Of “models” and “algorithms”

I was short with Joe Felsenstein in the comments section of “Stark Incompetence,” a post in which I address, well, um, the stark incompetence on display in a recent publication of Eric Holloway. I have apologized to Joe, and promised to make amends with a brief post on the topic that he wants to address. Now, the topic is a putative model that Eric introduced in “Mutual Algorithmic Information, Information Non-growth, and Allele Frequency” (or perhaps an improved version of the model). Here is a remark that I addressed to Joe:

Tom English: As you know, if a putative model is logically inconsistent, then it is not a model of anything. I claim that that EricMH’s putative model is logically inconsistent. You had better prove that it is consistent, or turn it into something that you can prove is consistent, before going on to discuss its biological relevance.

I will not have to go far into Eric’s post to identify inconsistencies. After explaining the inconsistencies, which I doubt can be eliminated, I will remark on why the “model” is not worth salvaging. The gist is that Eric’s attempted analysis puts a halting, output-generating simulator of a non-halting, non-output-generating evolutionary process in place of the process itself. An analysis of the simulator would not, in any case, be an analysis of the simuland.

Inconsistency

In the following passage from his post, Eric describes a randomized procedure, dubs it an evolutionary algorithm, and then asserts the existence of a halting program that implements the procedure.

The alleles are 1s and 0s, and the gene G a bitstring of N bits. A gene’s fitness is based on how many 1s it has, so fitness(G) = sum(G). The population consists of a single gene, and evolution proceeds by randomly flipping one bit, and if fitness is improved, it keeps that gene, otherwise it keeps the original. Once fitness(G) = N, the evolutionary algorithm stops and outputs G, which consists of N 1s. The bitstring that is N 1s will be denoted Y. We will denote the evolutionary algorithm E, and it is prefixed on an input bitstring X of length N that will be turned into the bitstring of N 1s, so executing the pair on a universal Turing machine outputs the bitstring of 1s: U(E,X) = Y.

The first thing to note is that the randomized procedure is not an algorithm: it halts with probability less than one. That is, by a simple inductive argument, for all natural numbers n, the probability is less than one that the procedure halts after n or fewer bit flips. Indeed, the probability is greater than zero that the procedure performs n bit flips without improving fitness. Thus if you were to turn the procedure into an algorithm by stipulating that it performs at most M bit flips, there would be a nonzero probability that gene G remains equal to input X \neq Y when the algorithm halts, no matter how large you make M. The problem is not the particular randomized procedure that Eric has chosen. Evolutionary procedures do not converge surely to local fitness maxima in discrete spaces (except in trivial cases).

It is gobsmacking for me, though probably not for you (I labored over “Stark Incompetence” in hope that everyone would be as astonished by something coming from Eric as I am by many of his claims), to see Eric flatly assert that the randomized “algorithm” is a program for a deterministic computer. To put it plainly, a universal Turing machine cannot flip bits randomly. Eric’s “model” is inconsistent, and thus is not a model. To get randomness, Eric must

  1. draw the deterministic bit-flipping program E randomly, or
  2. endow the deterministic bit-flipping program E with a pseudo-random number generator, and supply the program with a random seed as input (along with X).

However, this will not produce consistency, because Eric has predicated, with the expression U(E, X) = Y, that the program surely halts with an output that is maximal in fitness — no ifs, ands, or buts. His subsequent argument requires it. But his prior specification of the random bit-flipping procedure does not allow it.

The map is not the territory

Computer programs used by scientists to model evolutionary processes commonly signal the occurrence of events of interest to the scientists, and halt when the scientists are uninterested in gathering further data. An exceedingly naive response, most prominently on display in the “evolutionary informatics” of Marks, Dembski, and Ewert, is to analyze a program, and claim that the analysis applies to the modeled process — as though the evolutionary process itself signals the occurrence of events and halts.

I am not going to dig into Eric Holloway’s attempt at analysis. You should be able to see for yourself, if you have any business discussing what he has done, that it is literally the program E that enters into the analysis, and not the evolutionary process that is simulated by the program. It ought to be obvious that an evolutionary process does not “know” when fitness is maximized, let alone announce the genome for which fitness is maximal. The part of the program that detects and announces the event in which fitness is maximized, and subsequently halts, is not part of the (simulation of the) evolutionary process. It is a monitor of the simulated process, and can be decoupled from the simulation per se, even though it is usually tightly coupled with the simulation in practice. I advise against struggling to make Eric’s inconsistent “model” into one that is internally consistent, because the result would be a bogus, though consistent, “model” that mistakes the simulation software for the evolutionary process itself.

339 thoughts on “Of “models” and “algorithms”

  1. phoodoo: Which is more fit?

    You are dear phoodoo. You are oh so fit. I’ll leave you to your comic books, but before that you can have this again:

  2. colewd: When you offer something as vague as selection as a generator of information without the detail you essentially have nonsense.

    Tsk. You misspelled “mind”.

  3. Rumraket: So there are mutations with beneficial effects on various measures of performance.

    Tall people are better at basketball!

    I wonder who the last common ancestor of tall was? !

  4. colewd:
    You apparently don’t understand the problem here. To model evolution selected steps have to be identified. Without selectable steps between the tornado and the flying object evolution faces the tornado in a junkyard analogy.

    I understand the problem all right. Even after putting it in bold, you still failed to understand that when someone tells you that evolution is nothing like a tornado in a junkyard, insisting on asking the person to use a tornado in a junkyard “model” means that you did not understand what was said. here, for example, you started with a tornado in a junkyard “model” to then insist that a tornado in a junkyard applies. You’re basically saying: if evolution were like a tornado in a junkyard, then it would be like a tornado in a junkyard. Really?

    colewd:
    No one who is impartial is going to buy something as vague as fitness as a selectable step moving a sequence consistently toward function let alone a ubiquitin system that involves thousands of sequences and requires precise operation for a multicellular animal to form.

    Of course nobody would buy such a conceptual mess. Fitness is not a selectable step. What does it mean to move consistently towards function? Do you think that evolutionary biologists think that sequences went from no function whatsoever, to the functions they display today, after lots of intermediaries that had no functions whatsoever, yet moved “consistently”? What would “consistently” mean in such scenario? Why would evolutionary biologists propose such a thing? I ask because I’ve never seen such a proposal anywhere.

  5. DNA_Jock,

    Right Jock, I have already said here, I don’t know how many times, if one is born without legs, they are much less likely to get eaten by a tiger whilst out hunting for one. Could be a great advantage in certain villages. Sort of like Hemoglobin C.

    Likewise, if you are born with the LRP5 allele, you may end up looking sort of like an elephant man, BUT, if you lived underwater, you would have a great advantage, because you would float to the top like all those light boned suckers, ha!

    Behe sure was right. Evolution can destroy. And sometimes that’s good news! Now, what about creating??

  6. Entropy,

    What would “consistently” mean in such scenario? Why would evolutionary biologists propose such a thing? I ask because I’ve never seen such a proposal anywhere.

    This is the reality. If a sequence is not strongly directed toward a function mutation will break it down into non function. This we can model.

  7. phoodoo: I wonder who the last common ancestor of tall was?

    I believe you. I have no problem accepting that you truly wonder about that.

  8. colewd: If a sequence is not strongly directed toward a function mutation will break it down into non function.

    A functional sequence will eventually break down if it is not subject to purifying selection, sure.
    But even so, random sequences can evolve towards acquiring biological functions. Remember Hayashi et al 2003?

  9. Rumraket: But even so, random sequences can evolve towards acquiring biological functions.

    Of course they can, isn’t that what all of evolution is?

    But you guys hate that word random.

  10. phoodoo: Of course they can, isn’t that what all of evolution is?

    But you guys hate that word random.

    Phoodoo your comic books are waiting. Go read about flying blue men and lasor owls.

  11. Rumraket,

    But even so, random sequences can evolve towards acquiring biological functions. Remember Hayashi et al 2003?

    I do but you remember it was not the whole enzyme that was randomized only about 25%. Also the function it found was not the wild type. This is why Hyashi looked to a potentially deterministic mechanism like recombination to explain the existence of the wild type. I do agree with you that enzymes can have improved catalytic function with random change but not all cellular proteins are enzymes. A lot of cellular functions either work properly or they don’t.

  12. Rumraket,

    Did you know that people with a genetic mutation for being fat make better sumo wrestlers than those with a genetic mutation for skinny?

    Mindblowing.

  13. colewd:
    Entropy,
    This is the reality.If a sequence is not strongly directed toward a function mutation will break it down into non function. This we can model.

    Do you now understand that what you’re writing would not be like a tornado in a junkyard at all?

  14. colewd: I do but you remember it was not the whole enzyme that was randomized only about 25%

    It was a particular domain of a protein used when phage infects bacteria, not an enzyme. Without this domain which assists in infection, the organism had a level of infectivity over a millionfold less than normal. The loss of the domain incurred an incredibly large reduction in relative fitness. But not all the way to zero, it was not lethal.

    Also the function it found was not the wild type.

    You mean the level of function did not evolve back to the level observed in the wild type. Fitness was not completely restored to the original level.

    But that is irrelevant, the function was still found. Random mutations found the function the D2 domain used to perform, and improved it a lot from the ground up again. So from an arbitrary and random protein sequence, the function performed by D2 domain of phage protein g3p could be found again, despite having been entirely abolished.

    So random mutation combined with selection for fitness, can, in fact, evolve a random sequence towards acquiring a biological function. The fact that it did not completely restore fitness all the way back to the level observed in wild-type phage is irrelevant.

    I do agree with you that enzymes can have improved catalytic function with random change but not all cellular proteins are enzymes.

    Neither is the g3p protein an enzyme, and the D2 domain does not catalyze a chemical reaction. It binds to something.

    From: Holliger P, Riechmann L, Williams RL. Crystal structure of the two N-terminal domains of g3p from filamentous phage fd at 1.9 A: evidence for conformational lability. J Mol Biol. 1999 May 14;288(4):649-57. DOI: 10.1006/jmbi.1999.2720
    “Filamentous bacteriophages (Inoviridae) are a family of single-stranded DNA viruses that infect Gram-negative bacteria. The Filamentous bacteriophages (f1, fd, M13) infect Escherichia coli bearing an F0 pilus (Webster, 1996; Model & Russel, 1988; Marvin, 1998). Productive infection further requires three products of the tol operon, TolA, TolR and TolQ (Sun & Webster, 1986; Webster, 1991). Infection is mediated by the minor coat protein g3p located at the distal tip of the extended phage capsid. The g3p has a modular structure, comprising three distinct domains (D1, D2 and D3) separated by glycine-rich tetra- and pentapeptide repeats as well as a C-terminal transmembrane segment. Separate domains appear to encode separate functions. Relatively little is known about the functions of the C-terminal domain D3 and the transmembrane segment apart from their requirement for g3p incorporation into the phage particle (Stengele et al., 1990). The role of the two N-terminal domains, D1 and D2, in the infection process is better understood. Phage infection begins with the interaction of the middle domain D2 with the primary infection receptor for Ff phages, the tip of the F0 pilus.”

    A lot of cellular functions either work properly or they don’t.

    All cellular functions either work, or they don’t. Useless statement. The question is if functional sequences can evolve from nonfunctional ones, and they can.

  15. phoodoo: Mindblowing.

    Again, I believe you when you say your mind is blown from that. I can scarcely imagine how astonished you feel.

  16. colewd: Tom, I recently did a sequence comparison of skeletal muscle actin called alpha actin which has 377 amino acids in mammals. That is 20^377 possible arrangements. The alignment is between rats mice pigs and humans. The alignment is 100%. Given there should be billions of fixed neutral mutations since mice and rats split how do you explain this other that the original sequence was designed?

    The obvious explanation is… wait for it… selection!

  17. phoodoo: But you guys hate that word random.

    Nah, I have no problem accepting the fact that I exist by sheer dumb luck. It’s you and your ilk who can’t live with that. You need to believe that you were put here by some omni god, as if the universe couldn’t be complete without you. It’s sort of pathetic and narcissistic if you ask me, but to each their own, I guess

  18. Rumraket,

    All cellular functions either work, or they don’t. Useless statement. The question is if functional sequences can evolve from nonfunctional ones, and they can

    It is revenant or irrelevant depending the claim you are trying to make. If you are trying to claim the cause of the origin of the wild type enzyme that you are observing it is very relevant. If you are trying to claim how low level kinetic activity can evolve from a partially randomized sequence of a functional enzyme then I agree it is irrelevant.

  19. Tom English: Evolutionary biologists are not saying that biological evolution is an evolutionary algorithm executed by the Universe. What technologists like you and me do with an evolutionary algorithm is to use a simulated evolutionary process to sample the space of possible solutions to a problem. The component of the evolutionary algorithm that transforms the sample into a solution to a given problem is logically distinct from the component that generates the sample. There’s nothing “evolutionary” about the transformation of the sample. That is, there’s no analog of it in biological evolution.

    You’ve been beating a dead horse for months. Yet your problem is that algorithms and models are not anchored in reality. This has all been discussed right here http://theskepticalzone.com/wp/natural-selection-evolution-magic/
    …and here’s a quick summary:
    1. Natural Selection concept fails since phenotype does not determine survival which is also tautological with “best adapted”
    2. “Blind, mindless, purposeless, natural, and process” qualifiers fail
    3. Phenotype is an unstable infinite set (hence unknowable and theoretical)
    4. Fitness concept is redundant since never defined independently of survival
    5. “Selection” is Survival
    6. The only selection is Intelligent Selection – always done by an Intelligent Selector
    7. Selection is limited to a narrow set of adaptations – one cannot selected what is not there
    8. Selection and Mutations lack creativity, therefore cannot explain body designs
    9. We do not observe “divergence of character” but ‘limited variations around a mean’ (regression to the mean)
    10. Extinct organism were not flawed and their features were not “selected away”
    11. Intelligent Selection should replace Natural Selection but only if we ever transmutate organisms
    12. Humans do not apply Natural Selection because it doesn’t work
    13. Designs must cross an inevitable optimization gap making evolution impossible
    14. Breeding is much more than “artificial selection” and unrelated to any natural process

    “Natural selection” proponents must answer these simple questions – pick any biologic entity including populations and give the 80/20 Pareto without too much accuracy or precision :
    1. What is that biologic entity’s phenotype?
    2. What is its environment?
    3. What is its fitness function?
    4. What is the relationship between its phenotype, environment, fitness, and survival/reproductive success?

    The five ridiculous claims of “natural selection”
    1. “Design by multiple choice” is ridiculous
    2. “Multiple choice from ALL random answers” is ridiculous
    3. “Designing without trying” is ridiculous
    4. “Self design” is ridiculous
    5. “Design by incremental optimization” is ridiculous

    At a minimum, you should reply with your “fitness function”. And since you can’t, why push this “fitness” nonsense?

  20. colewd:

    This is because the mechanism that is offered is not capable of the task at hand.

    Bill has never been able to back up this assertion. Will you be supporting this claim here?

    Let’s look at a specific example. Show us the generation before and the generation after ubiquitin emerged in eukaryotes, and then show us how the differences between those generations could not be produced by mutation and selection.

  21. Nonlin.org: You’ve been beating a dead horse for months. Yet your problem is that algorithms and models are not anchored in reality. This has all been discussed right here http://theskepticalzone.com/wp/natural-selection-evolution-magic/
    …and here’s a quick summary:
    1. Natural Selection concept fails since phenotype does not determine survival which is also tautological with “best adapted”

    You fail right off the bat. All you need to do is create a mixture of antibiotic sensitive and resistance bacteria on an antibiotic plate, and then see which phenotype dominates.

  22. Tom English: Evolutionary biologists are not saying that biological evolution is an evolutionary algorithm executed by the Universe. What technologists like you and me do with an evolutionary algorithm is to use a simulated evolutionary process to sample the space of possible solutions to a problem. The component of the evolutionary algorithm that transforms the sample into a solution to a given problem is logically distinct from the component that generates the sample. There’s nothing “evolutionary” about the transformation of the sample. That is, there’s no analog of it in biological evolution.

    Nonlin.org: You’ve been beating a dead horse for months.

    I made similar remarks in “Evo-Info Sidebar: Conservation of Performance in Search.” That was 2-1/2 years ago. I don’t recall repeating myself since then. If I have returned to the point, then I’ve done so rarely.

    Nonlin.org: You’ve been beating a dead horse for months. Yet your problem is that algorithms and models are not anchored in reality. This has all been discussed right here http://theskepticalzone.com/wp/natural-selection-evolution-magic/
    …and here’s a quick summary: [Lists of 14, 4, and 5 points follow]

    I’ve not managed to find anything in your 23-point response that is relevant to my decomposition of evolutionary algorithms into two components, and explanation that only one of the two components is biologically inspired.

  23. Everyone:

    I’m not going to respond to comments on biology. There are people here who are much better equipped than I am to field them. It’s fine to discuss whatever you want.

    I count this thread as a success. I’ve catalyzed the discussion that Joe Felsenstein wants to have with Eric Holloway. Eric has acknowledged that his “model” is inconsistent, and has indicated that he will return with something better. Presumably the discussion of whatever he proposes next will be less painful for me to watch than the discussion what he proposed before.

  24. dazz: Nah, I have no problem accepting the fact that I exist by sheer dumb luck. It’s you and your ilk who can’t live with that. You need to believe that you were put here by some omni god, as if the universe couldn’t be complete without you. It’s sort of pathetic and narcissistic if you ask me, but to each their own, I guess

    That’s a caricature!

  25. Tom, very good cogent point in the OP. When I come to write (in a few days, I hope) on mutual information and natural selection, I will definitely note your point about random numbers and Turing machines. However I think I will not worry about the incoherence of Holloway’s argument, but instead just be in “even if” mode and say that even if his result were true …

  26. Here’s a paper which shows how to understand natural selection using mutual information.
    Natural Selection. V. How to read the fundamental equations of evolutionary change in terms of information theory

    https://www.researchgate.net/publication/233722364_Natural_Selection_V_How_to_read_the_fundamental_equations_of_evolutionary_change_in_terms_of_information_theory/link/5c8154b5299bf1268d448e7b/download

    Granted, this is not KMI, although KC does get mentioned in the article. But perhaps it will provide some ideas for Eric to use in trying to model how Levin’s result on non-increasing KMI can be used in a biological model in a way that contradicts this work. If indeed it can.

  27. BruceS, thanks for reminding me of Steven Frank’s paper — I’ve got a copy of it lying around somewhere on my computer and will make sure to reread it before writing a post on mutual information and evolution.

  28. Tom English: It’s two caricatures. Dazz has caricatured his own belief, just as he has yours. His comment is largely facetious, as are many of yours.

    So if you think Dazz doesn’t really believe in dumb luck for his existence, what does he put it down to?

  29. phoodoo: So if you think Dazz doesn’t really believe in dumb luck for his existence, what does he put it down to?

    His parents had sex.

    Of course, evolution is much more than just “dumb luck”. It’s also inheritance, natural selection, population mechanics, and the laws of physics and chemistry.

  30. phoodoo: So if you think Dazz doesn’t really believe in dumb luck for his existence, what does he put it down to?

    Evolution is a way to look at it, but of course evolution doesn’t really explain why I exist. My point was that I don’t mind the idea of being the byproduct of a large chain of natural events that you would qualify as “sheer dumb luck”. That’s the kind of thing that troubles you, not me.

  31. What’s annoying is that creationists often use phrases like “pure chance” and “dumb luck” to make it sound implausible that evolution could have led to fish that swim, or birds that fly, of humans who listen to creationist lectures. This is disingenuous on the part of creationist debaters, who should know better. But maybe some of them really don’t know better and don’t know that they should understand evolutionary biology before opening their mouths.

  32. Nonlin.org:
    The five ridiculous claims of “natural selection”

    Wow! I’m about to learn something!

    Nonlin.org:
    1. “Design by multiple choice” is ridiculous

    You should learnt o write with much more clarity. Are you saying that natural selection “proposes” that design by multiple choice is ridiculous? Or you’re saying that natural selection proposes that there’s design by multiple choice? Either way, I have not seen anything like that when natural selection is explained in textbooks. What do you mean by “design by multiple choice”?

    Nonlin.org:
    2. “Multiple choice from ALL random answers” is ridiculous

    Again, are you saying that natural selection “proposes” that multiple choice from ALL random answers is ridiculous, or that natural selection proposes that there’s “multiple choice from ALL random answers”? I never heard of such things when studying natural selection, and it doesn’t appear in any textbooks. So, no matter which one you meant, it shows that what you’re fighting is a straw man at best, while natural selection is far away from your reach and understanding.

    Nonlin.org:
    3. “Designing without trying” is ridiculous

    I agree that designing without trying is ridiculous, but I never heard that natural selection was about “designing without trying”, nor about “designing without trying being ridiculous.”

    Nonlin.org:
    4. “Self design” is ridiculous

    I disagree that self design is ridiculous. After all, at some point humans, whether we like it or not, might be designing humans. Yet, again, neither of both potential meanings you intended has anything to do with natural selection. natural selection is neither about self design, nor about self design being ridiculous.

    Nonlin.org:
    5. “Design by incremental optimization” is ridiculous

    I disagree. I know lots of engineers, and all of them produce designs by incremental optimizations. Now, as for natural selection it does not claim anything about whether design by incremental optimization is ridiculous, or about whether it happens.

    Seems like you have a very confused mind, and that you have no idea what natural selection means. looking at what you wrote above your five points that have nothing to do with natural selection, I’d imagine that you learned biology from creationist propaganda, and not the best of it.

  33. Joe Felsenstein: This is disingenuous on the part of creationist debaters, who should know better. But maybe some of them really don’t know better and don’t know that they should understand evolutionary biology before opening their mouths.

    This is a never-ending challenge of mine, to convince myself that they really don’t know better and are just speaking out of honest ignorance. It’s just very difficult to maintain that level of charity after having spent so much time trying to get the same thing across to the same small handful of individuals for so many years.

    There is of course a third option I have to remind myself of. They’re neither ignorant, nor disingenuous. Instead, they’re some sort of crazy.

  34. T_aquaticus,

    Let’s look at a specific example. Show us the generation before and the generation after ubiquitin emerged in eukaryotes, and then show us how the differences between those generations could not be produced by mutation and selection.

    This is the burden of evolution to show a model of a mechanism that can perform this task with the known species that exist. Whats known is the prokaryotic cell and eukaryotic cell. What is new is the spliceosome and the nuclear pore complex plus many other new organelles. Where is the model that can find the spliceosome? Where is the model that can find one of its proteins given the sequence homology observed (mutual information) by gpuccio? The model has to generate the DNA and protein sequences as Dawkins tried to generate with Weasel.

    My assertion is on pretty solid ground at this point. A mind plus the necessary attachments appears to be the unique mechanism that has the possibility of performing this very difficult task. How a mind can do this becomes a very interesting scientific question.

  35. colewd: This is the burden of evolution to show a model of a mechanism that can perform this task with the known species that exist.

    Yawn. Bill’s back with his latest installment of ignorance based personal incredulity theater.

    A mind plus the necessary attachments appears to be the unique mechanism that has the possibility of performing this very difficult task.

    So where are the necessary attachments which made your “magic mind POOFED biological life” into physical reality?

  36. Rumraket: This is a never-ending challenge of mine, to convince myself that they really don’t know better and are just speaking out of honest ignorance. It’s just very difficult to maintain that level of charity after having spent so much time trying to get the same thing across to the same small handful of individuals for so many years.

    Pretty sure all of us have felt the same frustration with the Bill Coles, the Joe Galliens, the Sal Cordovas of the world.

  37. colewd: Where is the model that can find the spliceosome?

    There is no “the spliceosome”. They’re different in many different ways basically between all known species. And, interestingly, the ways they are different largely recapitulates phylogeny, which is a fact only evolution by common descent explains.
    None of these spliceosomes were ever a “target” of evolution that we must accurately reproduce in some model. They’re historically contingent outcomes that evolved along different lineages from common ancestors. But we’ve been over all this before many times. I have personally spent an inordinate amount of time writing detailed posts explaining to you the selective pressures inferred to have caused the evolution of the spliceosomal machineries in eukaryotes, from their origin in prokaryotic group II self-splicing introns. I have explained, with references to the primary literature, the evidence that led scientists to these inferences, and how this explains numerous attributes of intron distribution and splicing in eukaryotic cells and genomes.

    But all that aside, your question is based on a fundamental misunderstanding about how historical inferences are made for the processes that led to any observed entity in science. Whether those entities are solar systems, stars, planets, continents, rivers, rocks of a particular nature, or evolved molecular machines in living organisms.

    We can take a cue from geology to see the ludicrousness of your demand here. In the same way the Mt. Everest is not a “target” outcome of plate tectonics, but how the pressures in the rocks happened to develop at the time. They resulted in an entire range of mountains called the Himalayas, of which the Mt. Everest is just one of many contingent outcomes of where the pressures happened to propagate. If the pressures had been different, the mountain would have formed differently.
    There will never be a model of plate tectonics that can faithfully reproduce the exact Mt. Everest as it is now, because we can’t know exactly how the pressures in the rocks happened to developed so far back in time. Nevertheless, we can say with great confidence that the Mt. Everest is the sort of thing that develops under the right circumstances, given certain patterns of pressures in the rocks over long periods of time. Scientists can build models that explain why there come to be mountain ranges, because there are these different forces acting in the rocks that cover our planet, but they do not have the capacity to exactly reproduce any particular mountain.

    It’s the same thing with evolution of the many different spliceosomes. We have a process that explains things like spliceosomes in a general sense, because there are these mechanisms acting on populations of reproducing organisms and their genomes, given certain selection pressures, even if we cannot reproduce all the exact chains of events that resulted in any specific and particular one of these outcomes.

    Now of course, another problem here is you have a double standard. A hypocritical double standard with respect to evidence and “modeling”. You have no model for the design of the spliceosome. You do not have a model where a designer has a prokaryote before him, and then decides to design and create any particular eukaryote with some particular spliceosome. You can not supply what you are demanding of others, and yet you still believe despite the complete absence of a design model for any biological entity, that all the biological entities were designed.

    Zero evidence, zero models. Nothing at all. Yet you believe in design hard, and are demanding evolutionary biology cross some unreasonable hurdle of modeling and evidence you demand from nothing else, which basically reveals how you are deeply biased against biology.

  38. So, let’s take a further look:

    Nonlin.org:
    1. Natural Selection concept fails since phenotype does not determine survival which is also tautological with “best adapted”

    It’s not natural selection that fails, but your poor understanding of what natural selection refers to. It doesn’t say that phenotype determines survival, it says that different phenotypes have different probabilities of surviving in a given environment. But survival is a mixture of happenstance, phenotype and environment. “Best adapted” is not “tautological” to natural selection, because it’s a concept applying at a different level. “Best adapted” would be the organisms with the best characteristics for their environment. We expect natural selection to increase the proportion of better adapted organisms to an environment. See how that’s different conceptual levels?

    Nonlin.org:
    2. “Blind, mindless, purposeless, natural, and process” qualifiers fail

    Are you really suggesting that the higher likelihood of survival can see, has a mind, has a purpose, is unnatural, and cannot be conceptualized as a process? Wow, you really have a very confused mind.

    Nonlin.org:
    3. Phenotype is an unstable infinite set (hence unknowable and theoretical)

    Oh how surprising! A concept is a concept! I never heard that before. The true surprise is that you think that because concepts are “theoretical” they’re “unknowable.” As per being unstable, that’s the fucking point Nonlin! Evolution cannot but happen because phenotypes are unstable. If they were stable then there would be no evolution.

    Nonlin.org:
    4. Fitness concept is redundant since never defined independently of survival

    And this is a problem because? By your “logic,” “gravitation” would be redundant because it’s never defined independently of mass. Oh! All of science is false! Things are defined in terms of other things!

    Nonlin.org:
    5. “Selection” is Survival

    Nope. It’s a metaphor referring to one of the factors in survival.

    Nonlin.org:
    6. The only selection is Intelligent Selection – always done by an Intelligent Selector

    Darwin decided to use selection as a metaphor to get the point across. I guess he never heard of idiots who cannot understand how concepts work, and their limitations. Here’s a bit of advice: think before making idiotic claims about the use of concepts and metaphors. In the end it’s whether you get the idea or not. If you find that there’s a point where the metaphor breaks, then don’t assume that the author wanted the metaphor to go that far. It was there just to help getting the main point across. that’s where your intelligence should help you go forward. You cannot blame Darwin for your stupidity. For your wanting to take the metaphor father than helpful.

    Nonlin.org:
    7. Selection is limited to a narrow set of adaptations – one cannot selected what is not there

    So? What’s the problem? Did anybody say that natural selection happens for things that are not there? Because I never heard such a thing.

    Nonlin.org:
    8. Selection and Mutations lack creativity, therefore cannot explain body designs

    You’re mistaking the map for the territory Nonlin. Of course “selection” and “mutations” lack creativity, they’re not people. They’re phenomena. Now, your claim that “body designs” cannot be explained by those two alone, I agree. the explanation needs a lot more understanding of the effects of the historical accumulation of successful genotypes/phenotypes, learning about their specific histories, the effects of random variations, etc. We’re just getting started. I don’t see why anybody would expect natural selection and mutations to explain it all, nor do I see why not being an all-inclusive explanation for everything would make natural selection problematic. Gravitation doesn’t explain everything either. So what?

    Nonlin.org:
    9. We do not observe “divergence of character” but ‘limited variations around a mean’ (regression to the mean)

    You might not observe such things. I do. Many people do. Changes in allele frequencies are observed all the time. Even generation to generation. It’s bound to happen. So much so that it’s “tautological.”

    Nonlin.org:
    10. Extinct organism were not flawed and their features were not “selected away”

    Do you really think that natural selection is a claim about why extinct species are extinct? You’re very lost in that confused mind of yours. A lot of factors play roles in survival Nonlin. All biologists understand that. None understands natural selection as the single reason for death, failure to reproduce, or extinction. None. What fails is your understanding Nonlin. Natural selection remains a useful concept. Sorry.

    Nonlin.org:
    11. Intelligent Selection should replace Natural Selection but only if we ever transmutate organisms

    WTF? What the hell is this supposed to mean? How the hell is this supposed to be about natural selection as phenomena or concept?

    Nonlin.org:
    12. Humans do not apply Natural Selection because it doesn’t work

    Humans cannot use natural selection because once humans are involved it’s not natural selection, by definition, any more Nonlin. This is a philosophical problem, not a problem with evolution or with natural selection. You truly have a confused mind.

    Nonlin.org:
    13. Designs must cross an inevitable optimization gap making evolution impossible

    Good luck proving that. I’d rather sit. You have a tendency to think that once you say so, it’s so, as if you were some kind of god. But, sorry, you’re not. You’re an idiotic creationists with a very confused mind, who cannot distinguish concepts from their referents, or appropriately use concepts and definitions.

    Nonlin.org:
    14. Breeding is much more than “artificial selection” and unrelated to any natural process

    Well, if we’re going to play with concepts, then since we’re natural, breeding would be a natural process. You have lots of trouble with concepts and their use. Either way, breeding was a metaphor used to try and explain the phenomena that Darwin (among others) identified. That it doesn’t apply 100% just means that metaphors have limited uses, and that, at some point, understanding should take the lead. You could use a bit of that from time to time Nonlin. As I said, you’re not some kind of god. You’re not as smart as you think you are. You actually come across as stupid beyond repair (as you will demonstrate if you even try and engage). I think you’re mostly mentally immature, which can be fixed. The question is whether you’re willing to fix it or not.

    See ya.

  39. Rumraket,

    Now of course, another problem here is you have a double standard. A hypocritical double standard with respect to evidence and “modeling”. You have no model for the design of the spliceosome. You do not have a model where a designer has a prokaryote before him, and then decides to design and create any particular eukaryote with some particular spliceosome. You can not supply what you are demanding of others, and yet you still believe despite the complete absence of a design model for any biological entity, that all the biological entities were designed

    You describe a speculation that information can be generated without a target. What I am demanding of others is a model that meets the claim that information (enough to create a single spliceosome protein) can be created de novo by the cell plus the environment providing feedback.

    At this point we don’t have a model that can come close to showing this even for the single central spliceosome protein that can get the party started.

    The design guys have put forward a mechanism that has a shot at this. This challenge will possibly integrate gpuccio’s work with Eric’s.

  40. colewd: The design guys have put forward a mechanism that has a shot at this.

    No, they have not. There is no design model that in any way “predicts” the genetic sequence of any known biological entity.

    What you just said is flatly false, Bill.

  41. colewd: My assertion is on pretty solid ground at this point. A mind plus the necessary attachments appears to be the unique mechanism that has the possibility of performing this very difficult task.

    Isn’t your position that the necessary attachments of a mind are the result of design? If so, isn’t that a potential problem for that hypothetical?

    How a mind can do this becomes a very interesting scientific question.

    And how the mind knew what to do, at present the only mind we have experience with is not capable.

  42. colewd: You describe a speculation that information can be generated without a target.

    Try this experiment Bill.

    Roll a pair of dice 100 times. Write down the string of 100 values. That is NEW INFORMATION.

    What was the target string of the dice rolling?

  43. colewd: At this point we don’t have a model that can come close to showing this even for the single central spliceosome protein that can get the party started.

    Bill Cole never met a lie about evolution he didn’t like, or wouldn’t repeat dozens of times despite being corrected.

  44. Rumraket,

    No, they have not. There is no design model that in any way “predicts” the genetic sequence of any known biological entity.

    Lets just say for a conservative claim that the design model easily solves the Weasel challenge. So can you generate the Weasel sentence without a target?

  45. colewd:
    Rumraket,
    Lets just say for a conservative claim that the design model easily solves the Weasel challenge.So can you generate the Weasel sentence without a target?

    The Weasel program isn’t an evolution simulator.

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