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

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March 19, 2023

Intelligent Design, Religion, Science

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Intelligent Design
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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

"why does there have to be a “why?” FP, You in grade school? Andrewasauber_{April 3, 2023
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Alan Fox writes:
Why there is a universe and why there are humans has not been answered yet.
A bigger question is why does there have to be a “why?” We may find a how, and for the most part I think we have filled in many of these gaps. And none of them point to a designer (a “why”).Ford Prefect_{April 3, 2023
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AF, and your scientifically falsified belief in common descent, (As Dr. Cornelius Hunter, (PhD – Biophysics), put it, “the dependency graph (intelligent design) model is astronomically superior compared to the (universal) common descent model.”)
New Paper by Winston Ewert Demonstrates Superiority of Design Model - Cornelius Hunter - July 20, 2018 Excerpt: Ewert’s three types of data are: (i) sample computer software, (ii) simulated species data generated from evolutionary/common descent computer algorithms, and (iii) actual, real species data. Ewert’s three models are: (i) a null model which entails no relationships between any species, (ii) an evolutionary/common descent model, and (iii) a dependency graph model. Ewert’s results are a Copernican Revolution moment. First, for the sample computer software data, not surprisingly the null model performed poorly. Computer software is highly organized, and there are relationships between different computer programs, and how they draw from foundational software libraries. But comparing the common descent and dependency graph models, the latter performs far better at modeling the software “species.” In other words, the design and development of computer software is far better described and modeled by a dependency graph than by a common descent tree. Second, for the simulated species data generated with a common descent algorithm, it is not surprising that the common descent model was far superior to the dependency graph. That would be true by definition, and serves to validate Ewert’s approach. Common descent is the best model for the data generated by a common descent process. Third, for the actual, real species data, the dependency graph model is astronomically superior compared to the common descent model. Where It Counts Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered — the actual, real, biological species data — the results were unambiguous. Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent. Darwin could never have even dreamt of a test on such a massive scale. Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other. We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand. Ten thousand is a big number. But it gets worse, much worse. Ewert used Bayesian model selection which compares the probability of the data set given the hypothetical models. In other words, given the model (dependency graph or common descent), what is the probability of this particular data set? Bayesian model selection compares the two models by dividing these two conditional probabilities. The so-called Bayes factor is the quotient yielded by this division. The problem is that the common descent model is so incredibly inferior to the dependency graph model that the Bayes factor cannot be typed out. In other words, the probability of the data set, given the dependency graph model, is so much greater than the probability of the data set given the common descent model, that we cannot type the quotient of their division. Instead, Ewert reports the logarithm of the number. Remember logarithms? Remember how 2 really means 100, 3 means 1,000, and so forth? Unbelievably, the 10,064 value is the logarithm (base value of 2) of the quotient! In other words, the probability of the data on the dependency graph model is so much greater than that given the common descent model, we need logarithms even to type it out. If you tried to type out the plain number, you would have to type a 1 followed by more than 3,000 zeros. That’s the ratio of how probable the data are on these two models! By using a base value of 2 in the logarithm we express the Bayes factor in bits. So the conditional probability for the dependency graph model has a 10,064 advantage over that of common descent. 10,064 bits is far, far from the range in which one might actually consider the lesser model. See, for example, the Bayes factor Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence. This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits. But It Gets Worse The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450. In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450. We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data. https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/
AF, your scientifically falsified belief in common descent, and your belief in the non-controversial claim of 'change over time', has exactly what to do with the fact that you are, self-admittedly, not in control of what you are writing in your posts? And although you, self admittedly, 'don't know' if you really are in control of writing your posts or not?
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,,,,”
And AF, why in blue blazes would you even entertain such an insane notion that you are not in control of what you are writing unless you were forced to take such an insane position by your apriori commitment to atheistic materialism? And again, If Alan Fox is self-admittedly not responsible for what he himself is writing in his posts, but his 'niche' is, why in blue blazes should anyone else pay him any attention?
(1) rationality implies a thinker in control of thoughts. (2) under materialism a thinker is an effect caused by processes in the brain (determinism). (3) in order for materialism to ground rationality a thinker (an effect) must control processes in the brain (a cause). (1)&(2) (4) no effect can control its cause. Therefore materialism cannot ground rationality. per Box UD
Of related note to us existing as 'real' persons, and not as 'neuronal illusions' as Darwinists hold,
I choose to hold that “I” exist —— to be clear, with “I” I refer to my consciousness, my viewpoint. I am the only one who has access to my “I”, put another way: no one but me can possibly have an informed opinion on this particular subject, therefor whatever I choose to believe about my “I” can only be my absolute responsibility, can only be the result of my fully self-determined choice. – – – – – – (1.) I do something. (2.) A thing that does not exist cannot do something —— from nothing nothing comes. From (1.) and (2.) (3.) I exist - Origenes https://uncommondescent.com/cosmology/from-iai-news-how-infinity-threatens-cosmology/#comment-766606
bornagain77_{April 3, 2023
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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,,,,”
What Alan Fox actually said: Yes, sort of, though I don’t know, as I said. The current mountain of evidence overwhelmingly supports the the ideas of common descent and change over time. Why there is a universe and why there are humans has not been answered yet.Alan Fox_{April 3, 2023
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Of supplemental note to the infinite Mind of God being the necessary foundational to any definition of 'reality' we may put forth, my question to atheists is this, "how is it remotely possible for something to become even ‘more real than real’ for a person having an Near Death Experience unless the infinite Mind of God truly is the ultimate basis for all of 'reality'?" In the following study, materialistic researchers who had an inherent bias against Near Death Experiences being real, set out to prove that they were merely ‘false memories’ by setting up a clever questionnaire that could differentiate which memories a person had were real and which memories a person had were merely imaginary. Simply put, they did not expect the results they found: To quote the headline 'Afterlife' feels 'even more real than real”
'Afterlife' feels 'even more real than real,' researcher says - Wed April 10, 2013 Excerpt: "If you use this questionnaire ... if the memory is real, it's richer, and if the memory is recent, it's richer," he said. The coma scientists weren't expecting what the tests revealed. "To our surprise, NDEs were much richer than any imagined event or any real event of these coma survivors," Laureys reported. The memories of these experiences beat all other memories, hands down, for their vivid sense of reality. "The difference was so vast," he said with a sense of astonishment. Even if the patient had the experience a long time ago, its memory was as rich "as though it was yesterday," Laureys said. http://www.cnn.com/2013/04/09/health/belgium-near-death-experiences/
And as the following study also found, 'memories of near-death experiences are recalled as ‘‘realer” than real events or imagined events.'
Characteristics of memories for near-death experiences - Lauren E. Moore, Bruce Greyson - March 2017 Abstract: Near-death experiences are vivid, life-changing experiences occurring to people who come close to death. Because some of their features, such as enhanced cognition despite compromised brain function, challenge our understanding of the mind-brain relationship, the question arises whether near-death experiences are imagined rather than real events. We administered the Memory Characteristics Questionnaire to 122 survivors of a close brush with death who reported near-death experiences. Participants completed Memory Characteristics Questionnaires for three different memories: that of their near-death experience, that of a real event around the same time, and that of an event they had imagined around the same time. The Memory Characteristics Questionnaire score was higher for the memory of the near-death experience than for that of the real event, which in turn was higher than that of the imagined event. These data suggest that memories of near-death experiences are recalled as ‘‘realer” than real events or imagined events. https://med.virginia.edu/perceptual-studies/wp-content/uploads/sites/360/2017/03/NDE-85-MCQ-ConCog.pdf
So again my question to atheists is, “how is it remotely possible for something to become even ‘more real than real’ for a person having an Near Death Experience unless the infinite Mind of God truly is the ultimate basis for all of ‘reality’?” And although atheists often dismiss Near Death Experiences as not being 'scientific', it is interesting to note the scientific evidence establishing the validity of Near Death experiences is far more robust than the scientific evidence for Darwinian evolution is,
Near-Death Experiences: Putting a Darwinist's Evidentiary Standards to the Test - Dr. Michael Egnor - October 15, 2012 Excerpt: Indeed, about 20 percent of NDE's are corroborated, which means that there are independent ways of checking about the veracity of the experience. The patients knew of things that they could not have known except by extraordinary perception -- such as describing details of surgery that they watched while their heart was stopped, etc. Additionally, many NDE's have a vividness and a sense of intense reality that one does not generally encounter in dreams or hallucinations.,,, The most "parsimonious" explanation -- the simplest scientific explanation -- is that the (Near Death) experience was real. Tens of millions of people have had such experiences. That is tens of millions of more times than we have observed the origin of species , (or the origin of life, or the origin of a protein/gene, or of a molecular machine), which is never.,,, The materialist reaction, in short, is unscientific and close-minded. NDE's show fellows like Coyne at their sneering unscientific irrational worst. Somebody finds a crushed fragment of a fossil and it's earth-shaking evidence. Tens of million of people have life-changing spiritual experiences and it's all a big yawn. Note: Dr. Egnor is professor and vice-chairman of neurosurgery at the State University of New York at Stony Brook. http://www.evolutionnews.org/2012/10/near_death_expe_1065301.html
In fact, we have far more observational evidence for the reality of immaterial minds/souls than we do for the Darwinian claim that unguided material processes can generate functional information. Moreover, the transcendent nature of 'immaterial' information, which is the one thing that, (as every ID advocate intimately knows), unguided material processes cannot possibly explain the origin of, directly supports the transcendent nature, as well as the physical reality, of the soul:
Oct. 2022 - So 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
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 3, 2023
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Alan Fox at 68 states: "Just to give Querius some respite from reality," "From reality"??? That is a very odd statement coming from a Darwinist. AF is pretending that he is being rational and that he is the one defending 'reality' and that Querius is somehow out of touch with reality. Nothing could be further from the truth. Darwinists, via their endless series of unsubstantiated 'wishful speculations' and 'just-so stories', are the ones who are, time and time again, shown to be the ones who are out of touch with 'reality'.
Dave Farina’s OOL “Experts” completely DEBUNKED by James Tour - Lee Cronin, Bruce Lipshutz, and Lee Smolin - video playlist https://www.youtube.com/watch?v=FP7ojkrZ1sc&list=PLILWudw_84t22BWvWsoXCmaXNllbfJ2h7
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.
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,,,,” https://uncommondescent.com/intelligent-design/at-evolution-news-for-darwinism-pregnancy-is-the-mother-of-all-chicken-and-egg-problems/#comment-771084
If Alan Fox is not responsible for what he himself if writing in his posts, why in blue blazes should anyone else pay him any attention? Anyways, as Alan Fox himself gives witness to, the entire concept of "reality" is far more problematic for Darwinists than they themselves apparently realize and/or will ever honestly admit. First off. any definition of 'reality' that we may put forth presupposes the existence of a conscious mind.
“The principal argument against materialism is not that illustrated in the last two sections: that it is incompatible with quantum theory. The principal argument is that thought processes and consciousness are the primary concepts, that our knowledge of the external world is the content of our consciousness and that the consciousness, therefore, cannot be denied. On the contrary, logically, the external world could be denied—though it is not very practical to do so. In the words of Niels Bohr, “The word consciousness, applied to ourselves as well as to others, is indispensable when dealing with the human situation.” In view of all this, one may well wonder how materialism, the doctrine that “life could be explained by sophisticated combinations of physical and chemical laws,” could so long be accepted by the majority of scientists." – Eugene Wigner, Remarks on the Mind-Body Question, pp 167-177.
Yet Darwinists deny the primacy of consciousness for any definition of 'reality ' we may put forth. And as a result of denying the necessary primacy of consciousness for any definition of 'reality' we may put forth, it is found that Darwinists/Atheists themselves are adrift in an ocean of fantasy and imagination with no discernible anchor for 'reality' to grab on to. First off, in their denial of the primacy of consciousness, Darwinists hold that we ourselves do not really exist as real persons, but our sense of self is merely a ‘neuronal illusion’ that is somehow, inexplicably, generated by, and/or emergent from, the unconscious material particles of the brain.
Sam Harris: “The self is an illusion.” – Michael Egnor Demolishes the Myth of Materialism (Science Uprising EP1) https://youtu.be/Fv3c7DWuqpM?t=267 The Brain: The Mystery of Consciousness – Steven Pinker – Monday, Jan. 29, 2007 Part II The Illusion Of Control Another startling conclusion from the science of consciousness is that the intuitive feeling we have that there’s an executive “I” that sits in a control room of our brain, scanning the screens of the senses and pushing the buttons of the muscles, is an illusion. - per academia press At the 23:33 minute mark of the following video, Richard Dawkins agrees with materialistic philosophers who say that: “consciousness is an illusion” A few minutes later Rowan Williams asks Dawkins ”If consciousness is an illusion…what isn’t?”. https://www.youtube.com/watch?v=HWN4cfh1Fac&t=22m57s The Confidence of Jerry Coyne – Ross Douthat – January 6, 2014 Excerpt: But then halfway through this peroration, we have as an aside the confession (by Coyne) that yes, okay, it’s quite possible given materialist premises that “our sense of self is a neuronal illusion.” At which point the entire edifice suddenly looks terribly wobbly — because who, exactly, is doing all of this forging and shaping and purpose-creating if Jerry Coyne, as I understand him (and I assume he understands himself) quite possibly does not actually exist at all? The theme of his argument is the crucial importance of human agency under eliminative materialism, but if under materialist premises the actual agent is quite possibly a fiction, then who exactly is this I who “reads” and “learns” and “teaches,” and why in the universe’s name should my illusory self believe Coyne’s bold proclamation that his illusory self’s purposes are somehow “real” and worthy of devotion and pursuit? (Let alone that they’re morally significant: But more on that below.) Prometheus cannot be at once unbound and unreal; the human will cannot be simultaneously triumphant and imaginary. https://douthat.blogs.nytimes.com/2014/01/06/the-confidence-of-jerry-coyne/?mcubz=3 “There is no self in, around, or as part of anyone’s body. There can’t be. So there really isn’t any enduring self that ever could wake up morning after morning worrying about why it should bother getting out of bed. The self is just another illusion, like the illusion that thought is about stuff or that we carry around plans and purposes that give meaning to what our body does. Every morning’s introspectively fantasized self is a new one, remarkably similar to the one that consciousness ceased fantasizing when we fell sleep sometime the night before. Whatever purpose yesterday’s self thought it contrived to set the alarm last night, today’s newly fictionalized self is not identical to yesterday’s. It’s on its own, having to deal with the whole problem of why to bother getting out of bed all over again.,,, – A.Rosenberg, The Atheist’s Guide to Reality, ch.10
Moreover, and as Descartes pointed out, to deny that our sense of self is real is to deny the most certain thing we can possibly know about reality. Rene Descartes, via his ‘method of doubt’, found that he could doubt the existence of all things save for the fact that he existed in order to do the doubting in the first place, “As Descartes explained, “we cannot doubt of our existence while we doubt….”
Cogito, ergo sum Cogito, ergo sum[a] is a Latin philosophical proposition by René Descartes usually translated into English as “I think, therefore I am”.[b] The phrase originally appeared in French as je pense, donc je suis in his Discourse on the Method, so as to reach a wider audience than Latin would have allowed.[1] It appeared in Latin in his later Principles of Philosophy. As Descartes explained, “we cannot doubt of our existence while we doubt….” A fuller version, articulated by Antoine Léonard Thomas, aptly captures Descartes’s intent: dubito, ergo cogito, ergo sum (“I doubt, therefore I think, therefore I am”).[c][d] The concept is also sometimes known as the cogito.[2] https://en.wikipedia.org/wiki/Cogito,_ergo_sum And from the conclusion that he could only be certain of the fact that he existed in order to do the doubting in the first place, Rene Descartes then went on to use that conclusion from his ‘method of doubt’ as a starting point to then argue for the existence of the person of God. René Descartes (1596—1650) Excerpt: 5. God a. The Causal Arguments At the beginning of the Third Meditation only “I exist” and “I am a thinking thing” are beyond doubt and are, therefore, absolutely certain. From these intuitively grasped, absolutely certain truths, Descartes now goes on to deduce the existence of something other than himself, namely God. https://www.iep.utm.edu/descarte/#SH4a
Besides claiming that our sense of self, (the one thing we can be most certain of existing), is merely a 'neuronal illusion', Darwinists are also forced to claim that many other things, (other things that everybody, including Darwinists themselves, consider to be real) are also illusions.
Basically, because of reductive materialism (and/or methodological naturalism), the atheistic materialist (who believes Darwinian evolution to be true) is forced to claim that he is merely a ‘neuronal illusion’ (Coyne, Dennett, etc..), who has the illusion of free will (Harris, Coyne), who has unreliable, (i.e. illusory), beliefs about reality (Plantinga), who has illusory perceptions of reality (Hoffman), who, since he has no real time empirical evidence substantiating his grandiose claims, must make up illusory “just so stories” with the illusory, and impotent, ‘designer substitute’ of natural selection (Behe, Gould, Sternberg), so as to ‘explain away’ the appearance (i.e. the illusion) of design (Crick, Dawkins), and who also must make up illusory meanings and purposes for his life since the hopelessness of the nihilism inherent in his atheistic worldview is simply too much for him to bear (Weikart), and who must also hold morality to be subjective and illusory since he has rejected God (Craig, Kreeft). Who, since beauty cannot be grounded within his materialistic worldview, must also hold beauty itself to be illusory (Darwin). Bottom line, nothing is truly real in the atheist’s worldview, least of all, beauty, morality, meaning and purposes for life.,,, - Jan. 2023 - defense of each claim https://uncommondescent.com/intelligent-design/is-the-galton-board-evidence-for-intelligent-design-of-the-universe/#comment-774417
Although the Darwinian Atheist and/or the Methodological Naturalist may firmly, and falsely, believe that he is on the terra firma of science (in his appeal, even demand, for naturalistic explanations over and above God as a viable explanation), the fact of the matter is that, when examining the details of his materialistic/naturalistic worldview, it is found that Darwinists/Atheists themselves are adrift in an ocean of fantasy and imagination with no discernible anchor for reality to grab on to. It would be hard to fathom a worldview more antagonistic to modern science, indeed more antagonistic to reality itself, than Atheistic materialism and/or methodological naturalism have turned out to be. In conclusion, if Alan Fox truly wants to portray himself as being the defender of 'reality', might it not first greatly behoove him to have a worldview that did not collapse into catastrophic epistemological failure? i.e. a worldview that did not collapse into a world of fantasies and illusions?
2 Corinthians 10:5 Casting down imaginations, and every high thing that exalteth itself against the knowledge of God, and bringing into captivity every thought to the obedience of Christ;
bornagain77_{April 3, 2023
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In @60, AF introduces the MAGICAL possibility that chemistry and physics MIGHTA changed over the lifetime of the universe . . . in fact, if it could do so, maybe 3.5 bya, the goddess Mother Nature touched the goddess Gaia with her wand, momentarily changing the laws of physics, to initiate The Origin of Life. Yes, life MIGHTA, MUSTA, EMERGED at this Magical Moment.
Alan Fox does not say this. I suggest readers compare my comment with Querius' egregious misrepresentation. Though it does confirm, I hope, we all agree that the measurable properties of the universe remain fixed and predictable. They don't change. If they did, science would be impossible. There are no miracles.Alan Fox_{April 3, 2023
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RNA is the catalyst that binds amino acids together after they have been specified by a rate-independent medium of information and presented for binding by the translation machinery.
You appear not to grasp the distinction between a precursor RNA world, with RNA being both replicator and catalyst, and what happens now.Alan Fox_{April 2, 2023
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.
AF: In the RNA world scenario? There is no mRNA. RNA is both storage and catalyst. UB: This is a blatant equivocation. The putative RNA replicator (which you do not have) is a purely dynamic entity. It cannot (and does not) contain information in the way mRNA does. AF: It is a fact.
It is a fact that your putative self-replicating RNA (which you do not have) is purely dynamic and cannot (and does not) contain information in the way that mRNA does. Yes, that is a fact. It is the central fact which you avoid at all cost. Its importance is in direct relation to your refusal to engage it. When you say “there is no mRNA, RNA is both storage and catalyst” you are suggesting that a self-replicating RNA somehow take over the role of mRNA, but that is not true. One is dynamic and the other is rate-independent. One can encode a sequence of amino acids and the other cannot. You are equivocating.
AF: There are RNA viruses in today’s world.
lol. RNA viruses hijack the cellular machinery of the host cell in order to execute their encoded information to build viral proteins and reproduce themselves. They require the very machinery that you are delighted to tell us your RNA replicator doesn’t have. One wonders why you brought it up. It appears to be an instance of saying something in order to have something to say.
Ribozymes are the central catalyst in protein synthesis.
RNA is the catalyst that binds amino acids together after they have been specified by a rate-independent medium of information and presented for binding by the translation machinery. Just like your persistent comments about base pairing, neither of these processes establish the medium of information, nor do they organize the machinery required to execute the code. Again, this appears to be another instance of saying something in order to have something to say.Upright BiPed_{April 1, 2023
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Look in that telescope, Cardinal
The Pope backed Galileo till Galileo betrayed him politically. The whole Galileo debate was a political one not one of religion or science. Then the Pope didn't deny Galileo's assertion only that it had not been proven. Galileo had no answer for the wind problem nor the parallax problem. It took 200 more years to solve those. Aside: Derogatory remarks are relied on to discredit someone but are especially ironic when the remark misses the target. Aside2: the evolution of non biological compounds require thousands of steps just as supposedly biological change does. But as in biological change, it is rarely or if ever one has seen a significant change or the steps necessary for it.jerry_{April 1, 2023
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I have watched Dr. Tour’s series on abiogenesis and appreciated the massive obstacles to forming anything of value by accident.
Look in that telescope, Cardinal, I dare you. Nick Lane acknowledges and discusses those very issues.Alan Fox_{April 1, 2023
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Just to give Querius some respite from reality, I'm busy with RL events tomorrow and over Easter weekend. The local tradition is a fête involving omelettes liberally flavoured with wild asparagus (and dancing). And I need to finish reading Transformer.Alan Fox_{April 1, 2023
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I'm about a quarter the way through Nick Lane's book, Transformer, and it turns out to be a potted history of biochemistry up to this point. Lane even has some kind things to say about Lehninger, both the man and his book.Alan Fox_{April 1, 2023
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Don't look in that telescope, Cardinal! :) :) :)Alan Fox_{April 1, 2023
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Bornagain77 @62, Thank you for not bothering linking to Nick Lane's paper on ATP, even for comedy relief. In his introduction, we encounter woulds like could have, mystery, infer, and possible. Maybe I should write a paper on what could have possibly be inferred to have happened to magically form ATP without any reason to do so or any mechanism to create the ATP-ADP cycle outside of the magic of science fantasy. I have watched Dr. Tour's series on abiogenesis and appreciated the massive obstacles to forming anything of value by accident. -QQuerius_{April 1, 2023
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As BA77 didn't link to Nick Lane's paper on a pre-biotic origin for adenosine triphosphate (ATP), here it is. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001437Alan Fox_{April 1, 2023
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Upright BiPed@58,
What you are doing is denying the validity of design inference based on your personal ideology, and you are doing so by fronting the unsupported assumption that there was once an RNA World that evolved into a description-based replicator. You then protect that assumption by absolutely refusing to engage with what is known to be required to establish a description-based self-replicator.
Exactly! Ideology now trumps reality. What's hilarious is that AF invokes one of the three gods-of-the-gaps arguments MUSTA, MIGHTA, and EMERGED in @61 (emergent), which is the intellectual equivalent of magical fairy dust. In @60, AF introduces the MAGICAL possibility that chemistry and physics MIGHTA changed over the lifetime of the universe . . . in fact, if it could do so, maybe 3.5 bya, the goddess Mother Nature touched the goddess Gaia with her wand, momentarily changing the laws of physics, to initiate The Origin of Life. Yes, life MIGHTA, MUSTA, EMERGED at this Magical Moment. All this baloney is a fantasy religion that's polluting science, and a great example of the OP and a complete waste of time. As Dr. James Tour puts it, "Ok, show me." -QQuerius_{April 1, 2023
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Of note:
Origin of Life: Controversial Chemist Shakes up Scientific Community | Problems with Primordial Soup - March 2023 https://www.youtube.com/watch?v=ZugOrSD7YL4 James Tour James Tour is the T. T. and W. F. Chao Professor of Chemistry, Professor of Computer Science, and Professor of Materials Science and NanoEngineering at Rice University. He has over 590 research publications and over 100 patents, and has received numerous scientific awards. https://inference-review.com/contributor/james-tour
Also of note regarding the OOL: A bit more of a layman's discussion on the science at hand starts at the 13:00 minute mark of the following interview of Prof. John Lennox.
Webinar: Prof John Lennox - Evolution - A theory in crisis? - Feb. 2023 https://youtu.be/Y0tQQCfrAK0?t=777
bornagain77_{April 1, 2023
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One of the emergent properties of RNA is that individual bases will pair bond (always Guanine with Cytosine, Adenine with Uracil) which is the basis of both replication and catalysis. This does not involve any genetic code.Alan Fox_{April 1, 2023
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This is a blatant equivocation.
It is a fact. There are RNA viruses in today's world. Ribozymes are the central catalyst in protein synthesis.
The putative RNA replicator (which you do not have) is a purely dynamic entity. It cannot (and does not) contain or convey information in the way mRNA does.
RNA is a molecule with specific properties that (if we accept that physical and chemical properties don't change) have been so for the lifetime of this universe.Alan Fox_{April 1, 2023
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Is Alan Fox suggesting that Coppedge's criticisms of Nick Lane's ATP hypothesis are invalid? Funny, Coppedge quoted from Lane's paper itself to establish the validity of most of his criticisms against Lane's hypothesis.. So, according to Alan Fox's 'reasoning' I guess we should ignore Lane himself whenever he admits to weaknesses in his own hypothesis? especially when ID proponents have the audacity to point them out? Moreover, why in blue blazes should I ever trust whatever Alan Fox's 'niche' has to say about OOL research over and above what Coppedge is saying?
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,,,,” https://uncommondescent.com/intelligent-design/at-evolution-news-for-darwinism-pregnancy-is-the-mother-of-all-chicken-and-egg-problems/#comment-771084 Game over. (1) rationality implies a thinker in control of thoughts. (2) under materialism a thinker is an effect caused by processes in the brain (determinism). (3) in order for materialism to ground rationality a thinker (an effect) must control processes in the brain (a cause). (1)&(2) (4) no effect can control its cause. Therefore materialism cannot ground rationality. per Box UD
bornagain77_{April 1, 2023
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.
In the RNA world scenario? There is no mRNA.
…and no way to specify and organize all the molecular components required for mRNA to function as a medium of information.
RNA is both storage and catalyst.
This is a blatant equivocation. The putative RNA replicator (which you do not have) is a purely dynamic entity. It cannot (and does not) contain or convey information in the way mRNA does.
You seen to not be able to grasp my point that what we know of how things are currently is not how they have always been.
There isn’t the slightest thing about what you are saying that is difficult to understand. Hello? What you are doing is denying the validity of design inference based on your personal ideology, and you are doing so by fronting the unsupported assumption that there was once an RNA World that evolved into a description-based replicator. You then protect that assumption by absolutely refusing to engage with what is known to be required to establish a description-based self-replicator. As a protectionist strategy, you don’t have to deal with the details because your assumption in true, and because your assumption is true, you don’t have to deal with the details. The game is as old as dirt.Upright BiPed_{April 1, 2023
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Link to Nick Lane’s book on Amazon. https://www.amazon.com/Transformer-Nick-Lane-ebook/dp/B07PDHXFB5Alan Fox_{April 1, 2023
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From BA's link: David Coppedge is a freelance science reporter in Southern California. He has been a board member of Illustra Media since its founding and serves as their science consultant. He worked at NASA’s Jet Propulsion Laboratory (JPL) for 14 years, on the Cassini mission to Saturn, until he was ousted in 2011 for sharing material on intelligent design, a discriminatory action that led to a nationally publicized court trial in 2012. Discovery Institute supported his case, but a lone judge ruled against him without explanation. A nature photographer, outdoorsman, and musician, David holds B.S. degrees in science education and in physics and gives presentations on ID and other scientific subjects. So no expertise in biology or biochemistry.Alan Fox_{April 1, 2023
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Who is David Coppedge? I've heard he was a JPL employee who was sacked for handing out DVDs in work time. Has he any expertise in biology or biochemistry?Alan Fox_{April 1, 2023
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Game Over? Nick Lane Wants Another Inning David Coppedge - October 7, 2022 Excerpt: The field of origin of life research has struck out at the bottom of the ninth. The crowds file out of the stands. Suddenly, eight players run onto the field! “Wait! Wait!” they cry. “Let us have a time at bat!”,,, Questions & Answers What about hydrothermal vents?, the referee asks. Aren’t those the preferred locations for prebiotic environments? “[O]ur results do not exclude submarine hydrothermal systems as potential environments for this chemistry,” they beam with pleasure. But it couldn’t happen today, they explain, because “high concentrations of Mg2+ (50 mM) and Ca2+ (10 mM) precluded ATP synthesis, implying that this chemistry would not be favoured in modern oceans.” The referee, frowning a bit, senses some special pleading going on. Other referees walk up to see what the commotion is about. After listening in, they start asking questions. Did you try this in a natural setting? No, we bought chemicals from Fischer and from Sigma-Aldrich, and then mixed them in our lab under controlled conditions. (See the Materials and Methods section.) How did you get the ingredients to link up? We used store-bought catalysts and mixed them with store-bought nucleotides and phosphorylating agents. Then we shook them and heated them. Why do you think that represents a plausible prebiotic environment? “AcP is unique among a panel of relevant phosphorylating agents in that it can phosphorylate ADP to ATP, in water, in the presence of Fe3+. AcP is formed readily through prebiotic chemistry and remains central to prokaryotic metabolism, making it the most plausible precursor to ATP as a biochemical phosphorylator.” Are you likely to find sufficient concentrations of AcP and ferric ion in natural water conditions for this to have happened on the early earth? Uh, we didn’t test that. Wait a second; adenosine is a nucleoside base that includes ribose. How did that form in water? That is a problem, we agree. Did you test for chirality? Uh, no. Did you come up with a plausible container to hold the ATP? That was not part of our investigation, no. OK, so you get some ATP under special conditions. ATP has a half-life of under 5 minutes in water. Do you expect it to hang around long enough to be useful in some protocell? We did not think about that in this paper, no. ATP is not alive, obviously. What would happen next? Presumably some primitive metabolic process could utilize it for energy. Like what? “Recent experimental work shows that the core of autotrophic metabolism can occur spontaneously in the absence of genes and enzymes. This includes nonenzymatic equivalents of the acetyl CoA pathway and parts of the reverse Krebs cycle, glycolysis and the pentose phosphate pathway, gluconeogenesis, and amino acid biosynthesis. Recent work demonstrates that some nucleobases can also be formed following the universally conserved biosynthetic pathways, using transition metal ions as catalysts. The idea that ATP could have arisen as a product of protometabolism starting from H2 and CO2 is therefore not unreasonable….” What, exactly, is “protometabolism”? Does it have any meaning outside of a living context? (Silent stares.) Who decides what is reasonable? I guess we do. The paper says that “biological purine synthesis specifically involves 6 phosphorylation steps that are catalysed by ATP in modern cells.” Adenine is a purine. How do you get past the chicken-and-egg problem of needing ATP to make ATP?“If ATP was indeed formed in a monomer word via a biomimetic protometabolism, then an earlier ATP equivalent must have driven the phosphorylation steps in purine synthesis.” Can you describe a plausible earlier ATP equivalent? Actually, “A major question for prebiotic chemistry is how could an energy currency power work” if not ATP. And how did ATP come to replace it, whatever it was? “Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery.” So how did your simple ATP-generating process get replaced by ATP synthase? Well, it is well known that “the ATP synthase powers a disequilibrium in the ratio of ADP to ATP, which amounts to 10 orders of magnitude from equilibrium in the cytosol of modern cells. Molecular engines such as the ATP synthase use ratchet-like mechanical mechanisms to convert environmental redox disequilibria into a highly skewed ratio of ADP to ATP.” But we cannot say how that happened. But how could a simple prebiotic system composed mostly of monomers sustain a disequilibrium in ATP to ADP ratio that powers work? Well, “One possibility is that dynamic environments could sustain critical disequilibria across short distances such as protocell membranes.” Didn’t you just assume the existence of a protocell with a membrane? Where did those come from? Look, we’re not trying to come up with a complete picture of how life originated. We’re just trying to explain why ATP is the universal energy currency for life as it exists today, and how it might have emerged. Emerged… by chance, you mean? Isn’t that circular reasoning? How so? What other possibility is there? There’s intelligence, the only cause ever observed that is capable of assembling complex parts into a functional whole. Sorry; we thought this was a scientific baseball diamond. It is. So what is your explanation for the functional information in the simplest life? Your paper admits that “ATP links energy metabolism with genetic information.” What is the source of that genetic information? Uh, some sort of intermediate or other. The referees convene and shout out, “GAME OVER!” https://evolutionnews.org/2022/10/game-over-nick-lane-wants-another-inning/
bornagain77_{April 1, 2023
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You don’t even have a successful autonomous self-replicating RNA in a pre-biotic environment, do you?
Did you spend any time looking at Nick Lane's work on origin of life? His latest book, Transformer: The Deep Chemistry of Life and Death, is available on Amazon, Kindle version at €15. I'm going to give it a read. Maybe you'd like to do the same, if only to get an idea of current thinking of professionals working in the field.Alan Fox_{April 1, 2023
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There is also no way to specify a protein from a medium of heritable information, like mRNA
In the RNA world scenario? There is no mRNA. RNA is both storage and catalyst. Once you have self-sustaining self-replicators, evolution can add functions. You seen to not be able to grasp my point that what we know of how things are currently is not how they have always been. Admittedly, I cannot provide every crossed "t" and dotted "i" for the last three and three-quarters billion years or so but what you are claiming (presumably), that there is no evolutionary pathway from first self-sustaining self-replicators to now, is avoiding the plausibility of RNA World. Playing devil's advocate, I suggest the hard problem is not whether RNA World is plausible, nor how DNA supplanted RNA's rôle as "genetic memory"* but how amino-acids, polymers like polyglycine, more complex polypeptides, and proteins became incorporated into cellular metabolism in small enough steps to allow an evolutionary process to be invoked. *If all you mean by "memory" is what you state in #50, fair enough.Alan Fox_{April 1, 2023
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.
There is no genetic code in the RNA World scenario
There is also no way to specify a protein from a medium of heritable information, like mRNA. By the way, you were invited to enlightened us on which RNA candidate you are talking about:
I don’t think Alan ever told us which type of RNA replicator he sees as the magic bullet here. Is it the type that can freely assemble itself, base by base, from a pool of available parts? That’s certainly a persnickety version. So far that version hasn’t been shown to be robust enough to even copy the RNA script causing the reaction, much less specify a protein on the side. Or maybe what Alan has in mind is the self-replicating ribozyme? That’s another tough one. But what about the cross-catalytic ligase ribozyme, from Gerald Joyce’s team? That’s the six-piece version where they create four specific RNA substrates that become linked together based on two complimentary RNA templates. Template 1 links two substrates together to create Template 2, and Template 2 does the same with the other two substrates to create Template 1. One template is 66 bases long, if I remember correctly, and the other is 78. It’s a reaction that can go on forever as long as a steady supply of the four individual substrates are created and fed into the system at balanced levels. If it falls out of balance, the system runs into troubles. The upside for Alan is that there is a short patch of bases in each template that are outside the catalytic domain, and aren’t critical – i.e. they can be changed around. Perhaps this is where Alan sees an opportunity to specify some protein? Of course, the downside is that the reaction fails in the presence of protein or other biological materials. So there’s that. When Gerald Joyce published on this cross-catalytic ligase ribozyme, he talked about the potential of forming autocatalytic networks of these replicators in order to study various concepts in replication, and he made a clear distinction between the type of templated RNA replication found in his experiments (which is based on the dynamic properties of RNA), versus the kind of replication that occurs in the living cell — that this, replication using the separate “replication machinery” of the aaRS, tRNA, ribosomes, etc. He stated “It is difficult to see how one would devise autocatalytic networks that allow optimization of a replicative machinery that is distinct from the templating properties of the molecule.“ Perhaps Alan intends to share something Gerald Joyce is missing.
You don’t even have a successful autonomous self-replicating RNA in a pre-biotic environment, do you? And even if you did, how do you get descriptions from dynamics? Any experimental results showing that?Upright BiPed_{April 1, 2023
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. Oh yes, Let us again argue over the word ”memory” Alan. Last month …
You want to play pitter-pat over the word “memory”. I have no intentions of doing that. You can call it “information storage” or “instructions” or “descriptions” or “stored specifications” or whatever you wish, it makes no difference. The measured physical reality remains the same. (btw, “DNA is the memory storage molecule of all living things” – National Science Foundation, “DNA is read-only memory, archived safely inside the cell” — RCSB Protein Data Bank
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You’ll pick a snappy angle that serves your purpose, yet all the documented empirical evidence against your position will remain untouched.
You can’t stop yourselfUpright BiPed_{April 1, 2023
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