Thursday, March 15, 2012

These New Protein Findings Might be a Problem Even According to the Evolutionist’s Own Numbers

The BSC4 gene in Saccharomyces cerevisiae, or baker’s yeast, was interesting to researchers because of its leaky stop codon but then it became more interesting because it only showed up in that one particular organism. The BSC4 gene is yet another example of a species-specific, or de novo, protein-coding gene. In this case, the protein appears to be involved in DNA repair and helping the organisms cope with nutrient-poor environments. And if this protein is anything like a typical protein, then evolution, even by the evolutionist’s own reckoning, would not be able to construct such low-probability designs. The BSC4 gene must have been constructed in only the past 10 million years or so. And evolutionists cannot appeal to speculative mechanisms. No exon shuffling, duplication, retroposition, fusion, fission or whatever for this gene. It must have arisen the old fashion way, by an evolutionary search through sequence space via random mutations. Is this feasible? The important numbers here are the number of attempts that are possible, and the number of attempts that are required. The two might not add up.

Evolutionists have estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit is 10^43 (a one followed by 43 zeros) obtained by multiplying 10^30 (cells in the world) by 10^4 (new genes generated per cell per year) by 10^9 (years). The lower limit is 10^21 obtained by multiplying 10^9 (bacteria species in the world) by 10^3 (unique sequences per species) by 10^9 (years).

While these estimates are incredibly optimistic for several reasons (even the evolutionists admit the upper limit is an “extreme upper limit”), we’re going by the evolutionist’s numbers for the moment. They need to be adjusted, however, because those estimates are for the entire history of the world and for all the species. For de novo genes such as BSC4, we’re dealing with a single species (with an effective population size of about ten million), and only about ten million years. In this case the upper and lower limits become 10^18 and 10^10, respectively.

And the numbers are even smaller for de novo genes found in humans. The time allowed goes down to about 5 million years and the effective population size goes down by at least two orders of magnitude, to about 10^5. So in this case the upper and lower limits become 10^14 and 10^10, respectively.

Studies have shown that even this many searches does not produce much. One study found that with 10^12 attempts all that was produced were a few proteins with weak ATP binding.

And for typical proteins, even these optimistic estimates of the number of attempts fall short by more than 50 orders of magnitude. And these deficits are according to the evolutionist’s own estimates of how many attempts would be required to find a typical protein. One study concluded that 10^63 attempts would be required for a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences.

Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required. In that case the protein was about the same length as that encoded by BSC4, but it was only a part of a larger protein which otherwise was intact, thus making the search easier.

The numbers don’t add up. The evolution of de novo genes can only count on from 10^10 to 10^18 attempts (and that’s optimistic). If the new proteins are anything like typical proteins, then these numbers show astronomical problems.

78 comments:

  1. Related notes:

    Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references
    http://www.vimeo.com/17135166

    A survey of orphan enzyme activities
    Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles.
    http://www.biomedcentral.com/1471-2105/8/244

    Age doesn't matter: New genes are as essential as ancient ones - December 2010
    Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked."
    http://www.sciencedaily.com/releases/2010/12/101216142523.htm

    New genes in Drosophila quickly become essential. - December 2010
    Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
    http://www.sciencemag.org/content/330/6011/1682.abstract

    Human Gene Count Tumbles Again - 2008
    Excerpt: Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences.
    http://www.sciencedaily.com/releases/2008/01/080113161406.htm

    Study Reports a Whopping "23% of Our Genome" Contradicts Standard Human-Ape Evolutionary Phylogeny - Casey Luskin - June 2011
    Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)
    http://www.evolutionnews.org/2011/06/study_reports_a_whopping_23_of047041.html

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  2. The BSC4 gene is yet another example of species-specific, or de novo, genes. The problem is that evolution, even by the evolutionist’s own reckoning, would not be able to construct such low-probability designs.

    From the quoted paper in the journal Genetics.

    Overall, our study identified and characterized a whole-gene de novo evolution case in S. cerevisiae for the first time. This gene originated from a previously noncoding but transcribed sequence.

    So, in the quoted case, de novo did not signify anything mysterious or problematic.

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    Replies
    1. Pedant:

      So, in the quoted case, de novo did not signify anything mysterious or problematic.

      Evolution is a given in normal science. At issue is not whether it evolved, that is a fact, but how it evolved. Their concern is to demonstrate that the gene is genuinely de novo.

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    2. Pedant:

      This gene originated from a previously noncoding but transcribed sequence.

      I suspect your thinking is as follows: Some already 'present' gene, that doesn't code for a protein, and hence is invisible to us, changes in some way, perhaps a very minor way, and this then begins to code, and is now seen.

      But, it can be asked: Where did the non-coding gene come from? If a similar type analysis/scenario is assumed to apply to the progenitor, then this process should walk itself back. Well, back to what? Where did the first "noncoding" gene come from?

      As far as I can see, neo-Darwinism has no answer for this.

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    3. CH: Evolution is a given in normal science. At issue is not whether it evolved, that is a fact, but how it evolved. Their concern is to demonstrate that the gene is genuinely de novo.

      I won't even bother pointing out exactly how evolution is a "fact" misrepresentation. We've been over this before.

      However, I will provide an illustration as to why we conclude these genes are genuinely de novo, rather than conclude this was a falsification of evolutionary theory.

      Imagine you brought three boxes of cupcakes to a birthday part. The party is winding down and you noticed the first box contains two cupcakes while the other two only contain one. You decided to consolidate the cupcakes by taking one from each of the two boxes, with you then discard, then place these two cupcakes in the first box, which already contained two.

      However, just as you close the lid, you realize you didn't get a chance to try of the cupcakes. To your surprise, when you open the lid again, you find only three cupcakes.

      Since you expected to find four cupcakes, one of your assumptions are wrong. So, my question is, where would you start in identifying this wrong assumption, and why?

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    4. Chocolate, of course.

      While I'm using cupcakes in this illustration, you could substitute them with anything that fits in a box.

      What's important is, when presented with this type of scenario, what assumption would you question first, and why would you start there, rather than somewhere else.

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    5. The original configuration of chocolate (iced?)cupcakes was box 1 = 2 , box 2 =1, box3 = 0, you said " the other two contain only contain 1" in total not each. The Jesuit education pays off again. Good choice of flavor

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    6. Scott, you didn't understand what CH said. He specifically said: "At issue is not whether it evolved, that is a fact, but how it evolved." What were interested in is whether this gene was build by chance or design. In order for you to prove that it was built by chance you need to cite some mathematics that prove that chance can stumble upon such a gene in the time given. Let's see some real science from you.

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    7. In your cupcake example, you're just assuming that the new cupcake got there by chance. In the real world cupcakes are designed by humans.

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    8. Scott, I encourage you to discuss this issue with me via skype. my skype id is kylefoley202

      Delete
    9. Kyle: Scott, you didn't understand what CH said.

      Didn't I? Here's a quote from CH….

      CH: Evolution is a given in normal science. At issue is not whether it evolved, that is a fact, but how it evolved. Their concern is to demonstrate that the gene is genuinely de novo.

      Again, my thought experiment is designed to illustrate why we conclude these genes are genuinely de novo, rather than conclude this was a falsification of evolutionary theory.

      You have a box that contains two items. You add two more items, close the box, then open it again and find three items. Since you assumed you would find four, one of your assumptions are wrong.

      Which assumption would you question first? Why would you start with this particular assumption, rather than some other assumption?

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    10. In other words, given the observations in this scenario, you've just made an observations that falsifies one of your assumptions.

      Which assumption would you consider this a falsification of? Why does it represent a falsification of *that* particular assumption, rather than falsifying *other* assumption in this very same scenario?

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    11. Scott, you're not an honest debater. You didn't even answer my challenge as to what evidence can you present that will establish your assertion that these new genes arose due to chance processes. You refused to provide us with mathematical rigorous evidence to support your thesis.

      If you have the courage of your convictions then you will discuss this matter with me over skype. Oral debate gives on a chance to discuss a broad range of issues, written debate allows one to discuss a few issues in great detail. Both have their advantages. If you're really interested in what I have to offer, just as I am interested in what you have to offer, then you will take up my challenge.

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    12. Kyle,

      I'm addressing an aspect of CH's OP which is relevant as to how probability is being used in regards to de novo proteins. The observations and means by which the probability was calculated is not in question. What is in question is, what rational conclusion should we reach from them?

      As such, my question is designed to illustrate how we rationally make theses types of decisions.

      On the other hand, your argument appears to be hand waving over large numbers in a scientific paper. This number is so "big" evolution must be false!

      But this puts cart before the horse. My question comes before your question, not merely because I posted it first, but because your question depends on it.

      Nor are we debating the observations or how the probabilities in this paper were calculated. We're debating what these observations and probabilities signify, if we approach them rationally.

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    13. "What is in question is, what rational conclusion should we reach from them? "

      exactly, are these genes due to chance or design. what evidence can you put forward that would support your assertion that they're due to a combination RM + NS? so far you have put none forward and have given me no reason to believe that these genes are due to RM + NS.

      "On the other hand, your argument appears to be hand waving over large numbers in a scientific paper. This number is so "big" evolution must be false! "

      Exactly, these numbers are so big therefore these genes are not due to RM + NS. Why do you believe that that is a faulty form of reasoning? Right now, all you have is an argument from ridicule. What you're basically saying is: it is ridiculous to think that big number falsify a position, therefore it's false. I need more from you than an argument from ridicule. As a Darwinist, you continually rely on ridicule to buttress your position.

      "We're debating what these observations and probabilities signify, if we approach them rationally."

      This statement is true, but it does not support Darwinism.

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    14. Apparently the Jesuits weren't successful

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    15. kyle foley

      Exactly, these numbers are so big therefore these genes are not due to RM + NS.


      No, that is not true. The "big numbers" CH sites are ones he took more or less at random from other scientific papers on different topics. They aren't relevant in the least to the OP topic, and don't in the least represent any insurmountable barrier for ToE. CH only offers them in the hopes of convincing ignorant laymen who don't understand the technical details of the science involves.

      Indeed, if CH's argument had any validity at all he could write them up and publish them in any major scientific journal, guaranteeing himself consideration for a Nobel Prize. But they don't, and he knows they don't. Like virtually all of CH's spin on science, he's just engaging in cheap rhetorical tricks.

      Why do you believe that that is a faulty form of reasoning? Right now, all you have is an argument from ridicule. What you're basically saying is: it is ridiculous to think that big number falsify a position, therefore it's false.

      No, we're saying bogus irrelevant big numbers don't make an argument just by being big.

      I need more from you than an argument from ridicule. As a Darwinist, you continually rely on ridicule to buttress your position.

      The problem is, science has known for decades that these "big number" arguments are 100% scientifically worthless. Still, Creationists keep trotting them out over and over and over again. After a while the only proper response to such inanity is ridicule.

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    16. Kyle,

      Cornelius is confusing two different kinds of unknowability. And he's doing so because he's either confused about evolutionary theory (which seems unlikely) or he's misrepresenting it.

      The first kind of unknowability are scenarios where the outcome is completely random. An example of this is Russian Roulette. As long as you know all of the possible outcomes, such as how many chambers are in the gun, which chambers contain bullets and how many times the trigger will be pulled, we can use probability to make choices about it. For example, if for some horrible reason, one had to choose between different versions of Russian Roulette with specific yet variable number of chambers, bullets and trigger pulls, one could use game theory to determine which variation would be most favorable.

      However, evolutionary theory isn't "just random". This is the fallacy in Cornelius' argument and a common misrepresentation made here by by creationists all the time.

      If the knowledge of how to build the biosphere was created over time, the ways in which life could have adapted would reflect the specific options that had been conjectured at each step. Specifically, the options by which an organism had at it's disposal at any time depended on what adaptations it could apply any particular environment. And these adaptations would have depended on which knowledge had be conjectured at each step.

      Unless we know if the gene for this protein started out from a specific existing protein, rather than a non-coding sequence which is current unavailable to us, one cannot use the probability numbers in these papers to claim evolution is unlikely, therefore false.

      As such, this is simply more hand waving, which we see regularly here on a regular basis.

      Now, Cornelius might not agree with the details of evolutionary theory. But this doesn't make statements such as These New Protein Findings Might be a Problem Even According to the Evolutionist’s Own Numbers any less disingenuous.

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    17. Thorton,

      "The "big numbers" CH sites are ones he took more or less at random from other scientific papers on different topics. They aren't relevant in the least to the OP topic, and don't in the least represent any insurmountable barrier for ToE."

      Well, if these numbers don't represent a barrier to ToE then let see some mathematical analysis of why that's true. All you have is a mere assertion that CH numbers are false. You present no counterproposal for a more plausible scenario. You have failed to produce positive evidence that genes are the result of RM + NS.



      "we're saying bogus irrelevant big numbers don't make an argument just by being big."

      Again, you don't show how they are irrelevant, you just assert it. You need to understand what makes a proper scientific argument and what doesn't.

      Delete
    18. "If the knowledge of how to build the biosphere was created over time, the ways in which life could have adapted would reflect the specific options that had been conjectured at each step. Specifically, the options by which an organism had at it's disposal at any time depended on what adaptations it could apply any particular environment. And these adaptations would have depended on which knowledge had be conjectured at each step."

      There is nothing in this argument that proves that BSC4 arose due to RM + NS. Further, there is nothing in this argument that even attempts to prove that a new trait can be built through darwinian processes. Staurt, each time you post something you evade the elephant in the room: Darwinists have never given a detailed for any gene arising through RM + NS. I have asked you about 3 times to point to a detailed attempt by Darwinists to show how each amino acid provided a definite selective advantage to the organism.

      "Unless we know if the gene for this protein started out from a specific existing protein, rather than a non-coding sequence which is current unavailable to us, one cannot use the probability numbers in these papers to claim evolution is unlikely, therefore false."

      I'd like to hear a good reason from you as to why. Right now, you have nothing more than a mere assertion. Just do the math. If the gene took less than 10 million years to arise. The point is the even darwinists accept mathematics as a means of determining whether or not chance can build genes. As CH pointed out
      http://www.ncbi.nlm.nih.gov/pubmed/2199970
      one study asserted that 10^63 attempts could build a relatively short protein (25 amino acids) which is probably even wildly optimistic, moreover, almost no proteins are that short. In the human most proteins run into 400 aa and humans have between 200 and 600 human specific genes. So your assertion that probability cannot be used to determine whether or not genes are due to chance is not even supported by darwinists.

      This is my challenge to you, Scott, either admit that darwinists have never given a detailed of any of the 10^12 proteins thought to exist, or provide a detailed account yourself. And when I say a detailed account, I mean show how each aa mutation provided a definite selected advantage to the organism.

      Here's something else I want an answer for. If humans have on average between 40 and 80 and if the average gene is 400 aa long, then why do you even think that a new gene can be built through chance. There are not even enough mutations to make a new gene in one generation and the odds of all those 80 mutations falling on the same portion of the genome are vanishingly small.

      Delete
    19. Kyle,

      It's unclear what part of my argument you're disagreeing with, as you have not addressed it.

      For example, do you disagree there are different kinds of unknowability? Or do you disagree as to what type of unknowability the evolution of *any* protein represents?

      Specifically, the question being asked in these papers represents one kind of unknowability in that that all of the choices are known. They are comparing a specific destination protein with a specific number of start proteins known to exist in common ancestors. As such, the use of probability is valid in categorizing these proteins as de novo.

      However, in regards to the question if any particular protein evolved at all, these probability calculations are invalid since not all start options are necessarily available to us. As such, It's a different kind of unknowability. Nor is it clear that this particular destination is the only type of protein could play the same role in some other organism, etc.

      So, until you clarify your position on these aspects of my argument, it's unclear how we can make progress.

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    20. kyle foley

      Well, if these numbers don't represent a barrier to ToE then let see some mathematical analysis of why that's true. All you have is a mere assertion that CH numbers are false. You present no counterproposal for a more plausible scenario. You have failed to produce positive evidence that genes are the result of RM + NS.


      RobertC already provide some detail scientific analysis on why CH's number are bogus in his post of Mar 15, 2012 03:15 PM below.

      You're new here, but the rest of us have seen CH trot out these same BS numbers for years now. His over-the-top claims about them have been conclusively show to be both dead wrong and deliberately misleading. Again, if CH could back up his remarkable claims he'd be a shoo-in for a Nobel Prize, but he can't. Right now the only prize he gets is a paycheck from the Discovery Institute for pushing their lies.

      Delete
    21. Kyle Foley

      Here's something else I want an answer for. If humans have on average between 40 and 80 and if the average gene is 400 aa long, then why do you even think that a new gene can be built through chance. There are not even enough mutations to make a new gene in one generation and the odds of all those 80 mutations falling on the same portion of the genome are vanishingly small.


      Evolution doesn't think or say the gene was built through chance. The evidence shows it evolved over time as the result of a long-term iterative feedback process involving genetic mutations being filtered by selection, with the beneficial (and neutral) ones being kept for subsequent generations.

      Why won't Creationists bother to learn even the most fundamental things of the science they're attacking?

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    22. Scott,

      What you have is an argument for agnosticism regarding the origin of genes, not an argument for Darwinism. If you're willing to give up Darwinism and assert that it cannot be known that genes are due to chance or not chance, then we can move further, otherwise, it is dishonest of you to move the goal post from defending Darwinism to defending agnosticism.

      In any case we do not need to come up with exact probabilities for the origin of genes by darwinian processes. We only need to have a rough idea of what the odds are to conclude if the construction of genes requires knowledge of the external world, then intelligence is a better explanation. As CH pointed out, Darwinists themselves attempt to pin these numbers down, so currently your argument is in tension with the darwinist community. Are you willing to address this point? Or will you ignore it and make another point?

      We humans, for example, have no way of knowing the probability that Obama does not know a word of English and is just getting lucky. After all, there is nothing that violates the laws of physics when a human randomly speaks coherent words from a language that they do not understand. We cannot know the exact probability but we can conclude that the odds are greater than 1 in 10^150 which is above Dembski's universal probability bound.

      As CH pointed out many scientists have attempted to show just how difficult constructing a functional protein is, which makes sense since often a protein will need to create a hydrophobic shield so that water cannot enter into the binding site and destroy the molecule that the protein is splitting. Creating a hydrophobic shield requires that all amino acids be arranged such that water is kept out.

      1. building a hydrophobic shield, requires knowledge of the properties of water
      2. chance has no knowledge
      3. the law of NS has no knowledge
      4. therefore intelligence is the best explanation.

      I invite you to discuss this issue with me through skype. You are contradicting yourself. You desire to discuss darwinism and you do not desire to discuss darwinism. My inference is that you lack the courage of your convictions.

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    23. [i]Evolution doesn't think or say the gene was built through chance. The evidence shows it evolved over time as the result of a long-term iterative feedback process involving genetic mutations being filtered by selection, with the beneficial (and neutral) ones being kept for subsequent generations.[/i]

      Of course, I'm familiar with Darwinian dogma. That post is just an assertion, let's see some evidence.

      [i]You're new here, but the rest of us have seen CH trot out these same BS numbers for years now. His over-the-top claims about them have been conclusively show to be both dead wrong and deliberately misleading. Again, if CH could back up his remarkable claims he'd be a shoo-in for a Nobel Prize, but he can't. Right now the only prize he gets is a paycheck from the Discovery Institute for pushing their lies.[/i]

      This is just a bunch of name calling and assertions. You present no evidence. Thorton, it's clear that you don't understand what an argument is. All you engage in is name-calling. I have concluded therefore that you have nothing to teach me and debate with you is fruitless. Your future posts will be ignored.

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    24. Thorton,

      "Evolution doesn't think or say the gene was built through chance."

      What part of random mutation do you not understand? Darwinism asserts that mutations are random, hence chance. Almost all chance processes act within the bounds of law, they are still chance. Take for example the movements of the molecules of gas. The molecules can still be described with laws, eg, their protons remain held together and their electrons change their orbits according to laws, they also cannot travel faster than the speed of light, however, their movement is still chance.

      It's the same with NS, mutations are random and they act within the context of law, eg, if the gene is disfunctional then the organism often cannot reproduce. At rock bottom, darwinian processes are still chance-like.

      That is something that darwinists have a very difficult time understanding because they know that the public does not attribute creative power to randomness.

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    25. Kyle,

      The topic of the post is These New Protein Findings Might be a Problem Even According to the Evolutionist’s Own Numbers.

      My comments in this thread are regarding the validity of these numbers in regards to evolutionary theory as a whole, rather than the context used in the actual papers.

      if you like to point out where you disagree with the argument I presented, then we can make progress. Otherwise, it would seem continued discussion will be fruitless.

      For example, you wrote: If you're willing to give up Darwinism and assert that it cannot be known that genes are due to chance or not chance, then we can move further, otherwise, it is dishonest of you to move the goal post from defending Darwinism to defending agnosticism.

      However, evolutionary theory does claim that genes are due to mere chance. As such, it represents a different kind of unknowability. Again, I illustrated this in length in this thread, among others.

      The knowledge used to build the biosphere, as found in the genome of organisms, was created by a form of conjecture and refutation. Specifically, conjecture, in the form of genetic variation, and refutation, in the form of natural selection.

      So, again… do you disagree there are different kinds of unknowability? Or do you disagree as to what type of unknowability the evolution of *any* protein represents?

      I can't tell as you simply seem to have no criticism. Rather, you just keep repeating the same assumption as if everybody knows it's true, therefore it's true.

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    26. Correction: However, evolutionary theory does NOT claim that genes are due to mere chance. As such, it represents a different kind of unknowability. Again, I illustrated this in length in this thread, among others.

      Delete
    27. "The topic of the post is These New Protein Findings Might be a Problem Even According to the Evolutionist’s Own Numbers. My comments in this thread are regarding the validity of these numbers in regards to evolutionary theory as a whole, rather than the context used in the actual papers."

      It's the Darwinists that have cooked up the following numbers. Let me quote CH: Evolutionists have estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit is 10^43 (a one followed by 43 zeros) obtained by multiplying 10^30 (cells in the world) by 10^4 (new genes generated per cell per year) by 10^9 (years). The lower limit is 10^21 obtained by multiplying 10^9 (bacteria species in the world) by 10^3 (unique sequences per species) by 10^9 (years).

      You haven't even addressed this point yet. What CH is trying to show is that the BSC4 gene even by darwinists own flawed numbers cannot have arisen in the known time period of 10 million years.

      "evolutionary theory does claim that genes are due to mere chance."

      Right now, all you have is a defensive argument that ToE is not a theory of chance. You don't have a positive argument in favor of darwinism. You have no math, nor any empirical evidence. Let me reiterate my argument that ToE is in fact a theory of chance. Here's what I wrote in response to Thorton:

      Darwinism asserts that mutations are random, hence chance. Almost all chance processes act within the bounds of law, they are still chance. Take for example the movements of the molecules of gas. The molecules can still be described with laws, eg, their protons remain held together and their electrons change their orbits according to laws, they also cannot travel faster than the speed of light, however, their movement is still chance. It's the same with NS, mutations are random and they act within the context of law, eg, if the gene is disfunctional then the organism often cannot reproduce. At rock bottom, darwinian processes are still chance-like.

      "The knowledge used to build the biosphere, as found in the genome of organisms, was created by a form of conjecture and refutation. Specifically, conjecture, in the form of genetic variation, and refutation, in the form of natural selection."

      You're going to have to explain what you mean by conjecture and refutation. I assume you mean a mutation occurs (conjecture), then it is refuted if the organism dies before reproducing, but I'm not sure.

      "So, again… do you disagree there are different kinds of unknowability? Or do you disagree as to what type of unknowability the evolution of *any* protein represents?"

      Sure, there are different kinds of unknowability. I don't see how that proves darwinism. With proteins we have positive evidence that the odds of a protein forming are well beyond the resources of chance. As CH pointed out: One study concluded that 10^63 attempts would be required for a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required. In that case the protein was about the same length as that encoded by BSC4, but it was only a part of a larger protein which otherwise was intact, thus making the search easier.

      Delete
    28. Kyle: It's the Darwinists that have cooked up the following numbers. […] You haven't even addressed this point yet.

      Again, the type of unknowability being referred to in those numbers is different than the type of unknowability you're referring to. As such, your application of them is invalid.

      You're inability to see the difference doesn't mean I haven't addressed this point. Nor have you criticized it. Rather, you keep repeating the same misrepresentations.

      At which point, further progress is unlikely.

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    29. Kyle: You don't have a positive argument in favor of darwinism. You have no math, nor any empirical evidence. Let me reiterate my argument that ToE is in fact a theory of chance.

      Your confusion is thinking these numbers somehow prove evolution is likely. But they are simply invalid either direction, as they neither prove evolution is likely or unlikely.

      Whether evolution is likely is a different sort of unlikeliness than whether a protein is classified as de novo.

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    30. The question is, does Cornelius present these numbers knowing full well they are invalid in respect to whether evolution is unlikely - resulting in the sort of comments above - or is he simply incompetent?

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    31. Scott,

      First, You failed to answer my proof that Darwinism is a mere theory of chance. Second, right now all you have is an argument from ridicule. What you're saying is: "This number is so "big" evolution must be false!" and the implication is that that is ridiculous. Yet you offer no rational argument as to why using big numbers is not a valid form of reasoning. Everyone resorts to using small probabilities to rule out chance hypotheses every day.
      1. you ride on airplanes because the probability that it will crash is so small that it is worth ignoring.
      2. you attribute the Rosetta Stone to intelligence because the odds that erosion caused it (chance) is so small that it is worth ignoring.
      3. you ignore the possibility of an asteroid hitting you when you walk outside (or inside) because the probability is so small.
      4. you disbelieve that Excel's random letter generator could write a string of more than 100 letters of coherent English text because the probability is so small.

      In fact, small probability is our only means of determining chance from intelligence. If we allow ourselves to believe that chance can routinely overcome small probabilities then we have no way of distinguishing chance from intelligence which would essentially make it impossible for us to function as rational beings.

      "What is in question is, what rational conclusion should we reach from them?"

      What I would like to hear from you is why you think it's rational to believe that it is more plausible that the BSC4 gene arose due to chance rather than intelligence.

      Delete
    32. Kyle Foley

      Yet you offer no rational argument as to why using big numbers is not a valid form of reasoning.


      The problem is you have no way of accurately determining any valid 'big numbers'. The ones offered are not applicable to the issue at hand.

      What I would like to hear from you is why you think it's rational to believe that it is more plausible that the BSC4 gene arose due to chance rather than intelligence.

      Your question is flawed and therefore meaningless. Only willfully ignorant Creationists with zero understanding of actual evolutionary theory say proteins arose solely by chance.

      Delete
    33. Kyle: First, You failed to answer my proof that Darwinism is a mere theory of chance.

      Let me guess…

      Kyle: Darwinism asserts that mutations are random, hence chance.

      However, this is a mischaracterization of Darwinism, as we've already pointed out.

      Kyle: Second, right now all you have is an argument from ridicule. What you're saying is: "This number is so "big" evolution must be false!"

      The fallacy in Cornelius argument is that he's presenting the probability calculations in these papers as if they are an accurate for the purpose of determining if evolution, as a whole, is unlikely. But they are not, for the reasons we've already pointed out.

      This invalidates all of your supposed probability examples as an analogy for evolutionary theory.

      Nor have you presented any criticism for the different types of unknowability. Rather, you merely keep repaying the same arguments, containing the same false assumptions.

      For a detailed explanation about how the creation of knowledge results in different types of unknowability, see the following talk: David Deutsch on optimism .

      Kyle: What I would like to hear from you is why you think it's rational to believe that it is more plausible that the BSC4 gene arose due to chance rather than intelligence.

      Kyle, my point is, likelihood is an *irrational* means of reaching conclusions in the case of evolutionary theory. It's simply not applicable. Nor does evolutionary theory hinge on any one particular set of experiments, as you're suggesting. Rather, it's based on an overwhelming observations in multiple, independent fields.

      So, it would seem this is yet another example of the sort of FUD generated by the fallacious arguments Cornelius posts here on a regular basis.

      Delete
    34. Scott,

      As for your assertion that Darwinism is not a theory of chance your only attempt at refuting my argument was to simply assert that I was wrong. This is hardly a strong argument and it represent a serious inability to argue on your part. You have no strong reasons for persuading anyone that ToE is nothing more than an assertion that all the diversity of species is due to chance with the obvious tautology thrown in that what does not reproduce will not reproduce.

      "The fallacy in Cornelius argument is that he's presenting the probability calculations in these papers as if they are an accurate for the purpose of determining if evolution, as a whole, is unlikely. But they are not, for the reasons we've already pointed out."

      Let me reiterate why CH's arguments are sound. Number one, he's using numbers that darwinists themselves have cooked up. So your arguments are in tension with the darwinist community. Let me remind you of them:

      Evolutionists have estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit is 10^43 (a one followed by 43 zeros) obtained by multiplying 10^30 (cells in the world) by 10^4 (new genes generated per cell per year) by 10^9 (years). The lower limit is 10^21 obtained by multiplying 10^9 (bacteria species in the world) by 10^3 (unique sequences per species) by 10^9 (years).

      Number two, you keep saying CH is wrong, but you will not say where he is wrong, what numbers are wrong, and what the proper numbers are, or why the proper numbers in principle are unknowable. For instance in a previous post you wrote: "My comments in this thread are regarding the validity of these numbers in regards to evolutionary theory as a whole, rather than the context used in the actual papers." Ok, why don't you demonstrate how these number violate ToE as a whole. Instead you simply assert it, hoping something magical will happen. Number three, you never analyze CH's numbers. You just say they're wrong. This is hardly a persuasive argument. For example, CH wrote:

      For de novo genes such as BSC4, we’re dealing with a single species (with an effective population size of about ten million), and only about ten million years. In this case the upper and lower limits become 10^18 and 10^10, respectively.

      You have never attempted to dispute this, instead it just flies over your head.

      Number four, you keep talking about unknowability. These are the only words I have found where you talk about unknowability at length: "Specifically, the question being asked in these papers represents one kind of unknowability in that that all of the choices are known. They are comparing a specific destination protein with a specific number of start proteins known to exist in common ancestors. As such, the use of probability is valid in categorizing these proteins as de novo. However, in regards to the question if any particular protein evolved at all, these probability calculations are invalid since not all start options are necessarily available to us. As such, It's a different kind of unknowability. Nor is it clear that this particular destination is the only type of protein could play the same role in some other organism, etc."

      Delete
    35. I want to reiterate that that is an argument no for ToE, it is just an argument in favor of agnosticism re the origin of species. You have yet to admit that. So your unknowability argument again is in tension with the darwinist community. Further, darwinists disagree with your assertions. As CH pointed out, darwinists attempt to put odds on the formation of proteins through chance:

      One study concluded that 10^63 attempts would be required for a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required.

      You have yet to address this. I have already pointed this out to you many times, but you keep repaying me with the same arguments.

      Scott wrote: "Nor have you presented any criticism for the different types of unknowability. Rather, you merely keep repaying the same arguments, containing the same false assumptions."

      As I said arguments from unknowability are arguments in favor of agnosticism, not darwinism. In any case, they are not sound arguments. All movement occurs due to chance, law or intelligence, as William Dembski has pointed out. Obviously proteins are not fashioned by law since law treats identical units identically, law would treat guanine the same in all situations in that clearly does not happen. That leaves only chance or intelligence. The darwinists themselves have pointed to math that overwhelmingly supports intelligence as the cause of proteins.

      Lastly: when movement demonstrates knowledge of the external world then it is more plausible that that movement is due intelligence than chance. It is simply common sense analogical reason: whenever we see movement that is aware of the structure of the external world that movement is due to intelligence. Chance never operates with knowledge of the external world. To build a protein you need knowledge of what molecules that protein is going to bind to, you need knowledge of what other proteins that protein is going to work with, you need knowledge of what temperature range that protein must stay in in order to function, you need knowledge of all the properties of the amino acids that that protein is composed of.

      Delete
    36. Kyle: As for your assertion that Darwinism is not a theory of chance your only attempt at refuting my argument was to simply assert that I was wrong. This is hardly a strong argument and it represent a serious inability to argue on your part.

      Huh? Your argument merely consists of: Darwinism asserts that mutations are random, hence chance. It's parochial because it appeals to an inappropriate level reductionism. This is a typical mischaracterization of evolutionary theory, which reveals your ignorance of the theory itself. Our attempts to point this out have gone in one ear and out the other.

      Apparently, the way you know evolutionary theory is false is by refusing to accept anything but this false characterization.

      Kyle: Let me reiterate why CH's arguments are sound. Number one, he's using numbers that darwinists themselves have cooked up. So your arguments are in tension with the darwinist community.

      No, I't's not "in tension with the darwinist community." That you think this the case illustrates how confused you are. Again, it's not the same kind of unknowability. Nor have you any criticism of why it's invalid. You just keep repeating the same non-sequitur.

      Kyle: Number two, you keep saying CH is wrong, but you will not say where he is wrong, what numbers are wrong, and what the proper numbers are, or why the proper numbers in principle are unknowable.

      There are no "proper numbers" because evolutionary theory isn't merely random!

      Again…

      The first kind of unknowability are scenarios where the outcome is completely random. An example of this is Russian Roulette. As long as you know all of the possible outcomes, such as how many chambers are in the gun, which chambers contain bullets and how many times the trigger will be pulled, we can use probability to make choices about it. For example, if for some horrible reason, one had to choose between different versions of Russian Roulette with different, yet specific number of chambers, bullets and trigger pulls, one could use game theory to determine which variation would be most favorable.

      However, evolutionary theory isn't "just random". This is the fallacy in Cornelius' argument and a common misrepresentation made here by by creationists all the time.

      If the knowledge of how to build the biosphere was created over time, the ways in which life could have adapted would reflect the specific options that had been conjectured at each step. Specifically, the options by which an organism had at it's disposal at any time depended on what adaptations it could apply any particular environment. And these adaptations would have depended on which knowledge had be conjectured at each step.

      As such, this is simply more hand waving, which we see regularly here on a regular basis.


      What part of his do you not understand? Please be specific.

      Again, likelihood is an *irrational* means of reaching conclusions in the case of evolutionary theory. It's simply not applicable. Nor does evolutionary theory hinge on any one particular set of experiments, as you're suggesting. Rather, it's based on an overwhelming observations in multiple, independent fields.

      Unless you have some sort of criticism specific to this, we're done.

      Delete
    37. Kyle Foley

      Let me reiterate why CH's arguments are sound. Number one, he's using numbers that darwinists themselves have cooked up. So your arguments are in tension with the darwinist community. Let me remind you of them:


      The argument is not sound because the numbers used are not applicable to the OP issue. CH dishonestly pulled "big numbers" from various papers that don't apply just to score cheap rhetorical points. His goal is to gull ignorant layman just like you Kyle. Looks like he succeeded.

      As an example you cite this

      "another study concluded that 10^70 attempts would be required."

      Turns out the 10^70 number was a rough calculation for a certain protein to achieve a level of fitness by random substitutions only. The very next sentence explains that's NOT how science thinks the protein formed, but that the process also used other mechanisms like homologous recombination. Of course CH conveniently "forgot" to pass on that important bit of info.

      Just because a number appears in a paper doesn't mean the number applies in all circumstances.

      Maybe a further example will help. Today's the 19th. 19 is a number. That means science has shown Kyle Foley's IQ is 19.

      That must be true because the number was in a paper, right?

      If you weren't such a clueless C&Ping cretobot and actually took the time to read and understand the actual research, maybe you wouldn't make such foolish mistakes.

      Delete
    38. Thornton,

      The argument is not sound because the numbers used are not applicable to the OP issue. CH dishonestly pulled "big numbers" from various papers that don't apply just to score cheap rhetorical points.


      Is that or is that not a mere assertion?


      His goal is to gull ignorant layman just like you Kyle. Looks like he succeeded.


      Is that or is it not a mere insult? It's the latter, which demonstrates a profoundly poor inability on your part to understand what constitutes a nonargument.


      Turns out the 10^70 number was a rough calculation for a certain protein to achieve a level of fitness by random substitutions only. The very next sentence explains that's NOT how science thinks the protein formed, but that the process also used other mechanisms like homologous recombination. Of course CH conveniently "forgot" to pass on that important bit of info. Just because a number appears in a paper doesn't mean the number applies in all circumstances.


      At least now you actually have an argument, turns out it's wrong. The BCS4 gene had to evolve according to the Darwinists story through random substitutions only. That means the 10^70 is justified. Let me quote the original paper which you overlooked:

      This study suggests that de novo evolution not only plays an important role in generating the initial common ancestral protein repertoire but also contributes to the subsequent evolution of an organism. However, it is nearly impossible to identify the noncoding origin of the initial ancestral proteins because of long-term accumulation of mutations.


      Thornton: is this or is it not a mere insult:

      Just because a number appears in a paper doesn't mean the number applies in all circumstances. Maybe a further example will help. Today's the 19th. 19 is a number. That means science has shown Kyle Foley's IQ is 19.

      And how about this, Thornton, is this not a mere insult:

      If you weren't such a clueless C&Ping cretobot and actually took the time to read and understand the actual research, maybe you wouldn't make such foolish mistakes.

      I'm through with you Thornton. You have no respect for reason, you have no idea what a nonargument is, you don't treat your interlocuters with respect. There's no point in arguing with you. I'm willing to talk to you through Skype, so that I can see what you're really made of, but you lack the courage of your convictions. My skype ID is kylefoley202

      Delete
    39. Scott,

      Huh? Your argument merely consists of: Darwinism asserts that mutations are random, hence chance.

      Apparently you forgot to read this part of my post: "Darwinism asserts that mutations are random, hence chance. Almost all chance processes act within the bounds of law, they are still chance. Take for example the movements of the molecules of gas. The molecules can still be described with laws, eg, their protons remain held together and their electrons change their orbits according to laws, they also cannot travel faster than the speed of light, however, their movement is still chance. It's the same with NS, mutations are random and they act within the context of law, eg, if the gene is disfunctional then the organism often cannot reproduce. At rock bottom, darwinian processes are still chance-like."

      This demonstrates a serious inability on your part to understand what your interlocuters are saying.

      likelihood is an *irrational* means of reaching conclusions in the case of evolutionary theory. It's simply not applicable.

      You've got to be kidding me. I seriously can't believe you just said that. Few darwinists would subscribe to such a claim. Likelihood is the foundation of all reasoning. To abandon likelihood is commit suicide. If we abandon likelihood in our calculations then the only thing we have left to go on is mere desire, which in no way makes reliable predictions about the future and with an inability to predict the future we will end up dead. Just imagine if we tried to fly to the moon based on equipment that seemed desirable and had nothing to do with the laws of physics. If you get to use desire in your calculations, then i get to use desire in my calculations. I desire that ToE is false. How do you prove me wrong? You prove me wrong by likelihood yet likelihood is the very thing you're abandoning. No serious scientist subscribes to such an approach.

      Nor does evolutionary theory hinge on any one particular set of experiments, as you're suggesting. Rather, it's based on an overwhelming observations in multiple, independent fields.

      Most likely you're making the same mistake that nearly every darwinist makes. ToE is four separate theses:

      1. change over time (evolution)
      2. common ancestry
      3. Natural Selection (a tautology)
      4. random mutation

      There is evidence for change over time but even that is questionable given Gould's punctuated equilibrium which states that organisms appear suddenly in the fossil record, remain unchanged, then disappear just as they were when they appeared. At most organisms grow bigger or smaller or adapt a few minor changes, such as scorpions replacing gills for lungs.

      there is very little evidence for the thesis that ALL mutations are random. That is what is at issue here. You are probably making the mistake of seeing that there is strong evidence for thesis 1 and then wrongly thinking that that evidence proves thesis 4. It doesn't.

      Delete
    40. Kyle Foley

      The BCS4 gene had to evolve according to the Darwinists story through random substitutions only.


      LOL! The paper doesn't say or imply that anywhere Kyle. In fact it says just the opposite

      "Recently evolved novel protein-coding genes provide us the opportunity to investigate the de novo evolution mechanism of protein-coding genes. This methodology on gene origination has been developed in Drosophila by Long et al. (Long and Langley 1993), which has led to many advances in understanding the mechanism of new gene origination, including gene duplication, retroposition, exon shuffling, and gene fission and fusion"

      Which means you were too lazy to actually read the paper and are just another creationist dimbulb regurgitating things he doesn't understand.

      You ignorant armchair philosophers are a hoot!

      Maybe you can use skype to call in for a clue.

      Delete
    41. Kyle: Few darwinists would subscribe to such a claim. Likelihood is the foundation of all reasoning. To abandon likelihood is commit suicide. If we abandon likelihood in our calculations then the only thing we have left to go on is mere desire, which in no way makes reliable predictions about the future and with an inability to predict the future we will end up dead.

      Kyle,

      How can we predict how knowledge we haven't even conceived of yet will effect the future?

      For example, people in 1900 didn't consider nuclear power or the internet unlikely. They didn't conceive of them at all. As such, it's unclear how they could have factored them into some sort of probability calculation about the future.

      So, I'd suggest it's actually the opposite. Making predictions about the future without taking into account how knowledge is created is irrational and a recipe for disaster. At best, we can make short term decisions under the assumption that no new discoveries would be made, but the scope of this is significantly limited.

      We can say the same about evolutionary theory, since it also uses a form of conjecture and refutation to create knowledge. As such, it's the same sort of unknowability with the same limitations.

      We could only make predictions if there was some way of mechanically extrapolating observations to create theories. But Popper has pointed out how this is a myth.

      For example, would you say we use likelihood to conclude the law of gravity is uniform?

      What we have are a overwhelming number of singular statements based on observations of gravity acting in a specific way at specific times and places. However, even this overwhelming number of observations are merely a drop in the bucket compared to the total possible number of locations in the universe we haven't measured the behavior of gravity, given it's size. And it's expanding at an exponential rate. Not to mention the estimated 13.7 billion years that we didn't exist to make measurements. And there's the possibility that future measurements anywhere in the entire universe could suggest otherwise, going billions of years forward.

      As such, if we combine this matrix of time and space, one could say it's beyond astronomically unlikely that gravity is a uniform law of nature. And it's getting exponentially more unlikely every second. Yet, I'm guessing you do not live in fear that objects might start falling up tomorrow, next week, next year, etc. Right?

      So, it would seem that even you do not actually consider "Likelihood is the foundation of all reasoning", after all.

      Delete
    42. Scott,


      What we have are a overwhelming number of singular statements based on observations of gravity acting in a specific way at specific times and places. However, even this overwhelming number of observations are merely a drop in the bucket compared to the total possible number of locations in the universe we haven't measured the behavior of gravity, given it's size. And it's expanding at an exponential rate. Not to mention the estimated 13.7 billion years that we didn't exist to make measurements. And there's the possibility that future measurements anywhere in the entire universe could suggest otherwise, going billions of years forward.


      What you have is a classic argument from ignorance. Theory A has worked 100% of the time in the past, theory B has worked 20% in the past. Does it follow that theory A will be more successful than theory B in the future? You're right, no, it does not. Does it follow that we should adopt theory B? No, it does not. Does it follow that it is more rational to adopt theory A over B? It certainly does. The foundation of reason rests on an assumption that the past will be like the future. If we abandon that logic look what happens: Theory A has been right in the past, therefore ANY theory will be right in the future. How do you choose which theory? You're only guide is desire. This is why this is an argument from ignorance. Arguments from ignorance have the structure: I do not know X, therefore Y is true. What you're asserting is:

      I do not know that theory A will work in the future,
      therefore, I know that theory B will.


      How can we predict how knowledge we haven't even conceived of yet will effect the future? For example, people in 1900 didn't consider nuclear power or the internet unlikely. They didn't conceive of them at all. As such, it's unclear how they could have factored them into some sort of probability calculation about the future.


      Again this is an argument from ignorance. What you're saying is:

      I do not know what will be discovered 50 years hence,
      therefore I know theory B is true.

      You're going straight from ignorance to knowledge.
      We have to build our worldview on what we know, not on some wild speculation as to what the future might bring.


      we can make short term decisions under the assumption that no new discoveries would be made, but the scope of this is significantly limited.


      Yes, the scope is limited. I never said that we have access to absolute knowledge. How does this support ToE?


      We can say the same about evolutionary theory, since it also uses a form of conjecture and refutation to create knowledge. As such, it's the same sort of unknowability with the same limitations.


      I don't understand what you mean. You're going to need to provide more details.


      if we combine this matrix of time and space, one could say it's beyond astronomically unlikely that gravity is a uniform law of nature. And it's getting exponentially more unlikely every second. I'm guessing you do not live in fear that objects might start falling up tomorrow, next week, next year, etc. Right?
      So, it would seem that even you do not actually consider "Likelihood is the foundation of all reasoning", after all


      The point is we have to worry about what applies to us humans, not what happened 6 billion years ago in a galaxy 300 million light years away. No one would be so irrational as to think: I'm going to jump off this cliff because there's a possibility that 6 billion years ago in a galaxy 300 light years away gravity was different. There is no instance of gravity behaving in wildly unpredictable ways in human history, therefore, there is no reason to think any shift is likely in the future. If you believe gravity is not constant, then why don't you jump off a cliff?

      Delete
    43. Kyle: The foundation of reason rests on an assumption that the past will be like the future.

      Again, this is a myth. If we thought the sun burned hydrogen at a rate faster that we currently think it does, we could conclude that the sun could supernova, at any time since it would run out of fuel.

      As such, it wouldn't necessarily rest on the assumption that sun will rise in the future merely because it's risen every day for billions of years in the past.

      Kyle: I do not know that theory A will work in the future, therefore, I know that theory B will.

      No, you're jumping to conclusions.

      Just as we do not conclude evolutionary theory is unlikely due to these probability numbers, we do not conclude it is likely due to these probability numbers either. Again, evolution represents a different kind of unknowability which makes the use of probability invalid either way.

      We accept evolutionary theory not merely because it's not unlikely. We accept it due to overwhelming number of collaborating observations across multiple, independent fields.

      So, you're presenting a false dichotomy between being likely or personal desire.

      Kyle: I do not know what will be discovered 50 years hence, therefore I know theory B is true.

      Why do you keep misrepresenting what I write?

      This is an example of the specific type of unknowability I'm referring to. As such, it's illustrates why probability is invalid in the case of this type of unknowability.

      Kyle: Yes, the scope is limited. I never said that we have access to absolute knowledge. How does this support ToE?

      Where did I say it did? Again, we do not accept evolutionary theory merely because it's not unlikely. We accept it due to overwhelming number of collaborating observations across multiple, independent fields.

      Kyle: The point is we have to worry about what applies to us humans, not what happened 6 billion years ago in a galaxy 300 million light years away.

      But the universal statement "the law of gravity is uniform" applies to us as well, as the exact same law is thought to be in effect everywhere. As such, a deviance in the law would effect human beings here as well.

      In fact the uniformity of the law of gravity is part of our explanation for space-time across the entire universe. So, we think that the law of gravity is uniform not because we we've developed some statistical calculations that show it's "probable" but because it's part of a hard to very explanation for space time in our vicinity, as well well as everywhere else in the universe.

      So, again, likelihood isn't the foundation of all reasoning.

      Delete
    44. Scott: We can say the same about evolutionary theory, since it also uses a form of conjecture and refutation to create knowledge. As such, it's the same sort of unknowability with the same limitations.

      I don't understand what you mean. You're going to need to provide more details.

      Probability is invalid for both the distant future and evolutionary theory because they are both based on the creation of knowledge. In the case of evolution, it's non-explantory knowledge.

      At best, we can use probability to classify whether a type of protein was de novo, not if the theory is likely as whole.

      see the folioing talk for details...

      David Deutsch on Optimism

      Delete
    45. Scott,


      likelihood isn't the foundation of all reasoning. … Probability is invalid for ... the distant future

      then what is valid? unlikelihood?

      What principle do you use to come to conclusion that jumping off a cliff would not be a good idea?



      If we thought the sun burned hydrogen at a rate faster that we currently think it does, we could conclude that the sun could supernova, at any time since it would run out of fuel.

      Well, we don't think it burns hydrogen at a faster rate so how is this an argument that more often than not the future is unlike the past.

      If the future were not like the past there would be no such thing as a law of nature.

      If you disbelieve that the future will be like the past then how do you decide what the future will be like?



      We accept evolutionary theory not merely because it's not unlikely. We accept it due to overwhelming number of collaborating observations across multiple, independent fields.


      "not likely" = likely. So you're contradicting your own arguments. Elsewhere you said "likelihood isn't the foundation of all reasoning," now you're using likelihood to justify the use of ToE.

      You're making the mistake of using the four separate theses of darwinism and claiming that evidence for one thesis justifies the other unrelated thesis. What overwhelming number of observations do you have that ALL mutations are random?


      the universal statement "the law of gravity is uniform" applies to us as well, as the exact same law is thought to be in effect everywhere. As such, a deviance in the law would effect human beings here as well.

      If gravity were off by so much as one order of magnitude in relation to the strong force, galaxies would not be able to form, so your idea that gravity is non-uniform throughout space has no basis in rational thought. You're only basis in believing it is possibility. Well, if there is a possibility that gravity is non-uniform, then there is a possibility that ID is correct. What principle do you use to exclude the hypothesis that ID is correct and include the hypothesis that gravity is non-uniform?

      Delete
    46. Scott: likelihood isn't the foundation of all reasoning. … Probability is invalid for ... the distant future

      Kyle: then what is valid? unlikelihood?

      What part of there are different kinds of unknowability do you not understand?

      Kyle: What principle do you use to come to conclusion that jumping off a cliff would not be a good idea?

      That would depend on what problem am I trying to solve by jumping off a cliff.

      Kyle: Well, we don't think it burns hydrogen at a faster rate so how is this an argument that more often than not the future is unlike the past.

      First, "more often than not "? you seem to be backpedaling.

      Second, because this is merely one of many examples I could make or propose which would conflict with the idea that "The foundation of reason rests on an assumption that the past will be like the future."

      Kyle: If the future were not like the past there would be no such thing as a law of nature.

      Laws of nature are universal statements. So, you're assuming there is some principle of induction that allows you to transform a number of singular statements based on observations into a uniform statement. However, you haven't elaborated on how this actually works, in detail.

      Kyle: If you disbelieve that the future will be like the past then how do you decide what the future will be like?

      We make decisions based on explanations, not the assumption that the future will resemble the past, as I've pointed out in my earlier example regarding the uniformity of gravity.

      Kyle: "not likely" = likely. So you're contradicting your own arguments. Elsewhere you said "likelihood isn't the foundation of all reasoning," now you're using likelihood to justify the use of ToE.

      Where did I say that?

      Just because something isn't unlikely doesn't mean it's likely. Things start out as logical possibilities that are neither likely or unlikely. And some things are neither likely or unlikely because probability is simply irrational means of drawing conclusions where the outcome influenced by the creation of knowledge.

      Kyle: You're making the mistake of using the four separate theses of darwinism and claiming that evidence for one thesis justifies the other unrelated thesis.

      No, you're the one who keep putting words in my mouth.

      Kyle: What overwhelming number of observations do you have that ALL mutations are random?

      Except, "ALL mutations are random" is a universal statement. And apparently, you're assuming that I too am an inductivist since you somehow think it's possible to turn singular statements based on observations into universal statements.

      But I'm not an inductivist. We create theories using conjecture, then test those theories for errors using observations. So, there is no number of overwhelming observations that possibly proves "ALL mutations are random". Rather we we've conjectured a theory that has withstood the criticism of an overwhelming number of observations.

      So, we tentatively accept evolutionary theory because it has yet to be refuted, not because a overwhelming number of observations somehow prove it, in particular, is true.

      Delete
    47. Kyle: If gravity were off by so much as one order of magnitude in relation to the strong force, galaxies would not be able to form, so your idea that gravity is non-uniform throughout space has no basis in rational thought.

      Which is precisely my point. The question is, why doesn't it have any basis in rational thought?

      Again, as I've pointed out, from the perspective of probability, it's astronomical unlikely that gravity actually is a uniform force, given observations alone. So, what are you appealing to other than likelihood?

      Kyle: You're only basis in believing it is possibility.

      No, gravity is an explanation for space time-itself. And it's a hard to vary explanation.

      Kyle: Well, if there is a possibility that gravity is non-uniform, then there is a possibility that ID is correct. What principle do you use to exclude the hypothesis that ID is correct and include the hypothesis that gravity is non-uniform?

      Again, why do you keep misrepresenting what I write?

      I'm not including the hypothesis that the law of gravity is non-uniform, I'm pointing out that both of us accept it as being uniform, despite the fact that it's astronomically unlikely, based on probability calculations.

      In other words, probability doesn't play the role you're claiming it does. Your own acceptance of it is a concrete example of this.

      Delete
    48. I have enough information to conclude that this debate will no longer serve a purpose. You're welcome to continue the debate via skype kylefoley202. good luck. it was a pleasure debating with you.

      Delete
  3. PaV Lino

    As far as I can see, neo-Darwinism has no answer for this.


    There's lots of things science doesn't have the answer for PaV. What's really curious is why you think that somehow invalidates all the things science does have a well supported answer for, like the mechanisms for common descent.

    Feel free to give us ID's explanation for the BSC4 gene data. We know CH won't have the spine to offer an alternative.

    You claim to know who the Designer is, so tell us when, where, and how he did this "design".

    ReplyDelete
    Replies
    1. Thorton:

      I'm flattered by your request to give my opinion on these matters. It makes feel right at home.

      Let me, instead, analyze your comments.

      There's lots of things science doesn't have the answer for PaV.

      Indeed, you are right. In fact, the more I study science, it seems that the more answers we have, the more questions it opens up. We seem almost to be falling behind. But, what does this have to do with anything?

      What's really curious is why you think that somehow invalidates all the things science does have a well supported answer for, like the mechanisms for common descent.

      This is a surprising statement from a couple of angles. First, did I say anything about "all the things science does", or, rather, did I say something about "neo-Darwinism" not having an answer for this. I think if you reread what you've quoted, you'll see it's the latter, and not the former. So, it would seem you're trying to put words into my mouth. Not good.

      Second, you're declaring that "science" has a "well-supported" answer for the "mechanisms for common descent."

      What does this mean, exactly? Is science saying that they can prove children are a lot like their parents? That each generation enjoys common descent from the previous generation? We know all of this before ever we begin talking about biology or evolution.

      Do you mean DNA? Is that what you're talking about? And, are Archea "descended" from protists? What do you mean? What "well supported" answer are you talking about? Please be more clear. And please provide details.

      Feel free to give us ID's explanation for the BSC4 gene data.

      The problem is not with the BSC4 gene data. The problem is the simplistic model employed as an explanation. In the end, it becomes logically incoherent. That was the exact point I made. Why don't you address this insufficiency? Trying to change the subject, are you?

      We know CH won't have the spine to offer an alternative.

      Yes, you're hoping I'll take the bait; CH has better sense than that. I'm getting there.

      You claim to know who the Designer is, so tell us when, where, and how he did this "design".

      I suppose that if I could tell you "when, where, and how" the Designer did what He did, then I would be as smart as the Designer. But I assure you, I'm not.

      But, please, since Darwinism so enlightens us, perhaps you'd like to explain "when, where and how" the progenitor BSC4 gene came about? We await.

      Delete
    2. PaV Lino

      T: "Feel free to give us ID's explanation for the BSC4 gene data."

      P: blah blah blah lots of meaningless evasive words and cowardly avoidance


      Thanks for demonstrating ID is so vacuous PaV.

      ID is 100% attack current science, 0% provide its own, better explanations.

      That's one of the many reasons why you clowns aren't taken seriously.

      Now where's your scientific evidence for the identity of the Designer?

      Delete

  4. You claim to know who the Designer is, so tell us when, where, and how he did this "design".


    Now wait a second. This is nothing more than a red herring designed to distract readers away from the main story that the Darwinian narrative has egg on its face (once again) and is woefully inadequate to explain the complexity of life.

    ID theory does not claim to know how or when a designer created life. All ID theory says is that some features of life and the universe are too complex to have arisen by accident and therefore must have required a designer.

    ID theory is fantastically easy to falsify. All you have to do is demonstrate a random process with no intelligent input creating the effect in question.

    Let's start with the origin of life. Have a random process create a primitive lifeform in a laboratory under the conditions of the early earth and you have falsified the ID claim that life is too complex to have arisen by accident.

    The obnoxious and silly Darwinists here are the ones claiming "aRandomProcessDidIt". Well let them put their money where their mouth us. Tell us how, why, where, and when said random process created a lifeform. Better yet, demonstrate this to us in a lab. There's no point getting your panties in a wad and trying shout down people who don't buy your story.

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    1. WG: Now wait a second. This is nothing more than a red herring designed to distract readers away from the main story that the Darwinian narrative has egg on its face (once again) and is woefully inadequate to explain the complexity of life.

      Is it? How do you explain how the knowledge this supposed deigned used to this protein, as found in the corresponding genes for BSC4, was created?

      Essentially, all ID proponents have done is push the food around on their plate, then claimed they've ate it. Yet, it's still there staring them in the face.

      A designer that "just was" complete with the knowledge of how to build BSC4, already present, serves no explanatory purpose. This is because one could more simply state that baker’s yeast "just appeared", complete with the knowledge of how to build BSC4, already present.

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    2. Correction: Is it? How do you explain how the knowledge this supposed designer used to build this protein, as found in the corresponding genes for BSC4, was created?

      In other words, BSC4 represents an adaption in the form of a protein. Adaptations require knowledge to build. And, in the case of biological organisms, this knowledge is found in the genes that result in BSC4.

      ID merely claims a designer put this knowledge in the genome. As such, is says nothing about the origin of this knowledge.

      My question is, what's you explanation as to how this knowledge was created?

      Delete
    3. wgbutler777Mar 15, 2012 01:54 PM

      T: "You claim to know who the Designer is, so tell us when, where, and how he did this "design"."

      Now wait a second. This is nothing more than a red herring designed to distract readers away from the main story that the Darwinian narrative has egg on its face (once again) and is woefully inadequate to explain the complexity of life.


      No it's not. On the 'probability' thread Pav Lino actually claimed to know the identity of the Designer. Since then he's clammed up and refused to name names. Maybe if you asked him what he meant he'd grow a spine.

      ID theory is fantastically easy to falsify. All you have to do is demonstrate a random process with no intelligent input creating the effect in question.

      LOL! Science doesn't have to falsify ID any more than it has to falsify the Easter Bunny or the FSM. There is no theory of ID to falsify, only some completely unsupported assertions with ZERO positive evidence.

      Let's start with the origin of life. Have a random process create a primitive lifeform in a laboratory under the conditions of the early earth and you have falsified the ID claim that life is too complex to have arisen by accident.

      I told you, I'll do that right after you have your Designer create an entire new universe from scratch. Ladies first.

      Delete
    4. Wb,fair enough ,just like evolutionary theory need not explain Abiogenesis, right?

      Delete
    5. Thorton:

      No it's not. On the 'probability' thread Pav Lino actually claimed to know the identity of the Designer. Since then he's clammed up and refused to name names. Maybe if you asked him what he meant he'd grow a spine.

      Are you jealous of my special knowledge? Is that why you want to know?

      Delete
    6. PaV Lino

      Thorton: No it's not. On the 'probability' thread Pav Lino actually claimed to know the identity of the Designer. Since then he's clammed up and refused to name names. Maybe if you asked him what he meant he'd grow a spine.

      Are you jealous of my special knowledge? Is that why you want to know?


      No PaV, It's because I expect you're lying through your teeth. I just like calling your bluff so the lurkers can watch you squirm and slime and avoid answering. Not that they need any more evidence of your incompetence, I mean specialness.

      Delete
  5. "Let's start with the origin of life. Have a random process create a primitive lifeform in a laboratory under the conditions of the early earth and you have falsified the ID claim that life is too complex to have arisen by accident."

    Oh is that all? How is it we're supposed to condense the resources of all the early earth across millions of years and get a result in a human lifetime or a few generations?

    Maybe PaV can help--his math allows a million liters in a few cubic feet.

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    3. RobertC:

      Maybe PaV can help--his math allows a million liters in a few cubic feet.

      I made the calculation on the fly. I should have divided by 2, instead of by 8, in my final step. That makes each molecule to be surrounded by 17 feet of water on each side, rather than just 4 feet. My point is not affected at all by that error. In fact, this only makes Musgrave's calculations less realistic. Does this bother you at all?

      And since, Robert, you're bringing this up here, what about it, Thorton: Are you ready to apologize for asserting that Musgrave's error was fixed two years ago, when, in fact, it wasn't?

      Delete
    4. PaV Lino

      RobertC: Maybe PaV can help--his math allows a million liters in a few cubic feet.

      Why don't you look at the calculation again. Maybe you'll notice that I took the cube root, and divided by 8. And then you can maybe figure out why.


      Yeah, and you screwed up the math again you moron. A million liters of water occupies the volume of a cube 10m on a side. Maybe you can explain how you got that down to a sphere 48" in diameter.

      Not as bad as you claiming a dice roll can have a "probability of 4.0", but still pretty dumb.

      Forget science and math PaV. Is there anything AT ALL you're not incompetent at?

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    5. Pav Lino

      And since, Robert, you're bringing this up here, what about it, Thorton: Are you ready to apologize for asserting that Musgrave's error was fixed two years ago, when, in fact, it wasn't?


      I didn't say the typo at TalkRational was was fixed you moron. I said it was "removed from the article", meaning the Wiki article we were discussing, where it had no relevance to his points anyway.

      Your desperation to defend Hoyle for his ridiculous claims by jumping on a typo is just pathetic PaV. Especially for a clown like you who can't even divide two numbers on a calculator.

      Delete
    6. Thorton:

      Maybe you can explain how you got that down to a sphere 48" in diameter.

      Yes, I can. I should have divided by 8 before taking the cube root, and not after.

      I guess that makes Musgrave right, and me wrong, correct? That's how you think, isn't it? It's not about who has a legitimate point and who doesn't. All you're interested in are any inaccuracies or mistakes others make, so that you can then feel justified in maintaining your position.

      But, of course, you conveniently forget about the mistakes and inaccuracies you make along the way--no matter how circumspect you try to be. (Of course, the miscalculation above only makes Musgrave's argument all the more senseless. But that doesn't bother you in the least, does it? You strain gnats and swallow camels.)


      For example, you write:

      I didn't say the typo at TalkRational was was fixed you moron.

      Here's my Thorton-esque reply: "You moron, I didn't say TalkRational, I said Talk.Origins."

      But, of course, I know what you meant, and will reply to the point you're making.


      You cite the Wikipedia "article" as a defense against Hoyle's argument. But the Wikipedia link doesn't address the Cytochrome C calculation. So why do you cite Wikipedia? You can't have replication unless Cytochrome C already exists. This calculation alone is reason enough to abandon the notion that life itself arose via strictly materialistic mechanisms. Hoyle clearly saw that.

      The only pertinent section of the Wikipedia page on Hoyle's fallacy has to do with the "analysis" section.

      Their argument is that Hoyle's myoglobin argument is wrong because he's assuming that every a.a. is important to function, when only those contributing to its 3D configuration are important to function.

      While I think this involves facile assumptions, let's just assume it is the case. And let's assume that 3/4 of the a.a.s are just along for the ride. Well, 20^153 (the actual number they use) becomes roughly 20^34, which is roughly 2^135. Is this suppose to make me confident in what random forces and differential death can bring about? And what if we were dealing with a protein that wa 350 a.a.s long? Then 90% of the a.a.s wouldn't have to effect function and you would still end up with the same improbability as above. And this is for but one protein.

      Besides the wikipedia link not addressing my specific argument. It presents an argument that when inspected lacks merit. And it includes mention of an article by Musgrave that is froth with its own errors, despite their knowing that some of the errors still exist.

      But you glibly cite these kinds of links as if they were the Gospel truth. It's all just as simple as that: provide a link here, provide a link there. See how simple life can be? You've become a fundamentalist of sorts.

      Your desperation to defend Hoyle for his ridiculous claims by jumping on a typo is just pathetic PaV.

      Not only is it you who are being pathetic, Thorton, you're not even being honest. If it was a typo, then why hasn't it been corrected? And, if Musgrave corrects it, then his numbers are off by a thousand, loosing their entire effect (as if they were of any significance given his suspect analysis). So who are you trying to kid?

      Delete
    7. "Your desperation to defend Hoyle for his ridiculous claims by jumping on a typo is just pathetic PaV. Especially for a clown like you who can't even divide two numbers on a calculator."

      Feb 17
      “You are a lying little troll nat. You already admitted it. You also spelled "you're" wrong."

      You've jumped onto others' typos too, Thorton. Do you hold yourself to the same standard?

      Delete
    8. LOL! PaV, you're just too funny!

      Go find a single biologist anywhere on the planet who agrees with Hoyle's nonsense.

      You're so desperate for any little pebble you can toss at ToE you're swallow anything, believe any bit of stupidity you read on Creationist websites.

      Look on the bright side PaV - CH's latest Gish Gallop of Creationist lies has pushed your "probability = 4.0" amazingly dumb boner off the main page. Bet you're relieved.

      Now when will you be presenting that scientific evidence for the identity of the Designer? You said you know so tell us. Your continued refusal to answer confirms you were just BSing. Of course ID has nothing to do with religion, right?

      Delete
    9. Smith

      T: You also spelled "you're" wrong."

      You've jumped onto others' typos too, Thorton. Do you hold yourself to the same standard?


      Everyone makes the occasional typo, and I certainly make my share. But continually misusing "you're" for "your" and "there" for "their" like natschuster and Tedford the idiot do aren't typos. They represent a fundamental ignorance of the English language. For someone like natschuster who claims to be a teacher the errors are inexcusable.

      Delete
    10. With that in mind, you and I should certainly hope that many others who comment on this blog are not employed in the field of teaching or dispensing knowledge due to the gross amount of grammatical, spelling and formatting errors consistently deployed.

      Delete
    11. Thorton:

      You're so desperate for any little pebble you can toss at ToE you're swallow anything, believe any bit of stupidity you read on Creationist websites.

      Thorton, I've been posting on this blog for two months now. You haven't made any kind of substantial contribution whatsoever. All you do is nitpick. And then you provide links to Talk.Origins and Wikipedia pages that are thoroughly dominated by evolutionists. Whenever I've asked you for analysis, you provide none.

      You see, in describing me, you've succeeded only in describing yourself---which is what liberals do all the time.

      You're but an acerbic pain-in-the-neck. It's no wonder CH ignores you all the time.

      Delete
    12. PaV Lino

      Thorton: You're so desperate for any little pebble you can toss at ToE you're swallow anything, believe any bit of stupidity you read on Creationist websites.

      Thorton, I've been posting on this blog for two months now. You haven't made any kind of substantial contribution whatsoever. All you do is nitpick. And then you provide links to Talk.Origins and Wikipedia pages that are thoroughly dominated by evolutionists. Whenever I've asked you for analysis, you provide none


      Sure PaV, tell us again what a great scientific analyst you are.

      Like your "analysis" where you concluded the probability of a dice roll = 4.0. Like where you calculated that a million liters of water occupies a sphere 48" in diameter. Like your "ID analysis" of the BSC4 data, which consisted solely of you waving your arms and running away.

      Now where's your list of biologists who support Hoyle's nonsense?

      Where's your scientific evidence for the identity of the Designer you claimed to have?

      Flounce back to UD little man if you can't stand being called on your ignorance and BS here. I'm sure Batspit77 and KariosFlatus love your work.

      Delete
  6. Let run through Hunter's big numbers game:

    John F. Reidhaar-Olson and Robert T. Sauer:
    "the estimated number of sequences capable of adopting the lambda repressor fold is still an exceedingly small fraction, about one in 10^63 of the total number of possible 92-residue sequences"

    Yockey:
    "The number of cytochrome c sequences is about 3·8 × 10^61. The probability of selecting one such sequence at random is about 2·1 ×10−65."

    Axe DD.
    "This implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77)."

    Hayashi et al.
    "The relative fitness of the wild-type phage, or rather the native D2 domain, is almost equivalent to the global peak of the fitness landscape. By extrapolation, we estimated that adaptive walking requires a library size of 10^70 with 35 substitutions to reach comparable fitness."

    So what does this have to do with the paper at hand. The authors find a protein coding gene emerge from a non-coding (RNA) one. It seems to confer some fitness.

    Do they claim:
    1) It is folded (it could be chaperoned, or unstructured)?
    2) That it has enzymatic activity (Axe).
    3) That it has reached its global fitness peak?
    4) That it is either cytochrome-c or lambda-repressor?

    No, seriously, this really highlights the issue with the big numbers game. There are 10^130 possible 100 amino acid proteins. (Putting aside that many proteins, even of that size are clearly repeats proteins or built up of smaller motifs). 4x10^61 of that pool are functional cytochrome C. 10^57 of that same pool are lambda repressors.

    What percent is of some function? Any function that increases fitness-even as a natively unfolded protein, or supported by chaperone proteins or complex partners?

    That is the question impacting this study. What are the odds this protein coding gene that emerged from a non-coding gene does something to improve Yeast fitness.

    And Hunter doesn't have the numbers for that.

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    1. RobertC:

      That is the question impacting this study. What are the odds this protein coding gene that emerged from a non-coding gene does something to improve Yeast fitness.

      The protein is implicated in DNA repair and coping with nutrient-poor environments. But nonetheless, I agree with your other points and edited the OP accordingly.

      Question: Does it matter? IOW, if a folded, enzymatically active protein was found, would that cast any doubt on evolution?

      The answer of course is "no."

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