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

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Due May 16, 2023:

At UK Spectator:

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

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

Comments
Hi Upright Biped.
The genetic code is established from genetic memory...
There is no genetic code in the RNA World scenario. But my problem is I don't understand what you mean by "genetic memory". Because a molecule can self-replicate, it has a memory? Is this just colourful language?Alan Fox
April 1, 2023
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There’s a third possibility. That your interpretation of the known facts is faulty. But don’t take my word for it. Publish somewhere you can be noticed.? I predict your “semiotic hypothesis” will impress nobody
More dogma, eh, Alan? Two things: 1) If the words of John Von Neumann, Francis Crick, and Sydney Brenner are ignored as a protectionist ploy, then really, what more could I do? This is pure rhetoric, and nothing else. 2) When your last refuge is dogma, well, you’ve lost on the science. When the horse is dead, get off.Upright BiPed
March 31, 2023
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. Alan, upthread you described a molecule of DNA and claimed it “indeed” determined the genetic code.
AF: The genetic code is indeed completely determined by physical behaviour, chemical and physical affinities, involving the inherent properties resulting in the iconic double helix conformation…
I reminded you that the DNA molecule is subject to the ‘minimum total potential energy principle’, and that those energetic forces cannot (and do not) determine the sequence of bases found along the length of the molecule — in other words, on an energetic basis, all sequences are effectively equal. I also added that the process of translation (where the genetic code is physically established) is both discontinuous and irreversible, not to mention the fact that it is has been well known for decades that the genetic code is established from encoded heritable memory. It is specified by the genes that code for the set of aminoacyl tRNA synthetases. The genetic code is established from genetic memory – just as it was predicted to be, first by John Von Neumann in 1948 when he was writing of the logical requirements of autonomous self-replication, and then again by Francis Crick in 1955 when he was doing research to understand exactly how the bases in DNA specified the amino acids in a protein. Both predictions were experimentally confirmed by the work of Hoagland and Zamecnik (1956-58). None of these facts are even contestable. Not only were you given Crick’s prediction verbatim, but you also saw that Sydney Brenner — who was actually on the ground collaborating with Crick at the time (i.e the person who named Crick’s famous “adapter hypothesis”) — you saw him make the exact same point that I am making, that is, that the genetic code is established by symbolic description held in heritable memory. In case this point is somehow lost on you; one of the most admired biologists of the era, a Nobel Laureate, is making the exact same point I make (which you deny). Brenner goes so far as to point out that this was the “fundamental distinction” that Von Neumann got right and Schrödinger got wrong … “the chromosome contains a description of the means” to execute the code “but not the means themselves”. It is just as Von Neumann predicted from Alan Turin’s symbol machine of 1933 (er, another point that Brenner makes). In 2012, Brenner went on to say that “the gene as a symbolic representation” is a “fundamental feature of the living world”. He stated this on the pages of the world’s most prestigious scientific journal, Nature. I believe I may have also mentioned the fact that Brenner’s statements are completely corroborated by five decades of publication on the subject by physicists such as Howard Pattee, as well as many others. Encoded symbolic descriptions are demonstrated to be the necessary physical basis for the system to function as it does — to specify something among alternatives. It is right there in the literature, for anyone to see. Judging by the content of your response, it appears you’d like to quietly abandon your claim. It is of little surprise; the claim was fairly ridiculous from the very start. I’m sure it can all be chalked up to you speaking carelessly in the heat of the moment, but unfortunately, it goes right up there with your companion claim that if SETI scientists received a signal from space containing encoded content they would not infer the presence of a previously unknown intelligence. I just wonder, why does it never bother you that you are forced to defend your position with such easily refuted (and supremely silly) claims. One after another. Over and over and over again. I remember a few years back sitting down for a lecture by a eminent psychologist, where he was discussing the problems that psychologists sometimes have to deal with regarding native languages. He was making the point that there are languages that have separate words that other languages simply do not have. For instance, English has a word for “shame” while other languages have several words to describe the different forms of “shame” that can manifest themselves in a person’s actions and motivations. Again, for instance, there is a sense of shame that is “toxic”, such that a person doesn’t perceive that they have “done something wrong” but instead, there is “something wrong with them”. That is “toxic” shame. Then there is also a healthy sense of shame that, as an example, says “don’t jump off the 10th floor roof” because you can’t fly. In other words, it is a protective, healthy sense of “shame” that serves the significant purpose of keeping a person in check with reality. I am no psychologist, but it occurs to me that you cannot even be sensibly “shamed” into stopping this continuous diatribe of yours. You are publicly pitching yourself against the well-documented history of science and experimental result, and it simply does not matter. As long as you can get in your little cut, or two, or three, in each and every response, then who gives a flying fuck about physics, experiment result, science, and reason. It is truly pitiable Alan. After more than a decade of this argument working on you (which you admit), you’ve reappeared on UD only to end up having your position be rendered intellectually pitiable. And you’ll do the whole claptrap again when you respond to this post. You’ll pick a snappy angle that serves your purpose, yet all the documented empirical evidence against your position will remain untouched. I’ll keep calmly repeating the literature and history, and in response, you’ll dig deeper and deeper into cuts at me. It will be that way because you have nothing else.Upright BiPed
March 31, 2023
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Upright BiPed @40, Looks like I need to retract my observation @42, that AF is hiding. After being plastered with three subsequent vacuous comments derisive of your post, AF is certainly present, but has distinctly avoided meaningful interaction with the information you provided. Instead, AF has, in fact, surrendered by resorting once again to ad hominem attacks such as
You need a better argument if you are to be taken seriously by genuine scientists.
Obviously, AF demonstrates skill in judgmental vituperation, hoping to cover for deficiencies in relevant knowledge. So, keep up the good work! -QQuerius
March 29, 2023
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Good grief Alan, you just described a molecule of DNA and claimed it determined “the genetic code”.
Not precisely. But how things are now is not as they always have been. RNA world as a precursor to what we observe today presents a plausible evolutionary pathway from first life to living organisms we observe now. You need a better argument if you are to be taken seriously by genuine scientists. Maybe you don't want to take that step. I can understand your reluctance.Alan Fox
March 29, 2023
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While Alan Fox has posted numerous critical comments on other topics, it looks like he’s been hiding from you.
Not really. I've made my central point, that RNA World avoids the issue Upright Biped raises in his "hypothesis". I enclose "hypothesis" in inverted commas* in this instance to question whether UB had actually ever clearly stated something that can be called a hypothesis. Also, the software glitch prevents me from commenting here at UD at times it is convenient for me to post comments. *When quoting people here, I invariably use blockquote tags. When I want to question the valid use of words or phrases, I use inverted commas, as in "Intelligent Design".Alan Fox
March 29, 2023
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@ Upright Biped, There's a third possibility. That your interpretation of the known facts is faulty. But don't take my word for it. Publish somewhere you can be noticed. I predict your "semiotic hypothesis" will impress nobody in the mainstream. Or if you prefer, carry on like the Ancient Mariner here. If the UD software manages to hold up, and if I'm spared, I'll keep pointing out your hypothesis needs more work.Alan Fox
March 28, 2023
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Upright BiPed @40, While Alan Fox has posted numerous critical comments on other topics, it looks like he's been hiding from you. But thanks for taking the time to post your response. I learned things that I didn't know! -QQuerius
March 28, 2023
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I’m placing this argument here because it is relevant to the assertion that ID per se does not have a religious purpose. It certainly supports most religions. But is not associated with any specific one. Here is a clear discussion of ID rationale.
Is the Human Neck a “Mistake of Evolution”? Walter Myers III in the context of biology, intelligent design intentionally makes no mention of who or what the designer is, or what the potential motivations of that designer might be. Moreover, intelligent design takes a straightforward abductive reasoning approach towards design, arguing that design is simply an inference to the best explanation. When we see the amount of human thought and work that goes into creating complex artifacts such as smartphones, automobiles, and jet airplanes, then it is at least reasonable to believe biological organisms, which are far more sophisticated than any human artifact, require thoughtful design.
https://evolutionnews.org/2021/10/is-the-human-neck-a-mistake-of-evolution/jerry
March 28, 2023
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AF: The genetic code is indeed completely determined by physical behaviour, chemical and physical affinities, involving the inherent properties resulting in the iconic double helix conformation…
Good grief Alan, you just described a molecule of DNA and claimed it determined “the genetic code”. lol Not only is your claim silly, but the molecule you described, according to physicists, is subject to the minimum total potential energy principle, which unambiguously demonstrates that the bonds that form in the structure of DNA do not establish the sequence of its bases. So, you just stated that something that cannot physically determine the genetic code, did “indeed” determine the genetic code. I know you really believe the things you say, but you’ll probably want to restate your claim with some colorful added assumptions about something else that determined the code, since the molecule can’t do it. Unfortunately, the problems for your claim don’t stop there. As is well known, the genetic code is the set of relationships between the spatial arrangement of bases in the various codons of DNA and the resulting amino acids being specified by those codons in a nascent protein. Those relationships are established during a well-described physical process, the process of translation. And here again, physicists will tell you that those relationships are rate-independent, and that the process in which they are established is discontinuous and irreversible. You already know this because I gave you the direct quote from Francis Crick in 1955 where he predicted the necessity of a set of mediating proteins, whose role it would be perform a “double-recognition” to establish the genetic code, and would themselves be specified from heritable memory. When Mahlon Hoagland and Paul Zamecnik confirmed the presence of that set of proteins and their “adapters”, they not only confirmed Crick’s famous adapter hypothesis, but also Von Neumann’s self-replicating automaton (with Alan Turing’s symbol machine in tow). You know this as well because you were given Nobel Laureate Sydney Brenner’s article in Nature confirming the connection, as well as Brenner’s video interview in his library making the same point. But hey, even if you hadn’t been given any of these things, all you have to do is study the process of translation for a moment to understand that the process is discontinuous and irreversible, and that the code is determined from heritable memory. So once again, either all the physics is wrong about this, or you are. It is you.Upright BiPed
March 24, 2023
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Haha, love it, Jerry! Thank you! Is there also a gene that compels people to come up with settled solutions to everything? Neat. Plausible. And wrong (hat tip to H.L. Mencken). -QQuerius
March 21, 2023
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A blast from the past. It explains everything that happens on UD. Ironic is how this is almost impossible to find on internet so has it been censored. https://www.facebook.com/thejohncleese/videos/we-scientists-have-discovered-the-god-gene/352475862739679/jerry
March 21, 2023
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Alan Fox @29,
Similarly? Oh my aching sides!
A vacuous, content-free troll post.
How do refineries separate hydrocarbons if not by exploiting their inherent (and emergent) physical and chemical properties?
Did refineries magically evolve or were they intelligently designed? Duh.
Engineering thinking misunderstanding biochemistry.
Magical Darwinian thinking is a misunderstanding of physical chemistry, which is entirely . . . physical and mechanical, not magical. It involves physical shapes of molecules that strongly or weakly lock with other molecules creating structures and chemical cycles in machinery based on electrostatic attractions and electron shells (along with homochirality and quantum effects--see https://www.pnas.org/doi/10.1073/pnas.2210505119). Engineering thinking avoids your magical thinking and consistently produces better results than your gods of the gaps: MUSTA, MIGHTA, and EMERGED. But at least you did succeed in wasting my time. -QQuerius
March 21, 2023
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AF at 35, That was incoherent. Care to elaborate?relatd
March 21, 2023
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Jeez, Relatd, Casey Luskin?Alan Fox
March 21, 2023
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AF at 27, Misleading people appears to be your purpose here. https://intelligentdesign.org/articles/molecular-machines-in-the-cell/relatd
March 21, 2023
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Kf at 32, A standard tactic here is to avoid the question and divert the reader's attention. The establishment of chemistry and chemical reactions on Earth required the Creation of physics, on the scale of the Universe, to allow all of this to happen. Alan Fox, and others, hope readers will miss this. They hope to exclude God from Creation and to attribute to nothing, three dimensional protein folding. This ignores the atomic-level precision involved, which has connections to the sub-atomic world. Hand waving is not a valid explanation of anything.relatd
March 21, 2023
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AF & Circle, I duly note, no substantial response to the metastability question. KFkairosfocus
March 21, 2023
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@ KF Name dropping? Physician, heal thyself! :)Alan Fox
March 21, 2023
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AF & circle, namedropping particular structural patterns that are part of protein folding does not avert the obvious metastability, barrier potential [thus possibly tunnelling], chemical and physical issue. I outlined. The prion, non functional state clearly has higher stability and that is why it can trigger a cascade of misfolding. There is a reason why we have molecular chaperones in the cell. And yes, that is a further degree of complexity in the functionally specific organisation of cell based life. KF PS, Wiki confesses:
In molecular biology, molecular chaperones are proteins that assist the conformational folding or unfolding of large proteins or macromolecular protein complexes. There are a number of classes of molecular chaperones, all of which function to assist large proteins in proper protein folding during or after synthesis, and after partial denaturation. Chaperones are also involved in the translocation of proteins for proteolysis. The first molecular chaperones discovered were a type of assembly chaperones which assist in the assembly of nucleosomes from folded histones and DNA.[1][2] One major function of molecular chaperones is to prevent the aggregation of misfolded proteins, thus many chaperone proteins are classified as heat shock proteins, as the tendency for protein aggregation is increased by heat stress.
The metastability energy uphill/downhill issues practically beg to be discussed. That starts with cooking and associated denaturing but continues all the way to prions. For a great many proteins, we see chaperoned folding to functional state, which practically screams, metastability issues.kairosfocus
March 21, 2023
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Similarly, the “G-code” in CNC machines, perhaps created from a DXF file, bears absolutely zero resemblance to the finished part, yet it directly controls every motion of a 3 or 5 axis machine as it manufactures the part that wasn’t originally designed with G-code.
Similarly? Oh my aching sides! How do refineries separate hydrocarbons if not by exploiting their inherent (and emergent) physical and chemical properties? Engineering thinking misunderstanding biochemistry.Alan Fox
March 21, 2023
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...more energetically stable but obviously non functional structure.
Beta sheet conformation occurs in functional proteins.Alan Fox
March 21, 2023
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@ KF Both alpha helix and beta sheet are common conformations in protein structure that emerge from the precise sequence of amino-acids in a polypeptide. Protein structure is a well understood field in biochemistry. Engineering thinking misleads ID proponents to an alarming extent.Alan Fox
March 21, 2023
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AF & circle, prions. The cascade of propagating misfolding suggests a falling downhill, more energetically stable but obviously non functional structure. An island of function issue with a potential barrier surmounted leading to falling downhill energy-wise and function- wise. KFkairosfocus
March 20, 2023
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Relatd, You might also like to google Rosalind Franklin and read about how she worked out that DNA molecules have a spiral arrangement.Alan Fox
March 20, 2023
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So, you claim proteins fold on their own, and automatically “know” how to assume the correct three-dimensional shape?
Proteins are molecules. Water molecules don't know how to arrive at 104.5° bond angle, each assumes the correct shape. Sucrose sugar crystals form with all molecules of identical shape. The 3D structure of protein, (whale) myoglobin, was first established by crystallizing it (guess what, the molecules in the crystal are identical) and passing x-rays through it. Relatd, I'd suggest you read up on some basic chemistry.Alan Fox
March 20, 2023
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JVL @20,
Then can ID explain how sections of DNA are transcribed into proteins?
While it's hard to believe after all this time, you still seem to be completely clueless about what ID actually means. So, let me translate your question into more familiar terms: "Then, can a mechanical engineer who is reverse-engineering a combustion engine on the premise that an intelligent agent designed the engine rather than it being the product of a mysterious explosion in a machine shop explain exactly how C5 and C6 alkanes are extracted from crude oil? A chemical engineer would know. And the chemical engineer would also understand that these alkanes didn't accidentally extract themselves from up to 100,000 compounds in crude oil, evolving into gasoline over millions of years."
If I create a code for encrypting text so that people who intercept my messages can’t read them then what I pick has nothing to do with what I am writing.
Similarly, the "G-code" in CNC machines, perhaps created from a DXF file, bears absolutely zero resemblance to the finished part, yet it directly controls every motion of a 3 or 5 axis machine as it manufactures the part that wasn't originally designed with G-code. -QQuerius
March 20, 2023
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Alan Fox, So, you claim proteins fold on their own, and automatically "know" how to assume the correct three-dimensional shape? If a misfold occurs, chaperones can correct the problem. But you claim that this knowledge comes from nowhere. Not a logical or compelling argument.relatd
March 20, 2023
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JVL at 15, You have an intricate machine and that machine contains sensors. Take DNA repair. The sensors detect a problem, instructions regarding how to fix it are sent. Once the repair is complete, the sensors detect that. They are always on. You cut your finger. Nothing major. Sensors detect a problem. Blood clotting instructions are sent. Wound healing/cell repair instructions are sent. A "being" has created an intricate machine that has damage/wound detection sensors, and repair instructions are sent to correct/fix the problem.relatd
March 20, 2023
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Querius: ID is simply pragmatic Then can ID explain how sections of DNA are transcribed into proteins? IF the genetic 'code' is an arbitrary, abstract code with no relationship to chemical affinities or mappings then someone or something would have to translate it EVERY SINGLE TIME it's read. Every single time. If I create a code for encrypting text so that people who intercept my messages can't read them then what I pick has nothing to do with what I am writing. It's just based on me making something up. That means that every single time someone decodes my messages they have to apply the decoding function. Every single time. It takes a person or computer to do it. A person or computer that is not part of the letter making or receiving process. Is that how DNA works? Is there someone or something that has to look up every single codon every single time one is 'read'?JVL
March 20, 2023
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