And the fact that these authors still are confident about the proposition that life arose via chemical mechanisms means something, too. The stuff @stcordova is posting here from Tan and Stadler’s book seems to utterly ignore these and other of the many, many other considerations that make OOL research vibrant and forward-thinking.
In fact, all the problems Sal refers to are comprehensively pointed out by and discussed by Benner and colleagues in multiple publications, and they are actively working on trying to solve them where possible.
I saw a staircase somewhere. Here is one that Fox made a generation ago:
fox1980Fig1.pdf (84.2 KB)
From Fox, S. W. (1980). Metabolic microspheres. Naturwissenschaften, 67(8), 378–383. doi:10.1007/bf00405480.
True, and to be fair, Benner in his own words:
Most of us hope that the second is the case, a **hope** that if realized would point to a very different solution to the “origins” problem. However unjustified this **hope** might be, classical research in “origins” has offered us little reason to abandon it. ... However, the concept of “paradox” should not be daunting. We expect that (**hope** that?) most of these paradoxes will be resolved by experiments that show that the theories that generate them are incorrect, incomplete, or inapplicable to particular molecular systems that just happen to have been present on early Earth.
I know these kind of threads can be frustrating but I appreciate you @Art and @Rumraket. I’m really learning stuff here. Much appreciated.
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From one of the things you found that describes the requirements for natural origin of ATP:
The half-life for hydrolysis of ATP to ADP is 6.3 years at 25 °C and neutral pH (Stockbridge and Wolfenden, 2009).
YIKES! That means even if it is made, its not going to float around for long!
It is indicated from the overviews that completion of the chemical evolution requires at least eight reaction conditions of (1) reductive gas phase, (2) alkaline pH, (3) freezing temperature, (4) fresh water, (5) dry/dry-wet cycle, (6) coupling with high energy reactions, (7) heating-cooling cycle in water, and (8) extraterrestrial input of life’s building blocks and reactive nutrients. The necessity of these mutually exclusive conditions clearly indicates that life’s origin did not occur at a single setting; rather, it required highly diverse and dynamic environments that were connected with each other to allow intra-transportation of reaction products and reactants through fluid circulation. Future experimental research that mimics the conditions of the proposed model are expected to provide further constraints on the processes and mechanisms for the origin of life.
6.3 years is quite a long time in terms of chemical reactions, why are you so shocked by that number? The ATP we produce in our bodies doesn’t hang around for years, it’s broken down to produce energy. That what it’s used for, remember?
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I have university access, but could not get the paper. But from the abstract:
Interaction of a solution of ATP with a suspension of microparticles of basic and acidic thermal proteinoids produces the dinucleotide and trinucleotide of adenine. The basic proteinoid in solution alone promotes the production of dinucleotide. The results with the particles provide a model for the origin of cellular Synthesis of polynucleotide. In association with other concepts the results strengthen the concept of cells prior to contemporary nucleic acid and protein.
This is only a tri-nucleotide. Tan and Stadler review a much longer complex in their book, so this is probably moot.
In the early 1990s, under prescribed conditions including proper concentration, temperature, pH, and appropriate catalysts, Ferris and Ertem demonstrated the formation of dinucleotides (i.e., the connection of two nucleotides) and trace amounts of longer polymers [114]. The longest observed chain contained eleven monomers, with a yield of 0.0003. However, one-third of the phosphodiester bonds were incorrect…
monomers) and the highest production of molecules with the correct bonds have been achieved in the presence of montmorillonite clay [115–118]. With purine nucleotides (adenosine and guanine), the percentage of correct phosphodiester bonds actually exceeded that of the incorrect bonds. However, the addition of each monomer to the chain comes with a probability of incorrect bonding, and one incorrect bond irreversibly destroys the homolinkage of the growing polymer, just as a train with one derailed boxcar can destroy the entire train.
Tan, Change. The Stairway To Life: An Origin-Of-Life Reality Check . Evorevo Books. Kindle Edition.
Still, basically a train wreck.
The Jungck and Fox study was published in 1973. Analytical methods were pretty crude back then, and I would bet that much longer molecules were produced, but at levels below the sensitivities of the crude (by modern standards) methods. But that’s beside the point. Antievolutionists like to claim that any sort of oligo/polynucleotide synthesis requires what are in essence modern enzymes, which could not possibly exist in the prebiotic world. Jungck and Fox refutes this claim categorically. Their study also shows how @stcordova’s claims about nucleotide structure and possible chemical reactions are pretty irrelevant.
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Thanks for the kind words.
That ATP isn’t going wait around for the other parts of the proto-cell to come to existence, unlike living things that already exist.
Is the idea that there is a constant stream of ATP from a non-biological source until life gets going?
BUT before insinuations are made that Tan and Stadler didn’t allude to issues in the paper cited, this shows Tan and Stadler were cognizant of these developments and did indeed allude to them:
Nucleotides adsorb on montmorillonite via van der Waals’interaction between the silicate layer of the montmorillonite and the purine and pyrimidine bases of the nucleotides at neutral pH (Lailach et al., 1968, Ferris, 2006). The strength of the binding of purine nucleotides is greater than that of the corresponding pyrimidine ones owing to the larger size of the planar purine ring (Ertem and Ferris, 1997).
But before that, in the paper you provided:
The polymerization of nucleotides in water is an unfavorable reaction in both thermodynamics and kinetics. The Gibbs energy necessary to synthesize a mole of phosphodiester bond is 5.3 kcal at 25 °C and pH 7 (Dickson et al., 2000). The value indicates that an equilibrium molar ratio of dimer over monomer of nucleotide is only ∼0.01% even when the monomer concentration is as high as 1M. The half-life of the phosphodiester bond of oligonucleotides is in the range of 1 hour–10 day, 2–70 s and 0.01–0.9 s at 100 °C, 200 °C, and 300 °C, respectively (Kawamura, 2004). Consequently, attempts to polymerize nucleotide in aqueous solution result in a formation of short oligonucleotides in very poor yields (Ogasawara et al., 2000). Alternative approaches proposed so far include a dry heating of nucleotides at high temperature (>100 °C; Morvek, 1967) and mixing with organic activating agents such as cyanamide and water-soluble carbodiimides (Ibanez et al., 1971a, Ibanez et al., 1971b, Ferris et al., 1989). Both approaches, however, have failed to make oligomers longer than dimers in acceptable yields (Orgel, 2004). Nucleoside 5′-polyphosphates (e.g., ATP) are high-energy phosphate esters, but are unreactive in aqueous solution.
NONE of this is very promising for OOL. It shouldn’t be advertised as progress nor breakthrough, it shows how train wrecks develop in OOL.
Why should the generation of ATP be a one time event? Do you think that the expectation was that a whole bunch of ATP was generated and then hung around for millions of years? You’re making up scenarios that no one is proposing, finding that they’re implausible, and then reacting “YIKES!” As though anyone else is supposed to be surprised.
The two quotes you mention in the rest of your comment have nothing to do with ATP generation.
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If I’m not mistaken, that was the paper you put on the table regarding ATP generation. No?
But thanks again for the paper. I can at least point out non-biological sources of ATP thanks to you.
You had only Table 3 as an explanation. But even then Table 3 assumed nucleobases, which isn’t exactly promising either:
Note that nucleobases have relatively short lifetimes in aqueous solution; the half-lives of A , C , G , T and U at 100 °C and pH 7 are 1 year, 19 days, 0.8 years, 56 years and 12 years, respectively (Levy and Miller, 1998). To accumulate nucleobases in prebiotic environments, they must be synthesized at higher rates than their decomposition.
I don’t know how feasibly a nucleobase generated from one reaction can be expected to migrate to another reaction center in any usable concentration.
BUT, Again thanks for the info on non-biological sources of ATP. That was extremely helpful. A data point that should be passed on, notwithstanding the considerations I laid out about half-lives.
A simple algebraic analysis of a steady-state process will reveal that, even if breakdown rates exceed synthesis rates, the concentrations of ATP will not be zero.
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@stcordova
Sal, I have tried on multiple occasions, and with all the sincerity I can muster, to get you to understand the Law of Large Numbers, and still you have it wrong. This will be my final attempt, after which I’m just going to let you be wrong.
The sum of values from a random sample, or the results of a random additive process, will tend to be closer to the population mean, or the process mean. If the sample is large enough we can say the sample will tend to follow a Normal distribution. LLN applies only to sums, not to individual observations from the original population (unless you know that population to be Normal).
One house of cards is neither a sample nor random. One protein is not random process. LLN refers to what we can learn about a larger population using a random sample that is smaller than the population.
Throwing a 52-card deck in the air so cards land randomly, by LLN we should expect (over many repeats of this experiment) an average of 26 face-up cards, with a standard deviation of ~3.5 (square root of 13, my assumptions are the cards land independently face-up following a Bernoulli distribution with probability 0.5). I can make a good approximate the distribution of the “face-up” counts with the normal distribution because there are a sufficiently large number of cards and “face-up” is not a rare event.
Thrown cards stacking on each other is not LLN, because it’s not an additive process. Counting face-up cards IS an additive process. There are Extreme Value laws which describe non-additive sampling processes, but the card analogy no longer works. What you should be saying is that thrown cards have a random distribution in which cards are unlikely to stack. There is no appeal to LLN.
Your usage of LLN to describe probability of proteins is wrong because it’s in no way an additive process. This should be obvious because you don’t have any numbers to describe the result of the sample and how it desribes to the population - something you should be able to do if you can legitimately apply LLN.
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Dan, I specifically cited a scientific paper that applies the law of large numbers to a component of protein evolution, namely the homochirality of it.
In case I’m not stating it explicitly enough, I’m NOT saying every aspect of protein evolution is governed by the law of large numbers, but specifically the homochirality and the homogenous linkage.
Here is the paper:
The law of large numbers determines that, in the absence of any chiral polarization, the racemic composition will always be obtained.
So, what I said is not solely my own, it is in a peer reviewed paper and other places.
Of course there are mechanisms to overcome this problem, and I stated explicitly examples like plants catabolizing D-amino acids.
To clarify again, I do not use LLN to explain the house of cards, though someone might make a not-so-elegant attempt at doing so and might be right.
Just because someone else appealed to LLN doesn’t not mean your usage is correct. Even without seeing the original, I suspect the following usage is wrong.
If Dr. Tan didn’t say LLN, there might be good reason for that.
And this …
Here can’t tell what you are saying, but LLN makes no sense in the context you are using it.
You posted here for comments and review. I try to be sincerely helpful, and you continue to argue against math. I can ask you to correct your understanding of the Law of Large Numbers, but I can’t make you do it. Enough.
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I never said it did. In the case of proteins, each amino acid that forms the protein in a pre-biotic environment can be treated as an individual Bernouli trial.
So for would-be proto-protein of 1000 amino acids, there are 1000 individual Bernouli trials, so that is a population of 1000 trials.
That corresponds to what the peer-reviewed papers was saying:
I’m not alone in referencing the Law of Large numbers in evolution of groups of chemicals.
I’m not trying to be polemic here, but I want to point out, I’m not out on a limb in my usage of LLN. If I’m wrong, I’m wrong, but I’m not out on a limb based on OOL literature that uses similar descriptions of the problems I’m highlighting.
Here is another essay that connects law of large numbers to the problem of homochirality (for the amino acid components of proteins):
This is a consequence of the energy degeneracy between the enantiomers and of the law of large numbers acting in the thermodynamic limit [45]. In summary, chiral statistical fluctuations around a stable racemic configuration cannot be amplified.
And another paper:
However, the abundance of various substances on a prebiotic Earth means effective averaging of the rates of catalytic reactions over all available catalysts for a given reaction and having the large value of enantioselectivity of the averaged rates seems questionable due to the law of large numbers.
This paper shows how the problem really bad and has been understated in the literature for YEARS.
Suppose we have a clay catalyst that makes L-amino acids. Well, there could be another catalyst that makes D-amino acids nearby. It might create a local concentration of L or D types, but then they can cross contaminate and make a mix of L and D, and that will destroy the ability of proteins to make certain structures like alpha helices and beta sheets. It certainly helps to have clay catalysis, but it’s not without its problems.
The paper I just cited looks awesome and is mostly consistent with what I, Dr. Tan and Dr. Stadler have been saying. The paper points out mistakes in previous models (and presumably papers):
Surprisingly, total enantioselectivity was “allowed” to deviate from that identically zero value in a substantial number of models and for quite a large number of years. However, since current work is not about the analysis of the previous mistakes, we will not perform any further review of that matter.
Science actually self-corrected in this case, but not in favor of naturalistic OOL. The authors were guarded in their language, but they called out some faulty science that persisted for years.
I give up.
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