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 enzymes. All 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.”
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 enzymes. All 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.”
Last edited by Otangelo on Thu May 06, 2021 9:53 am; edited 3 times in total
