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Defending the Christian Worldview, Creationism, and Intelligent Design

This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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Defending the Christian Worldview, Creationism, and Intelligent Design » Origin of life » Professor Dave attempting to refute James Tour - a review

Professor Dave attempting to refute James Tour - a review

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Professor Dave attempting to refute James Tour - a review

https://reasonandscience.catsboard.com/t3137-professor-dave-attempting-to-refute-james-tour-a-review

Response to James Tour: 700 Papers and Still Clueless (Part 1 of 2)
https://www.youtube.com/watch?v=ghJGnMwRHCs&t=429s


Professor Dave ( PD): James does research on molecular machines which have nothing to do with biological systems, and even less to do with abiogenesis.
Reply: The origin of proteins ( molecular machines ) stays right at the core of the question of how life arose on earth. No proteins, no life. So how did the first minimal protein set emerge prebiotically? Rather than providing compelling answers, science has rather unraveled how unlikely it is that proteins could emerge prebiotically, and much less, a minimal proteome, necessary for life to start.

The factory maker argument
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument

The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  14   They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. This probability is hard to imagine but an illustration may help.

Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^55.

Proteins and Protein synthesis
https://reasonandscience.catsboard.com/t2706-main-topics-on-proteins-and-protein-synthesis

“What we lack is a hypothesis for the earlier stages, where you don’t have this spectrum of enzymatic activities, active sites and folds from which selection can identify starting points. Evolution has this catch-22: Nothing evolves unless it already exists.
https://www.asbmb.org/asbmb-today/science/092313/close-to-a-miracle

PD:  There is not one single recipe for life. The way it emerged was bottom-up,   and does not even remotely resemble some kind of manufacturing assembly line. It complexified incrementally, and the processes that produced life were not directed, so this is not a valid analogy. It hasn’t ever been a valid analogy. It was debunked 300 years ago by David Hume before modern biology even existed.
Reply:  Here, professor Dave makes a bunch of unwarranted assertions.

Metabolite pool
In certain ways, a metabolic pathway is similar to a factory assembly line. Products are assembled from parts by workers who each perform a specific step in the manufacturing process. Enzymes of a cell are like workers on an assembly line; each is only responsible for a particular step in the assembly process.
https://en.wikipedia.org/wiki/Metabolite_pool#:~:text=In%20certain%20ways%2C%20a%20metabolic,step%20in%20the%20assembly%20process.

Irreducible Complexity: The existence of irreducible interdependent structures in biology is an undeniable fact
https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#2133

The whole is more than the sum of the parts. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.  Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal.
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.

The argument of irreducible complexity is obvious and clear. Subparts like a piston in a car engine are only designed, when there is a goal where they will be mounted with specific fitting sizes and correct materials, and have a specific function in the machine as a whole. Individually they have no function. Same in biological systems, which work as factories ( cells ) or machines ( cells host a big number of the most various molecular machines and equal to factory production lines ) For example, in photosynthesis, there is no function for chlorophyll individually, only when inserted in the light-harvesting complex, to catch photons, and direct their excitation energy by Förster resonance energy transfer to the reaction center in Photosystem one and two. Foreplanning is absolutely essential. This is a  simple fact, which makes the concept of  Irreducible complexity obvious concept. Nonetheless, people argue all the time that it's a debunked argument. Why? That's as if genetic mutations and natural selection had enough probability to generate interdependent individual parts being able to perform new functions while the individual would have no function unless interconnected.

PD:  He wants to distribute his car parts around the  world, like hidden treasure. The implication here is that all the individual parts needed to make a living cell originated in different regions of  
the world and had to wait millions of years for a favorable gust of wind to unite them.   It is baffling that a research scientist would say something so idiotic.
Reply: And I am baffled that Professor Dave would answer with such a staggeringly idiotic claim & reply.

A. G. CAIRNS-SMITH Seven clues to the origin of life, page 58
Vast times and spaces do not make all that much difference to the level of competence that pure chance can simulate. Even to get 14 sixes in a row (with one dice following the rules of our game) you should put aside some tens of thousands of years. But for 7 sixes a few weeks should do, and for 3 sixes a few minutes. This is all an indication of the steepness of that cliff-face that we were thinking about: a three-step process may be easily attributable to chance while a similar thirty-step process is quite absurd.

Time makes everything become possible. Really?
https://reasonandscience.catsboard.com/t2025-time-makes-everything-become-possible-really

PD:  From the abstract, we can see that a variety of organic compounds are synthesized in these nebulae, and subsequently spread throughout the galaxy. Apart from such compounds likely  
being present in the material that coalesced to form our solar system, including Earth,   we can, more importantly, presume that much more was delivered to the surface of the Earth soon after its formation from impacting bodies.
Reply: Panspermia is not a viable explanation for the origin of life.  Blank and her NASA team claimed that amino acids can survive a comet’s entrance into Earth’s atmosphere and subsequent surface impact. But this presents a big problem. Calculations and measurements show that both events generate so much heat (atmosphere = 500°+ Centigrade while the collision = 1,000°+ Centigrade) that they break down the molecules into components useless for forming the building blocks of life molecules. This was confirmed by NASA when they sent the Stardust Spacecraft to the comet 81P Wild in 2004 to recover samples, which were returned to Earth and analyzed for organic molecules. The only amino acid indisputably detected in the sample was glycine at an abundance level of just 20 trillionths of a mol per cubic centimeter

Life chemistry demands homochirality (same chirality). Proteins cannot assemble unless all the chiral amino acids (20 out of the 21 bioactive amino acids are chiral) are either 100 percent left-handed or 100 percent right-handed. Likewise, DNA and RNA molecules cannot assemble unless all pentose sugars are 100 percent left-handed or right-handed. All organisms on Earth manifest only left-handed chiral amino acids and right-handed pentose sugars. 7

A chiral excess of isoleucine exists in GRA 95229, indicating that some mechanism must produce it. But still it is questionable if this relatively low level of chiral excess in isoleucine can explain the origin of homochirality. A 14% surplus of one enantiomer is a far cry from the 100% required for living systems. 3

Life chemistry demands homochirality (same chirality). Proteins cannot assemble unless all the chiral amino acids (20 out of the 21 bioactive amino acids are chiral) are either 100 percent left-handed or 100 percent right-handed. Likewise, DNA and RNA molecules cannot assemble unless all pentose sugars are 100 percent left-handed or right-handed. All organisms on Earth manifest only left-handed chiral amino acids and right-handed pentose sugars.

chiral excess in Earth’s oceans will not promote homochirality in life molecules, but, in fact, detracts from it. 6

a chiral excess of isoleucine exists in GRA 95229, indicating that some mechanism must produce it. But still it is questionable if this relatively low level of chiral excess in isoleucine can explain the origin of homochirality. A 14% surplus of one enantiomer is a far cry from the 100% required for living systems. 4

several pieces of evidence are deal-killers for one or both those theories. Among them: the richness of deuterium, which the Tagish Lake Meteorite and most comets have. Heavy hydrogen forms when water absorbs neutrons. That can happen only from an event that releases many neutrons. The tremendous earthquakes of the Global Flood likely produced that swarm of neutrons. An exploding planet between Mars and Jupiter could have produced such a swarm. But an interstellar meteor stream or dust or gas cloud could not. (The exploded planet theory has a deal-killer of its own, namely all the ice on the Moon and Mercury.)

So an interstellar origin defies logic and is well-nigh impossible. Without that, panspermia is equally impossible. 5

More: 
https://reasonandscience.catsboard.com/t1362-panspermia-not-a-viable-explanation-for-the-ool

PD:   Which compounds, he asks? Many, such as these,   which are supremely relevant to abiogenesis, and  can be used to arrive at simple biomolecules.
Reply:  No prebiotic selection !!  If a machine has to be made out of certain components, then the components have to be made first.'

Molecules have nothing to gain by becoming the building blocks of life. They are "happy" to lay on the ground or float in the prebiotic ocean and that's it. Being incredulous that they would concentrate at one building site in the right mixture, and in the right complex form, that would permit them to complexify in an orderly manner and assembly into complex highly efficient molecular machines and self-replicating cell factories, is not only justified but warranted and sound reasoning. That fact alone destroys materialism & naturalism. Being credulous towards such a scenario means to stick to blind belief. And claiming that "we don't know (yet), but science is working on it, but the expectation is that the explanation will be a naturalistic one ( No God required) is a materialism of the gaps argument.

A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids 10 December 2020
The prebiotic seas contained L- and D-amino acids, and non-Polar AAs and Polar AAs, and minerals could adsorb all these molecules. Besides amino acids, other molecules could be found in the primitive seas that competed for mineral adsorption sites. Here, we have a huge problem that could be a double-edged sword for prebiotic chemistry. On the one hand, this may lead to more complex prebiotic chemistry, due to the large variety of species, which could mean more possibilities for the formation of different and more complex molecules. On the other hand, this complex mixture of molecules may not lead to the formation of any important molecule or biopolymer in high concentration to be used for molecular evolution. Schwartz, in his article “Intractable mixtures and the origin of life”, has already addressed this problem, denominating this mixture the “gunk”. 5

Intractable Mixtures and the Origin of Life 2007
A problem which is familiar to organic chemists is the production of unwanted byproducts in synthetic reactions. For prebiotic chemistry, where the goal is often the simulation of conditions on the prebiotic Earth and the modeling of a spontaneous reaction, it is not surprising – but nevertheless frustrating – that the unwanted products may consume most of the starting material and lead to nothing more than an intractable mixture, or -gunk.. The most well-known examples of the phenomenon can be summarized quickly: Although the Miller –Urey reaction produces an impressive set of amino acids and other biologically significant compounds, a large fraction of the starting material goes into a brown, tar-like residue that remains uncharacterized; i.e., gunk. While 15% of the carbon can be traced to specific organic molecules, the rest seems to be largely intractable 

Even if we focus only on the soluble products, we still have to deal with an extremely complex mixture of compounds. The carbonaceous chondrites, which represent an alternative source of starting material for prebiotic chemistry on Earth, and must have added enormous quantities of organic material to the Earth at the end of the Late Heavy Bombardment (LHB), do not offer a solution to the problem just referred to. The organic material present in carbonaceous meteorites is a mixture of such complexity that much ingenuity has gone into the design of suitable extraction methods, to isolate the most important classes of soluble (or solubilized) components for analysis.

Whatever the exact nature of an RNA precursor which may have become the first selfreplicating molecule, how could the chemical homogeneity which seems necessary to permit this kind of mechanism to even come into existence have been achieved? What mechanism would have selected for the incorporation of only threose, or ribose, or any particular building block, into short oligomers which might later have undergone chemically selective oligomerization? Virtually all model prebiotic syntheses produce mixtures. 6

Life: What A Concept! https://jsomers.net/life.pdf
Craig Venter: To me the key thing about Darwinian evolution is selection. Biology is a hundred percent dependent on selection. No matter what we do in synthetic biology, synthetic genomes, we're doing selection. It's just not
natural selection anymore. It's an intelligently designed selection, so it's a unique subset. But selection is always part of it.

More:
Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759

PD: But the obvious conclusion is that if it is so  simple for these molecules to form abiotically   that they even form in outer space, then these  building blocks of building blocks, as James  
calls them, are ubiquitous, and can be presumed as starting material for prebiotic chemistry.  an enormous percentage of his series is just  him rambling endlessly about lab syntheses that  have nothing to do with the origin of life.  Because it makes him sound like a bigshot.

Reply:  Lab experiments attempt to recreate what might have happened on the early earth, to go from simple molecules laying around on the prebiotic earth, to what goes on in the cell, which is a chemical factory, producing the basic building blocks through complex enzymatic metabolic pathways. In order to make the basic building blocks of life, the following is the number of enzymes employed in the chemical cell factory:

https://reasonandscience.catsboard.com/t2894-prevital-unguided-origin-of-the-four-basic-building-blocks-of-life-impossible#8358

De novo Nucleotide synthesis
Folate is necessary for the production of DNA  and RNA . The synthesis of NADPH requires 6 enzymes 6 proteins are required in the folate pathway.   The pyrimidine synthesis pathway requires six regulated steps, 7 enzymes, and energy in the form of ATP. The starting material for purine biosynthesis is product of the highly complex pentose phosphate pathway, which uses 12 enzymes.  De novo purine synthesis pathway requires ten regulated steps, 11 enzymes, and energy in the form of ATP. In total 31 enzymes.  The replacement of RNA as the repository of genetic information is done by its more stable cousin, DNA, provides a more reliable way of transmitting information. DNA uses thymine (T) as one of its four informational bases, whereas RNA uses uracil (U).  At the C2' position of ribose, an oxygen atom is removed. The remarkable enzymes that do this are named Ribonucleotide reductases (RNR).  The  enzyme is essential for DNA synthesis, and most essential enzymes of life.  Uracil bases in RNA are transformed into thymine bases in DNA. The synthesis of thymine requires 7 enzymesAll in all, not considering the metabolic pathways and enzymes required to make the precursors to start RNA and DNA synthesis requires at least 26  enzymes.   In total, 57 enzymes.

De novo Amino Acid synthesis
Transamination reactions and other rearrangements promoted by enzymes containing pyridoxal phosphate (PLP), which requires 8 enzymes to be synthesized.  Transfer of one-carbon groups, with either tetrahydrofolate or S-adenosylmethionine as a cofactor; tetrahydrofolate is derived from the folate pathway,  Transfer of amino groups is derived from the amide nitrogen of glutamine. As implied by the root of the word (amine), the key atom in amino acid composition is nitrogen. All organisms contain the enzymes glutamate dehydrogenase and glutamine synthetase, which convert ammonia to glutamate and glutamine, respectively.
A minimum of 112 enzymes are required to synthesize the 20 (+2) amino acids used in proteins.

Carbohydrates
LUCA used the simplest and most ancient of the six known pathways of CO2 fixation, called the acetyl–CoA (or Wood–Ljungdahl) pathway. It uses nine enzymes. 

Phospholipid Membranes
At least 74 enzymes are required for phospholipid synthesis in prokaryotes 29


1. On the one side, we have the putative prebiotic soup with the random chaotic floating around of the basic building blocks of life, and on the other side,  the first living self-replicating cell ( LUCA ), a supposed fully operational minimal self-replicating cell, using the highly specific and sophisticated molecular milieu with a large team of enzymes which catalyze the reactions to produce the four basic building blocks of life in a cooperative manner, and furthermore, able to maintain intracellular homeostasis, reproduce, obtaining energy and converting it into a usable form, getting rid of toxic waste, protecting itself from dangers of the environment, doing the cellular repair, and communicate.  
2. The science paper: Structural analyses of a hypothetical minimal metabolism proposes a minimal number of 50 enzymatic steps catalyzed by the associated encoded proteins. They don't, however, include the steps to synthesize the 20 amino acids required in life. Including those, the minimal metabolome would consist of 221 enzymes & proteins. A large number of molecular machines, co-factors, scaffold proteins, and chaperones are not included, required to build this highly sophisticated chemical factory.
3. There simply no feasible viable prebiotic route to go from a random prebiotic soup to this minimal proteome to kick-start metabolism by unguided means. This is not a conclusion by ignorance & incredulity, but it is reasonable to be skeptic, that this irreducibly complex biological system, entire factory complexes composed of myriads of interconnected highly optimized production lines, full of computers and robots could emerge naturally defying known and reasonable principles of the limited range of random unguided events and physical necessity. Comparing the two competing hypotheses, chance vs intelligent design, the second is simply by far the more case-adequate & reasonable explanation.

And more problems:
What are the odds to have a functional interactome for the smallest known living cell?
https://reasonandscience.catsboard.com/t3120-what-are-the-odds-to-have-a-functional-interactome-for-the-smallest-known-living-cell

1. All organisms have a genome. Some an epigenome and all life has a proteome, a metabolome, and less known, as well, an interactome, which defines all cellular interactions, amongst it, all protein-protein interactions of a cell.
2. Protein-protein interactions (PPIs) are one of the most important components of biological networks. Proteins, in order to perform their functions, often need to be interlinked in an interdependent manner with other proteins to form production line-like associations to produce the various molecules, building blocks, co-factors, and proteins of the cell. Without the right interdependent linkages, there would be no life on earth.
3. Besides explaining the origin of a minimal protein set on early earth ( the smallest proteome of a free-living cell is 1350 proteins by Pelagibacter ubique) it must also be explained how they got interlinked together.
4. The odds to connect all 1350 proteins in the right, functional order ( supposing that all outcomes would be equally likely. In other words, every connection would have an equal chance of being chosen. The odds of an event occurring are equal to the ratio of favorable outcomes to unfavorable outcomes) would be 4.1431^3641. That is an unimaginably large number. ( with 3641 zeroes! ) There are 10^22 stars in the knowable universe !! This is the odds on top of the odds to have a functional proteome, which is in the case of Pelagibacter, again with 1350 proteins, average 300 Amino Acids size: 10^722000 ) It should be evidently clear, by the astronomical odds, that having a functional interactome of the currently known smallest life form, Pelagibacter, on top of a functional proteome, is in the real of the ABSOLUTELY impossible !!

PD: Autocatalytic cycles are the key to continuously developing organized structures of increasing complexity,   beginning with physical phenomena, followed by chemical phenomena, then autocatalytic cycles,   and finally living systems. Autocatalytic systems are truly the crucial step in the   selection process of the molecules of life.
Reply:  The Implausibility of Metabolic Cycles on the Prebiotic Earth Leslie E Orgel†
Almost all proposals of hypothetical metabolic cycles have recognized that each of the steps involved must occur rapidly enough for the cycle to be useful in the time available for its operation. It is always assumed that this condition is met, but in no case have persuasive supporting arguments been presented. Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of the reverse citric acid cycle was present anywhere on the primitive Earth, or that the cycle mysteriously organized itself topographically on a metal sulfide surface? The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own. 
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060018

Carbon metabolism, which is the most basic aspect of life: by design, or chemical evolution?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world#7746

PD: This paper is a bit lengthy but is linked below,  and it’s a great read for anyone interested   in how the emergence of complex systems is  specifically prompted by thermodynamic principles,
Reply:   Life in any form is a very serious enigma and conundrum. It does something, whatever the biochemical pathway, machinery, enzymes etc. are involved, that should not and honestly could not ever "get off the ground". It SPONTANEOUSLY recruits Gibbs free energy from its environment so as to reduce its own entropy. That is tantamount to a rock continuously recruiting the wand to roll it up the hill, or a rusty nail "figuring out" how to spontaneously rust and add layers of galvanizing zinc on itself to fight corrosion. Unintelligent simple chemicals can't self-organize into instructions for building solar farms (photosystems 1 and 2), hydroelectric dams (ATP synthase), propulsion (motor proteins) , self repair (p53 tumor suppressor proteins) or self-destruct (caspases) in the event that these instructions become too damaged by the way the universe USUALLY operates. Abiogenesis is not an issue that scientists simply need more time to figure out but a fundamental problem with materialism

The natural tendency of proteins is to fall apart; for proteins to be synthesized, the reaction must be driven up the thermodynamic hill, away from equilibrium. The same is true of other biochemical processes: the transport of nutrients against a concentration gradient, the generation of physical force or electrical potentials, even the accurate transmittal of genetic information, all represent work in the thermodynamic sense. They can take place only because of cells couple the work function to a source of energy. This, in fact, is how energy is defined: it is the capacity to do work. Bioenergetics revolves around the sources of biological energy and the mechanisms by which energy is coupled to useful work

Transformation of Energy to Maintain a Low Entropy State and Perform Work
https://reasonandscience.catsboard.com/t2572-transformation-of-energy-to-maintain-a-low-entropy-state-and-perform-work#6856

More:
Thermodynamics, and the origin of life
https://reasonandscience.catsboard.com/t2718-thermodynamics-and-the-origin-of-life

PD: These two phenomena comprise  a single physico-chemical continuum,  with no clear distinction between them.
Reply: The Origin of the First Hereditary Replicators.
This process is still an unsolved problem. By itself, this transition is not an evolutionary one because, without hereditary replicators, no Darwinian evolution is possible.
https://www.pnas.org/content/112/33/10104

Darwin probably didn’t propose a theory for the origin of life simply because applying Darwin’s mechanism of natural selection to the emergence of life, as done by Dawkins (1976), is like comparing apples with pears (Johnson 2010). What’s more, the idea that a self-replicating molecule with an information content casually appeared in a primordial soup, as imagined by Dawkins (1976) (“At some point a particularly remarkable molecule was formed by accident. We will call it the Replicator.”) appears to be statistically groundless (Yockey 1977).
https://www.springer.com/gp/book/9783030259617

Is life a gamble? Scientist models universe to find out April 21, 2020
Scientists suspect that the complex life that slithers and crawls through every nook and cranny on Earth emerged from a random shuffling of non-living matter that ultimately spit out the building blocks of life.
https://www.livescience.com/origin-of-life-rna-universe-model.html

Darwin persuades us that the seemingly purposeful construction of living things can very often, and perhaps always, be attributed to the operation of natural selection. Natural selection requires three processes: reproduction, variation, and inheritance.

If you have things that are reproducing their kind;
if there are sometimes random variations, nevertheless, in the offspring;
if such variations can be inherited;
if some such variations can sometimes confer an advantage on their owners;
if there is competition between the reproducing entities -
if there is an overproduction so that not all will be able to survive to produce offspring themselves -
then these entities will get better at reproducing their kind. What is needed for natural selection are things that conform to those 'ifs'. Self-replicating cells  are prerequisites for evolution. None of this was available prebiotically to explain the origin of the first life form.

A. G. CAIRNS-SMITH Seven clues to the origin of life, page  36:
And if you ask me how the next stage happened, how the smallish 'molecules of life' came together to make the first reproducing evolving being, I will reply: 'With time, and more time, and the resource of oceans.' I will sweep my arms grandly about. 'Because, you see. in the absence of oxygen the oceans would have accumulated "the molecules of life". The oceans would have been vast bowls of nutritious soup. Chance could do the rest.

The possible mechanisms to explain the origin of life
https://reasonandscience.catsboard.com/t2515-abiogenesis-the-possible-mechanisms-to-explain-the-origin-of-life

PD: Below I will link this 2021 review of  autocatalysis, which neatly summarizes   the breadth of application this concept  presents, only part of which is the origin of   life. It covers essential background information  regarding kinetics that James might want to study,   as well as dozens of examples of autocatalysis  in a variety of contexts, including the strictly   organic and feasibly prebiotic, such as the  formose reaction he so frequently brings up.
Reply: The formose reaction is of great importance to the question of the origin of life as it explains part of the path from simple formaldehyde to complex sugars like ribose and from there to RNA. All sugars have fairly similar chemical properties; thus, it is difficult to envision simple physicochemical mechanisms that could (1) preferentially concentrate ribose from a complex mixture or (2) enhance the yield of the d-ribose relative to that of its biologically inactive mirror image. The inherent instability of ribose poses yet another problem with respect to its prebiotic availability. Under neutral conditions (pH 7), the half-life for the decomposition of ribose is 73 minutes at 100C and only 44 years at 0C (Larralde, Robertson, and Miller 1995).

More:
The RNA world, and the origins of life
https://reasonandscience.catsboard.com/t2024-the-rna-world-and-the-origins-of-life

PD: There’s also the 2012 study I alluded to in  my previous video but didn’t specifically   cite as I was keeping things brief for the  layperson. Here it is now, with the abstract   outlining how “mixtures of RNA fragments that  self-assemble into self-replicating ribozymes   spontaneously form cooperative catalytic cycles  and networks.”
Reply: Neeraja Sankaran: Revisiting the RNA World with its inventor September 6, 2017
The RNA World Hypothesis is a model for the early evolution of life on earth proposed in 1986 by the molecular biologist Walter Gilbert, in which he posited that the earliest forms of life were likely composed entirely of RNA molecules. According to this scenario, the two fundamental functions of life, namely metabolism, and the closely associated process of catalysis, and replication, namely the passing on of the information about various activities to the next generation of offspring, performed in contemporary living systems by proteins and DNA respectively, were both carried out by RNA.

Today, thirty years after the RNA World was first proposed, no one has seen an actual living system that is completely based in RNA. Nevertheless, the hypothesis lives on in the origins of life research community, albeit in a hotly debated, highly contentious atmosphere. Although there are strong opponents, many researchers agree that although far from complete, it remains one of the best theories we have to understand “the backstory to contemporary biology.” Gilbert himself expressed some disappointment that “a self-replicating RNA has not yet been synthesized or discovered” in the years since he predicted his hypothesis, but he remains optimistic that it will emerge eventually.
[url=https://atlasofscience.org/revisiting-the-rna-world-with-its-inventor/#:~:text=The RNA World Hypothesis is,composed entirely of RNA molecules.]https://atlasofscience.org/revisiting-the-rna-world-with-its-inventor/#:~:text=The%20RNA%20World%20Hypothesis%20is,composed%20entirely%20of%20RNA%20molecules.[/url]

My comment:  So, nobody has been able to confirm the hypothesis in 30 years. And there are reasons for that.

PHILIP BALL: Flaws in the RNA world 12 FEBRUARY 2020
Self-replicating RNA may lack the fidelity needed to originate life
The hypothesis of an ‘RNA world’ as the font of all life on Earth has been with us now for more than 30 years, the term having been coined by the biologist Wally Gilbert in 1986. You could be forgiven for thinking that it pretty much solves the conundrum of how the replication of DNA could have avoided a chicken-and-egg impasse: DNA replication requires protein enzymes, but proteins must be encoded in DNA. The intermediary RNA breaks that cycle of dependence because it can both encode genetic information and act catalytically like enzymes. Catalytic RNAs, known as ribozymes, play several roles in cells.
It’s an alluring picture – catalytic RNAs appear by chance on the early Earth as molecular replicators that gradually evolve into complex molecules capable of encoding proteins, metabolic systems and ultimately DNA. But it’s almost certainly wrong. For even an RNA-based replication process needs energy: it can’t shelve metabolism until later. And although relatively simple self-copying ribozymes have been made, they typically work only if provided with just the right oligonucleotide components to work on. What’s more, sustained cycles of replication and proliferation require special conditions to ensure that RNA templates can be separated from copies made on them. 


More:
The origin of replication and translation and the RNA World
https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world

Lee Cronin:  And basically all I was saying is that very basic chemistry introduces the concept of molecules and reactions and complexity. And with those ideas together and some time you are able to get to evolution.
Reply: This is a staggeringly simplistic, and simply wrong concept.

The factory maker argument
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument

Cells are factories in a literal sense:
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#6959

1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over forty epigenetic languages, translation systems, and signaling networks. These information systems prescribe and instruct the making and operation of cells and multicellular organisms. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like,  autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.

2. The origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.

3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes.

Herschel 1830 1987, p. 148:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”



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Lee Cronin:  That is what the current scientific consensus is saying, it’s what all the experiments are showing.
Reply:  Much of the "settled science" that even geologists and other degree-holding "scientists" accept is really not established fact, it's only most "widely accepted theory", and some actually ignores evidence that might support other and better inferences from available evidence, because that evidence indicates something other than the "consensus opinion" on a subject.
Never mind that almost all the most groundbreaking and world-changing scientific and mathimatical breakthroughs from Galileo to Newton, to Pasteur, to Pascal and Einstein, etc. were made by people who rejected conventional wisdom or went well beyond what "everybody knows". Stephen Lucas

There are until numbers if dissenters and all it takes is one to disprove the orthodoxy.
Most proponents of darwinism never actually examine their theory critically. They just assume it to be true in part because, well, it's the consensus after all! That's called group think.

Michael Crichton
“I want to pause here and talk about this notion of consensus, and the rise of what has been called consensus science. I regard consensus science as an extremely pernicious development that ought to be stopped cold in its tracks. Historically, the claim of consensus has been the first refuge of scoundrels; it is a way to avoid debate by claiming that the matter is already settled. Whenever you hear the consensus of scientists agrees on something or other, reach for your wallet because you're being had.

Let's be clear: the work of science has nothing whatever to do with consensus. Consensus is the business of politics. Science, on the contrary, requires only one investigator who happens to be right, which means that he or she has results that are verifiable by reference to the real world. In science consensus is irrelevant. What is relevant is reproducible results. The greatest scientists in history are great precisely because they broke with the consensus.

There is no such thing as consensus science. If it's consensus, it isn't science. If it's science, it isn't consensus. Period.”
 
“I would remind you to notice where the claim of consensus is invoked. Consensus is invoked only in situations where the science is not solid enough. Nobody says the consensus of scientists agrees that E=mc2. Nobody says the consensus is that the sun is 93 million miles away. It would never occur to anyone to speak that way.”

It begins with Stump's appeal to authority. This is a common evolutionary argument, but the fact that a majority of scientists accept an idea means very little. Certainly expert opinion is an important factor and needs to be considered, but the reasons for that consensus also need to be understood. The history of science is full of examples of new ideas that accurately described and explained natural phenomena, yet were summarily rejected by experts. Scientists are people with a range of nonscientific, as well as scientific influences. Social, career and funding influences are easy to underestimate. There can be tremendous pressures on a scientist that have little to do with the evidence at hand. This certainly is true in evolutionary circles, where the pressure to conform is intense.

More:
Is consensus in science an indicator for truth?
https://reasonandscience.catsboard.com/t1646-is-consensus-in-science-an-indicator-for-truth

Lee Cronin:  you can make molecules that can do what would be like proteins and be like genetic material at the same time, mutually interacting.  And they started off from an inorganic salt.
Reply:  How do you go from that proposed scenario to the one performed by modern cells to make proteins ?

For even a single protein to be successfully expressed in the cell, a huge number of molecules need to interact with one another in exactly the right way, at exactly the right time, and in exactly the right order.
https://philpapers.org/archive/NICOBT-2.pdf

The Emergence of Life
The organization of various biological forms and their interrelationships, vis-à-vis biochemical and molecular networks, is characterized by the interlinked processes of flow of information between the information-bearing macromolecular semantides, namely DNA and RNA, and proteins (Zuckerkandl and Pauling 1965).
https://link.springer.com/article/10.1007/s11214-019-0624-8

To make proteins, and direct and insert them to the right place where they are needed, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps are required. Each step requires extremely complex molecular machines composed of numerous subunits and co-factors, which require the very own processing procedure described below, which makes its origin an irreducible  catch22 problem:

THE GENE REGULATORY NETWORK "SELECTS" WHEN, WHICH GENE IS TO BE EXPRESSED
INITIATION OF TRANSCRIPTION BY RNA POLYMERASE
TRANSCRIPTION ERROR CHECKING BY CORE POLYMERASE AND TRANSCRIPTION FACTORS
RNA CAPPING
ELONGATION
SPLICING
CLEAVAGE
POLYADENYLATION AND TERMINATION
EXPORT FROM THE NUCLEUS TO THE CYTOSOL
INITIATION OF PROTEIN SYNTHESIS (TRANSLATION) IN THE RIBOSOME
COMPLETION OF PROTEIN SYNTHESIS  
PROTEIN FOLDING
MATURATION
RIBOSOME QUALITY CONTROL
PROTEIN TARGETING TO THE RIGHT CELLULAR COMPARTMENT
ENGAGING THE TARGETING MACHINERY BY THE PROTEIN SIGNAL SEQUENCE
CALL CARGO PROTEINS TO LOAD/UNLOAD THE PROTEINS TO BE TRANSPORTED
ASSEMBLY/DISASSEMBLY OF THE TRANSLOCATION MACHINERY
VARIOS CHECKPOINTS FOR QUALITY CONTROL AND REJECTION OF INCORRECT CARGOS
TRANSLOCATION TO THE ENDOPLASMIC RETICULUM
POSTRANSLATIONAL PROCESS OF PROTEINS IN THE ENDOPLASMIC RETICULUM OF TRANSMEMBRANE PROTEINS AND WATER-SOLUBLE PROTEINS
GLYCOSILATION OF MEMBRANE PROTEINS IN THE ER ( ENDOPLASMIC RETICULUM )
ADDITION OF OLIGOSACCHARIDES
INCORRECTLY FOLDED PROTEINS ARE EXPORTED FROM THE ER, AND DEGRADED IN THE CYTOSOL
TRANSPORT OF THE PROTEIN CARGO TO THE END DESTINATIONS AND ASSEMBLY

Paul Davies, the origin of life, page 59
Proteins are a godsend to DNA because they can be used both as building material, to make things like cell walls, and as enzymes, to supervise and accelerate chemical reactions. Enzymes are chemical catalysts that ‘oil the wheels’ of the biological machine. Without them metabolism would grind to a halt, and there would be no energy available for the business of life. Not surprisingly, therefore, a large part of the DNA databank is used for storing instructions on how to make proteins. Here is how those instructions get implemented. Remember that proteins are long chain molecules made from lots of amino acids strung together to form polypeptides. Each different sequence of amino acids yields a different protein. The DNA has a wish list of all the proteins the organism needs. This information is stored by recording the particular amino acid sequence that specifies each and every protein on the list. It does so using DNA's four-letter alphabet A, G, C and T; the exact sequence of letters spells out the amino acid recipe, protein by protein – typically a few hundred base pairs for each. To turn this dry list of amino acids into assembled, functioning proteins, DNA enlists the help of a closely related molecule known as RNA (for ribonucleic acid). RNA is also made from four bases, A, G, C and U. Here U stands for uracil; it is similar to T and serves the same purpose alphabetically. RNA comes in several varieties; the one of interest to us here is known as messenger RNA, or mRNA for short. Its job is to read off the protein recipes from DNA and convey them to tiny factories in the cell where the proteins are made. These mini-factories are called ribosomes, and are complicated machines built from RNA and proteins of various sorts. Ribosomes come with a slot into which the mRNA feeds, after the fashion of a punched tape of the sort used by old-fashioned computers.

More:
The interdependent and irreducible structures required to make proteins
https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins

Lee Cronin:So I think that   that’s an important thing about the need for some  kind of advanced information to already be there, invoking this creator, that is incorrect. We’ve shown that is false.
Reply:  Even let's suppose that scenario were true, how do you go from this scenario to the information contained in the most simple know life form?

Pelagibacter unique bacteria are known to be the smallest and simplest, self-replicating, and free-living cells. Pelagibacter genomes (~ 1,300 genes and 1,3 million base pairs ) devolved from a slightly larger common ancestor (~2,000 genes). Pelagibacter is an alphaproteobacterium. In the evolutionary timescale, its common ancestor supposedly emerged about 1,3 billion years ago. The oldest bacteria known however are Cyanobacteria,  living in the rocks in Greenland about 3.7-billion years ago.  With a genome size of approximately  3,2 million base pairs ( Raphidiopsis brookii D9) they are the smallest genomes described for free-living cyanobacteria. This is a paradox. The oldest known life-forms have a considerably bigger genome than Pelagibacter, which makes their origin far more unlikely from a naturalistic standpoint.  The unlikeliness to have just ONE protein domain-sized fold of 250amino acids is 1 in 10^77. That means, to find just one functional protein fold with the length of about 250AAs, nature would have to search amongst so many non-functional folds as there are atoms in our known universe ( about 10^80 atoms).   We will soon see the likeliness to find an entire functional of genome Pelagibacter with 1,3 million nucleotides, which was however based on the data demonstrated above, not the earliest bacteria....

Pelagibacter has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,3 million base pairs and code for 1,300 proteins.  The chance to get its entire proteome would be 10^722,000.  The discrepancy between the functional space, and the sequence space, is staggering.


Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events
https://reasonandscience.catsboard.com/t2508-abiogenesis-uncertainty-quantification-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-events

PD:  Here’s a schematic of the cross-replicating  ribozymes, including a closer look at the   pair with the fastest rate of exponential  growth, which was 20-fold after five hours.
Reply: PHILIP BALL: Flaws in the RNA world 12 FEBRUARY 2020
Self-replicating RNA may lack the fidelity needed to originate life
The hypothesis of an ‘RNA world’ as the font of all life on Earth has been with us now for more than 30 years, the term having been coined by the biologist Wally Gilbert in 1986. You could be forgiven for thinking that it pretty much solves the conundrum of how the replication of DNA could have avoided a chicken-and-egg impasse: DNA replication requires protein enzymes, but proteins must be encoded in DNA. The intermediary RNA breaks that cycle of dependence because it can both encode genetic information and act catalytically like enzymes. Catalytic RNAs, known as ribozymes, play several roles in cells.
It’s an alluring picture – catalytic RNAs appear by chance on the early Earth as molecular replicators that gradually evolve into complex molecules capable of encoding proteins, metabolic systems and ultimately DNA. But it’s almost certainly wrong. For even an RNA-based replication process needs energy: it can’t shelve metabolism until later. And although relatively simple self-copying ribozymes have been made, they typically work only if provided with just the right oligonucleotide components to work on. What’s more, sustained cycles of replication and proliferation require special conditions to ensure that RNA templates can be separated from copies made on them.

PD: These papers are tangible examples of   “evolution-like” behavior from molecules outside  of a living system, demonstrating how Jim’s idea   that there are no selection mechanisms outside  of life is completely wrong. This behavior also   strongly suggests that certain molecules DO  have an innate tendency to generate life,   which again contradicts Jim’s favorite mantra.
Reply: The role of natural selection in the origin of life
Unlike living systems that are products of and participants in evolution, these prebiotic chemical structures were not products of evolution. Not being yet intricately organized, they could have emerged as a result of ordinary physical and chemical processes.
https://www.ncbi.nlm.nih.gov/pubmed/20407927

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life? July 6, 2011
The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution.
https://sci-hub.tw/https://www.annualreviews.org/doi/10.1146/annurev-micro-090110-102801

Functional proteins from a random-sequence library
Anthony D. Keefe & Jack W. Szostak
Functional primordial proteins presumably originated from random sequences
https://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Keefe_Szostak_Nature_01.pdf?fbclid=IwAR0giOg_aZfFRKQALk7CB22nVIx32ShiN0Vp78cwtAYwmwQ_0RJicfxpR1M

When we consider how life might have arisen from nonliving matter, we must take into account the properties of the young Earth’s atmosphere, oceans, and climate, all of which were very different than they are today. Biologists postulate that complex biological molecules first arose through the random physical association of chemicals in that environment.
LIFE The Science of Biology, TENTH EDITION, page 3

Neither Evolution nor physical necessity are a driving force prior dna replication. The only two alternatives are either a) creation by an intelligent agency, or b) Random, unguided, undirected natural events by a lucky "accident". 


PD:  say that selection can’t exist on a prebiotic  Earth, you are doing nothing but demonstrating   your spectacular ignorance towards an entire  subfield of chemistry.
Reply: In regards to the prebiotic synthesis of the basic building blocks of life, I list 23 problems directly related to the lack of a selection mechanism on the prebiotic earth. This is one of the unsolvable problems of abiogenesis. 
Selecting the right materials is absolutely essential. But a prebiotic soup of mixtures of impure chemicals would never purify and select those that are required for life. Chemicals and physical reactions have no "urge" to join, group, and start interacting in a purpose and goal-oriented way to produce molecules, that later on would perform specific functions, and generate self-replicating factories, full of machines, directed by specified, complex assembly information. This is not an argument from ignorance, incredulity, or gaps of knowledge.

William Dembski: The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability. Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better inference. Occam's razor also boils down to an argument from ignorance: in the absence of better information, you use a heuristic to accept one hypothesis over the other.
http://www.discovery.org/a/1256

Out of the 27 listed problems of prebiotic RNA synthesis, 8 are directly related to the lack of a mechanism to select the right ingredients.
1.How would prebiotic processes have purified the starting molecules to make RNA and DNA which were grossly impure? They would have been present in complex mixtures that contained a great variety of reactive molecules.
2.How did fortuitous accidents select the five just-right nucleobases to make DNA and RNA, Two purines, and three pyrimidines?
3.How did unguided random events select purines with two rings, with nine atoms, forming the two rings: 5 carbon atoms and 4 nitrogen atoms, amongst almost unlimited possible configurations?
4.How did stochastic coincidence select pyrimidines with one ring, with six atoms, forming its ring: 4 carbon atoms and 2 nitrogen atoms, amongst an unfathomable number of possible configurations?
5.How would these functional bases have been separated from the confusing jumble of similar molecules that would also have been made?
6.How could the ribose 5 carbon sugar rings which form the RNA and DNA backbone have been selected, if 6 or 4 carbon rings, or even more or less, are equally possible but non-functional?
7.How were the correct nitrogen atom of the base and the correct carbon atom of the sugar selected to be joined together?
8.How could right-handed configurations of RNA and DNA have been selected in a racemic pool of right and left-handed molecules? Ribose must have been in its D form to adopt functional structures ( The homochirality problem )

Out of the 27 listed problems of prebiotic amino acid synthesis, 13 are directly related to the lack of a mechanism to select the right ingredients.
1. How did unguided stochastic coincidence select the right amongst over 500 that occur naturally on earth?
2. How were bifunctional monomers, that is, molecules with two functional groups, so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
3. How could achiral precursors of amino acids have produced/selected and concentrated only left-handed amino acids? ( The homochirality problem )
4. How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
5. How would natural causes have selected twenty, and not more or less amino acids to make proteins?
6. How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
7. How were bifunctional monomers, that is, molecules with two functional groups so they combine with two others selected, and unifunctional monomers (with only one functional group) sorted out?
8. How could achiral precursors of amino acids have produced and concentrated/selected only left-handed amino acids? (The homochirality problem)
9. How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
10. How would natural causes have selected twenty, and not more or less amino acids to make proteins?
11. How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
12. How did nature "know" that the set of amino acids selected appears to be near ideal and optimal?

Out of the 12 listed problems of prebiotic cell membrane synthesis, 2 are directly related to the lack of a mechanism to select the right ingredients.
1. How did prebiotic processes select hydrocarbon chains which must be in the range of 14 to 18 carbons in length?  There was no physical necessity to form carbon chains of the right length nor hindrance to join chains of varying lengths. So they could have been existing of any size on the early earth.
2. How would random events start to produce biological membranes which are not composed of pure phospholipids, but instead are mixtures of several phospholipid species, often with a sterol admixture such as cholesterol? There is no feasible prebiotic mechanism to select/join the right mixtures.

PD:  even with a 10% yield for a reaction the first  time around, at the end of many cycles, all the   useless impurities that are not reproducing  will have purged themselves spontaneously,  and you will have highly purified products. If James wants to get out of his sad  little box and actually learn about this field,   he has to dig into the literature on autocatalysis  which he is busy pretending is not relevant,  starting with the early theory and  comprehensive mathematical models,   followed by a mountain of experimental science  leading all the way up to that 2021 review.
Reply:  Why has what you claim not been demonstrated in the Lab ?

Do natural clays catalyze this reaction?
June 2006 Robert Shapiro
The attractiveness of this oligonucleotide synthesis rests in part in the ready availability of the catalyst. Montmorillonite is a layered clay mineral-rich in silicate and aluminum oxide bonds. It is widely distributed in deposits on the contemporary Earth. If the polymerization of RNA subunits was a common property of this native mineral, the case for RNA at the start of life would be greatly enhanced.
However, the “[c]atalytic activity of native montmorillonites before being converted to their homoionic forms is very poor” (Ertem 2004:567). The native clays contain bound polyvalent cations, such as Cu2, Fe3, and Zn2, that interfere with phosphorylation reactions. This handicap was overcome in the synthetic experiments by titrating the clays to a monoionic form, generally sodium, before they were used. Even after this step, the activity of the montmorillonite depended strongly on its physical source, with samples from Wyoming yielding the best results (Ferris et al. 1989; Ertem 2004). Eventually the experimenters settled on Volclay, a commercially processed Wyoming montmorillonite provided by the American Colloid Company. Further purification steps were applied to obtain the catalyst used for the “prebiotic” formation of RNA.
https://sci-hub.ren/https://www.jstor.org/stable/10.1086/506024?seq=1

PD: The matter is the information. In this  case it is the sequence of nucleotides.  That’s all.
Reply: Information is not physical
https://arxiv.org/pdf/1402.2414.pdf
Information  is a disembodied abstract entity independent of its physical carrier. ”Information is always tied to a physical representation. It is represented by engraving on a stone tablet, a spin, a charge, a hole in a punched card, a mark on paper, or some other equivalent. This ties the handling of information to all the possibilities and restrictions of our real physical word, its laws of physics and its storehouse”. However, the legitimate questions concern the physical properties of information carriers like ”stone tablet, a spin, a charge, a hole in a punched card, a mark on paper”, but not the information itself.  Information is neither classical nor quantum, it is independent of the properties of physical systems used to its processing.


https://biosemiosis.net/?fbclid=IwAR1xTZ-JWsSeSaTHqN5MmsaXpPN6dlFQz4liWCcOYzt6ugib-TVWv9y8YIE
Information is not a tangible entity, it has no energy and no mass, it is not physical,  it is conceptual.

- Life is a software/information-driven process.
- Information is not physical it is conceptual.
- The only known source of semiotic information is prior to intelligence.
- Life is therefore the direct product of a deliberate creative intellectual process.

The algorithmic origins of life
https://reasonandscience.catsboard.com/t3061-the-algorithmic-origins-of-life

PD: Information is just a word we use  to describe certain patterns. Early complex  pre-biological structures evolved together in  synergy with systems of mixtures of chemicals  
Reply:  OPEN QUESTIONS IN ORIGIN OF LIFE: EXPERIMENTAL STUDIES ON THE ORIGIN OF NUCLEIC ACIDS AND PROTEINS WITH SPECIFIC AND FUNCTIONAL SEQUENCES BY A CHEMICAL SYNTHETIC BIOLOGY APPROACH February 2014
There is a conceptual problem, namely the emergence of specific sequences among a vast array of possible ones, the huge “sequence space”, leading to the question “why these macromolecules, and not the others?” One of the main open questions in the field of the origin of life is the biogenesis of proteins and nucleic acids as ordered sequences of monomeric residues, possibly in many identical copies. The first important consideration is that functional proteins and nucleic acids are chemically speaking copolymers, i.e., polymer formed by several different monomeric units, ordered in a very specific way.

The information stored in DNA can be described by man, but it is instructional assembly information. It instructs the sequence that amino acids must join together to bear functionality by means of functional folding, which permits proteins to become functional.

Barbieri: Code Biology:
"...there is no deterministic link between codons and amino acids because any codon can be associated with any amino acid.  This means that the rules of the genetic code do not descend from chemical necessity and in this sense they are arbitrary."
"...we have the experimental evidence that the genetic code is a real code, a code that is compatible with the laws of physics and chemistry but is not dictated by them."
https://www.sciencedirect.com/journal/biosystems/vol/164/suppl/C

[Comment on other biological codes]: "In signal transduction, in short, we find all the essential components of a code: (a) two independents worlds of molecules (first messengers and second messengers), (b) a set of adaptors that create a mapping between them, and (c) the proof that the mapping is arbitrary because its rules can be changed in many different ways."

What we see operating in cells is not like a code, but genuinely is a code—therefore its “true and sufficient” explanation is intelligence. 

Coded information comes always from a mind
https://reasonandscience.catsboard.com/t1312-coded-information-comes-always-from-a-mind

PD:  life almost certainly predates DNA,
Reply:  Does a DNA-less cellular organism exist on Earth?  2011 Nov 17.
All the self-reproducing cellular organisms so far examined have DNA as the genome.
https://pubmed.ncbi.nlm.nih.gov/22093146/

DNA is “the Blueprint of Life.” It contains the data needed to make every single protein that life can't go on without. No DNA, no proteins, no life. RNA has a limited coding capacity because it is unstable.

RNA is inherently unstable
RNA is often considered too unstable to have accumulated in the prebiotic environment. RNA is particularly labile at moderate to high temperatures
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149711/

PD: Origin and evolution of the genetic code. Yet  again, whether or not this paper or any other has  the details precisely correct, the key concept  James can’t seem to understand is selection
Reply:  The origin of the genetic code is an entirely different question, than the origin of the information stored in DNA, which uses codon words, which then are translated through the ribosome using the genetic code, which is a non-random assignment of triplet codons to amino acids.

Origin and evolution of the genetic code: the universal enigma
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

There are many problems about the quest of the origin of the genetic code, which seems unsolvable.

1. Did the dialects, i.e., mitochondrial version, with UGA codon (being the stop codon in the universal version) codifying tryptophan; AUA codon (being the isoleucine in the universal version), methionine; and Candida cylindrica (funges), with CUG codon (being the leucine in the universal version) codifying serine, appear accidentally or as a result of some kind of selection process?
2. Why is the genetic code represented by the four bases A, T(U), G, and C?
3. Why does the genetic code have a triplet structure?
4. Why is the genetic code not overlapping, that is, why does the translation apparatus of a cell, which transcribes information, have a discrete equaling to three, but not to one?
5. Why does the degeneracy number of the code vary from one to six for various amino acids?
6. Is the existing distribution of codon degeneracy for particular amino acids accidental or some kind of selection process?
7. Why were only 20 canonical amino acids selected for the protein synthesis?
8. Why should there be a genetic code at all?
9. Why should there be the emergency of stereochemical association of a specific arbitrary codon-anticodon set?
10. Aminoacyl-tRNA synthetases recognize the correct tRNA. How did that recognition emerge, and why?
11. Is this very choice of amino acids accidental or some kind of selection process?
12. Why don’t we find any protein sequences in the fossils of ancient organisms, which only have primary amino acids?
13. Why didn’t the genetic code keep on expanding to cover more than 20 amino acids? Why not 39, 48 or 62?
14. Why did codon triplets evolve, and why not quadruplets? With 44 = 256 possible codon quadruplets, coding space could have increased, and thus a much larger universe of possible proteins could have been made possible.

The Genetic Code was most likely implemented by intelligence.
1. In communications and information processing, code is a system of rules to convert information—such as assigning the meaning of a letter, word, into another form, ( as another word, letter, etc. ) 
2. In translation, 64 genetic codons are assigned to 20 amino acids. It refers to the assignment of the codons to the amino acids, thus being the cornerstone template underling the translation process.
3. Assignment means designating, dictating, ascribing, corresponding, correlating, specifying, representing, determining, mapping, permutating.    
4. The universal triple-nucleotide genetic code can be the result either of a) a random selection through evolution, or b) the result of intelligent implementation.
5. We know by experience, that performing value assignment and codification is always a process of intelligence with an intended result. Non-intelligence, aka matter, molecules, nucleotides, etc. have never demonstrated to be able to generate codes, and have neither intent nor distant goals with a foresight to produce specific outcomes.  
6. Therefore, the genetic code is the result of an intelligent setup.

The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin

PD:  Tweedledum are stuck on pretending thermodynamics forbids the emergence of life when in fact it is specifically thermodynamics that prompts it.
Reply:  Establishing the flow of information depends not only on hardware and software, ( an information storage device, and the stored instructional blueprint  ),  but also on the transfer of energy to perform the exchange from a disordered state ( random letters on the floor ) to an ordered state - an informational sentence ( the ordered sequence of letters, correctly lined up that form the phrase ).

The same occurs in living organisms. Energy input in the form of ATP is required to produce information-rich, organized structures such as proteins and nucleic acids. An essential Origin of Life research problem is not only the availability of the basic building blocks of life on a prebiotic earth but how could they have been brought and concentrated to one construction site, where they would all have been available at the same time, and then put into the right order to create information, according to the secular narrative, first through the formation of RNA polymers, which in sequence, began self replication.

https://reasonandscience.catsboard.com/t2590-origins-what-cause-explains-best-our-existence-and-why#5811
The emergence of concentrated suites of just the right mix thus remains a central puzzle in origin-of-life research.

That is not a trivial task, but science has no compelling hypothesis how that could have occurred. Fred Hoyles Tornado sweeping through a Junkyard, unjustly dismissed by naturalists, is a good analogy. In the engineering lab of Boeing, the formation of a blueprint to make 747's would hardly emerge by random forces of ink and paper or self-forming computer-aided design, but by the precise order of writing down information by the guiding hand of highly skilled, trained and intelligent engineers, that would store the instructional information that is transmitted to the factory to the workers to make the airplanes.  

On early earth, the basic chemical elements would have, somehow, to be transformed, non enzymatically, without the aid of molecular machines that would speed up the process, into the essential molecules of life, namely amino acids, sugars, fatty acids, and nucleotides. Biological Cells use highly complex assembly lines to make these essential basic molecules.  ( In our analogy, the letters for the informational sentences have to be formed from raw materials )  Life uses ultracomplex metabolic pathways, and a myriad of enzymes, but these pathways were non-existent on early earth. To perform just ONE of seven reactions to make pyrimidines, one of the two types of bases to make RNA and DNA nucleotides, enzyme expert Dr Richard Wolfenden, of the University of North Carolina, showed in 1998 that the reaction performed by OMP decarboxylase enzymes, is ‘“absolutely essential” in creating the building blocks of DNA and RNA, would take 78 million years in water’, but was speeded up 10^18 times by that enzyme. ( it is the fastest enzyme known ) If by some unknown event, prebiotic mechanisms would have produced the intermediate product, Orotidine 5'-monophosphate, until nonenzymatic reactions would have transformed it into uridine monophosphate, the last product in the pathway, after 78mio years,  the molecule would have disintegrated long ago by ultraviolet light and other environmental factors.  

Thermodynamics, and the origin of life
https://reasonandscience.catsboard.com/t2718-thermodynamics-and-the-origin-of-life

PD: And  UV photons play a particular role, one that is  crucial to the formation of nucleosides, not  their degradation as James naively presumes.  Of course James wants to see the synthetic routes.  Here’s one for purines starting exclusively with   hydrogen cyanide.
Reply: Life uses just five nucleobases to make DNA and RNA. Two purines, and three pyrimidines. Purines use two rings with nine atoms, pyrimidines use just one ring with six atoms. Hydrogen bonding between purine and pyrimidine bases is fundamental to the biological functions of nucleic acids, as in the formation of the double-helix structure of DNA. This bonding depends on the selection of the right atoms in the ring structure. Pyrimidine rings consist of six atoms: 4 carbon atoms and 2 nitrogen atoms. Purines have nine atoms forming the ring: 5 carbon atoms and 4 nitrogen atoms.

Remarkably, it is the composition of these atoms that permit that the strength of the hydrogen bond that permits to join the two DNA strands and form Watson–Crick base-pairing, and well-known DNA ladder.  Neither transcription nor translation of the messages encoded in RNA and DNA would be possible if the strength of the bonds had different values. Hence, life, as we understand it today, would not have arisen.

Now, someone could say, that there could be no different composition, and physical constraints and necessity could eventually permit only this specific order and arrangement of the atoms. Now, in a recent science paper from 2019, Scientists explored how many different chemical arrangements of the atoms to make these nucleobases would be possible. Surprisingly, they found well over a million variants.   The remarkable thing is, among the incredible variety of organisms on Earth, these two molecules are essentially the only ones used in life. Why? Are these the only nucleotides that could perform the function of information storage? If not, are they perhaps the best? One might expect that molecules with smaller connected Carbon components should be easier for abiotic chemistry to explore.

According to their scientific analysis, the natural ribosides and deoxyribosides inhabit a fairly redundant ( in other words, superfluous, unnecessary, needless,  and nonminimal region of this space.  This is a remarkable find and implicitly leads to design. There would be no reason why random events would generate complex, rather than simple, and minimal carbon arrangements. Nor is there physical necessity that says that the composition should be so. This is evidence that a directing intelligent agency is the most plausible explanation. The chemistry space is far too vast to select by chance the right finely-tuned functional life-bearing arrangement.

In the mentioned paper, the investigators asked if other, perhaps equally good, or even better genetic systems would be possible.  Their chemical experimentations and studies concluded that the answer is no. Many nearly as good, some equally good, and a few stronger base-pairing analog systems are known. There is no reason why these structures could or would have emerged in this functional complex configuration by random trial and error. There is a complete lack of scientific-materialistic explanations despite decades of attempts to solve the riddle.

What we can see is, that direct intervention, a creative force, the activity of an intelligent agency, a powerful creator, is capable to have the intention and implement the right arrangement of every single atom into functional structures and molecules in a repetitive manner, in the case of DNA, at least 1,300,000  nucleotides to store the information to kick-start life, exclusively with four bases, to produce a storage device that uses a genetic code, to store functional, instructional, complex information, functional amino acids, and phospholipids to make membranes, and ultimately, life.  Lucky accidents, the spontaneous self-organization by unguided coincidental events, that drove atoms into self-organization in an orderly manner without external direction, chemical non-biological are incapable and unspecific to arrange atoms into the right order to produce the four classes of building blocks, used in all life forms.


Fine-tuning of the force of the hydrogen bonds that hold nucleotides together to form Watson-Crick base-pairing of DNA stands
https://reasonandscience.catsboard.com/t2591-biochemical-fine-tuning-essential-for-life#7845

PD: Time is a problem in synthesis. Yes, some of the molecules of life as we know   it are not totally stable, and clearly this is  because they must be hydrolyzed from time to time.  But they are still stable enough to lead to life.  Stability and equilibria are not the issues here.  
Reply: The Asphalt Paradox 
Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  the literature reports (to our knowledge) exactly  ZERO CONFIRMED OBSERVATIONS where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. 

Decomposition of Monomers, Polymers and Molecular Systems: An Unresolved Problem 2017 Jan 17
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment.


Paradoxes in the Origin of Life
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-virtually-impossible#7309


PD: It is also known that amino acids  which crystallize as racemates can   spontaneously deracemize upon sublimation. Yes,  deracemization, meaning going from being racemic   to enantiomerically pure. So nature provides  us with very simple ways to resolve several   naturally occurring amino acids, something  James does not seem to know anything about
Reply: Neither do the authors of following papers know anything about your solution. I wonder if professor Dave has solved a puzzle that lasts since Louis Pasteur discovered biochemical homochirality about 150 years ago....

Homochirality Originates from the Handedness of Helices 2020 November 20
https://pubs.acs.org/doi/10.1021/acs.jpclett.0c02144
Homochirality is a common feature of amino acids and carbohydrates, and its origin is still unknown.

On the possible origin of protein homochirality, structure, and biochemical function December 26, 2019
How L-chiral proteins emerged from demi-chiral mixtures is unknown.The lack of understanding of the origins of the breaking of demi-chirality found in the molecules of life on Earth is a long-standing problem, and models to date either focused on the RNA world hypothesis, which does not explain how RNA became chiral, or the use of chiral templates (e.g., chiral crystal surfaces). The alternative view due to Dyson conjectures that metabolism, likely from proteins, came first, followed by replication. But how did the ultimately homochiral proteins responsible for metabolism emerge from the short peptides that formed spontaneously and probably contained a mixture of D and L amino acids? The foldamer hypothesis suggests that such oligomers acted as templates to catalyze the synthesis of likely demi-chiral proteins. Other mechanisms such as molecular mutualism or the spontaneous peptide formation from aminonitriles might have been operative. By whatever means, we assume that, somehow, proteins, whose lengths range from 50 to 300 residues, were generated.
https://www.pnas.org/content/116/52/26571

Tan,Stadler. The Stairway To Life:
In all living systems, homochirality is produced and maintained by enzymes, which are themselves composed of homochiral amino acids that were specified through homochiral DNA and produced via homochiral messenger RNA, homochiral ribosomal RNA, and homochiral transfer RNA. No one has ever found a plausible abiotic explanation for how life could have become exclusively homochiral.

Homochirality, an unresolved issue
https://reasonandscience.catsboard.com/t1309-homochirality

PD: In nature there could have been millions of crystallization, and one day a pool with nearly  100% ee for L amino acids may have been washed by rain and then dried up, giving enantiomerically  pure crystals.
Reply: This is a purely baseless assertion. Unwarranted speculation without evidence to back up the claim. The problem of the origin of the first amino acid set to produce life goes, btw. far beyond just solving the question of homochirality. Many other problems are unsalved, and most likely never will because there was no selection mechanism.

Chemical evolution of amino acids and proteins ? Impossible !!
https://www.youtube.com/watch?v=1L1MfGrtk0A

https://reasonandscience.catsboard.com/t2887-chemical-evolution-of-amino-acids-and-proteins-impossible

https://reasonandscience.catsboard.com

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