Brian Miller vs. Jeremy England, Round 2

_{Denyse O'Leary

May 20, 2020

Intelligent Design, Origin Of Life}

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Round 1 was at Inference Review: A Sizzling Exchange On The Origin Of Life

England rightly states that the fluctuation theorems allow for the possibility that some mechanism could drive matter to both lower entropy and higher energy (higher free energy), thus potentially solving the problem of the origin of life, at least in theory. In contrast, I addressed the likelihood that, given the practical constraints, realistic natural processes on the early earth could generate a minimally complex cell. In that context, England indirectly affirmed the main points of my argument and thus reinforced the conclusion that an undirected origin of life might be possible in principle, but it is completely implausible in practice.
Brian Miller, “On the Origin of Life, Here Is My Response to Jeremy England” at Evolution News and Science Today

Origin of life is more fun when it is a genuine discussion rather than a speculation based on a chance finding.

See also: The Science Fictions series at your fingertips – origin of life What we do and don’t know about the origin of life.

Comments

JVL
So, is it possible that an RNA chain could form even without an enzyme? It seems to be able to with the enzyme so why not without?
And why does it have to be a protein based enzyme? An enzyme is nothing but a catalyst, and the world is full of very simple catalysts. Elements catalyze chemical reactions trillions of times every day.Ed George_{June 5, 2020
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That’s because I argued for a plausible origination for the precursor of a self-replicator. Once you have that then the real show starts.
A de facto acknowledgement of the empirical case made for ID.
You think the existing biological system could not have arisen via purely chemical processes.
No, that is not the argument I have presented.
I have presented research which suggests it could have. Perhaps you should address that research.
I already have. It's a purely dynamic reaction. The existence of dynamic reactions are not under debate. The system of symbols, constraints and semantic closure is the target you must avoid. Getting from dynamics to that system is the issue at hand. It is the issue you are avoiding in each and every comment you make.Upright BiPed_{June 5, 2020
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Uprigtht BiPed: So, no details whatsoever connecting dynamics to the necessary conditions of symbols, constraints, and semantic closure. That's because I argued for a plausible origination for the precursor of a self-replicator. Once you have that then the real show starts. There has perhaps not been a more clear recent example on these pages of an ideologue being confronted with documented science and history that they cannot refute, and transparently choosing to assume their conclusion anyway – even while being told upfront what their next move will be. And you’ll be back here again tomorrow, doing the same thing. You think the existing biological system could not have arisen via purely chemical processes. I have presented research which suggests it could have. Perhaps you should address that research.JVL_{June 5, 2020
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EugeneS: I am referring to the differences between a search in a parametric space and a random walk. The differences between the two are large. Evolution does not pursue future function. It cannot search for it either. It can just stumble upon it randomly. It can only select from among existing functions. I hope you can see already what challenge you are up against. I am also saying that it's possible for biology to be pursuing many avenues at the same time! It's not searching for anything, it's just expanding. And the expansion flows along viable lines. If you can’t explain the starting point, it is no use discussing what may or may not follow. I was presenting a passible starting point. And surely not all peaks, but only available ones: reachable and, remember, selectable. There is a limited number of organisms on earth and there is a limited amount of time available to evolution. Again, the amount of functional information explainable by evolution is dwarfed by comparison with observed biological functional complexity. The organisms that arose were not a goal. You are making the sharp-shooter fallacy. The chance of arriving at a particular goal is minuscule, the chance of arriving at a goal is much greater.JVL_{June 5, 2020
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. So, no details whatsoever connecting dynamics to the necessary conditions of symbols, constraints, and semantic closure. There has perhaps not been a more clear recent example on these pages of an ideologue being confronted with documented science and history that they cannot refute, and transparently choosing to assume their conclusion anyway - even while being told upfront what their next move will be. And you'll be back here again tomorrow, doing the same thing.Upright BiPed_{June 5, 2020
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JVL
Remember, when biology finds something that works it tends to pursue it even if it’s not optimal.
I am referring to the differences between a search in a parametric space and a random walk. The differences between the two are large. Evolution does not pursue future function. It cannot search for it either. It can just stumble upon it randomly. It can only select from among existing functions. I hope you can see already what challenge you are up against.
Evolution can be climbing all peaks at the same time!!
If you can't explain the starting point, it is no use discussing what may or may not follow. And surely not all peaks, but only available ones: reachable and, remember, selectable. There is a limited number of organisms on earth and there is a limited amount of time available to evolution. Again, the amount of functional information explainable by evolution is dwarfed by comparison with observed biological functional complexity.EugeneS_{June 5, 2020
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EugeneS: It is possible to estimate the number of states an evolutionary random walk can visit. It is O(2^140) at best. It is also possible to estimate independently, the amount of functional information in biological systems. There is a many orders of magnitude mismatch between the two… Which evolutionary random walk? Remember, when biology finds something that works it tends to pursue it even if it's not optimal. Search assumes a fitness function and control over system states by fitness function gradients. Evolution does not have that. All evolution has is a random walk. It can climb peaks but because the fitness landscape is rugged, evolution stagnates in local peaks. However, there is evidence suggesting that extant biological systems are globally optimized. Evolution can be climbing all peaks at the same time!! Life spreads out wherever it can. Again, I think of it like water, it seeps and flows everywhere it can.JVL_{June 5, 2020
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Upright BiPed: You do not know this. You have no test to establish this. It is merely your non-falsifiable assumption against universal evidence to the contrary. It is just as I predicted from the start of this conversation; you are forced by documented science to defend your position by assuming your conclusion. Research seems to have shown that the raw materials for building RNA combined with an enzyme will create a strand of genetic material which can lead to some kind of self-replicator (which may depend on that same enzyme but it already exists). Enzymes accelerate chemical reactions but the reactions might happen anyway. Probably much less often. That is all science. Why not pursue that avenue of investigation to see if more steps can be added to those? That's the nature of research is it not? To see if something is possible. Dr Pattee seemed to think it was; he didn't warn against it anyway. I'm in favour of trying stuff to see if it works. There were people in the 19th century that said it was impossible for humans to survive travelling more than 50 mph; their logic told them so. They were wrong because one of their underlying assumptions was wrong. Logic is great but if one of your axioms doesn't hold then . . . .JVL_{June 5, 2020
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JVL
I think, eventually, unguided processes tend to check out every nook and cranny.
This is wishful thinking, I am afraid. It is possible to estimate the number of states an evolutionary random walk can visit. It is O(2^140) at best, which is an equivalent of 140 functional bits max. It is also possible to estimate independently, the amount of functional information in biological systems. There is a many orders of magnitude mismatch between the two... Search assumes a fitness function and control over system states by fitness function gradients. Evolution does not have that. All evolution has is a random walk. It can climb peaks but because the fitness landscape is rugged, evolution stagnates in local peaks. However, there is evidence suggesting that extant biological systems are globally optimized.EugeneS_{June 5, 2020
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ET: Spiegelman’s Monster is not a self replicator. And it existence demonstrates that nature tends towards the more simple. Alright, that particular example probably depends on the enzyme but, again, an enzyme just accelerates a chemical reaction. So, is it possible that an RNA chain could form even without an enzyme? It seems to be able to with the enzyme so why not without? I think it's worth doing the research. I think it's exciting! I'd like to know. I'm not going to prejudge the work. I'm not going to condemn it to failure util someone checks it out thoroughly.JVL_{June 5, 2020
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JVL: people are testing bits of possible paths that will get you there.
You do not know this. You have no test to establish this. It is merely your non-falsifiable assumption against universal evidence to the contrary. It is just as I predicted from the start of this conversation; you are forced by documented science to defend your position by assuming a non-falsifiable conclusion. This is your defense against science.Upright BiPed_{June 5, 2020
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ET: You don’t have a mechanism capable of producing the necessary enzyme. Enzymes encourage chemical reactions but the reaction would happen anyway, just more slowly. So . . . you probably don't even need the enzyme. Archaeology and forensic science prove that they don’t. Those aren't studying unguided processes though. Also, you should read about Spiegelman’s Monster. If you're referring to the fact that mostly it seems to shorten a genome then I still say it's a self-replicator and the question is can such a thing arise without the supposed precursors. And it sounds to me like . . . yeah, maybe it can. Maybe chemistry can create a self-replicator upon which natural selection can act.JVL_{June 5, 2020
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JVL:
As was stated in the quote Qbeta replicase (which is an enzyme and contains no genetic material) was put into a mix of the building blocks of RNA and was able to synthesise RNA which was then able to form into something like Spiegelman’s Monster which is a self replicator.
'Spiegelman's Monster is not a self replicator. And it existence demonstrates that nature tends towards the more simple.ET_{June 5, 2020
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JVL- You don't have a mechanism capable of producing the necessary enzyme.
I think, eventually, unguided processes tend to check out every nook and cranny.
Except for every case in which they don't. Archaeology and forensic science prove that they don't. Also, you should read about Spiegelman's Monster.ET_{June 5, 2020
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AS, more of the notion that there is a convenient vast continent of smoothly varying function, allowing hill climbing. Only, the evidence is for deeply isolated islands of function just on requisites of complex multipart coherent function. Where, remember life has to invent a machine code and execution machinery out of molecular noise on these models. Patent implausibility to maximal degree. It is ideological imposition so it MUST have happened and any questioning is pounced on that has locked in what Lakatosian thinking would identify as a degenerate research programme/paradigm. KFkairosfocus_{June 5, 2020
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"life continues to expand into every niche" I'm not sure what this means, but it's more poetry than it is science. Andrewasauber_{June 5, 2020
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JVL, consider very large config spaces. The problem is not to climb a mountain but to get to a shoreline of function in a vast sea of non function. As was pointed out over and over, for years; functionality comes in isolated islands as very specific combinations are required to get coherent functionality, and vastly more possibilities will be non functional. Dynamic systems tend to have low contingency if dominated by mechanical necessity and stochastic disturbances do not provide resources to search config spaces of 500 - 1000+ bits. . It is obvious that there is not a genuine discussion here at this point. I am just noting unresponsiveness to key issues. That is the root problem. KFkairosfocus_{June 5, 2020
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EugeneS: You can’t get through the dynamically changing maze without knowledge, foresight, planning and control. The way I see it, life continues to expand into every niche. The ones that are more productive generate more generations to continue from their locations while others may be exploring a different path. It's like filling a maze with water. Eventually an exit is found with no foresight or plan or control.JVL_{June 5, 2020
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Asauber: With Natural Selection, it’s not even climbing. It could be going sideways, down, or nowhere. I think, eventually, unguided processes tend to check out every nook and cranny. The productive options tend to leave more offspring a bit further down a particular path than those a few generations back and start their 'search' from a different point.JVL_{June 5, 2020
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JVL
I think it’s more like climbing a mountain and every time a step is shown to be possible a path up the entire thing becomes more plausible.
On the contrary! The more is known about how cell operates, the more desperate the case becomes for naturalists. The moon is getting further away from the person climbing a tree. You can't get through the dynamically changing maze without knowledge, foresight, planning and control. Even to climb a mountain one needs planning, equipment, a map, and skill. The blind watchmaker paradigm has ended up in a fiasco.
when progress is being made
Oh, boy.EugeneS_{June 5, 2020
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"I think it’s more like climbing a mountain" With Natural Selection, it's not even climbing. It could be going sideways, down, or nowhere. Andrewasauber_{June 5, 2020
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Upright Biped: your cite appears to be a complete air ball. There is no claim here against dynamic processes. Take a molecule out of an extant cell, place it in a man-made environment and feed it raw materials. It will do what it does, The raw materials can be found outside of a cell, perhaps not in the same concentrations but they are 'around'. If the enzyme (which contains no genetic material) can possibly generate outside of a cell then you have a possible generation point. And an enzyme is just a chemical molecule. Again, origin of life research checks out little tiny steps like this and then checks possible steps on either side. If one of the steps is highly improbable then that bit of path becomes less likely. I think such work is exciting and I don't think it's time to throw in the towel when progress is being made. The step from this to a self-replicator has been shown so it seems worth seeing if the path continues in the other direction. Except of course, we already know its possible to climb a mountain, so lets just stick with reality: you have to get from dynamics to a semantically-closed system of symbols and constraints. And people are testing bits of possible paths that will get you there. Surely it's worth doing that research? Dr Pattee even had suggestions of where researchers should focus their attentions.JVL_{June 5, 2020
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I think it’s more like climbing a mountain
Except of course, we already know its possible to climb a mountain, so lets just stick with reality: you have to get from dynamics to a semantically-closed system of symbols and constraints.Upright BiPed_{June 5, 2020
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. JVL, your cite appears to be a complete air ball. There is no claim here against dynamic processes. Take a molecule out of an extant cell, place it in a man-made environment and feed it raw materials. It will do what it does, And so?Upright BiPed_{June 5, 2020
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ET & Upright BiPed As was stated in the quote Qbeta replicase (which is an enzyme and contains no genetic material) was put into a mix of the building blocks of RNA and was able to synthesise RNA which was then able to form into something like Spiegelman's Monster which is a self replicator. It's a very interesting experiment. The entire paper is available at the link provided. The point being that with the right combination of raw materials and the right enzyme you can get strands of genetic material without having any present. EugeneS: OOL research is like someone climbing a tree and saying: I am getting closer to the moon, with every step. Yes, closer but it does not count because by climbing a tree you will never reach it. I think it's more like climbing a mountain and every time a step is shown to be possible a path up the entire thing becomes more plausible.JVL_{June 5, 2020
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JVL Just as an illustration, the challenge that naturalists are facing is akin to this with the exception that in reality it is dynamic and more complex. Trying to explain the end result as just an interplay of selection and variation is a fool's errand. You need foresight and other things which the naturalistic toolkit does not have.EugeneS_{June 5, 2020
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. JVL, this has been a discussion about the necessary conditions of autonomous open-ended self-replication, as established over documented history -- from abstract theory and logic, to published prediction, to experimental confirmation, followed by complete physical analysis. Please, do tell us – how exactly does the experiment you reference have any impact on obtaining the required conditions for autonomous open-ended self-replication? Can you point to any details of actual substance?Upright BiPed_{June 5, 2020
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JVL:
The paper was trying to see if one particular step in a long process could have occurred.
That is the very thing! One particular step... The laws of nature (natural regularities) can explain how ink flows on paper but they are just not enough to explain the meaning of my comment. This is because the meaning of it is not reducible to physicality. As simple as that. It is possible to instantiate logic and meaning into physicality by arranging boundary conditions on the motion of matter in the system. But that requires foresight and planning. This irreducibility can easily be demonstrated: semantically the same message can be conveyed by entirely physically different means: as a gesture, with ink and paper, by voice or by RNA, for that matter. A bit of correction on your word usage: process: a series of actions or steps taken in order to achieve a particular end. Nature does not do things like that because it simply lacks vision or foresight. It cannot process anything. Unfortunately, scientific terminology has adopted a misnomer, a random process, which, strictly speaking, is no process at all. OOL research is like someone climbing a tree and saying: I am getting closer to the moon, with every step. Yes, closer but it does not count because by climbing a tree you will never reach it.EugeneS_{June 5, 2020
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JVL:
Are you sure that bacteriophage Qbeta and Qbeta replicase are the same thing?
I didn't say they were. I cut an pasted what you posted.
In your opinion.
Nope, it's a fact. You can't even provide a testable hypothesis for unguided evolution with respect to producing protein machines.
What about the people who started out believing some kind of ID and then changed their minds?
What about them?ET_{June 5, 2020
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ET: You cannot use what needs to be explained- bacteriophage Qbeta replicase- to do the explaining. The paper was trying to see if one particular step in a long process could have occurred. It was not trying to explain the whole kit-and-kaboodle. Are you sure that bacteriophage Qbeta and Qbeta replicase are the same thing? The people who say that ID has not “proven” its case are the same people who don’t have any science to support their own claims. In your opinion. Others think differently. All they have is their dislike of ID. And that is due to personal biases. What about the people who started out believing some kind of ID and then changed their minds? What would have caused that?JVL_{June 5, 2020
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