Can you disprove this secular argument against evolution?

Hi forexhr and welcome.The first problem with your premise is that you are conflating evolution and abiogenesis. While that may seem to you to be a logical connection, it really is not. Evolution deals with biological life and how it changes over time and how those changes lead to the origin of new species. What you seem to be describing is the implausibility that life arose naturalistically, not the implausibility that organisms can modify existing patterns to produce novel proteins. If you are trying to describe evolution as implausible, you will need a completely different set of premises and calculations.Not all of us who accept evolution as the best explanation for the diversity of life believe in a wholly naturalistic account. I understand the question of origins in a theistic evolution context, although I don't particularly like the label. I simply do my best to learn what is true and then I accept it. If I find out later that something I hold to be true is not, I will change what I believe. This is a strange way to put it and I would argue this statement is not a good representation of a key evolutionary premise. Yes, CHONOPS are the most abundant elements of life and are required for all known lifeforms and rearrangements of those elements occur during evolution, but to put it in this way, as a fundamental premise of evolution, is well... odd at best, but seems more like disingenuous. Evolution doesn't beg that question. That is a question for origin of life theories, such as abiogenesis or creationism or ID. Evolution starts with living entities that are capable of replication. How those entities came to be is not part of evolutionary theory.But anyway, let's consider your arguments "against evolution" This is an example of how using CHNOPS is odd/misleading. Proteins don't arrange CHNOPS, they arrange amino acids (which yes, are made of CHNOPS) but I don't understand why you would need to bring up CHNOPS, why not just talk about proteins and amino acids? It seems to me that you didn't actually read these papers that you referenced. The way you are using the information you cite from them is basically dishonest.The paper "Functionally acceptable substitutions in two alpha-helical regions of lambda repressor. " does state that 10⁶³ figure, but it is in reference to the gamma-repressor folds, not all functional sequences in general. Your statement is that there are only 1 in 10⁶³ functional proteins - meaning with any function. But that is not what the paper claims.

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Nevertheless, the estimated number of sequences capable of adopting the gamma repressor fold is still an exceedingly small fraction, about 1 in 10⁶³ of the total number of possible 92-residue sequences.

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They did not determine how many "functional proteins" could possibly be formed from a 92-residue sequence, but how many ways a functional protein could be mutated and still retain its unique functional fold.Here is the paper that is not behind a pay wall if any one wants to actually read it: Functionally acceptable substitutions in two a-helical regions of gamma repressorThe second citation is just as bad. Just reading the abstract suggests that the paper does not support your position.

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We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency.

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So, your using their "data" to suggest the opposite conclusion without arguing against their position is kind of uhmmm.... shady.I challenge you to find the information you cite in that paper "maximum number of mutations or CHNOPS re-arrangements at 10⁴³". It's not there. Here is the only places where the number 10⁴³ is used.

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This gives an extreme upper limit of 410⁴³ different amino acid sequences explored since the origin of life. The contribution to this number of sequences by viral and eukaryotic genomes is difficult to estimate but it is very unlikely to be orders of magnitude greater than the 410⁴³ sequences from bacteria.

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It does not say the same thing your statement does.Here is some other quotes from the paper

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Protein sequence space is often viewed as a limitless desert of maladjusted sequences with only a few oases of working sequences linked by narrow pathways. The navigation over this space by natural selection is difficult and could take many different routes thus resulting in organisms with largely different protein compositions. This idea of contingency, if taken at the level of species, led Gould to suggest that if one was to rerun the ‘tape of life’ then evolution would take a totally different path and we, as a species, would only appear as a highly improbable accident. However, if there is any merit to our simple calculation then protein sequence analysis provides no support for the idea of contingency at a molecular level and it provides strong support for the ideas of convergence. If one was to rerun the tape, then the protein composition of organisms would be similar. Our calculation removes the almost impossibly unrealistic pressure on natural selection to navigate through protein sequence space avoiding the vast number of functionless sequences by simply indicating that most sequences have been tried are useful in some way, and that there are many possible routes to obtain proteins with desirable functions.

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Finally, we conclude that the number 20¹⁰⁰ and similar large numbers are simply ‘straw men’ advanced to initiate discussion in the same spirit as the ‘Levinthal paradox’ of protein folding rates. 20¹⁰⁰ is now no more useful than the approximate 210^1834097 books present in Borges' (1999) fantastical ‘Library of Babel’ and has no connection with the real world of amino acids and proteins. Hence, we hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.

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The paper is saying the complete opposite of what you are arguing and yet you lift a number out of it and assign it a different context and then cite the paper as support of your position.I'd be willing to bet you did not formulate this argument and the information you cited did not come from your reading of these papers.So, I would say there is not much to the argument, and it is pretty much just a lame attempt at the same old "improbability" canard.HBDEdited by herebedragons, : No reason given.

It would be better to reply to each post individually I suspect that English may not be your first language, this sentence doesn't make a lot of sense... "share of bio-functionality in organic matter composed of 92 amino acids" ? I certainly didn't argue against that since I don't know what it even means.My point about your statement regarding "1 functional in 10⁶³ protein sequences" being dishonest is that you cite a paper for the figure, but change the context. Basically, you are making the figure up... you took the number from the paper, but not the context with which the number was used. So you don't have 1/2 of your equation, you don't know what proportion of the possible sequences are functional. This is certainly NOT obvious. What does it mean to "extract from organic matter"? Are you thinking that an organism that has no protein with a gamma fold and then moves into an environment that it would be useful in and has to go to a pool of amino acids and try to assemble a 92-aa sequence that results in a functional gamma fold? Because this is an extremely unrealistic expectation of how evolution works. Which is why we don't believe that protein sequences and complex biological systems, such as hearts and kidneys, just pop up spontaneously without a predecessor.HBD

I would like to remind you that there are several posts on this thread that deal directly with your point but you are not addressing them. First point you have not addressed. You have not established the proportion of structures in a given set of possible structures that are "bio-functional." Your 1 in 10⁶³ number was improperly cited and improperly applied to your problem. You calculations do not appear to take into account the physical reality of amino acid interactions within a peptide chain. As one of your own sources showed, there are large numbers of residues within a peptide chain that can be mutated without changing the basic shape or function. That is because a relatively small proportion of residues determines the shape of the molecule. So although mathematically there may be 'x' number of possible combinations, physics constrains the real set of possibilities to a much smaller number.As a simple example, 1 oxygen atom and 2 hydrogen atoms (3 particles) when combined will produce 1 and only 1 3D structure H-O-H with a bond angle of 105^o; your calculations say there is 2 possible structures. Likewise, H₂O₂ (4 particles) will only form 1 3D structure although your math predicts 5. Same idea goes for peptides. Your calculations do not reflect reality.Another example could be a Zinc-Finger motif that has a sequence of CXX(XX)CXXXXXXXXXXXXHXXXH This is a portion of a peptide that is at least 23 amino acids long. But only 4 positions make any difference to the bio-functionality of this section. Where the 'X's are could be any of the other amino acids and where the '(XX)' could be any length of any series of amino acids. Your calculations do not take this into account.In addition, this motif exists in 100's proteins just within the human genome, which demonstrates that this section does not need to be recreated whole cloth for every new peptide, just the backbone changes. Your calculations do not take this into account. So now you want to discuss evolutionary models? The fact is, your caricature of evolutionary theory is a strawman with no resemblance to the actual theory of evolution.Case in point: No one is claiming this is how it happens. We don't suggest that molecules float around in space and randomly bump into one another and form a heart. So pointing out how the actual theory works is entirely relevant to the discussion. However, it is not necessary to argue from the position of how evolution actually works because the principles of your argument are flawed anyway. So please tell us, how many actual structures can a sequence of 92 amino acids form? Not your false enumeration concept, but actual structures based on real amino acid interactions.Then tell us what proportion of those structures has bio-functionality, and not just gamma-fold bio-functionality, but functionality to a biological system.I contend you don't know the answer to either of these questions and you are just making up very large numbers that may seem to some to indicate the implausibility of evolution. But you neither actually address evolution nor do you actually address the reality of molecular interactions. This is just the same old "tornado in a junk yard" PRATT.HBD

But you are supposing that to find a solution, an organism needs to create a new peptide from scratch and "extract bio-functionality" from some random assembly of molecules. This is what keeps being pointed out to you, evolution starts with pre-existing materials and modifies them. There is no need to create new proteins from scratch to produce functional enzymes. There are lots and lots of ways organisms deal with issues like this, many (most) involve regulation rather than protein modification. Your calculations don't take that into account either.HBD

Agreed. However, one of the references he provided in the OP, although it does not support his position and he took the cited data quite out of context, makes an interesting argument. He argues that evolution does not proceed based on contingency but rather convergence, which would be a form of directionality. Not directionality based on purpose or end-game reasoning, but based on functional necessity.

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However, if there is any merit to our simple calculation then protein sequence analysis provides no support for
the idea of contingency at a molecular level and it provides strong support for the ideas of convergence. If one was to rerun the tape, then the protein composition of organisms would be similar.

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Here is the paper again. Its a pretty easy read. How much of protein sequence space has been explored by life on Earth?HBD

Actually, no. This is what you are presupposing... that evolutionary change requires these "jumps" across vast wastelands of "junk."A single nucleotide mutation can change the affinity of a transcription factor and alter the expression of a gene. This can result in significant changes in morphological structures and fitness of the organism. Not a huge "jump" though a wasteland of "junk."Most evolutionary progress comes from changes in regulatory functions rather than mutations in significant regions of protein sequences. These changes in regulation do not require huge "jumps" through a wasteland of "junk."There are examples of genes that have been duplicated and then one of them truncated and are serving a different function than the original gene. Not a huge "jump" through a wasteland of "junk."Actual studies of the evolution of genomes shows a general step-wise modification of pre-existing genes, not huge "jumps" through a wasteland of "junk."You also make the assumption that all bio-functional structures are very, very far apart on this functional landscape. However, you have not demonstrated this to be the case. In order to do this you would need to identify all such bio-functional structures and determine distance between them. Lets say there are the bio-functional structures 'A' 'B' 'C' 'D' 'E' and 'F' in a particular sized polypeptide. You have only given the calculation for the distance between no structure and each of the final structures A, B, C, D, E, and F (which I have already pointed out is a flawed calculation to begin with), not the distance between the structures. You don't know this, and you have not demonstrated it to be true; it is an assumption you are making. You do not know if the functionality landscapes of two bio-functional structures overlap, since you have no data regarding that.Therefore, your model of bio-functionality landscapes is flawed.I also note that although you say you don't want to discuss evolutionary models but the extraction of bio-functional combinations, you ignore direct arguments against your maths and focus on those comments that refer to evolutionary models. eg. you skipped my Message 66 and instead replied to Message 67.HBD

As I pointed out several times now, you citation was bogus. Do we need to go over it again as to why it is not a valid citation in support of your premise? Ignoring responses that demonstrate why your assumption is wrong doesn't make them go away.HBD

Right, but no one (other than you) claims the we need to jump from a bacterium to a gear in a plant hopper in one step. Your faulty requirement is that each of these systems need to come into existence from nothing, poof! One day it's a bacterium the next day it's a leaf hopper insect. But you have not established this as a fact. You simply lifted the number from a paper out of context. 1 in 10⁶³ is only for a particular function. There is nothing about other functions that the arrangement might take on. I don't know how I can explain this any better to you...If I ask you how many different combinations can you get from a 90-aa protein? You would respond with something like "90!" .Then I ask how many are functional? And you respond 1 in 10⁶³ (which means there are 10⁷⁵ functional combinations - which is a lot). BUT, these are ONLY those combinations that result in a specific structural function.How many different functional structures could a chain of 90-aa produce? I don't know... and neither do you. But I would guess it's an awful lot. You have not considered those "other" functions and how far it is to each of them on your functional landscape or what proportion of all 90-aa sequences would perform a function of some kind.You keep insisting that each new protein needs to be created from scratch, but this is not the case. You can't take data from a source out of context and claim it is evidence of another context. Which is what you did with the 1 in 10⁶³ number and your claim of only 10⁴³ mutations since life began. Both taken out of context and used to support a different (opposite) context. It's not the opposite position that's the problem, it is taking the data out of context and pretending it means something it doesn't. The sources you cited do not support your claim and the way you are using the information in them is not honest. Just read the paper and you will see what I mean.HBD

You mention 3 evolutionary concepts that were "falsified" (none of which have actually been "falsified") but then go on to say: If several key evolutionary concepts have indeed been "falsified," then they are not "unfalsifiable" are they? It would be nice if creationists and IDists would look in a mirror when they start talking about the "unfalsifiable stories" of evolution.Learning new things and modifying a theory is not the same as that theory being falsified.Descent with modification applies to populations, not individuals. Each generation is modified from the previous generation. That is not about individuals. The point is that individuals themselves do not evolve. You are right in that individuals are the units being selected. But they will pass on more or less offspring to the next generation, but just that "more or less" indicates a population because "more or less" according to what? It is this passing on of more or less offspring that will change the composition of a population and will eventually lead to a new phenotype displacing a previous phenotype.Individuals themselves do not evolve. Yes, the individual must bear the burden or benefit of a specific mutation and that mutation will determine if the organism lives or dies before it can pass on its genes to the next generation. If that is what you mean by evolution, that an individual is affected by the combination of mutations it inherits and the environment it lives in, then no, that is not "evolution" that is "fitness."HBD

Well, I guess forexhr was talking about individuals evolving, so the straw man comes to life and becomes a real boy.

Oh great,now I'm getting a lecture about logical fallacies. I have several times And... The evidence of what I said is in the papers you cited and had you actually read them you would have noticed.If I were given your article to peer-review for publication, I would reject it on these grounds. Were there just one such citation problem, I would have suggested that you offer an additional citation and/or add justification why the arguments and conclusions in the cited paper were inaccurate. But with two of them and they are both foundational to your argument, there would be no way I would accept this paper for publication. This is data-mining, cherry-picking whatever you want to call it but it is dishonest.And of course, you would cry foul... discrimination against Intelligent Design. Rejection because I don't like the conclusion. But that's not the case. I accept intelligent design, even creation, just not the false pseudoscience of the "-isms."Your citations are seriously flawed, and if you can't see why I would object to them, please don't lecture me about logical fallacies.HBD

This same kind of BS was put up regarding the bacterial flagella, the eye and the human immune system. But then when plausible step-wise evolutionary pathways were proposed for each of these, the goalposts were moved to "prove that it actually DID happen."What it boils down to is "this system is so complex and we can't understand how it could have evolved therefore it must have been designed." Design is not the null hypothesis.What IDists and Creationists need to do is stop focusing on how evolution can't be true and start providing some positive evidence that design or creation IS true. Those are very different endeavors.The idea that since we don't know EVERY single step in the history of the evolution of every system in the biological world that evolution must be false is just absurd. The knowledge and unification that the ToE brings to biology makes it worth accepting, even if it is not completely right. The power of explanation it does have makes it the best theory we have to explain the diversity of life. IDism and Creationism have no explanatory power at this point, only arguments against evolution.HBD

Well, forexhr, I can see that debate with you is pointless. I can no longer waste my time in this discussion.HBD

So when you ask: What you really mean is "Can an evolutionist go back in time and watch the gradual development of complex systems over the course of millions of years?" Well I have to admit, then that the answer is "No, we can't." I guess that resolves the issue then, huh?This is a prime example of why it is a waste of time debating with you.HBD

Yea, and the sad part is, the argument is actually a fairly good one especially as compared to other arguments of the type and I thought it was going to provide a decent discussion. But obviously forexhr is not willing (or maybe even capable of - doubt he/she came up with the argument him/herself) to defend the argument against scrutiny except to say that he is right because evolution is a fairy-tail.Yaaaawwn...HBD