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The Death Knell for Life from an RNA world

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The RNA world hypothesis, to be true, has to overcome  major hurdles:

https://reasonandscience.catsboard.com/t2024-the-rna-world-and-the-origins-of-life#3414

1. Life uses only right-handed RNA and DNA. The homochirality problem is unsolved. This is an “intractable problem” for chemical evolution
2. RNA has been called a “prebiotic chemist’s nightmare” because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability. Many bonds in RNA are thermodynamically unstable with respect to hydrolysis in water, creating a “water problem”. Finally, some bonds in RNA appear to be “impossible” to form under any conditions considered plausible for early Earth.   In chemistry, when free energy is applied to organic matter without Darwinian evolution, the matter devolves to become more and more “asphaltic”, as the atoms in the mixture are rearranged to give ever more molecular species. In the resulting “asphaltization”, what was life comes to display fewer and fewer characteristics of life.
3. Systems of interconnected software and hardware like in the cell are irreducibly complex and interdependent. There is no reason for information processing machinery to exist without the software and vice versa.
4. A certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded
5. RNA catalysts would have had to copy multiple sets of RNA blueprints nearly as accurately as do modern-day enzymes
6. In order a molecule to be a self-replicator, it has to be a homopolymer, of which the backbone must have the same repetitive units; they must be identical. In the prebiotic world, the generation of a homopolymer was however impossible.
7. Not one self-replicating RNA has emerged to date from quadrillions (10^24) of artificially synthesized, random RNA sequences.  
8. Over time, organic molecules break apart as fast as they form
9. How could and would random events attach a phosphate group to the right position of a ribose molecule to provide the necessary chemical activity? And how would non-guided random events be able to attach the nucleic bases to the ribose?  The coupling of ribose with a nucleotide is the first step to form RNA, and even those engrossed in prebiotic research have difficulty envisioning that process, especially for purines and pyrimidines.”
10. L. E. Orgel:  The myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist’s view of RNA’s catalytic potential.
11. Macromolecules do not spontaneously combine to form macromolecules
125. The transition from RNA to DNA is an unsolved problem. 
13. To go from a self-replicating RNA molecule to a self-replicating cell is like to go from a house building block to a fully built house. 
14. Arguably one of the most outstanding problems in understanding the progress of early life is the transition from the RNA world to the modern protein-based world. 31
15. It is thought that the boron minerals needed to form RNA from pre-biotic soups were not available on early Earth in sufficient quantity, and the molybdenum minerals were not available in the correct chemical form. 33
16. Given the apparent limitation of double-stranded RNA (dsRNA) genomes to about 30 kb, together with the complexity of DNA synthesis, it appears dif¢cult for a dsRNA genome to encode all the information required before the transition from an RNA to a DNA genome. Ribonucleotide reductase itself, which synthesizes deoxyribonucleotides from ribonucleotides, requires complex protein radical chemistry, and RNA world genomes may have reached their limits of coding capacity well before such complex enzymes had evolved.

Comments
And here's Dr. Tour's latest video, which destroys a popular conception of how RNA "musta" formed with with the paradoxes in the data already published by Origin of Life researchers: https://www.youtube.com/watch?v=atxmIZw3DdA What Dr. Tour asserts is that however RNA was formed on the early earth, this is not it! -QQuerius
January 24, 2023
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Ram @161,
Let’s be content to be brothers in ID friendliness.
Cheerfully agreed! :-) -QQuerius
January 24, 2023
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Querius: Matthew is loaded with problems. But this isn't a bible study site. Let's be content to be brothers in ID friendliness. :) RAMram
January 23, 2023
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PyrrhoManiac1 @159,
I don’t have answers for these questions — I’m only trying to think about the problem from a systems-theory perspective.
The set of Fox locations traversed, a1-h8, are data. The rules for either storing or recording 5 card sets of successful Hound evasions is the information producing the data from random noise. What you're thinking of strongly reminds me of some conversations I once had with mathematician, William Bricken. His closed non-intersecting boundary curves remind me of Fox paths (although these paths often do intersect, which can be avoided by adding an othogonal Time dimension to create x, y, T coordinates). One of his excursions was into abbreviating the paths into fewer curves, yet maintaining the same general shape. This destructively simplifies and compresses the data into your "pattern." If you're interested, here's a relevant link: https://wbricken.com/htmls/01bm/01-math.html And more broadly . . . https://iconicmath.com/ -QQuerius
January 19, 2023
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@152 Oh, I quite agree that the game you described doesn't involve any new information. Though I do wonder: if one were to film many trials of this game, and then watch the resulting film at 5X or 10X the initial speed, would one perceive patterns that were not intelligible at the outset? Could one then construct a description of those patterns that is shorter than a bit-map of the patterns themselves? If so, would that description appear to be 'information' that is not mechanistically derived from the rules of the game itself? I don't have answers for these questions -- I'm only trying to think about the problem from a systems-theory perspective.PyrrhoManiac1
January 19, 2023
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Bornagain77 @157, Thanks for the link. I felt a little sorry for Dr. Tour as Eric Metaxas tried to be funny and then made Dr. Tour slow down to an excruciatingly slow pace to explain everything to presumably a heterogeneous audience and keeping things to monosyllabic words. On a few occasions, Dr. Tour was able to mischievously get even with Eric Metaxas, catching him in his own trap. I guess it was okay. The audience seemed to love it, but I wasn't able to sit through it all. The problem that Dr. Tour or anyone giving a technical presentation (or teaching) encounters has to do with finding a good abstraction level appropriate for that audience, avoiding complex terminology, jargon, and acronyms. Story: Once when I took a cab to the airport for a business trip, the cab driver made the mistake of asking me what I did for a living. In reply, I made a heroic but ugly attempt at explaining the technology at a high-enough level for a cabby to understand. After allowing me to struggle through my description, the wicked young man informed me that this was actually the area he was studying in college and that he was merely driving cab to help pay for his education. You can just imagine what I felt like! -QQuerius
January 18, 2023
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Just uploaded: Dr. James Tour (& Eric Metaxas): How Did Life Come into Being? https://www.youtube.com/watch?v=9qxoH7u3FXw A conversation between Dr. James Tour and Socrates in the City host Eric Metaxas on the topic "How Did Life Come into Being?" Dr. Tour is presently 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 is widely regarded as among the leading nano-scientists in the world. This event took place at the River Oaks Country Club in Houston, Texas in October 2022. Learn more about Socrates in the City at socratesinthecity.com.bornagain77
January 18, 2023
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Drc466 @149, Great point and an excellent summary! What bothers me is the all-too-common lack of intellectual honesty in overstating some things and understating or ignoring others. Politics is the worst, but I deeply sympathize with Dr. Tour as he tries to untangle the stilted and convoluted language in the papers he reviews! Poor guy! I once saw a funny rendition of 1+1=2 that was inflated into a monster equation by substitution. The wag who posted it claimed that 1+1=2 was boring, but his result was far more impressive and commanded Massive Respect! -QQuerius
January 17, 2023
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Relatd @150, Agreed.drc466
January 17, 2023
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Ram @147,
As an Orthodox Jew, I can say it’s far more than that.
And so also was Yeshua Ha’Nazeret. :o Otherwise, I don’t think he would have said the following:
“Do not think that I came to abolish the Law [Torah] or the Prophets; I did not come to abolish but to fulfill. For truly I say to you, until heaven and earth pass away, not the smallest letter or stroke shall pass from the Law until all is accomplished. Whoever then annuls one of the least of these commandments, and teaches others to do the same, shall be called least in the kingdom of heaven; but whoever keeps and teaches them, he shall be called great in the kingdom of heaven.” – Matthew 5:17-19 NASB
As an Orthodox Jew, you might be in agreement with the title of the song, “I Knew Jesus Before He Was a Gentile.” (smile)
But when it comes to ID, we’re on the same side.
Yes, indeed! Hashem is absolutely brilliant! -QQuerius
January 17, 2023
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Jerry @146,
Good idea, you are out of your depth on economics.
I am as well, and I’ve even studied some basic economics (Samuelson). -QQuerius
January 17, 2023
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PyrrhoManiac1 @145,
The more I look into systems theory and biosemiotics, the more it seems to me that the RNA world hypothesis rests on a conceptual error — though a very widespread one!
Considering this definition of systems theory . . .
Systems theory seeks to explain and develop hypotheses around characteristics that arise within complex systems that seemingly could not arise in any single system within the whole. This is referred to as emergent behavior. If a complex system expresses emergent behavior, that means it has characteristics its properties do not display on their own.
How would you reconcile the presumed emergence of information? Let me start with something tangible. Imagine a chessboard with two pieces: a hound and a fox: - The Hound patrols in a square path (c3 – f3 – f6 – c6) one square at a time. - The Fox starts in one of the four central squares, let’s say e4 and moves one square in one of four random directions (North, South, East, or West) controlled by the suit of a shuffled deck of cards. - If the Hound lands on the Fox, the Fox loses and the initial locations of the Hound and Fox are reset to the beginning. - Any time that the 5th card is played without the Fox being trounced, those 5 cards are saved in a set and the Fox continues. If the Fox is trounced that set is discarded. - The Fox wins if it goes through the entire deck without being trounced or escapes off the edge of the chessboard. Question: Does this generate information? (I don’t think it does) -QQuerius
January 17, 2023
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Vividbleau @144,
Awesome that means I can steal it and claim authorship.
No, you can’t. It’s actually authored by the amazingly prolific author, anon. ;-) Thanks for the fun story! I was involved in a situation where I received a prestigious award for my work, but later found out that someone not involved claimed ownership all over the internet. I really, honestly don’t care. History is replete with people like him. Maybe he’ll get a dead-end street named after him. LOL I’m having way too much fun with new ideas and creating things! -QQuerius
January 17, 2023
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Drc466 at 149, I've read about the attempts to make life from chemicals and about a 'minimal cell,' which is the minimum number of components needed to make a working/living cell. And of what little progress that has been made required intelligent agents - the scientists doing the work. And even IF an attempt produces something like a living cell, at least two things need to be pointed out: 1) It is not known if "nature" actually used any method found. 2) The experiments will require intelligent agents. And there is also the problem of reproduction. In synthetic biology, successful production of biological components for industry has occurred. This was done by modifying certain organisms to produce these products.relatd
January 17, 2023
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Regarding the whole Dr. Tour vs. Professor Dave imbroglio (and tangentially related to the RNA topic at hand), knowing who is right and who is wrong is actually quite simple and requires very little knowledge of synthetic chemistry. It only requires the answer to one question. To wit: What are OoL scientists currently researching? If Dr. Tour is correct, they will still be researching prebiotically relevant methods of obtaining the requirements ("building blocks") for a living cell (amino acids, polypeptides, sugars, carbohydrates, lipids, homochirality, etc.) as (he claims) they have been for the last 50 years. If Professor Dave is correct, they will have moved on past this type of research, and will be working on actually creating living cells from these building blocks of life. I won't answer the question for you. Feel free to peruse the current literature and come to your own conclusion. Starting with the research currently being investigated by the Harvard OoL Initiative, and Dr. Benner's Foundation might be a good jumping off point. This also applies to the RNA World hypothesis that O references - what is the state of current research? Are they advancing, or repeating the same types of research?drc466
January 17, 2023
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Querius at 139, I urge you to present examples and supporting evidence regarding any changes in Christianity. First, from the beginning there were misunderstandings. Some thought that salvation was only for the Jews, no one else. Acts 28:28 "Therefore let it be known to you that this salvation of God has been sent to the Gentiles; they will listen.” Other disagreements led to other Christian denominations being formed.relatd
January 17, 2023
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Querius:... 4. Christianity is objectionable because a. I don’t understand why God allows evil in the world. b. I don’t understand why God sends or predestines innocent people to eternal torture for relatively trivial reasons. c. I suffered abuse in a church of some kind in the past. d. I want to live life my way, I’m comfortable, and I don’t want anyone telling me what I should do. e. “Can God create a rock that he cannot lift?” “If God was the cause of the universe, what was the cause of God?”
As an Orthodox Jew, I can say it's far more than that. But when it comes to ID, we're on the same side. Cheers RAMram
January 17, 2023
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I’d like to get back on topic as well
Good idea, you are out of your depth on economics.jerry
January 17, 2023
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@140
In the current topic, what I’d like to do is understand and discuss the perspectives and problems of the RNA World hypothesis. Is that bad?
I'd like to get back on topic as well. The more I look into systems theory and biosemiotics, the more it seems to me that the RNA world hypothesis rests on a conceptual error -- though a very widespread one!PyrrhoManiac1
January 17, 2023
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Q “I have no idea who originally came up with it.” Awesome that means I can steal it and claim authorship. For some reason this brings to mind a funny story. When I was younger I was lucky enough to have earned a football scholarship at a large D1 university. I was not the most talented but I did enjoy a good deal of success as a starter on a very good team When I was a senior a very talented QB enrolled at the school, this QB started every game and went on to the NFL and subsequently the Super Bowl. One day I got a call .from my Daughter and she asked me “Dad does the name such and such mean anything to you” ? I told her the name was not familiar to me why do you ask. Well she told me that this person died and in his obituary it said that he played at the time I was a player and in it claimed that the talented QB was his back up. I laughed and said honey that’s crazy he never was a back up to anyone but by the time I die I will be in the NFL hall of fame! LOL. If no one knows anything one can claim anything after their dead! Vividvividbleau
January 17, 2023
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Vividbleau @142,
What a great observation!
It is! And not that surprising. I have no idea who originally came up with it. -QQuerius
January 16, 2023
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Q • The Greeks turned the teachings of Jesus into a philosophy • The Romans, into a system • The Europeans, into a culture • And the Americans, into a business. What a great observation! Vividvividbleau
January 16, 2023
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Dr. Tour's new video is up: Dr. Tour MINES Data on Origin of Life Claims - Steve Benner, Part 02 https://www.youtube.com/watch?v=cL0NIFk1grE Previous episodes Episode 1: https://youtu.be/4rwPi1miWu4 Episode 2: https://youtu.be/aUOZh4zmrXo Episode 3: https://youtu.be/v3A8_ezYlZY Episode 4: https://youtu.be/N_on6LK6Etc Episode 5: https://youtu.be/t5PfBzQUjW8 Episode 6: https://youtu.be/ZtitTE2BavU Episode 8 premieres next Monday, January 23th! SUBSCRIBE so you'll be notified!bornagain77
January 16, 2023
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Vividbleau @132,
Besides this is not a proper forum for this type of discussion.
I also heartily agree. Nevertheless, the subject emerges surprisingly often, at least to me it does. Typically, people follow some version of this path: 1. Intelligent Design is simply creationism in drag. (I vehemently disagree) 2. Creationism is the unique domain of Christianity. (This is false) 3. Christianity is ideologically repugnant to scientists and anyone else with a logical mind. (This is also false) 4. Christianity is objectionable because a. I don't understand why God allows evil in the world. b. I don't understand why God sends or predestines innocent people to eternal torture for relatively trivial reasons. c. I suffered abuse in a church of some kind in the past. d. I want to live life my way, I'm comfortable, and I don't want anyone telling me what I should do. e. "Can God create a rock that he cannot lift?" "If God was the cause of the universe, what was the cause of God?" I know that each of these objections have excellent answers, and I'd encourage anyone bothered by these to find them on a forum focused on these questions. In the current topic, what I'd like to do is understand and discuss the perspectives and problems of the RNA World hypothesis. Is that bad? -QQuerius
January 16, 2023
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Vividbleau @124,
but first I think it would be instructive do delve into the question of what exactly is a Christian. This would seem to be on the face of it a simple exercise but the term Christian has been so bastardized that in todays world it has no meaning at all.
Excellent question and I agree. There are three common types of answers: a. Someone born into a predominantly “Christian” culture and is not something else. b. Someone who identifies with and subjects themselves to a set of church teachings and practices. These vary considerably. c. What Yeshua ha Nazaret actually taught as recorded by his direct disciples. I also researched what early Christians, believed and how they behaved individually and corporately up until around 300 A.D. at the maximum, where Christianity started to change. It’s c. that interests me personally.
One of the most common misconceptions about Christian’s held by non believers is that Christians think they are good and morally better than non Christians. This is false . . .
Yes, I heartily agree! An amusing but gross oversimplification was that • The Greeks turned the teachings of Jesus into a philosophy • The Romans, into a system • The Europeans, into a culture • And the Americans, into a business. -QQuerius
January 16, 2023
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Try here https://uncommondescent.com/geo-strategic-issues/a-note-on-technology-driven-economic-long-waves-aka-the-ghost-of-kondratiev-roars/kairosfocus
January 16, 2023
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If you wish to understand economic growth and transformation, the Kondratiev-Schumpeter approach to long waves of transformation may be advisable, I have seen a survey of 19 such waves all the way back to the Song Dynasty in China
That's interesting! Do you still remember the source? I can probably track it down with some clever Googling if not.PyrrhoManiac1
January 16, 2023
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PM1, if you want a theory of technological evolution, there is one, TRIZ. Developed in Russia in the days of the USSR, through investigating principles of invention expressed in patents. If you need to understand innovation, product markets and product life cycles, you would be better advised to consult that sub discipline of strategic marketing. If you wish to understand economic growth and transformation, the Kondratiev-Schumpeter approach to long waves of transformation may be advisable, I have seen a survey of 19 such waves all the way back to the Song Dynasty in China. KFkairosfocus
January 16, 2023
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@105
There is no doubt that the mainstream of “scientific socialism” built on dialectic materialism and historical materialism, both deriving from the Marx-Engels collaboration and laid out a dynamic of economic production modes and relations with class conflict based thesis-antithesis, then a next stage. The epochs envisioned were: primitive communalism > ancient slave state > feudal state > capitalist state > socialist state > [stateless] communist golden age.
I'm not a huge fan of Marx's philosophy of history and I definitely think that his claims to have established socialism on a scientific basis are vastly exaggerated. But I do think Marx helps us appreciate how changes in technology ripple throughout society: how the ability to build higher-temperature furnaces unleashes the power of iron vs bronze, or how the stirrup affects horsemanship. What goes missing in Marx is the way in which culture affects how and why certain technologies get adopted. For example, many Islamic societies did not print the Koran, even though they knew of printing, because they thought it important that the Koran be written by hand, where the path taken by the hand inscribes the breath that gives live to the text when it is read aloud. That's an attitude about the nature of writing that Christians did not have, and so they had no objection to printing the Bible. In any event, I definitely do not think there is anything inevitable about a socialist revolution. And as I've said many times, I think it's very clear that Marx identifies a communist society with a post-scarcity society. It's a nice question whether there would be any need for a state in a post-scarcity society. There very well might be, but it's not clear exactly why.
The USSR consciously modelled a transition beyond capitalism and it failed, having already discredited itself as utterly lawless, murderous and destructive.
The USSR never succeeded in going beyond capitalism, regardless of what they claimed. But "lawless"? This puzzles me. There was no absence of laws in the USSR. The problem is that their laws were not just and that there was no constitution that limited state power.
There is a better path, to re-establish lawfulness, first built in law, the lawful state, responsible reformation, constitutional, lawful state democratic self government following the stream laid down on July 4, 1776.
I don't entirely disagree, but I don't entirely agree, either. I think it's absolutely crucial to notice that every revolution is unlawful, including the American Revolution. The Constitution was established in the wake of that revolution, to establish a new law to replace the old law that was violently cast off. Ultimately, I don't really care about law and order, in that I don't think law and order are the highest goods. What matters to me is justice -- and there are plenty of unjust laws, past and present. American chattel slavery was unjust but legal, and helping a slave escape was illegal, and yet the right thing to do. The same point applies to the Constitution itself. What matters to me is not whether a law is constitutional but whether the constitution is morally just. Law and order are not so intrinsically good as to make reform always preferable to revolution. As Rosa Luxemborg (murdered by reformists on 15 January, 1919) put it:
Every legal constitution is the product of a revolution. In the history of classes, revolution is the act of political creation, while legislation is the political expression of the life of a society that has already come into being. Work for reform does not contain its own force independent from revolution. During every historic period, work for reforms is carried on only in the direction given to it by the impetus of the last revolution and continues as long as the impulsion from the last revolution continues to make itself felt. Or, to put it more concretely, in each historic period work for reforms is carried on only in the framework of the social form created by the last revolution.
PyrrhoManiac1
January 16, 2023
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O Love you bro Vividvividbleau
January 16, 2023
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