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

James Tour on Origin-of-Life Dealbreakers April 8, 2023 On a new episode of ID the Future, distinguished synthetic organic chemist James Tour of Rice University explains why the goal of synthesizing life from non-life in conditions similar to those of the early Earth appears further away than ever. It’s not an illusion, he explains. The illusion was how close OOL researchers thought they were 50-70 years ago. They were never close, and the more we learn about how mind-bogglingly sophisticated even the simplest cells are, and how the complexity is essential for biological life, the more we realize just how far we are from constructing a plausible scenario for the mindless origin of the first life. Tour points out that even granting a great deal of intelligent design in the form of the highly skilled and interventionist work of the origin-of-life researchers in the lab, they still can’t engineer into existence all the key building blocks of a living cell. What if you handed them all the building blocks in the right proportions? They’re still nowhere near being able to intelligently design those ingredients into a living cell, Tour says. It has to do with what’s termed the interactome — that is, all the interdependent molecular interactions in a particular cell, many of which may initially appear unimportant but turn out to be crucial. https://evolutionnews.org/2023/04/james-tour-on-origin-of-life-dealbreakers/ Podcast https://idthefuture.com/1731/

bornagain77

Uploaded 2 days ago,

The TRUTH About the Shroud of Turin w/Fr. Robert Spitzer | Chris Stefanick Show https://www.youtube.com/watch?v=5xxiR37eUt8

from the comment section,

What an absolutely totally incredible account of the crucifixion of Jesus Christ! It gave me the most calming peaceful feeling for my soul! I pray people, will watch this video to reassure their faith in our Lord Jesus to believe and know he is the Son of God! The Shroud of Turin is a gift for humanity and proof the Bible is the word from God Almighty! Thank You, Fr. Robert Spitzer, forever and ever I’m very grateful for hearing the Blessed accounting during Holy Week!

and

I couldn’t help but come to tears in the graphic description of our Savior’s wounds and suffering. What He did for us we can never repay. Thank you Jesus. I love you

Verse:

John 20:7-8 The cloth that had been around Jesus’ head was rolled up, lying separate from the linen cloths. Then the other disciple, who had reached the tomb first, also went in. And he saw and believed.

bornagain77

Related: The first hyper-realistic body of Christ based on the Holy Shroud is on exhibit in Spain. Gosh, he looks very white. JVL

Good Friday at the Vatican: Papal preacher warns against relativism and ‘vortex of nihilism.’ https://www.catholicnewsagency.com/news/254047/good-friday-at-the-vatican-papal-preacher-warns-against-relativism-and-vortex-of-nihilism relatd

The first hyper-realistic body of Christ based on the Holy Shroud is on exhibit in Spain. https://www.catholicnewsagency.com/news/252551/the-first-hyper-realistic-body-of-christ-based-on-the-holy-shroud-is-on-exhibit-in-spain relatd

Denial and fatuous comment right on schedule . . . Querius

Seems Uncommon Descent needs some TLC. Alan Fox

AF disingenuously tried to claim that polyglycine is to be considered a legitimate functional protein.

Poly-glycine has structural properties akin to collagen. Alan Fox

Bornagain77,

A few small problems for AF. First, polyglycine is not consider a functional protein but is considered a ‘homopolymer’.

Ouch, that must have hurt. Ok, waiting for a troll to deny this or post something fatuous to change the subject. Thanks for the link in 159. What a great summary! I respect James Tour's scientific openness in not saying anything is impossible. Generally, ingenious people figure out ways of doing things or discovering things once thought to be impossible. -Q Querius

Ba77 at 159, Even the writer of this article is, it appears unintentionally, naively optimistic, since he adds "... anytime soon." Does he really believe that? Or is he so caught up in prevailing Darwinian dogma to the point where he cannot exclude the possibility? In a presentation I watched, atomic-scale assembly is the goal. But, and this is my observation, even if individual atoms can be arranged in atomically precise ways, this does not mean human beings can create life this way. Computers might be created this way, at some point. One aspect of life is its connection to the quantum world. This connection is not purely mechanistic. It is a built-in connection. relatd

Just uploaded at ENV:

Do Present Proposals on Chemical Evolutionary Mechanisms Point Toward the First Life? James M. Tour - April 7, 2023 Excerpt: Working in synthetic chemistry, building relatively simple nanomachines, has led to being sceptical of proposals for the origin of the requisite chemical building blocks necessary for life. Some biologists seem to think that there are well-understood prebiotic molecular mechanisms for the synthesis of carbohydrates, proteins, lipids, or nucleic acids. They have been grossly misinformed. Others think that, if not yet known, such chemical pathways will soon be identified. To me, these biologists are naively optimistic. What they hope for will not happen anytime soon. https://evolutionnews.org/2023/04/are-present-proposals-on-chemical-evolutionary-mechanisms-accurately-pointing-towards-the-first-life/

bornagain77

Ba77, Without actual scientific evidence, people like Richard Dawkins propose "climbing Mount Improbable," where - somehow - life can self-upgrade and in a directional, purposeful way. But, as you've pointed out, even in a lab and even with significant manipulation, this cannot be done. Craig Venter, it is claimed, created "synthetic life." In reality, his 'minimal cell' required actual, living cell components to function. As a businessman, he hopes to hijack the machinery of the cell in order to create biological substances which can be sold. https://www.jcvi.org/research/first-minimal-synthetic-bacterial-cell relatd

I stated: "Tell you what AF, if you want to be taken seriously, and not be viewed as a dogmatic Darwinian troll who is impervious to reason, experimentally show us completely natural processes creating just a single protein. At least then you will have a tiny smidgeon of real-time empirical evidence supporting your atheistic materialism, and you will not be completely reliant on imaginary just-so stories as you are now." AF responded,"The simplest possible protein is poly-glycine, which is achiral." A few small problems for AF. First, polyglycine is not consider a functional protein but is considered a 'homopolymer'. As the following article explains, ",,, proteins have a defined and complex sequence that includes all 20 of the amino acids, but polyglycine is a homopolymer formed only from glycine residues."

Polyglycine (Molecular Biology) Excerpt: Polyglycine is the name given to the polyamino acid formed from glycine. Like proteins, the polyglycine polymer is formed by condensation of the amino group of one amino acid and the carboxyl group of another amino acid. On the other hand, proteins have a defined and complex sequence that includes all 20 of the amino acids, but polyglycine is a homopolymer formed only from glycine residues. http://what-when-how.com/molecular-biology/polyglycine-molecular-biology/

AF trying to pass off polyglycine as a functional protein formed by completely natural processes is disingenuous to say the very least. Secondly, and as was already shown to AF at post 135, AF's belief that achirality preceded homochirality is wrong. As Dr. Tour observed, ",, 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.",,,

“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 other words, homochirality must be solved before life appeared, not after. AF, nor any other Darwinists, have any scientific evidence that such is possible in a prebiotic environment. So thus, when pressed for empirical evidence for a simple protein forming by completely natural processes, AF disingenuously tried to claim that polyglycine is to be considered a legitimate functional protein. And then, on top of that, AF tried to imply that achirality preceded the homochiral proteins we find in life. i.e. "Early proteins, with useful structural properties, emerged before enzymes?" AF simply has no real-time empirical evidence that such a scenario from a hypothetical prebiotic pool of achiral amino acids to homochiral functional proteins is remotely possible. Nor, as Dr. Tour explained, can life even exist until the problem of homochiral proteins is solved. (Not to mention the problem of homochiral DNA). Despite AF trying to hand-wave the homochirality problem off with unsubstantiated just-so stories, homochirality has been, and remains, a huge and vexing problem for Darwinian atheists. A huge problem that, much like the proverbial elephant in the living room, simply refuses to go away.

Dr. James Tour – (Problems with) Abiogenesis Theory – Homochirality https://youtu.be/tqbpd3CmBgE

Moreover, as Dr. Tour pointed out in his interview from 3 weeks ago, the problems for Darwinian atheists go far deeper that just trying to explain the origin of homochiral proteins (and DNA).

"There is no such thing as a simple cell every cell is is amazingly complex. This has been calculated. I've not done the calculation this was done by by biophysicists.,, They have figured this out. They give the pieces that are needed to build a simple cell. So it's a it's about 15 different pieces you would need to build for there to be a simple cellular life. Of those 15 pieces zero, ZERO, have been made by origin of Life researchers. Even in their Laboratories. Even with all their equipment. I'm not talking about under a rock or in some pool by the side of the ocean. I'm talking in the pristine Laboratories building up these molecules and making any of those 15 pieces.,,, You have to have each one of these pieces none of them, ZERO of them, have been made." - James Tour - Origin of Life: Controversial Chemist Shakes up Scientific Community | Problems with Primordial Soup https://youtu.be/ZugOrSD7YL4?t=1393

In fact, it is not just that ZERO of the 15 pieces that were calculated to be necessary for 'simple' life have ever been made in pristine laboratories, and as Dr Tour stated elsewhere, even if you were somehow able to make all of the different pieces that are required for life, still no one would have any realistic clue as to how to put all those different pieces together.

(July 2019) “We have no idea how to put this structure (a simple cell) together.,, So, not only do we not know how to make the basic components, we do not know how to build the structure even if we were given the basic components. So the gedanken (thought) experiment is this. Even if I gave you all the components. Even if I gave you all the amino acids. All the protein structures from those amino acids that you wanted. All the lipids in the purity that you wanted. The DNA. The RNA. Even in the sequence you wanted. I’ve even given you the code. And all the nucleic acids. So now I say, “Can you now assemble a cell, not in a prebiotic cesspool but in your nice laboratory?”. And the answer is a resounding NO! And if anybody claims otherwise they do not know this area (of research).” – James Tour: The Origin of Life Has Not Been Explained – 4:20 minute mark (The more we know, the worse the problem gets for materialists) https://youtu.be/r4sP1E1Jd_Y?t=255

What Dr. Tour touched upon in that preceding comment is the fact that having the correct sequential information in DNA and proteins is not nearly enough. Besides having the correct the sequential information in DNA there is also a vast amount of ‘positional information’ that must somehow be accounted for as well in order to explain life. In short, and to cut to the chase, only a vastly superior Intelligence can provided the vast amount of 'positional information' that is necessary to explain 'simple life', (i.e. 10 to the 12 bits of information), and overcome the tremendous 'thermodynamic hurdle' that prevents non-life from ever forming a 'simple' cell. https://uncommondescent.com/intelligent-design/researchers-surface-bubbles-could-have-somehow-become-earths-first-cells-hey-james-tour-will-love-this-um-not/#comment-725762 bornagain77

The point is that there is a structural aspect here. Silk, nylon, collagen, all repetitive strings of monomers via CONH bonds. Early proteins, with useful structural properties, emerged before enzymes? Alan Fox

The simplest possible protein is poly-glycine, which is achiral. A bit long but fascinating. https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/cbic.202100658 Alan Fox

AF: "My question is how the phenomenon of CISS is supposed to be an issue for biochemistry and molecular biology" It is not an issue for biochemistry and molecular biology. In fact, it is finding of biochemistry and molecular biology. But CISS, and homochirality in general, is a HUGE issue for the pseudo-science of Darwinian evolution since Darwinian evolution can't realistically explain how they came about. In fact, the sciences of biochemistry and molecular biology have no need whatsoever for the just-so stories of Darwinian evolution.

"In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, and physiology, have not taken evolution into account at all." - Marc Kirschner, founding chair of the Department of Systems Biology at Harvard Medical School, Boston Globe, Oct. 23, 2005 "While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that “Nothing in biology makes sense except in the light of evolution”, most can conduct their work quite happily without particular reference to evolutionary ideas. Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superflous one.” - Adam S. Wilkins, editor of the journal BioEssays, Introduction to "Evolutionary Processes" - (2000). "Biologists must constantly keep in mind that what they see was not designed, but rather evolved. It might be thought, therefore, that evolutionary arguments would play a large part in guiding biological research, but this is far from the case. It is difficult enough to study what is happening now. To figure out exactly what happened in evolution is even more difficult. Thus evolutionary achievements can be used as hints to suggest possible lines of research, but it is highly dangerous to trust them too much. It is all too easy to make mistaken inferences unless the process involved is already very well understood." - Francis Crick - What Mad Pursuit (1988) "Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No. I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss. In the peer-reviewed literature, the word "evolution" often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for "evolution" some other word – "Buddhism," "Aztec cosmology," or even "creationism." I found that the substitution never touched the paper's core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology.,,, Darwinian evolution – whatever its other virtues – does not provide a fruitful heuristic in experimental biology." - Philip S. Skell - (the late) Emeritus Evan Pugh Professor at Pennsylvania State University, and a member of the National Academy of Sciences. - Why Do We Invoke Darwin? - 2005 http://www.discovery.org/a/2816

Moreover, even your cited paper trying to solve the problem of homochirality for Darwinists is a joke as far as the real sciences of molecular biology and biochemistry are concerned, since they, via a model, and not via any real world evidence, estimated "around 300 thousand years plus or minus a couple of orders of magnitude" to reach homochirality. In other words, your cited paper is just another just-so-story in an endless series of just-so stories from Darwinists.

Atheist and Darwinian Science and Story Telling, part 1 of 9 Excerpt: (Darwinists) must deal with the fact that abiogenesis (abiotic synthesis) is not observed anywhere and is not producible in any experiments (and if it was it would be evidence of intelligent design).,,, What is their answer? They can imagine a time, long, long ago in the Earth’s past, when everything happened just so and abiogenesis was possible. What about filling the various gaps in our knowledge? They can imagine a time in the distant future when their beliefs will be proven true: in other words they think that eventually material causes will be discovered for all material effects including the universe itself.,, Herein lies the fallacies: they merely regress to an unknown past in which they can imagine thing occurring that do not occur today (what happened to uniformitarianism?) and they can project into an equally unknown future at which time we will discover that absolute materialism is true. Atheists of this sort appeal to inaccessible, unobserved, un-experimented upon, ideal and self-service concepts and replace evidence for imagination. As long as they can imagine it, it must be true: this appears to be what Richard Dawkins meant by being an intellectually fulfilled atheist. https://truefreethinker.com/atheist-and-darwinian-science-and-story-telling-part-1-of-9/

Tell you what AF, if you want to be taken seriously, and not be viewed as a dogmatic Darwinian troll who is impervious to reason, experimentally show us completely natural processes creating just a single protein. At least then you will have a tiny smidgeon of real-time empirical evidence supporting your atheistic materialism, and you will not be completely reliant on imaginary just-so stories as you are now.

Origin: Probability of a Single Protein Forming by Chance https://www.youtube.com/watch?v=W1_KEVaCyaA Mathematical Basis for Probability Calculations Used in (the film) Origin Excerpt: Putting the probabilities together means adding the exponents. The probability of getting a properly folded chain of one-handed amino acids, joined by peptide bonds, is one chance in 10^74+45+45, or one in 10^164 (Meyer, p. 212). This means that, on average, you would need to construct 10^164 chains of amino acids 150 units long to expect to find one that is useful. http://www.originthefilm.com/mathematics.php Minimal Complexity Relegates Life Origin Models To Fanciful Speculation - Nov. 2009 Excerpt: Based on the structural requirements of enzyme activity Axe emphatically argued against a global-ascent model of the function landscape in which incremental improvements of an arbitrary starting sequence "lead to a globally optimal final sequence with reasonably high probability". For a protein made from scratch in a prebiotic soup, the odds of finding such globally optimal solutions are infinitesimally small- somewhere between 1 in 10exp140 and 1 in 10exp164 for a 150 amino acid long sequence if we factor in the probabilities of forming peptide bonds and of incorporating only left handed amino acids. https://uncommondescent.com/intelligent-design/minimal-complexity-relegates-life-origin-models-to-wishful-speculation/ The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1 “We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions.” - James Tour – considered one of the top ten leading synthetic chemists in the world - The Origin of Life: An Inside Story - March 2016 https://www.youtube.com/watch?v=_zQXgJ-dXM4

Verse:

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

Bornagain77 @137,

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.

Yes, of course. People who are ideologically poisoned by a failed 19th-century racist theory cannot and will not acknowledge any evidence that contradicts their fundamentalist quasi-religious science fantasy. For example, in @142, Alan Fox mocks “A hypothesis of “Intelligent Design,” but just like Critical Rationalist, he cannot provide a simple definition of what he’s mocking. Also notice that in @133, Alan Fox claims “a quick glance at that Tour video.” Dr. Tour has an open challenge to anyone to explain to him how any of this science fantasy is supposed to work. He promises only to ask questions, but has no takers so far. So here’s what any of the debaters and their sock puppets here can do. Send Dr. Tour an email (on his web page, https://www.jmtour.com/) accepting his challenge. Then, they can let us know how it went. -Q Querius

As always, the mainstream in the biological sciences are working away oblivious to UD commenters telling them their research is impossible.

Great work in generics. We await your analysis on the significance of this for Evolution. How about making your next comment an explanation of how this supports your claims for naturalized Evolution. We don’t mind waiting 6-8 months for you to get it right. We know you want to get it so all the plebes here can understand just how it works. jerry

As always, the mainstream in the biological sciences are working away oblivious to UD commenters telling them their research is impossible. https://link.springer.com/article/10.1007/s11084-022-09632-9 Alan Fox

Alan at 144 has the audacity to still pretend that CISS, i.e homochirality, is no problem for his atheistic worldview?

My question was what does Phil regard as problematic for biomolecules and biochemistry? After all you raised the subject.

Whatever Alan, chase your own tail in a circle. ? ,,, I have MUCH better things to do today than try to be reasonable with someone who simply refuses to ever be reasonable.

No answer, then. The subject of CISS was just a distraction. Alan Fox

We do not come from blind particles out of nowhere. Who'd a thunk it? Origenes

Ba77, The defense of atheistic naturalism must continue regardless of claims to the contrary. The Soviet Union existed for a number of years prior to collapsing in on itself in the early 1990s. The atheist Workers' Paradise is still admired by some. Intelligent Design points to a designer - as opposed to nothing. As opposed to a mindless process that some still support. The alternative is too frightening to contemplate. God created. And since God created, and we can know this on our own, the truly terrible part is that we are responsible. What we say and do matters. Of course, Christians who fear God understand that He is just. relatd

Alan at 144 has the audacity to still pretend that CISS, i.e homochirality, is no problem for his atheistic worldview? :) Whatever Alan, chase your own tail in a circle. :) ,,, I have MUCH better things to do today than try to be reasonable with someone who simply refuses to ever be reasonable. bornagain77

AF: "Presuming there is such a thing as “atheistic nihilism”." There is, and the psychological, and physical, effects of atheism are bad on humans.

“I maintain that whatever else faith may be, it cannot be a delusion. The advantageous effect of religious belief and spirituality on mental and physical health is one of the best-kept secrets in psychiatry and medicine generally. If the findings of the huge volume of research on this topic had gone in the opposite direction and it had been found that religion damages your mental health, it would have been front-page news in every newspaper in the land.” - Professor Andrew Sims former President of the Royal College of Psychiatrists - Is Faith Delusion?: Why religion is good for your health - preface “In the majority of studies, religious involvement is correlated with well-being, happiness and life satisfaction; hope and optimism; purpose and meaning in life; higher self-esteem; better adaptation to bereavement; greater social support and less loneliness; lower rates of depression and faster recovery from depression; lower rates of suicide and fewer positive attitudes towards suicide; less anxiety; less psychosis and fewer psychotic tendencies; lower rates of alcohol and drug use and abuse; less delinquency and criminal activity; greater marital stability and satisfaction… We concluded that for the vast majority of people the apparent benefits of devout belief and practice probably outweigh the risks.” - Professor Andrew Sims former President of the Royal College of Psychiatrists - Is Faith Delusion?: Why religion is good for your health – page 100 https://books.google.com/books?id=PREdCgAAQBAJ&pg=PA100#v=onepage&q&f=false Can attending church really help you live longer? This study says yes – June 1, 2017 Excerpt: Specifically, the study says those middle-aged adults who go to church, synagogues, mosques or other houses of worship reduce their mortality risk by 55%. The Plos One journal published the “Church Attendance, Allostatic Load and Mortality in Middle Aged Adults” study May 16. “For those who did not attend church at all, they were twice as likely to die prematurely than those who did who attended church at some point over the last year,” Bruce said. https://www.usatoday.com/story/news/nation-now/2017/06/02/can-attending-church-really-help-you-live-longer-study-says-yes/364375001/ Study: Religiously affiliated people lived “9.45 and 5.64 years longer…” July 1, 2018 Excerpt: Self-reported religious service attendance has been linked with longevity. However, previous work has largely relied on self-report data and volunteer samples. Here, mention of a religious affiliation in obituaries was analyzed as an alternative measure of religiosity. In two samples (N = 505 from Des Moines, IA, and N = 1,096 from 42 U.S. cities), the religiously affiliated lived 9.45 and 5.64 years longer, respectively, than the nonreligiously affiliated. Additionally, social integration and volunteerism partially mediated the religion–longevity relation. https://uncommondescent.com/intelligent-design/study-religiously-affiliated-people-lived-religiously-affiliated-lived-9-45-and-5-64-years-longer/ Can Religion Extend Your Life? - By Chuck Dinerstein — June 16, 2018 Excerpt: The researcher's regression analysis suggested that the effect of volunteering and participation accounted for 20% or 1 year of the impact, while religious affiliation accounted for the remaining four years or 80%. https://www.acsh.org/news/2018/06/16/can-religion-extend-your-life-13092 Harvard Researchers Have Linked Spirituality To Healthier Lives And Longer Lifespans - August 17, 2022 Excerpt: “This study represents the most rigorous and comprehensive systematic analysis of the modern-day literature regarding health and spirituality to date,” said Tracy Balboni, lead author and senior physician at the Dana-Farber/Brigham and Women’s Cancer Center and professor of radiation oncology at Harvard Medical School. “Our findings indicate that attention to spirituality in serious illness and in health should be a vital part of future whole person-centered care, and the results should stimulate more national discussion and progress on how spirituality can be incorporated into this type of value-sensitive care.” https://uncommondescent.com/spirituality/at-scitech-daily-harvard-researchers-have-linked-spirituality-to-healthier-lives-and-longer-lifespans/

bornagain77

Phil says:

...I have no earthly clue how anyone on God’s green earth could ever find ANY comfort whatsoever in the utter despair that is Atheistic Nihilism

Presuming there is such a thing as "atheistic nihilism", what would that have to do with scientific research and explanations in the realm of evolutionary biology? Alan Fox

Alan, already addressed at 135. i.e. “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.”

My question is how the phenomenon of CISS is supposed to be an issue for biochemistry and molecular biology. It appears to be measurable but how is the effect bad news? Be Is there some biological process that has to be revised to take account of the effect? I'm predicting no. Alan Fox

Sri: "RNA-world has imploded. Let’s move on." Yes, true. But alas Origenes, naturalistic OOL pipe dreams are all that Darwinists have to keep them warm at night. (Although I have no earthly clue how anyone on God's green earth could ever find ANY comfort whatsoever in the utter despair that is Atheistic Nihilism).

The Despair of Atheism - KYLE BUTT, M.Div. - 2019 Excerpt: Nothing left but Despair What is left in a world where meaninglessness reigns supreme, but its human inhabitants are wired to need meaning in their lives? As Lawrence Krauss so brazenly reminds his readers and listeners: “And by the way, that’s the second of the two things I wanted to remind you of. The first is that you’re insignificant. And the second, the future is miserable.”25 French humanist, Voltaire, encapsulated this recognition of misery in his “Poem on the Lisbon Disaster,” in which he wrote: “What is the verdict of the vastest mind? Silence: the book of fate is closed to us. Man is a stranger to his own research; He knows not whence he comes, nor whither goes. Tormented atoms in a bed of mud, devoured by death, a mockery of fate.”26 So, humans are “insignificant,” “miserable,” “tormented atoms in a bed of mud.” Yet, atheism is not finished painting humanity’s sad plight with the pale colors of despair. Peter Atkins opined: “We are children of chaos, and the deep structure of change is decay. At root, there is only corruption, and the unstemmable tide of chaos. Gone is purpose; all that is left is direction. This is the bleakness we have to accept as we peer deeply and dispassionately into the heart of the Universe.”27 Albert Camus quoted Kirkegaard, who said: “If man had no eternal consciousness…what would life be but despair?” Camus then wrote: “This cry is not likely to stop the absurd man. Seeking what is true is not seeking what is desirable. If in order to elude the anxious question: ‘What would life be?’ one must, like the donkey, feed on the roses of illusion, then the absurd mind, rather than resigning itself to falsehood, prefers to adopt fearlessly Kierkegaard’s reply: ‘despair.’”28 Bertrand Russell bemoaned: “Brief and powerless is Man’s life; on him and all his race the slow, sure doom falls pitiless and dark. Blind to good and evil, reckless of destruction, omnipotent matter rolls on its relentless way; for Man, condemned today to lose his dearest, tomorrow himself to pass through the gate of darkness….”29 Into this chaos of bleakness, meaninglessness, insignificance, torment, and despair, Christianity offers a hope that can anchor the soul (Hebrews 6:19) and a truth that does not need a “noble lie” to make it palatable. Christianity provides the only system that can give humanity a reason to get up in the morning and live life to the fullest. A Response to Atheism’s Despair Madalyn Murray O’Hair was the founder of the American Atheist organization. She lived a life in complete rebellion against her God. Her rabid atheism prodded her to attack the idea of God whenever she could. But her atheism could not bring her joy, only a forlorn heart of desperation. When her personal belongings were auctioned, it was discovered that on six different pages of her writings was the heartbreaking cry: “Somebody, somewhere, love me!”30 The greatest tragedy of atheism is that it strips the world of everything meaningful, including real love. Atheist Dan Barker admitted that, according to atheism, “In the end of the cosmos it’s not going to matter. You and I are like ants or rats or like pieces of broccoli, really, in the big picture…there is no value to our species…we are no different than a piece of broccoli in the cosmic sense.”31 As we have seen, according to atheism, humans are nothing more than matter in motion, “tormented atoms in a bed of mud.” Our actions will not determine where we spend eternity. And any “feeling” that one person may have for another person can only be “skin deep.” It can only be a product of the physical brain. As much as atheists try to discuss love, hope, honor, or any of the elevated human virtues, they cannot explain how such can exist in a world without God. Sadly, just like O’Hair, there is a world full of people who want someone to love them, but they refuse to recognize that there is Someone Who does. Their Creator, God, loves them so much that He came to die on the cross for them. Jesus Christ, God in the flesh, gave His life to prove His love for humanity and to show humans that they are not cosmic accidents, but intentionally designed persons who have a meaning and purpose in life. And He gave His life so that those humans who choose to obey Him can live eternally in heaven. “For God so loved the world that He gave His only begotten Son, that whoever believes in Him should not perish but have everlasting life” (John 3:16). But God’s love has a limit. He will not force anyone to believe in Him. He loves each person enough to let us all freely choose whether or not to believe in and obey Him. And our choice will determine our eternal destiny. Moses once wrote to the Israelites: “I call heaven and earth as witnesses today against you, that I have set before you life and death, blessing and cursing; therefore choose life” (Deuteronomy 30:19). The failure to choose the right beliefs and actions in this life has real consequences. These are not imagined consequences that have to be endowed with meaning by subjective, arbitrary feelings. On the contrary, the consequences are objectively real. We are not ultimately like broccoli or rats. Our decisions really matter, for now and for eternity. Those who refuse to acknowledge God can have no hope for an afterlife or joy in death, only despair. Agnostic Bart Ehrman, who once claimed to be a Christian, wrote: “The fear of death gripped me for years, and there are still moments when I wake up at night in a cold sweat.”32 The Bible explains that Christ came to defeat death, and “release those who through fear of death were all their lifetime subject to bondage” (Hebrews 2:15). The only solution to the fear of death and the deep, abiding despair that stems from atheism is to seek God and His will. Madalyn Murray O’Hair’s cry, “Somebody, somewhere, love me!” echoes across the world from millions of voices who are trying to find love and hope apart from God. The irony of it all is that they have shut their ears to the voice of God, Who through His Son, calls from the cross, “I love you.” Instead of the bleak, tormented, useless, meaningless, purposeless, pitiless, miserable despair that atheism demands, let us turn our faces to the true light, hope, joy, and love that our Creator provides.33 https://apologeticspress.org/the-despair-of-atheism-5713/

bornagain77

RNA-world has imploded. Let’s move on.

Who's us and what will you move on to? A hypothesis of "Intelligent Design"? Alan Fox

RNA-world has imploded. Let's move on. Origenes

Alan, already addressed at 135. i.e. "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." bornagain77

And the issue with CISS is what, exactly, Phil? Alan Fox

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-779373 bornagain77

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

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

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

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

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

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. -Q Querius

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

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

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. KF kairosfocus

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

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

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

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

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. KF kairosfocus

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

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 -Q Querius

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

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

a sign of the bankruptcy of the evolutionary materialistic dogma and its fellow travellers.

See this, UB? This is attacking the messenger. Alan Fox

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

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. KF kairosfocus

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 on Alan Fox

Or will you continue to attack the messenger instead?

How is pointing out a major flaw in your argument a personal attack? Alan Fox

I still don't understand why Upright Biped doesn't get together with BIO-Complexity and work on publishing a paper. Alan Fox

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

. 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

...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

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

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

.

the fact that RNA World is a plausible precursor still stands. RNA is still both replicator and catalyst today.

You continue to assume your conclusions while avoiding the physical detail (the science). - - - - - - - - - - - - - - - - - - - - - - This is how you lose an argument by assuming your conclusions, and then spare yourself of the reason: AF: Upright Biped! Upright Biped! Upright Biped! AF: your whole “semiosis” argument fails on the existence of RNA and its dual role as replicator and catalyst. UB: Being able to play a “dual role” (as a catalyst and as an information carrier like mRNA) implies that there are certain conditions that enable the RNA to play those two roles. AF: My challenge is to propose the steps that could have taken RNA world to DNA-protein world. AF: One! The answer to your question, Upright Biped, (now you have clarified) is one. AF: No I don’t suggest any biochemically active suite of proteins can be constructed from polymers consisting of a single amino acid. AF: RNA World does not have to explain the genetic code and protein synthesis. (thud) - - - - - - - - - - - - - - - - - …and despite having glorious funding and a hardy open door at every suitable institution on the surface of the planet for decades on end, you don’t even have an autonomous self-replicating RNA, do you. Upright BiPed

For Upright Biped: Anyway, the fact that RNA World is a plausible precursor still stands. RNA is still both replicator and catalyst today. RNA World scenario allows evolutionary processes to add polypeptides, genetic code, aminoacyl tRNA synthetases incrementally. But no doubt you will continue to claim I have not refuted your argument. But what can you do? Nobody actually working in the field of OoL has heard of you or your “hypothesis”. Over a decade and counting with no progress. Are people cowering in fear of your mighty insight? I don’t think so. But my claim is testable. Why don’t you test it? Publish a paper where it might get noticed. Bio-Complexity should be beating a path to your door. Alan Fox

Q, sadly yes. bornagain77

Bornagain77, See what I mean? -Q Querius

• 'The Church “proclaims that by the light of reason the human intellect can readily and clearly discern purpose and design in the natural world, including the world of living things.” • “Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science.” ' "Christoph Cardinal Schönborn is archbishop of Vienna and general editor of the Catechism of the Catholic Church." relatd

It’s a pity that Alan Fox won’t ever listen to this information, because he finds it ideologically incompatible with his beliefs.

Oh, physician heal thyself. Alan Fox

Likewise, Relatd! Bornagain77 @97, What a great clip of the brilliant expert, Dr. Tour! Thank you. It's a pity that Alan Fox won't ever listen to this information, because he finds it ideologically incompatible with his beliefs. All we get is denials and vacuous unsupported assertions in reply. What a waste. But others of us appreciated it. -Q Querius

Ba77, Your posts are much appreciated. "CHURCH: But none of us has recreated that,,. SHAPIRO: There must have been much more primitive ways of putting together. CHURCH: But prove it." My comment to these men would be: If it is so simple, why hasn't it been done in a lab? relatd

The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm Inferring efficiency of translation initiation and elongation from ribosome profiling - 2020 Abstract Excerpt: Our method distinguishes between the elongation rate intrinsic to the ribosome’s stepping cycle and the actual elongation rate that takes into account ribosome interference. This distinction allows us to quantify the extent of ribosomal collisions along the transcript and identify individual codons where ribosomal collisions are likely. When examining ribosome profiling in yeast, we observe that translation initiation and elongation are close to their optima and traffic is minimized at the beginning of the transcript to favour ribosome recruitment. https://academic.oup.com/nar/article/48/17/9478/5895331 Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service - 2009 Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act." https://www.science.org/doi/full/10.1126/science.326_346 Armed Forces in the Cell Keep DNA Healthy - September 8, 2015 Excerpt: According to Prof. Hurt, the production of ribosomes is an extremely complex process that follows a strict blueprint with numerous quality-control checkpoints. The protein factories are made of numerous ribosomal proteins (r-proteins) and ribosomal ribonucleic acid (rRNA). More than 200 helper proteins, known as ribosome biogenesis factors, are needed in the eukaryotic cells to correctly assemble the r-proteins and the different rRNAs. Three of the total of four different rRNAs are manufactured from a large precursor RNA. They need to be "trimmed" at specific points during the manufacturing process, and the superfluous pieces are discarded. "Because these processes are irreversible, a special check is needed," explains Ed Hurt. http://www.evolutionnews.org/2015/09/armed_forces_in099121.html Ribosomes Optimized for Speed, Flexibility - August 2, 2017 Excerpt: The DNA translation machines in the cell show unexpected complexity, forcing molecular biologists to revise what they thought they knew about ribosomes. In particular, they appear optimized for speed of self-duplication and modularized for flexibility.,,, if you think of “orchestrated function” again, the sheet music won’t do any good if the stage isn’t already set up and the players aren’t in their seats.,,, The “orchestrated function of hundreds of proteins” has time limits. The conductor is pounding his foot and tapping his baton on the podium, rushing the orchestra to get in place. Imagine how much harder if each player, instrument, chair, and music stand has to make a copy of itself first for a show across town!,,, https://evolutionnews.org/2017/08/ribosomes-optimized-for-speed-flexibility/ Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013 Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within cells consisting of tightly stacked sheets of membrane studded with the molecules (ribosome machines) that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell. "The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,, ,, this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,, http://www.sciencedaily.com/releases/2013/07/130718130617.htm

Moreover, (and as if the inference to intelligent design needed any more help), the Ribosome of the cell is also found to be very similar to a CPU in an electronic computer:

Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf

bornagain77

AF, "Remnants of RNA World exist now. Ribosomes are essentially ribozymes, their catalytic site consists of an RNA molecule. RNA is very versatile, performing many rôles in cellular metabolism." LOL, :)

LIFE: WHAT A CONCEPT! Excerpt: The ribosome,,,, it's the most complicated thing that is present in all organisms.,,, you find that almost the only thing that's in common across all organisms is the ribosome.,,, So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be? George Church http://www.edge.org/documents/life/church_index.html Leading Biologists Marvel at the "Irreducible Complexity" of the Ribosome, but Prefer Evolution-of-the-Gaps - Feb, 2008 Excerpt: VENTER: Below ribosomes, yes: you certainly can’t get below that. But you have to have self-replication. CHURCH: But that’s what we need to do — otherwise they’ll call it irreducible complexity. If you say you can’t get below a ribosome, we’re in trouble, right? We have to find a ribosome that can do its trick with less than 53 proteins. VENTER: In the RNA world, you didn’t need ribosomes. CHURCH: But we need to construct that. Nobody has constructed a ribosome that works well without proteins. VENTER: Yes. SHAPIRO: I can only suggest that a ribosome forming spontaneously has about the same probability as an eye forming spontaneously. CHURCH: It won’t form spontaneously; we’ll do it bit by bit. SHAPIRO: Both are obviously products of long evolution of preexisting life through the process of trial and error. CHURCH: But none of us has recreated that,,. SHAPIRO: There must have been much more primitive ways of putting together. CHURCH: But prove it. http://www.evolutionnews.org/2008/02/leading_biologists_marvel_at_t004789.html Of note, although the ribosome is present in all life, and is necessary for life, it is not uniform (i.e. conserved) across all life as is presupposed within Darwinian theory, i.e. the 'non-conserved' nature of ribosomes falsify Darwin's theory. Ribosomes Excerpt: Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth) differ in their size, sequence, structure, and the ratio of protein to RNA. https://sites.google.com/site/jjohnsonelps301/home/animal-cell-structure/ribsomes Information Processing Differences Between Bacteria and Eukarya—Implications for the Myth of Eukaryogenesis by Change Tan and Jeffrey P. Tomkins on March 25, 2015 Excerpt: In a previous report, we showed that a vast chasm exists between archaea and eukarya in regard to basic molecular machines involved in DNA replication, RNA transcription, and protein translation. The differences in information processing mechanisms and systems are even greater between bacteria and eukarya, which we elaborate upon in this report. Based on differences in lineage-specific essential gene sets and in the vital molecular machines between bacteria and eukarya, we continue to demonstrate that the same unbridgeable evolutionary chasms exist—further invalidating the myth of eukaryogenesis. https://answersingenesis.org/biology/microbiology/information-processing-differences-between-bacteria-and-eukarya/

bornagain77

The RNA world does not exist now, and never has existed, in the real world.

Remnants of RNA World exist now. Ribosomes are essentially ribozymes, their catalytic site consists of an RNA molecule. RNA is very versatile, performing many rôles in cellular metabolism. See this list. Alan Fox

AF: "RNA World does not have to explain the genetic code and protein synthesis. It merely has to exist as a precursor" The RNA world does not exist now, and never has existed, in the real world. But has only ever existed in the fevered imagination of Darwinian atheists and, in a highly limited sense, in highly manipulated laboratory conditions.

Abiogenesis Hypothesis ULTRA Pack! Free Course w/ Rice University Chemist - Dr. James Tour Episode 8 - Nucleotides, DNA, and RNA - RNA self-replication - 4:49 mark https://youtu.be/WKLgQzWhO4Q?t=17378

bornagain77

Perhaps most importantly, an RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins.

RNA World does not have to explain the genetic code and protein synthesis. It merely has to exist as a precursor, where self-sustaining self-replicators are thus subject to evolutionary processes and the various steps in incorporation of amino-acids into cellular metabolism can be added incrementally. Alan Fox

Robert Shapiro was professor emeritus of chemistry at New York University. He is best known for his work on the origin of life, having written two books on the topic...@

I hold fond memories of professor Shapiro, with whom I had extensive email interaction in 2005 over claims his review of Darwin's Black Box amounted to peer review. It was reading his books that led me to my former position of being skeptical of RNA World. I thoroughly recommend Planetary Dreams which advocates researching other worlds for evidence of life, which would give us much insight into OoL. I now think the circumstantial evidence for RNA World has piled up since such that Shapiro would take a different view, were he alive today. Alan Fox

Alan Fox: "the fact that RNA World is a plausible precursor still stands." Others disagree.

The RNA world hypothesis: the worst theory for the early evolution of life (except for all the others) - July 2012 Excerpt: "The RNA World scenario is bad as a scientific hypothesis" - Eugene Koonin “The RNA world hypothesis has been reduced by ritual abuse to something like a creationist mantra” - Charles Kurland "I view it as little more than a popular fantasy." - Charles Carter https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/ Putting the RNA World to the Test with "Pistol" - February 24, 2017 Excerpt: In Susan Mazur's book The Origin of Life Circus, leading origin-of-life researchers describe the utter disaster of the RNA world scenario in one-on-one interviews she recorded in person. *Lawrence Krauss tells her (p. 35): "The question is, can RNA result naturally? That's been a big stumbling block." *David Deamer tells her (p. 43) that the RNA and DNA monomers don't link up naturally: "the laws of thermodynamics do not allow them to polymerize because there is a tremendous energy barrier to getting them to form bonds." That's especially true in water, he says, which breaks down (hydrolyzes) RNA. *Sara Walker tells Mazur that researchers need to move away from the RNA World, "because most of the origin-of-life community don't think that's the definitive answer." Walker herself says, "I don't see how an RNA world with only RNA can work" (p. 68). *Loren Williams tells her the original RNA World ("all RNA, all the time, and nothing else") is unreasonable and dead. RNA can't have done everything originally claimed. "Another problem is related to the origin of RNA itself. Where did RNA come from? Where did RNA precursors come from?" (p. 96). *Steven Benner tells Mazur (p. 81), "we don't know how useful function is distributed among sequence spaces. You have 4 raised to the power of 100 different sequences of RNA 100 nucleotides long. We don't know how productive function is distributed there compared to destructive function." Chances are destructive processes are increased as much as productive processes, he adds. On page 151-152, Benner lists four major "paradoxes" of the RNA world: the tar problem, the water problem, the entropy problem and the destruction problem. *RNA-world champion Nick Hud has abandoned the idea that RNA would form on its own. He's looking for candidates of not only proto-RNA, but "pre-proto-RNA" because, as Mazur reminds him, "RNA itself falls apart" (p.87). *Stuart Kauffman tells Mazur that they "tried for 40 years to get single-stranded RNA molecules to replicate, perhaps hundreds of chemists, and they all failed. It should work. But it hasn't. And after 40 years or 50 years, you think - maybe it's the wrong idea. People really tried hard" (p. 111). *Jack Szostak ups the time estimate to 60 years that researchers have worked on this problem of non-enzymatic replication. "The problem is RNA falls apart," he says (p. 218). *Norm Packard tells Mazur, "There are issues with the RNA world approach. The main one is how do you get RNA starting to get produced in the first place" (p. 297). He envisions an enzyme doing it. This speculation, of course, leads to an obvious problem: "But how do you get that enzyme?" *Pier Luigi Luisi is merciless in his attack, calling the RNA world a "baseless fantasy." Mazur puts his criticisms in bold print on pages 362-363, where he finds it "full of conceptual flaws," including its origin, the thermodynamics, the sequencing problem, the concentration problem, and more. The story of RNA turning into ribozymes he calls "chemical non-sense" (p. 363). http://www.evolutionnews.org/2017/02/putting_the_rna103513.html Can the Origin of the Genetic Code Be Explained by Direct RNA Templating? Stephen C. Meyer, Paul A. Nelson Abstract Motivated by the RNA world hypothesis, Michael Yarus and colleagues have proposed a model for the origin of the ‘uni- versal’ genetic code, in which RNA aptamers directly template amino acids for protein assembly. Yarus et al. claim that this “direct RNA templating” (DRT) model provides a stereochemical basis for the origin of the code, as shown by the higher-than- expected frequency of cognate coding triplets in aptamer amino acid-binding sites. However, the DRT model suffers from several defects. These include the selective use of data, incorrect null models, a weak signal even from positive results, an implausible geometry for the primordial RNA template (in relation to the universally-conserved structures of modern ribo- somes), and unsupported assumptions about the pre-biotic availability of amino acids. Although Yarus et al. claim that the DRT model undermines an intelligent design explanation for the origin of the genetic code, the model’s many shortcomings in fact illustrate the insufficiency of undirected chemistry to construct the semantic system represented by the code we see today. https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.2/BIO-C.2011.2 "As a medical biochemist (aka chemical pathologist) and a biologist with training in evolutionary biology, I can’t help but comment on Jack Szostak ideas regarding the issue of the origin of the genetic code. None of what he said about the issue in the context of the RNA world idea, and none of what is presented in one of the recent paper mentionned (Radakovic 2022 PNAS) has any chemical plausibility in my opinion.,,, As usual with RNA and ribozymes, catalytic activities are very weak and molecules are unstable. This has always plagued the RNA world hypothesis and no one has ever solved this inconvenient fact. And as usual with OoL research, the probability of any of these sorts of reactions occurring in natural prebiotic conditions is indistinguishable from zero. For example, the amino acid they used, Lysine, is, as they concede, not reasonably expected to be found in prebiotic environment:,,, That this sort of wild, totally implausible, speculation is allowed to appear in a respectable journal like PNAS is embarrassing.,,, Outside living cells, we know of no other chemical reaction governed by a code, not a single one, why ? The question is thus, how can chemistry become linguistic/informatics? So far, nobody has any clue." - Jblais - July 2022 https://uncommondescent.com/intelligent-design/at-evolution-news-gunter-bechly-repudiates-professor-daves-attacks-against-id/#comment-760263 ”Definitely embarrassing:” Nobel Laureate retracts non-reproducible paper in Nature journal - December 5, 2017 Excerpt: Some researchers who study the origins of life on Earth have hypothesized that RNA evolved before DNA or proteins. If true, RNA would have needed a way to replicate without enzymes.,,,, The errors were “definitely embarrassing,” Szostak told us: "In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been (and as Tivoli was) in interpreting these experiments." http://retractionwatch.com/2017/12/05/definitely-embarrassing-nobel-laureate-retracts-non-reproducible-paper-nature-journal/ Life What A Concept! - Robert Shapiro – video http://www.youtube.com/watch?&v=ku9wUbbPVYg#! (The late) Professor Robert Shapiro~ quote from preceding video “I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable. I’m always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words “To be or not to be, that is the question,” that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn’t be functional until it attained a certain length and could copy itself — appearing on the Earth.” Robert Shapiro was professor emeritus of chemistry at New York University. He is best known for his work on the origin of life, having written two books on the topic: The End of the RNA World Is Near, Biochemists Argue - December 19, 2017 Excerpt: Perhaps most importantly, an RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins. Finding a set of rules robust enough to do that would take far too long with RNA alone, said Peter Wills, Carter’s co-author at the University of Auckland in New Zealand — if the RNA world could even reach that point, which he deemed highly unlikely. In Wills’ view, RNA might have been able to catalyze its own formation, making it “chemically reflexive,” but it lacked what he called “computational reflexivity.” “A system that uses information the way organisms use genetic information — to synthesize their own components — must contain reflexive information,” Wills said. He defined reflexive information as information that, “when decoded by the system, makes the components that perform exactly that particular decoding.” The RNA of the RNA world hypothesis, he added, is just chemistry because it has no means of controlling its chemistry. “The RNA world doesn’t tell you anything about genetics,” he said. https://www.quantamagazine.org/the-end-of-the-rna-world-is-near-biochemists-argue-20171219/

bornagain77

You telling me that I “just don’t understand” that the RNA World didn’t have or need all that stuff is nothing more than hand-waiving (sic) under the big bright lights.

Bright lights? The bulbs are getting a bit dim here at UD. Anyway, the fact that RNA World is a plausible precursor still stands. RNA is still both replicator and catalyst today. RNA World scenario allows evolutionary processes to add polypeptides, genetic code, aminoacyl tRNA synthetases incrementally. But no doubt you will continue to claim I have not refuted your argument. But what can you do? Nobody actually working in the field of OoL has heard of you or your "hypothesis". Over a decade and counting with no progress. Are people cowering in fear of your mighty insight? I don't think so. But my claim is testable. Why don't you test it? Publish a paper where it might get noticed. Bio-Complexity should be beating a path to your door. What's the alternative? Alan Fox

. Alan at 72. You come back at me again with the “you just don’t understand” bit? (ahem) Are you not going to tell me that I carelessly, but quite mistakenly, have some dates and experimental findings and their authors incorrect? Crick’s adapter hypothesis surely came out in 1955 at Cavendish, and it surely says what it says. And could Francis Crick have been any more clear? Could Von Neumann have been more clear? Could Brenner? Could the physicist, Pattee? I don’t think so. Are you not, then, going to tell me that my “interpretation” of the experimental history is wrong – wasn’t that your earlier claim. Is the physics wrong? Are you not going to argue that Hoagland and Zamecnik never confirmed Crick’s protein constraints and Von Neumann’s symbolic descriptions? It is hard to pull that off when there are papers upon papers making the same case in physical terms, not to mention having a Nobel Laureate – the guy who actually named the adapter hypothesis – speaking openly about it and making the exact same connection on the pages of the world’s most prestigious journal … which, by the way, was claim written 45 years after RNA was first suspected of having some catalytic properties and 30 years after it was confirmed. One might stumble upon the conclusion that Brenner (apparently like me today) didn’t understand the RNA World hypothesis when he wrote those words and conclusions in Nature, but I am betting that he did. He wrote them because the experimental history is correct. The physics is correct. Apparently, the fact that nucleic bases pair-up, and can sometimes have enzymatic activity, doesn’t change the fact that you have to have encoded descriptions in a transcribable medium to establish the gene — to physically enable the origin of specification, control, and heredity (i.e. life). For those descriptions to exist, as was predicted, it requires all the components and organization that make encoded descriptions physically possible in the first place. As a matter of the historical record, like a big cherry on top, it was the finding of all those components that confirmed the predictions. You telling me that I “just don’t understand” that the RNA World didn’t have or need all that stuff is nothing more than hand-waiving under the big bright lights. Its pitiable, Alan. The case has been made. Neither your dismissal nor your dogma is going to make it go away. Cheers Upright BiPed

Bornagain77 @88,

The ‘near perfect’ finding for ATP synthase, (and for other molecular systems), is far more problematic for dogmatic Darwinists, such as AF, than they will ever honestly admit to the public.

Of course. For them, abiogenesis has just GOTTA be true despite all evidence to the contrary. Similarly, in spite of the experiments of Redi, Spallanzani, and Pasteur, their own opponents never admitted they were wrong either.

Félix-Archimède Pouchet, (born Aug. 26, 1800, Rouen, Fr.—died Dec. 6, 1872, Rouen), French naturalist who was a leading advocate of the idea of the spontaneous generation of life from nonliving matter. Pouchet was director of the Rouen Museum of Natural History and the Rouen Jardin des Plantes (1828) and later a professor at the School of Medicine at Rouen (1838). In his major work, Hétérogénie (1859), he detailed the conditions under which living organisms supposedly were produced by chemical processes such as fermentation and putrefaction. His supporters were primarily among those whose religious or philosophical beliefs required the concept of spontaneous generation. Pouchet’s theory was discredited when Louis Pasteur proved the existence of microorganisms in the air. Today Pouchet’s elaborate arguments are mere curiosities. - Britannica

Louis Pasteur falsified abiogenesis using swan-necked flasks together with his germ theory and corresponded with Pouchet. Nevertheless, Pouchet defiantly published his book on abiogenesis later that same year. Similarly, the vacuous arguments and fatuous noise from the detractors here, who consistently avoid the scientific challenge from James Tour and others, will eventually become mere curiosities of history, and their desperate struggle against mounting scientific evidence will be forgotten as well. -Q Querius

Assauber writes:

“why does there have to be a “why?” FP, You in grade school?

Nice mature response. Now, do you want to try to address the concept that “why” is not the question that science is designed to answer? The point of science is to try to answer “how.” Asking “why” instills an inherent bias to the research. It assumes an intention when an intention may not be a factor. We can hope that science can help us figure out how the universe formed, or how humans came to exist. But science can never be used to infer/imply/conclude “why” they did. Ford Prefect

Ba77, I think this sums it up: "... an unfalsifiable religion for atheists." It would explain a necessary - for some - defense of this idea regardless of evidence against it. relatd

AF now claims, "I don’t and never have subscribed to strict determinism. I, from first-person experience, am convinced I am able to choose among viable and constrained possible actions. They use “near-perfect” in the title and throughout the paper:" Yet previously AF claimed that his 'niche', not AF himself, was responsible for what he was writing in his posts

BA77: “So AF holds that the ‘niche”, not AF himself, is responsible for the information that he himself is writing in his posts?” Alan Fox: “Yes, sort of, though I don’t know,,,,”

So I guess AF now wants a 'do over' from this previous comment? :)

"I think I need a do over" https://media.tenor.com/SvVMlwxdZpYAAAAd/i-think-i-need-a-do-over-bad-day.gif

:) Of further note to ATP synthase in particular, David Coppedge just posted this over at ENV:

Denton’s “Puzzle of Perfection,” Then and Now David Coppedge - April 3, 2023 Excerpt: They use “near-perfect” in the title and throughout the paper: "ATP synthase produces most of the ATP in respiratory and photosynthetic cells. It is a rotary motor enzyme and its catalytic portion F1-ATPase hydrolyzes ATP to drive rotation of the central ? subunit. Efficiency of chemomechanical energy conversion by this motor is always near-perfect under different ATP hydrolysis energy (?GATP) conditions." Any deviation from perfection, however, could be due to experimental error. In their graph, the error bars transverse the slope for 100 percent efficiency (that is, for conversion of chemical energy to mechanical work). It may well be as close to perfect as is physically possible. What’s even more striking is that this “near-perfect” level of efficiency is maintained throughout a “broad range” of operation conditions.,,, https://evolutionnews.org/2023/04/dentons-puzzle-of-perfection-now-and-then/

The 'near perfect' finding for ATP synthase, (and for other molecular systems), is far more problematic for dogmatic Darwinists, such as AF, than they will ever honestly admit to the public. As William Bialek found, "Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark,,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants."

William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them the superb efficiency with which bacterial cells will close in on a food source; the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head; and the way a shark can find its prey by measuring micro-fluxes of electricity in the water a tremulous millionth of a volt strong — which, as Douglas Fields observed in Scientific American, is like detecting an electrical field generated by a standard AA battery “with one pole dipped in the Long Island Sound and the other pole in waters of Jacksonville, Fla.” In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.html

And as William Bialek further noted, "While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks."

William Bialek Excerpt: A central theme in my research is an appreciation for how well things ‘work’ in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks. https://www.princeton.edu/~wbialek/wbialek.html William Bialek is the John Archibald Wheeler/Battelle Professor in Physics, and a member of the multidisciplinary Lewis-Sigler Institute for Integrative Genomics, at Princeton University.

In fact, 'adaptation' itself is found to be 'perfect' As the following article states, “There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.”,,, Moreover, the "amazing and surprising" outcome of the study is applicable to any living organism or biochemical network of any size.,,,”

Math sheds light on how living cells 'think' - May 2, 2018 Excerpt: "Proteins form unfathomably complex networks of chemical reactions that allow cells to communicate and to 'think' --,,, "We could never hope to measure the full complexity of cellular networks -- the networks are simply too large and interconnected and their component proteins are too variable. "But mathematics provides a tool that allows us to explore how these networks might be constructed in order to perform as they do.,,, Dr Araujo's work has focused on the widely observed function called perfect adaptation -- the ability of a network to reset itself after it has been exposed to a new stimulus. "An example of perfect adaptation is our sense of smell," she said. "When exposed to an odour we will smell it initially but after a while it seems to us that the odour has disappeared, even though the chemical, the stimulus, is still present. "Our sense of smell has exhibited perfect adaptation. This process allows it to remain sensitive to further changes in our environment so that we can detect both very faint and very strong odours. "This kind of adaptation is essentially what takes place inside living cells all the time. Cells are exposed to signals -- hormones, growth factors, and other chemicals -- and their proteins will tend to react and respond initially, but then settle down to pre-stimulus levels of activity even though the stimulus is still there. "I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.,,, Professor Lance Liotta, said the "amazing and surprising" outcome of Dr Araujo's study is applicable to any living organism or biochemical network of any size.,,, https://www.sciencedaily.com/releases/2018/05/180502094636.htm

To break this down for you AF, these empirical findings are NOT good news for Darwinists, and should count as yet another falsification of Darwin's theory. And these findings would count as an empirical falsification of Darwin's theory if Darwin's theory were a normal science that was subject to empirical testing instead of being, basically, an unfalsifiable religion for atheists.

1 Thessalonians 5:21 but test all things. Hold fast to what is good.

Of supplemental note to this finding of 'perfect adaptation', Lewontin himself stated in an article entitled 'Adaptation" that, "It was the marvelous fit of organisms to the environment,,, that was the chief evidence of a Supreme Designer.,,,"

Adaptation - by Richard C. Lewontin - 1978 Excerpt: Organisms fit remarkably well into the external world in which they live. They have morphologies, physiologies and behaviors that appear to have been carefully and artfully designed to enable each or­ganism to appropriate the world around it for its own life. It was the marvelous fit of organisms to the environment, much more than the great diversity of forms, that was the chief evidence of a Supreme Designer.,,, https://dynamics.org/~altenber/LIBRARY/REPRINTS/Lewontin_Adaptation.1978.pdf

bornagain77

Tonight o the Alan Fox Show. Alan sings The Niche. You definitely want to miss it. :) relatd

Besides being out of touch with reality regarding OOL research, and as Alan Fox himself gives witness to, Alan Fox is also out of touch with reality regarding his own actions in the universe. Specifically, Alan Fox, via his denial of free will, denies that he himself is responsible for writing his own sentences.

Here's one straw-man. I don't and never have subscribed to strict determinism. I, from first-person experience, am convinced I am able to choose among viable and constrained possible actions. Alan Fox

Alan Fox @84,

Whether or not the straw-men he has flailed at have been demolished, they don’t represent my views.

Seems to me that Upright BiPed did an excellent job. Maybe you should try addressing his points if you can.

I’d write more but UD keeps freezing up when I try to comment.

I wouldn't say that UD is "freezing up" in your case. I think it's simply cringing. :D -Q Querius

Ba77 has thoroughly debunked your claims.

Well, not really. Whether or not the straw-men he has flailed at have been demolished, they don't represent my views. I'd write more but UD keeps freezing up when I try to comment. Alan Fox

Bornagain77 @74, Thank you! Looks like Rowan Williams and Anthony Kenny demolished Richard Dawkin's speculations about consciousness. And I was astonished at Dawkins' quasi-religious description in one gigantic run-on sentence blown out in a single breath that fantasizes . . .

. . . I think that um it is a thing most wonderful almost too wonderful to be that at least on this planet and possibly on billions of other planets but certainly on this one the laws of physics have conspired to make the collisions of atoms get together to produce nothing that any physicist would have dreamed of but to produce things like us to produce plants, trees, kangaroos, uh insects, and us to produce collections of matter collections of atoms that don't just obey Newton's laws in a passive way they don't obviously disobey them but not in a passive way but which move and jump and spring and hunt and flee and mate, and think at least in our case which is a quite astonishing thing to have happened and we know since 1859 how it happened and it's almost too wonderful to believe but we have to believe it because we now know it's true it's almost too wonderful to believe that um the laws of physics working through this very remarkable process that Darwin called natural selection has produced these gigantic collections of apparently purposeful beings which look overwhelmingly as though they had been designed they carry a a terrific illusion of design which fooled humanity until the middle of the 19th century um now I think that Darwin's achievement in doing that was not only a magnificent achievement in itself but it was a triumph of science which can be generalized to science generally because once Darwin had solved the problem of how you can get big complicated purposeful and apparently designed things out of very simple beginnings once Darwin has solved that problem, it then gives courage to the rest of science that the same thing can be done in general and that we shall end up understanding literally everything as springing from almost nothing or according to some modern physicists even literally nothing and I think that that is a truly wonderful thought when i say almost too wonderful to be it's a thought that is extremely hard to comprehend and believe and many people have great difficulty in believing it and resort to uh what in my view is is an unsatisfactory uh resolution to the problem which is to say an intelligence did it that seems to me to be an invasion of the question an invasion of the scientific responsibility to understand how things come about how complicated things come about in terms of of simple things . . .

Later, Dawkins wonders whether consciousness is an illusion, and (after hundreds of more words) how babies meld such illusions into a unified identity that somehow explains consciousness. Pure, hilarious entertainment! -Q Querius

AF at 76, Ba77 has thoroughly debunked your claims. relatd

Q, I had problems connecting to UD Thursday evening and over the weekend. Andrew asauber

Asauber @79, But WHY does there have to be a "Why does there have to be a why?" Rinse and repeat. LOL -Q P.S. I'm having a hard time accessing UD. Yesterday was impossible. It always seems to be timing out. Anyone else have that problem? Querius

"why does there have to be a “why?” FP, You in grade school? Andrew asauber

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

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

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

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

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

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

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

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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

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

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

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

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

Don't look in that telescope, Cardinal! :) :) :) Alan Fox

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. -Q Querius

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.3001437 Alan Fox

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." -Q Querius

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

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

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

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

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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

Link to Nick Lane’s book on Amazon. https://www.amazon.com/Transformer-Nick-Lane-ebook/dp/B07PDHXFB5 Alan Fox

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

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

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

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

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

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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

. 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 yourself Upright BiPed

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

.

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

. 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

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! -Q Querius

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

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

@ 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

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! -Q Querius

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

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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

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). -Q Querius

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

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. -Q Querius

AF at 35, That was incoherent. Care to elaborate? relatd

Jeez, Relatd, Casey Luskin? Alan Fox

AF at 27, Misleading people appears to be your purpose here. https://intelligentdesign.org/articles/molecular-machines-in-the-cell/ relatd

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

AF & Circle, I duly note, no substantial response to the metastability question. KF kairosfocus

@ KF Name dropping? Physician, heal thyself! :) Alan Fox

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

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

...more energetically stable but obviously non functional structure.

Beta sheet conformation occurs in functional proteins. Alan Fox

@ 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

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. KF kairosfocus

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

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

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. -Q Querius

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

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

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

Jerry: You haven’t a clue what you are talking about. Well can you explain how the genetic 'code' works? That is: how, physically, a sequence of DNA is interpreted as a protein works. IF the genetic 'code' is a code that is purely arbitrary (just made up with no relationship to biological processes) then something or someone would have to interpret it EVERY SINGLE TIME it's 'read' or processes. Every single time. This has nothing to do with epigenetics (which affects which genes are read and when) this has to do with the way the condones are translated into proteins. Every single time. If it's not a basic chemical process then how does it work? PS Jerry: your excerpt on epigenetic didn't actually explain what it is. Nor did it support ID in any way. Did you actually watch that particular 'course' or just copy-and-paste a bit of its introduction? JVL

On the contrary, ID is simply pragmatic while ". . . simply won’t let go. Like a dog with a bone" is more fitting to the 19th century theory that's been acting as a pseudo-scientific rationale for racism, European colonialism, and eugenic genocides, which has frequently been surprised, embarrassed, and falsified. -Q Querius

In layman vernacular, “code” and “selection” are intentional acts by individuals with some level of intelligence. This is not how biologists use these terms, but IDists simply won’t let go. Like a dog with a bone.

You haven't a clue what you are talking about. First, the people here do not represent ID. They are at best a group of informed amateurs and do not speak for ID. Second, many of the ID writers, only one here is Denyse, are biologists or have studied some aspects of biology. Denyse is not a biologist but has written books on ID. From a course on Epigenetic by the Great Courses

WHAT IS EPIGENETICS? Epigenetics is the science of living DNA. Modern biology began with genes and genetics and the discovery that genes are made of DNA, the basic code for life. However, the famous Watson-Crick double helix was just a statue. And while the x-ray pictures that Rosalind Franklin took verified the double-helix structure, the DNA she photographed was dead. Indeed, to understand the science of living DNA, you have to go beyond genetics and into the realm of epigenetics, where epi- is from the Greek meaning “over” or “beyond.” Epigenetics is built around genetics—the pure DNA itself. At the center of your DNA is a series of As, Ts, Gs, and Cs—your base pair code. These letters spell out the basic code —the genetic code —as given by your genes.

I can guarantee that the author, Dr Charlotte Mykura, is not ID friendly and teaches biology. jerry

JVL@8, I would agree that IDists latch on to terms used by biologists, terms such as “code” and “selection” in a way not intended by biologists. In layman vernacular, “code” and “selection” are intentional acts by individuals with some level of intelligence. This is not how biologists use these terms, but IDists simply won’t let go. Like a dog with a bone. Ford Prefect

Relatd: Out to muddy the waters? Code means instructions. If the 'code' has nothing to do with the physical reactions of the constituent parts then does that not mean that EVERY SINGLE TIME the 'code' is read some higher function has to translate the code? That is my question. All of this requires a master programmer. A being who codes for all cellular functions. Do you think that every single time a bit of DNA is 'read' and 'decoded' some being has to do the translation? A purely arbitrary code would require that because a purely arbitrary code could not be processed by purely mechanical processes. We all agree that the genetic 'code' is a table showing what condones create what proteins. The question is: IF the code is NOT related to chemical reactions then who or what is doing the translation? EVERY SINGLE TIME the DNA is being 'read'. I just want to be clear on what people are saying happens. JVL

From the paper Relatd links to: Most proteins fold into specific three-dimensional conformations to carry out their unique biological roles (1). Alan Fox

Meaning what? In order to fold correctly, proteins require chaperones.

Nope. Proteins generally will fold into a specific confirmation spontaneously. Chaperones speed up the process. Alan Fox

"spontaneously"? Meaning what? In order to fold correctly, proteins require chaperones. https://www.science.org/doi/10.1126/sciadv.add0922 relatd

That portion of DNA that codes for proteins means a protein with a precise shape can be built using instructions. There is no other way to do it.

Proteins will fold into shapes with precise structure spontaneously in vivo and in vitro with the right environment, temperature, pH etc. Alan Fox

OR is the ‘code’ in question even partially determined by physical behaviour and chemical affinities?

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 spontaneously achieved in aqueous solution within pH and temperature limits. Alan Fox

JVL at 8. Out to muddy the waters? Code means instructions. For a cell to function, and to reproduce, instructions are required. Further, the cell contains machinery and this machinery requires instructions. There are molecular switches inside cells that turn on and off when needed and other switches that stay open for a precise period to get water and nutrients to the cell. All of this requires a master programmer. A being who codes for all cellular functions. That portion of DNA that codes for proteins means a protein with a precise shape can be built using instructions. There is no other way to do it. A three-dimensonal image of a protein shows a precision at the sub-atomic level, the quantum level. relatd

Relatd: There is one poster here who denies genetic codes are codes even though the word code is used in the description. I think the disagreement comes down to what a 'code' is defined to be. Is the 'code' in question purely arbitrary, based on some criteria which has nothing to do with the natural physical behaviour of the objects in question? OR is the 'code' in question even partially determined by physical behaviour and chemical affinities? Mathematicians use the term differently from others. AND, I think, when the biologists called it the genetic 'code' they could have picked a better term. Just like with natural 'selection'. They both carry vestiges of definitions that might not be appropriate for the situation in question. If the 'code' in question is purely arbitrary, not based on physical constraints or chemical affinities then, the question must be, how is it implemented? That is: what process reads the encoded text and translates it and conveys that to the interpretive medium? That would have to happen every single time IF the code had no physical ties at all, if it was purely arbitrary. JVL

Querius: The bottom line is that humans don’t live by the scientific method and logic alone. Thankfully! These magisteria cannot deliver art and beauty, equity and justice, love and joy, athletic prowess, or personal qualities and transcendence to the majority of humanity. I suspect it is possible to 'breed' athletic prowess but otherwise I agree. Thus, it’s not unreasonable to anticipate that most people maintain a balance between physical, social, intellectual, and spiritual aspects of their lives. Sure . . . difference balance points for different people of course. In that case, art and beauty, equity and justice, love and joy, athletic prowess, or personal qualities and transcendence are also tricks we play on ourselves while waiting to reproduce and die. I don't think so, meaning I choose to believe otherwise. I think, when you're honest with yourself about what you like, what moves you, what speaks to you, you are responding to . . . things which 'speak' to you personally for some reason. I just love the works of Raphael. I also really like Michelangelo and Da Vinci but Raphael connects with me more deeply. I don't know why. I don't really care why. I just know I figured that out without being told who to appreciate. Same with Elizabeth Vigee Lebrun. (Interestingly enough, in some cases, I think I have figured out why some artists (meaning painter or musicians or writers) appeal to me more that others. But, the important thing was NOT to try and analyse it.) I think, when your honest, what you like and don't like somehow connects with parts of you that you may not be aware of. And that is at least interesting and, at best, enlightening. AND when you surround yourself with things that sing (to you), you life is more joyous and more up-lifting. JVL

Jery at 5, You mean the Marxist-Atheist-Darwinist Dictatorship? There is one poster here who denies genetic codes are codes even though the word code is used in the description. relatd

Aside: There is only one truth so correct science and one possible religion will always be in agreement with the truth. The problem is that there are a zillion religions and a almost as many versions of science. So maybe in one of each there is agreement. We do not know which. ID tries to do the science but most definitely stays away from the zillion religions. But we have those who want to do both and for them, religion is the motivating goal (both for and against) and science be damned if it conflicts with their ideology. jerry

Jerry at 1, Get a clue. The majority of the 'arguments' here are between atheists and theists. Science is part of it, but at the end of the day, that's the conflict. relatd

"... what is religion but a trick we play on ourselves? – David Wootton (March 18, 2023)" So, man's desire to run away from God is great. This is nothing new. I hope some here do not believe that ignoring God is a good thing - a worthy pursuit. It is strange to see the above message repeated over and over like a marketing slogan. Power and wealth are temporary, eternity is not. We prepare now, and work now, for what is to come. relatd

What this book marks, in fact, is the quiet triumph of meta-science over faith . . .

The bottom line is that humans don't live by the scientific method and logic alone. These magisteria cannot deliver art and beauty, equity and justice, love and joy, athletic prowess, or personal qualities and transcendence to the majority of humanity. Thus, it's not unreasonable to anticipate that most people maintain a balance between physical, social, intellectual, and spiritual aspects of their lives. Perhaps, a sequel will attempt to enlighten us about the tangled history of science and art, beaming about the quiet triumph of meta-science over artistic expression.

. . . . and what is religion but a trick we play on ourselves?

In that case, art and beauty, equity and justice, love and joy, athletic prowess, or personal qualities and transcendence are also tricks we play on ourselves while waiting to reproduce and die. Unless, of course, a Creator exists and has a purpose. But that would be a topic for a different forum. -Q Querius

I am going to leave this comment here because it is as good a place as any. I stumbled on a twitter remark and then a Substack post and found some great insight.

Why Smart People Believe Stupid Things Intelligence is not rationality

This could explain 80% of the comments on UD, some of which has gone on in full view this last 72 hours. https://gurwinder.substack.com/p/why-smart-people-hold-stupid-beliefs Some of the featured tweets in this essay

An absurd ideological belief is a form of tribal signalling. It signifies that one considers their ideology more important than truth, reason, sanity. To one's allies, this is an oath of unwavering loyalty. To one's enemies, it is a threat display When intelligent people affiliate themselves to ideology, their intellect ceases to guard against wishful thinking, and instead begins to fortify it, causing them to inadvertently mastermind their own delusion, and to very cleverly become stupid The greatest enemy of truth is the desire to win arguments

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The 10 Best Ideas I Learned in 2022

I like

2. Cunningham's Law: The best way to get the right answer on the internet is not to ask a question, but to post the wrong answer, because people are more interested in criticizing others than helping them.

https://gurwinder.substack.com/p/the-10-best-ideas-i-learned-in-2022 jerry