodiester linkages form in the face of a set of competing reactions, including hydrolysis, 2? to 5? linkages, 5? to 5? linkages, and so on. Given these problems, it has been suggested that the first molecules to possess both catalytic activity and information storage capabilities may have been polymers that resemble RNA but are chemically simpler (Figure 6-93). We do not have any remnants of these compounds in present-day cells, nor do such compounds leave fossil records. Nonetheless, the relative simplicity of these “RNA-like polymers” make them better candidates than RNA itself for the first biopolymers on Earth that had both information storage capacity and catalytic activity.
So, it's on to pre-RNA now. And of course these issues sound a lot like points Dr Tour long since raised. KFkairosfocus_{April 5, 2023
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Only in the imagination of Darwinists is the RNA world "empirically supported by several pieces of research as Alan has shown." As Dr. Tour mentioned in his video about Joyce's research, "This RNA that was made and all the things that were replicated, these nucleotides that were used were not made prebiotically, they were taken from nature to be used. Nobody knows how we got these in the first place …" https://youtu.be/WKLgQzWhO4Q?t=17378 And as Dr. Tour highlighted previous to that comment, small molecules to RNA has never been shown without illegitimately 'borrowing" from nature, and/or from massive intelligent intervention from highly trained Chemists.
- "Small molecules" to RNA has never been shown, https://youtu.be/CYiguQYCSio?t=1619
My question to Darwinists is this, "Just how much intelligent intervention from highly trained Chemists is allowed in your 'natural' precursor OOL scenarios before you will honestly admit that intelligent design is required to explain life?"
Atheist's logic 101 - cartoon "If I can only synthesize life here in the lab it will prove that no intelligence was necessary to create life in the beginning" http://dl0.creation.com/articles/p073/c07370/Scientist-synthesize-life-machine.jpg
bornagain77_{April 5, 2023
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Kairosfocus writes:
And, RNA world is an empirically bankrupt just so story,
That is empirically supported by several pieces of research as Alan has shown. And you accuse others of ideologically driven dismissiveness.Ford Prefect_{April 5, 2023
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Just a snippet from the paper I linked to in comment #125 We found that non-canonical vestige nucleosides8–12, which are key components of contemporary RNAs6,7, are able to equip RNA with the ability to self-decorate with peptides. This creates chimeric structures, in which both chemical entities can co-evolve in a covalently connected form13, generating gradually more and more sophisticated and complex RNA–peptide structures.Alan Fox_{April 5, 2023
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Here's a more recent paper, 2022. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9095488/ I think I have some reading to do. I'll try and sit through Tour's video, too. Fingers crossed, UD holds together a bit longer. In which case: I'll be back!Alan Fox_{April 5, 2023
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AF, evolutionary materialistic scientism and fellow traveller ideologies are just that, ideologies that are multiply intellectually bankrupt. Persons, they are not. And, RNA world is an empirically bankrupt just so story, as Dr Tour among others has shown at adequate length. KFkairosfocus_{April 5, 2023
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Thanks folks for indirectly leading me to Gerald Joyce's 2009 paper on self replication of RNA. Here's the link to the full paper. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652413/ I'm curious what other work has been done since 2009. The paper has been widely cited.Alan Fox_{April 5, 2023
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Bornagain77 @120,
AF apparently can’t see, or more likely simply refuses to see, that appealing to already existent life that uses RNA as his main support for his claim that the RNA world generated life is a blatant example of ‘circular reasoning’, and/or ‘assuming his conclusion’. i.e. AF is guilty of ‘begging the question’.
Yes, exactly. Also notice that implicit in the response is an appeal to the second of the three Darwinian gods of the gaps, MUSTA. ". . . RNA is central to cellular metabolism across all species" etc. etc., so there MUSTA been an RNA world to make it all happen. Pure science fantasy. Too bad Alan Fox refuses to watch this segment of Dr. Tour's rebuttal of RNA world: https://youtu.be/WKLgQzWhO4Q?t=17378 -QQuerius_{April 5, 2023
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Bornagain @97 Thank you for linking to the James Tour video. https://youtu.be/WKLgQzWhO4Q?t=17378 I did not know that "RNA-world" was in such bad shape. RNA must be extracted from nature, no one knows how to make it. Degradation is an enormous problem. Next, RNA, under pristine laboratory conditions, cannot self-replicate more than once! Only 6% self-replicates, but no part of that 6% can self-replicate further; no further daughters ensue ... What are we even talking about? "RNA-world" cannot be considered serious science.
James Tour: … in the RNA world explorations researchers have made specially designed primed RNA that can replicate itself without exogenous enzymes. Gerald Joyce is one of the leaders in this field. But these self-replicating RNA enzymes are limited far from a general application and they have not duplicated a significant portion of themselves where further daughters could ensue. For example a short RNA of 189 bases could replicate an 11-mer from primed template strands (6% of the strand was copied). So only six percent of something that was set up to self-replicate could self-replicate. It had an error rate of 1.1 % per nucleotide which is a high error rate. … You can't deal with an error rate like this. The largest it was able to replicate was a 14-mer which is also too short for self-replication [in won’t self-replicate further]. The record is 20 bases long but again too short for further replication [it won’t self-replicate further].So these ones that replicated could never replicate anymore and it didn't replicate the whole thing, only short segments. And these were primed set up in a laboratory under pristine conditions. Obviously all the component nucleotides were isolated from natural sources. This RNA that was made and all the things that were replicated, these nucleotides that were used were not made prebiotically, they were taken from nature to be used. Nobody knows how we got these in the first place …
Origenes_{April 5, 2023
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KF: "In short, as James Tour and many others have shown, RNA world is yet another empirically unsupported just so story dressed up in a lab coat." AF responds: "Unsupported, apart from the fact that RNA is central to cellular metabolism across all species. It is the working core of ribosomes, it is copied from DNA in order to transfer sequence information for protein synthesis. It is a most versatile molecule." AF apparently can't see, or more likely simply refuses to see, that appealing to already existent life that uses RNA as his main support for his claim that the RNA world generated life is a blatant example of 'circular reasoning', and/or 'assuming his conclusion'. i.e. AF is guilty of 'begging the question'
Circular reasoning Circular reasoning (Latin: circulus in probando, "circle in proving";[1] also known as circular logic) is a logical fallacy in which the reasoner begins with what they are trying to end with.[2] Circular reasoning is not a formal logical fallacy, but a pragmatic defect in an argument whereby the premises are just as much in need of proof or evidence as the conclusion, and as a consequence the argument fails to persuade. Other ways to express this are that there is no reason to accept the premises unless one already believes the conclusion, or that the premises provide no independent ground or evidence for the conclusion.[3] Circular reasoning is closely related to begging the question, and in modern usage the two generally refer to the same thing.[4] https://en.wikipedia.org/wiki/Circular_reasoning
AF goes on, "and if that (RNA world) is all you have; then, in an environment where you are first and without competition, you don’t need perfection and you can flourish while evolutionary processes kick in." AF's belief that the hypothetical RNA world can possibly generate the ribosome is a mighty big 'if" that AF is presupposing to be true
Imagine How It Happened! "Evolution Presents" the Ribosome, "Nature's Masterpiece" - July 9, 2014 Excerpt: There are even more reasons to reject the evolutionary hypothesis in the PNAS paper on which the film was based. The authors provide no evidence that the "common core" (Phase 1 in the film) of the large ribosomal subunit (LSU) was able to do anything on its own. There is a small ribosomal subunit (SSU) that has to match it. Even more important, a ribosome is useless without a genome! How do they handle that? "In our model, the LSU has evolved in distinct phases," the paper speculates. "This process started with the formation of the P site, possibly in an RNA world, and continues today in eukaryotes." So they lean on the RNA world scenario, which we have shown many times is untenable. This is recognized even by evolutionists, such as Niles Lehman, whom Casey Luskin quoted as saying, "The odds of suddenly having a self-replicating RNA pop out of a prebiotic soup are vanishingly low." This stops the tale before it even starts. The authors try to make the "common core" look small and simple, but the LSU of the simplest bacterium contains on the order of 3,000 nucleotides. The small rRNA subunit (SSU) contains another 1,500 more. These are much larger (and more complex) than anything that origin-of-life researchers could ever hope for in an RNA world. Even more problematic for evolution, both ribosomal subunits for the simplest bacterium contain dozens of protein parts integrated with the RNA parts. But the proteins had to be translated by the very ribosome the evolutionists are trying to explain! It's a profound chicken-and-egg problem that Williams and his co-authors gloss over,,, http://www.evolutionnews.org/2014/07/imagine_how_it2087611.html 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
On top of "The odds of suddenly having a self-replicating RNA pop out of a prebiotic soup are vanishingly low" AF also has no empirical evidence whatsoever that a 'prebiotic soup' ever even existed in the real world.
"We get that evidence from looking at carbon 12 to carbon 13 analysis. And it tells us that in Earth's oldest (sedimentary) rock, which dates at 3.80 billion years ago, we find an abundance for the carbon signature of living systems. Namely, that life prefers carbon 12. And so if you see a higher ratio of carbon 12 to carbon 13 that means that carbon has been processed by life. And it is that kind of evidence that tells us that life has been abundant on earth as far back as 3.80 billion years ago (when water was first present on earth).,,, And that same carbon 12 to carbon 13 analysis tells us that planet earth, over it entire 4.5662 billion year history has never had prebiotics. Prebiotics would have a higher ratio of carbon 13 to carbon 12. All the carbonaceous material, we see in the entire geological record of the earth, has the signature of being post-biotic not pre-biotic. Which means planet earth never had a primordial soup. And the origin of life on earth took place in a geological instant" Hugh Ross - Origin of Life - 11 minute mark https://youtu.be/I417jWea0C0?t=672
In fact, and again, the only place that the RNA world has even been observed existing in the real world is in highly manipulated laboratory conditions where intelligent intervention by highly trained chemists is rampant. As James Tour observed,
",,, and these were primed. Set up in a laboratory under pristine conditions. Obviously all the component nucleotides were isolated from natural sources. This RNA that was made, and all the things that were replicated, these nucleotides that were used were not made prebiotically. They were taken from nature to be used. Nobody knows how we got these (prebiotically) in the first place",,, – Dr. James Tour Episode 8 – Nucleotides, DNA, and RNA – RNA self-replication – 4:51:06 mark https://youtu.be/WKLgQzWhO4Q?t=17378
Thus in conclusion, AF may repeatedly 'assume his conclusion' to try to claim that the existence of the ribosome itself proves that the RNA world hypothesis must be true, but, as far as empirical science itself is concerned, AF simply has no empirical evidence whatsoever that a prebiotic soup ever even existed on the early earth, nor does he have any evidence that it is mathematically, and/or chemically probable for RNA self-replication to spontaneously appear in the non-existent prebiotic soup.. Nor, as Dr. Tour has shown, do chemists even use prebiotically relevant conditions to generate the limited RNA self replication they achieved in laboratories. In short, AF has only his blind faith, and no real-time empirical evidence whatsoever, to support his apriori belief in the RNA world (and/or his apriori belief in atheistic materialism)bornagain77_{April 5, 2023
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a sign of the bankruptcy of the evolutionary materialistic dogma and its fellow travellers.
See this, UB? This is attacking the messenger.Alan Fox_{April 5, 2023
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In short, as James Tour and many others have shown, RNA world is yet another empirically unsupported just so story dressed up in a lab coat.
Unsupported, apart from the fact that RNA is central to cellular metabolism across all species. It is the working core of ribosomes, it is copied from DNA in order to transfer sequence information for protein synthesis. It is a most versatile molecule and if that is all you have; then, in an environment where you are first and without competition, you don't need perfection and you can flourish while evolutionary processes kick in.Alan Fox_{April 5, 2023
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AF et al:
the evolution of the genetic code happens after RNA World is ~~established [--> imposed per evolutionary materialist dogma]~~
In short, as James Tour and many others have shown, RNA world is yet another empirically unsupported just so story dressed up in a lab coat. Myths like this cannot be devastating blows. The only actually empirically well supported biological life is protein using, encapsulated, smart gated, metabolising, cell based life, with DNA and mRNA using coded, algorithmic symbolic information to build proteins. The imposition of the RNA World myth as if it were fact is a sign of the bankruptcy of the evolutionary materialistic dogma and its fellow travellers. KFkairosfocus_{April 5, 2023
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RNA World does not have to explain the genetic code and protein synthesis. (thud)
Really, the evolution of the genetic code happens after RNA World is established. It is not an ingredient in RNA World. I realize this is a devastating blow to your argument but you'll have to address it at some point. Or move onAlan Fox_{April 5, 2023
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Or will you continue to attack the messenger instead?
How is pointing out a major flaw in your argument a personal attack?Alan Fox_{April 5, 2023
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I still don't understand why Upright Biped doesn't get together with BIO-Complexity and work on publishing a paper.Alan Fox_{April 5, 2023
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AF, for the sake of argument, lets assume that the scientific literature demonstrates the fulfilled prediction that an autonomous open-ended self-replicating cell (life) requires a system of encoded symbols and constraints.
I'll acknowledge the problem and wonder "what next?". Now you? 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 5, 2023
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. AF, for the sake of argument, lets assume that the scientific literature demonstrates the fulfilled prediction that an autonomous open-ended self-replicating cell (life) requires a system of encoded symbols and constraints. What will be your next step? - - - - - - - - - - - - - - - - - - - - - - By the way, this is effectively the question I asked you at the very top of this conversation months ago. Can you allow yourself to acknowledge the legitimacy of the history, the science and reason — even if you personally believe that some day the inference will be falsified? Can you even walk away? Or will you continue to attack the messenger instead? Thus far, you’ve made your choice abundantly clear. You’ve answered the question.Upright BiPed_{April 4, 2023
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...you don’t even have an autonomous self-replicating RNA, do you?
The inherent properties of RNA (pair bonding between cytosine and guanine, adenine and uracil) is autonomous. RNA bases will polymerize under the right conditions, temperature, pH level, concentration, energy source.Alan Fox_{April 4, 2023
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UB writes:
[Alan Fox's] challenge is to propose the steps that could have taken RNA world to DNA-protein world.
That is an important challenge. I readily confirm I don't know the details of such steps. What there is, once you have self-sustaining self-replicators, is time and opportunity. There's a grey area between "this pathway is impossible" and "this is what happened". I can live with doubt on details while research continues.Alan Fox_{April 4, 2023
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