Natural Selection – Evolution Magic

Natural Selection is described as “the differential survival and reproduction of individuals due to differences in phenotype”. To this, some add “blind, mindless, and purposeless environmental process” that nonetheless is imagined turning random genetic mutations into superior new features enhancing descendants’ survivability (fitness). Accumulation of these features supposedly turns one lifeform into another over time. Natural Selection seeks to explain the appearance of design in nature without appealing to a designer.

This definition however fails the simplest test as different phenotypes survive different environments thus delinking phenotype from survivability. In a small farm, only organisms closely related to their wild cousins survive, but agribusinesses select for chickens with oversize breasts and research labs select for populations with specific genetic mutations requiring tight environments to survive. Although all these have different phenotypes, they do not possess an intrinsic phenotype “fitness” independent of the environment. In addition, who decides what is natural and what is not? Darwin considered domestication natural enough to include it as supporting argument. And as far as “blind, mindless, and purposeless”, all these are impossible to prove in addition to being utterly incompatible with the anthropic concepts of “better adapted” and “better fit”, both of which cannot be evaluated independent of survivability anyway.

Natural Selection is supposed to tie both ways survivability with phenotype, but this leaves out the environment which not only affects survivability directly, but also phenotype, itself a sum of genotype plus the environment, and even genotype that is a recurrent function of previous genotypes and the environment again. So in the end, survivability is a recurrent function of genotype, an infinite continuum of environments, and other unknown factors. While survivability can be measured as can be the individual genotype, measuring a population’s genotype is daunting at best, and the impact of the ever changing environment is simply impossible to evaluate. Phenotypes are impossible to define and measure in entirety even for one individual and, in addition, phenotype changes constantly from birth to adult to old age. We do see genetic mutations (unknowable if random) and we do know that, given a similar environment, extreme genotypes reduce survivability, yet we also know that a large variety of genotypes survive just fine in any population.

Fitness is never defined independently of survivability – this renders the fitness concept redundant especially since survivability can be measured while fitness cannot. Evolutionary Fitness is defined as the quantitative representation of natural and sexual selection (reproductive success) of a genotype or phenotype in a given environment. “Survival of the fittest” is interpreted as: “Survival of the form (phenotypic or genotypic) that will leave the most copies of itself in successive generations.” Not only is survivability the only measure, but survivability also changes with the environment.

Natural Selection is Intelligent Selection which is always done by an Intelligent Selector such as Darwin’s breeder which is an intelligent and willful player that takes intentional actions to reach preset goals. Predators, plants, birds, insects or bacteria, all show intelligence and the willful pursuit of predetermined goals. When interacting with the inert environment, organisms self-select rather than being selected by this environment. As soon as the organism dies and becomes part of the lifeless universe, all selection of that entity ceases.

Selection is limited to a narrow set of possible adaptations – what is not there, cannot be selected. Among the most common adaptations are body color/size/shape, hair type, antibiotic/chemical resistance, and behavior, and even these are limited in scope. Farmers would like to grow walking chicken breasts the size of hogs that grow much faster and come in various flavors, but this is not happening despite their best efforts. Antibiotic resistant bacteria still cannot survive extreme temperatures and chemical concentrations and their resistance decreases when the stimulus is removed. Rabbits cannot turn green when hopping over grass and white just over winter, despite the clear advantage such camouflage would bring. Size of tails, horns, beaks, trees, etc. are all stable over time as tradeoffs limit their growth. Human intelligence, flying, swimming, venom, and all other desirable capabilities remain restricted to specific organisms. Domestication has greatly helped mankind’s progress, but it has not changed the nature of the target animals and plants despite intensive efforts to accelerate their evolution. Instead, humans only enhanced the built in characteristics of domestic organisms and simply did without – a huge civilization disadvantage – when those plants and animals were unavailable. Hence, selection does not “design”, is limited in scope to a few available characteristics, and is reversed as soon as the selection pressure ends.

Extinct organism were not flawed and their features were not “selected away”. Most characteristics of the extinct survive just fine in current organisms of which some changed so little over time they are called living fossils. Sure, the mammal eye might provide superior vision to insect eye, but nothing comes for free and tradeoffs ensure both survive. Organisms that have completely vanished cannot be characterized as flawed and it would not take much imagination to see them thriving in a current landscape. The environment may have changed dramatically over time, however on a macro scale, the environment affected all organisms making the “natural selection” explanation highly doubtful regarding why some organisms survived in their old form, why some went extinct and why others would survive in a changed form. Humans and apes shared the same environment in Africa so common genotype would not have caused our dramatic differences just as lions are not that different than leopard, the cheetah and the others.

What if anything should replace Natural Selection? Humans have applied the most intensive and targeted selective pressure on us and others with great results for our existence. Yet we have not transformed even one organism into another – not even the lowly eColi after decades of laboratory work (Lenski). Our dogs are still basic canines and our cats are still basic felines, not much different than their wild cousins. If anything, we had to adapt to them rather than them to us. The finch, the moth, the antibiotic resistant bacteria are still the original organisms, their hailed changes having reverted or proven simple adaptations. We are no smarter, more powerful or longer living (in absolute) than out primitive ancestors. Selection is not transformative, much less creative.

Humans would apply the Natural Selection method if feasible. But we don’t because it isn’t. A Natural Selection software would use a random generator and a selection criteria to maximize survivability in an available niche. For instance, a family vehicle should optimize the transport function (survivability) given a set of environmental constraints (regulations) and an existing design as starting point. Random minute changes could be tested and retained if the transport function is improved. However, this method can only remove minor oversights but will never create any new designs. Any significant departure such as a new fuel, material or environment either results in a suboptimal design, or requires a cascade of changes to improve the survivability function. That is why the auto industry, like most other industries, introduces minor redesign annually and major revamps every few years. And while even the minor improvements must come in harmonized packages rather than one off (to reduce negative ramifications), in the absence of those major redesigns a firm would shortly go extinct.

Designs do not transform into better designs without crossing an inevitable optimization gap. Given a certain environment, once a design is optimized for a certain function, it becomes suboptimal as soon as the function, the structure, or the materials changes. Until the new design is optimized for that particular change, it remains inferior to an old design already optimized to that environment. Humans optimize new designs (with multidimensional differences from previous versions) conceptually before abruptly replacing old designs. A Darwinist biologic gradual design transition would thus be impossible hence never observed in nature. Had the compound eye been optimized first, a transition to non-compound eye would inevitably had to be suboptimal for a while and vice versa. Only if all eye designs had started from the same point, each following an independent path and at the same pace would we have so many different designs today, each optimized for its function. This however implies a coordinated original grand design incompatible with Darwinian evolution.

Pro-Con Notes

Con: What about organic design? Isn’t that natural selection at work?

Pro: No. This is just iterative optimization of a given design. In this case, the wing shape, the material, the environmental forces and the optimization target are all given. The algorithm will not generate a new wing shape or material and it will stop converging as soon as the environment is less than perfectly defined. In addition, this design is radically different from the previous one, and the next iteration will certainly be radically different than this one (no gradualism).

Con: You just don’t understand natural selection.

Pro: If “natural selection” were hard to understand it would not be taught to young children. Instead, “natural selection” is more like very bad street magic where the bus is covered with the cloth and we then are asked to imagine it disappeared without even removing the cloth and showing us the empty space.

663 Replies to “Natural Selection – Evolution Magic”

  1. Adapa
    Ignored
    says:

    colewd:

    The origin of flight is very strong evidence of intelligent design.So is the origin of the flight feather.

    If you click your heels together and repeat that lie while ignoring all the evidence you’ve been shown, do you think you’ll go to Kansas?

  2. Neil Rickert
    Ignored
    says:

    Nonlin.org: For some reason they won’t publish my reply to your other comment.

    I found your reply attempts flagged as spam. They were probably flagged because of the number of links.

    For now, I will move those to trash since they mostly duplicate what you have now managed to post.

    Note, also, that your post (the one to which I am replying) breaks the rules. I did consider moving it to guano. But I’ll give it a pass for now.

  3. John Harshman John Harshman
    Ignored
    says:

    Nonlin.org: You’re not answering the questions, nor are you hand typing: “There is no such thing as Natural Selection!”

    Hey, I thought I was supposed to be the intelligent person you wanted to talk to. Now you’re acting as if I’m just as stupid as everybody else here. Such a quick descent from the heights! I have indeed answered the questions, or at least the fraction that were intelligible. (Incidentally, have you ever considered the possibility that you are not being absolutely clear, and that some further explanation might be required?) I might add that you seem oddly arrogant for a person who appears to know nothing about the subject.

    You don’t know what 80/20 is?!? Embarrassing, especially for those with internet access. Hint: Pareto. One of your “arguments” was a dead end link – a waste of time link that didn’t answer anything. Don’t do it – its unprofessional.

    OK, now that we know what 80/20 means, how does it make your question intelligible? Still don’t see it. And what do you mean by “dead-end link”? The only link I can think of was to my paper on crocodylians. It wasn’t broken, and I think it was quite relevant to your question. I even think I explained why it was relevant. Where did I go wrong?

    For some reason they won’t publish my reply to your other comment. So here it is: Quit being such a whiny prima-donna. In my experience, people complaining about this, “not understanding” that, recommending the other, asking silly questions, assuming, etc. do it because they don’t have solid arguments.

    You should pull back from yourself a little. You don’t get automatic obeisance. You have to work for it. When I say I don’t understand your question, I mean I don’t understand it and invite you to explain further, which is what you should have done. I’m not sure what you mean by “recommending the other”, so perhaps that would be an opportunity to explain. Also, it would be good not to just assume my questions are silly; the polite thing would be to answer them as best you can. I consider your response to be whiny, by the way.

    1.What individual? You don’t know your own dogma? “Natural selection” is not about the individual. For a population, survival is reproductive success.

    Sorry, but reproductive success is something that individuals have. Selection happens to individuals and results in evolution in the population. This is something I understand and you don’t.

    2.Fine. Don’t answer if “not your claim”.

    What is this even responding to? The last thing I did was ask what you mean. How can I answer until I know?

    3.Really? Zebra’s survival (pardon me: “reproductive success”) hinges on its stripes?!? Only on its stripes? Curious since they don’t even know the role of those stripes.

    Why “only”? How would that be relevant? There is some evidence that stripes deter tsetse flies from biting. Do you think that might impact survival or reproductive success?

    4.No, I am not saying “fitness depends on environment”. I am saying “no such thing as fitness”… and not on phenotype either: “In a small farm, only organisms closely related to their wild cousins survive, but agribusinesses select for chickens with oversize breasts and research labs select for populations with specific genetic mutations requiring tight environments to survive. As shown, all these different organisms may or may not survive regardless of their phenotype. “

    That makes no sense to me. I’ll throw some words at it in hopes of hitting your point. You may be saying that there is a stochastic element to survival (or reproductive success), and that’s correct. But it doesn’t invalidate natural selection. It just means that you have to get data from many individuals to test it, so as to average out the noise. And of course different environments select for different characteristics, which you have said isn’t your point.

    5.For the species? “Reproductive success is defined as the passing of genes onto the next generation in a way that they too can pass on those genes.” Only possible if the species survives. Reverse is also true.

    I find that a trivial and useless point. Yes, a species survives only if some individuals reproduce. But the causation is all in one direction. Individuals don’t reproduce only if the species survives; species survival is just the result. Your quote contradicts your claim.

    6.Aren’t you forgetting something? In what environment? See 4. example

    No, I don’t think I’m forgetting something. The environment determines which genotypes are favored. How is this a problem?

    7.I know that “ape to human” as proposed by Darwinistas is a pipe dream: http://nonlin.org/human-evolution/ . We’re also 69% rats and 50% bananas according to the DNA but DNA is not what you think: http://nonlin.org/dna-not-essence-of-life/.

    You should know that I’m not going to your web site, since your postings here suggest that I will find only nonsense. If you want to present some evidence, present it here. Your figures of 69% and 50% represent two incommensurable measures, and even if they were the same sort of thing your interpretation is unclear and, I strongly suspect, nonsensical. All things being equal, the more closely related to a species we are the more similar its genome will be to ours, by whatever measure you care to consult. You have no idea what I think DNA is. And the evidence for human relationships to other taxa is overwhelming. I could explain some of it to you if you cared, which I suspect you don’t. Hey, I see you didn’t answer my question.

    8.Have you considered that it’s only your imagination running wild? Also, who cares? Scientific method is not imagination. We need proof. Experiments clearly show that selection does not design, is limited in scope to a few available characteristics, and is reversed as soon as the selection pressure ends.

    Your are mistaken. Science doesn’t deal in proof, just evidence. Experiments don’t show what you suppose, though evolution can be reversible over the short term.

    9.Why should I care that you do astrology? Don’t just send me to a dead end link as substitute for an argument. What I think happens instead is not the issue – we’re debating “natural selection”. Stay on topic.

    The argument is simple. The evidence shows common descent. The genetic differences among species are of the sort that can be accounted for by the types of mutations we observe. Given all that, what can account for the differences in morphology? Do you have a hypthesis, or do you reject the data?

    10.Google: Deleterious = damaging; Flawed = damaged. They go together.

    Did you actually find that from Google? I’m suspicious.

    11.“Phylogenetic analysis” presupposes “evolution”. Can’t use it to demonstrate transmutation aka “evolution”. Circular logic. Deep time = hocus pocus

    So you’re a young-earth creationist, then. Pity. No, phylogenetic analysis doesn’t presuppose evolution. Why would you think so? Do you know anything about it?

    12.The only provable experience with new designs is human design. Did you test “Antibiotic-resistance is a reversible adaptation “? Aren’t we just as natural as the ape and banana? And it doesn’t matter – if “natural selection” worked, we would just apply it anyway. But it doesn’t.

    If natural selection doesn’t work, how does antibiotic resistance arise? Sure, it’s reversible. Usually it’s on a plasmid, and the plasmid can be lost. Often it’s deleterious in an environment lacking in antibiotics. But not always. The problem with human design is that life doesn’t look anything like it.

    13.Forget fossils. The fossil record lends no support for Darwinian evolution because: it is sketchy at best inviting proponents to make whatever desired of it via artistic license, it is static hence one must presume evolution to see evolutionary links (the animation movie), and fossils are not positively linked to one another hence likely part of other animation movies altogether. Alternative hypotheses such as “independent development” (aka Convergent Evolution) and “directed development” (aka Intelligent Design) would have yielded the same fossil record without confirming the Darwinist model of evolution. Did I say anything about bumblebees?!?

    I see you’re incapable of noticing or understanding metaphors. Pity.

    The fossil record is clearly good for some things, and one of those things is presenting examples of intermediate forms you claim can’t exist. That’s true even if you discount all possibility of evolution. It also offers taxa for phylogenetic analysis, which makes no prior assumptions of relationship and doesn’t require any connecting of dots. This is another subject you seem to know nothing of.

  4. Corneel Corneel
    Ignored
    says:

    Nonlin.org: Bad example. We do know “how and why a car moves”.

    Excellent example. I found us some common ground to start off a real discussion.

    Nonlin.org: Yes cars are precisely designed and tested. Yes we do know what happens if the spark plug fails. Yes, they think of every little detail when designing those cars. And yet no one claims “fitness” for the cars. Why? because “fitness” is nonsense.

    You claim organisms are designed. So what is the function that organisms need to fulfill? I would say reproductive success.

    Nonlin.org: Also the phenotype of the car is known an mostly static (except the fluid levels).

    I agree that living organisms are very different from human-made devices, but remember that the argument from analogy comes from your side of the fence; Don’t blame me for its inadequacy.
    Still, I think the analogy holds reasonably well here; A car has plenty of moving parts, and its parts are subject to wear and tear. But you immediately see that it is silly to claim that in has an infinity of parts, just because you can observe those parts at infinitisemally small time intervals. This is exactly what you were claiming for organisms. There is limited change due to development and senescence, but that will not amount to an infinity of phenotypic traits.

  5. Corneel Corneel
    Ignored
    says:

    Nonlin.org: Adaptive is not the opposite of design. We do design devices to be as adaptive as possible.

    Yes, I understood that. But how can we recognise designed adaptations if the phenotype is unknowable? We need to somehow establish that it fulfills some function, right?

  6. OMagain
    Ignored
    says:

    Nonlin,
    If the only provable experience with new designs is human design, then is your claim that humans designed humans?

  7. Entropy Entropy
    Ignored
    says:

    colewd:
    I would agree that gene duplication could add genetic diversity but there are problems that duplications can cause.It has the potential to add information but this is yet to be established as a reliable way to add information.

    Remains to be established? We’re looking at it when we see those multiplied keratin genes in birds.

    colewd:
    Whether the genes identified in the paper are by duplication or design is not understood.

    Of course it is. For one, designer is philosophically nonsensical, for another, patterns expected from duplications are present.

    colewd:
    I am skeptical of the amount of gene duplication they are claiming.

    If two genes look too similar tone the result of chance, the only option left is duplication.

    colewd:
    What we don’t know from the paper is all the TF’s that are involved in feather manufacturing.

    At least some of them are counted in that very figure. I don’t see the big deal either way. Tis are often duplicated and diverge in the sites they bind. Binding sites in DNA for TFs evolve easily (they’re short sequences).

    colewd:
    I think the bigger issue is how rapidly a gene will break down due to mutation. If you claim rapid purifying selection then you limit variation.

    Only if variation meant mutations deleterious enough to be subject to purifying selection, yet we see that there’s enormous variety that survives, therefore lots of variability that escapes purifying selection. See how easy that is?

    colewd:
    If you don’t then the sequence will rapidly degrade with a very rare possibility of natural selection.I think gene duplication plus mutation is a very poor theory since it requires the goldilocks scenario: too much purifying selection or alternatively finding advantage before the sequence breaks down.

    Have you considered that maybe the life forms whose lineages have succeeded have succeeded precisely because they’ve evolved into a “goldilocks scenario”? It seems like the most obviously evolvable feature of them all.

  8. Neil Rickert
    Ignored
    says:

    OMagain: If the only provable experience with new designs is human design, then is your claim that humans designed humans?

    Humans design humans; bats designed bats; spiders designed spiders. That at least makes more sense to me than what the ID people are arguing.

    If there is design, then it is mostly self-design (occurs during development) and design by the population (otherwise known as “evolution”).

  9. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    The feather paper shows us that new structures require new regulatory elements. New regulatory elements require genetic change that is very poorly explained by the blind watchmaker.

    Why? It’s easy to evolve a new transcription factor binding site; they’re short, and there’s a lot of wiggle room in the sequence that will bind.

    A wing that can support flight requires a large series of regulatory changes not limited to the construction of feathers. The mechanism must produce a group of different feathers that make up the wing structure. These represent large genetic changes from non flying animals.

    I see no evidence that large genetic changes are required. Lots of non-flying theropods have feathers on their arms in a pattern similar to that in a bird.

    Yet you have not observed this process.You are assuming it happened.

    Again, a story without evidence or feasibility.

    Again with the misunderstanding of science. You don’t have to observe (as in watching with your eyes in real time) in order to infer an event. All science is inference from data. The data show that very little morphological change would be needed to turn a small, flightless theropod into a flying one. The data show that all the various beta-keratins evolved through gene duplication and divergence. This appeal to the “Were you there?” syndrome is creationist ignorance at its worst.

    Again, a story that ignores the genetic changes required to achieve navigated powered flight.The flight wing is irreducibly complex starting with bone shape and structure, muscle shape and structure, neurological control , multiple feather types and navigation.All these require coordinated genetic changes of which the blind watchmaker provides no direction.

    Simply repeating your original assertion is not an argument, especially when the data have already shown it to be wrong. The existence of Archaeopteryx and other maniraptoran intermediates falsifies all that. What bone shape and structure? What muscle shape and structure? You inability to go into specifics shows that you have no case. Further, the point of WAIR and other pathways is that they show how precursors to flight could be advantageous and thus facilitate the evolution of structures later useful in flight. You, on the other hand, have no explanation at all for the existence of intermediates.

    The origin of flight is very strong evidence of intelligent design.So is the origin of the flight feather.

    Again, simply repeating your assertion is not an argument and does not deal with the evidence. Have you ever looked at a fossil or at the paleontological literature?

  10. colewd
    Ignored
    says:

    Entropy,

    Remains to be established? We’re looking at it when we see those multiplied keratin genes in birds.

    You’re looking at similar keratin genes and inferring gene duplication. Gene insertions and deletions are associated with many diseases. While you are stating a possible inference it may be wrong.

    Of course it is. For one, designer is philosophically nonsensical, for another, patterns expected from duplications are present.

    This is where you are blocking evidence due to you philosophical beliefs. We have talked through this and I believe you have thought through this as well as anyone but you are now looking at data that may contradict your conviction. Lets go where the data is taking us and not arbitrarily shut off a possible explanation. The more I look at gene duplication the more problematic it looks.

    If two genes look too similar tone the result of chance, the only option left is duplication.

    The option that you are not considering is design. If you dismiss it out of hand there is no chance for you to absorb the magnitude of the data pointing in this direction.

    Only if variation meant mutations deleterious enough to be subject to purifying selection, yet we see that there’s enormous variety that survives, therefore lots of variability that escapes purifying selection. See how easy that is?

    You’re reasoning here is circular. You are assuming that random mutation is the cause of the pattern of the data. Again, the cause maybe design.

    Have you considered that maybe the life forms whose lineages have succeeded have succeeded precisely because they’ve evolved into a “goldilocks scenario”? It seems like the most obviously evolvable feature of them all.

    Genes are mathematical sequences of nucleotides that code for functional proteins. A theory that starts with random change suggests that this will through serendipity cause benefit. I think this whole concept is problematic no matter how powerful you think natural selection is.

  11. Entropy Entropy
    Ignored
    says:

    colewd:
    You’re looking at similar keratin genes and inferring gene duplication.Gene insertions and deletions are associated with many diseases. While you are stating a possible inference it may be wrong.

    The only other option is random similarity, and the probability is infinitesimally small.

    colewd:
    This is where you are blocking evidence due to you philosophical beliefs.

    Not beliefs at all. Just reasoning. Point to any designer that’s not composed of the very things you’re trying to explain with a designer. Can you do that?

    colewd:
    We have talked through this and I believe you have thought through this as well as anyone but you are now looking at data that may contradict your conviction.

    Not at all. The proposal of a designer is very poor philosophy, which includes extreme cherry-picking (the only feature about actual designers that you take into account is the capacity to design, but you don’t want to take into account anything else) and circular logic, compounded by argument from ignorance (you don’t know, or, rather, you refuse to understand, therefore “design”), etc.

    colewd:
    Lets go where the data is taking us and not arbitrarily shut off a possible explanation. The more I look at gene duplication the more problematic it looks.

    Since the data point to gene duplication, I stand by that explanation. I don’t see anything problematic about it. I don’t understand why you refuse to understand something this simple. Looks like a duplication, has hallmarks of duplications (for example, in the kinds of sequences surrounding the duplicated genes looking like those of the other gene copy), therefore it’s a duplication. Another possibility is horizontal gene transfer, but the hallmarks would be somewhat different, and the probability, in multicellular organisms, seems rather small. But, should more evidence for HGT arise I’d consider that.

    colewd:
    The option that you are not considering is design. If you dismiss it out of hand there is no chance for you to absorb the magnitude of the data pointing in this direction.

    The problem here is beyond the poor philosophy. It’s also your lack of understanding about how easily duplications can and do happen. There’s plenty of gene-copy (and DNA-segment) variation with no-big-deal phenotypic effects, even in humans. You only know about the problematic ones because scientists study bad phenotypic effects for obvious reasons (because they’re bad!), while healthy people are rarely studied (there’s little money to study non-disease, right?).

    colewd:
    You’re reasoning here is circular. You are assuming that random mutation is the cause of the pattern of the data. Again, the cause maybe design.

    My reasoning is circular? It’s you who refuses to consider that natural processes have done all of this. It’s you who refuses to understand how large, and old, nature is, and thus how easily natural processes can solve these “problems.” It’s you who doesn’t notice that a “goldilocks situation” would be a very easy-to-understand example of an evolvable feature. I suspect that you think it’s circular precisely because it looks so naturally, obviously, evolvable.

    colewd:
    Genes are mathematical sequences of nucleotides that code for functional proteins.

    Nonsense. You conceptualize them as mathematical sequences, but they’re just biochemical polymers. We went through this before. You should not mistake your concepts for what your concepts are trying to represent.

    colewd:
    A theory that starts with random change suggests that this will through serendipity cause benefit.

    Not at all. The theory starts with random mutations causing variation across many individuals. Many individuals don’t make it. The ones that make it have variations, the variations might be beneficial. It has a huge cost in millions upon millions of life forms that just won’t make it. I would not call that serendipity.

    colewd:
    I think this whole concept is problematic no matter how powerful you think natural selection is.

    What you think is inconsequential to what nature can and has done. The question as to the smallest details about how, might be somewhat open, but that would be our problem in understanding, not nature’s problem in performing.

    From where I sit, when I confront something I cannot explain (which is not the case here), that means I’m ignorant about something. Being ignorant about something doesn’t make a “designer” any less of a nonsensical, philosophically poor, “explanation.”

  12. Nonlin.org
    Ignored
    says:

    Neil Rickert,

    What rules is it breaking?

  13. Neil Rickert
    Ignored
    says:

    Nonlin.org:
    Neil Rickert,

    What rules is it breaking?

    Criticizing the person (poster) rather than the content.

  14. Nonlin.org
    Ignored
    says:

    John Harshman: Hey, I thought I was supposed to be the intelligent person you wanted to talk to. Now you’re acting as if I’m just as stupid as everybody else here. Such a quick descent from the heights! I have indeed answered the questions, or at least the fraction that were intelligible. (Incidentally, have you ever considered the possibility that you are not being absolutely clear, and that some further explanation might be required?) I might add that you seem oddly arrogant for a person who appears to know nothing about the subject.

    OK, now that we know what 80/20 means, how does it make your question intelligible? Still don’t see it. And what do you mean by “dead-end link”? The only link I can think of was to my paper on crocodylians. It wasn’t broken, and I think it was quite relevant to your question. I even think I explained why it was relevant. Where did I go wrong?

    You should pull back from yourself a little. You don’t get automatic obeisance. You have to work for it. When I say I don’t understand your question, I mean I don’t understand it and invite you to explain further, which is what you should have done. I’m not sure what you mean by “recommending the other”, so perhaps that would be an opportunity to explain. Also, it would be good not to just assume my questions are silly; the polite thing would be to answer them as best you can. I consider your response to be whiny, by the way.

    Sorry, but reproductive success is something that individuals have. Selection happens to individuals and results in evolution in the population. This is something I understand and you don’t.

    What is this even responding to? The last thing I did was ask what you mean. How can I answer until I know?

    Why “only”? How would that be relevant? There is some evidence that stripes deter tsetse flies from biting. Do you think that might impact survival or reproductive success?

    That makes no sense to me. I’ll throw some words at it in hopes of hitting your point. You may be saying that there is a stochastic element to survival (or reproductive success), and that’s correct. But it doesn’t invalidate natural selection. It just means that you have to get data from many individuals to test it, so as to average out the noise. And of course different environments select for different characteristics, which you have said isn’t your point.

    I find that a trivial and useless point. Yes, a species survives only if some individuals reproduce. But the causation is all in one direction. Individuals don’t reproduce only if the species survives; species survival is just the result. Your quote contradicts your claim.

    No, I don’t think I’m forgetting something. The environment determines which genotypes are favored. How is this a problem?

    You should know that I’m not going to your web site, since your postings here suggest that I will find only nonsense. If you want to present some evidence, present it here. Your figures of 69% and 50% represent two incommensurable measures, and even if they were the same sort of thing your interpretation is unclear and, I strongly suspect, nonsensical. All things being equal, the more closely related to a species we are the more similar its genome will be to ours, by whatever measure you care to consult. You have no idea what I think DNA is. And the evidence for human relationships to other taxa is overwhelming. I could explain some of it to you if you cared, which I suspect you don’t. Hey, I see you didn’t answer my question.

    Your are mistaken. Science doesn’t deal in proof, just evidence. Experiments don’t show what you suppose, though evolution can be reversible over the short term.

    The argument is simple. The evidence shows common descent. The genetic differences among species are of the sort that can be accounted for by the types of mutations we observe. Given all that, what can account for the differences in morphology? Do you have a hypthesis, or do you reject the data?

    Did you actually find that from Google? I’m suspicious.

    So you’re a young-earth creationist, then. Pity. No, phylogenetic analysis doesn’t presuppose evolution. Why would you think so? Do you know anything about it?

    If natural selection doesn’t work, how does antibiotic resistance arise? Sure, it’s reversible. Usually it’s on a plasmid, and the plasmid can be lost. Often it’s deleterious in an environment lacking in antibiotics. But not always. The problem with human design is that life doesn’t look anything like it.

    I see you’re incapable of noticing or understanding metaphors. Pity.

    The fossil record is clearly good for some things, and one of those things is presenting examples of intermediate forms you claim can’t exist. That’s true even if you discount all possibility of evolution. It also offers taxa for phylogenetic analysis, which makes no prior assumptions of relationship and doesn’t require any connecting of dots. This is another subject you seem to know nothing of.

    Yes, you do seem to be the most intelligent Darwinista from this bunch – let this not go to your head 🙂
    Fine, you get the benefit of the doubt. Silly question was: “did you ever read a scientific paper?” It’s not arrogance – if you are honest, you will eventually agree with me. The link was not an argument, hence “dead end”. If you don’t read mine, should I read yours? 🙂

    To know what we’re talking about, here is my “Natural Selection” summary again:
    1. Natural Selection fails its definition – survival is not directly tied to phenotype
    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’
    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

    1. How did we get to your comment? Point is, phenotype is not enough. Wikipedia definition fails. Google’s definition mentions the environment, but not phenotype and introduces “better adapted”. Well duh – tautology.
    2. Do you attach those qualifiers above to “natural selection”? If not, let’s move on.
    3. Maybe stripes help with comfort. Would zebra go extinct without them? You have no idea, but that can be tested. Address the claim from the list.
    4. Example given shows “fitness” is whatever you want to be. The only measure is survival of descendants (there is no fitness without survival). What data other than survival of descendants? Environment doesn’t select – see 5.
    5. “Individuals don’t reproduce only if the species survives”?!? Yes, individuals reproduce only if the species survives. An extinct species does not reproduce. Reproduction = Survival and Survival = Reproduction. Why is this so hard for you?
    6. When interacting with the inert environment, organisms self-select rather than being selected by this environment. They do not go where they cannot survive. Humans and bacteria will move away from harm. It is intelligent selection. Even plants follow the sun when possible.
    7. What’s the point of asking if you’re not interested in the evidence? “The more similar” is not necessarily “evolution” – witness similarity between car models. Anyway, we deviated from the initial claim 7 above. Address that.
    8. You’re just denying without arguments and not even addressing claim 8 above.
    9. The evidence does not show “common descent” – you’re presupposing that. Darwin, Lamarck, etc. had the philosophy before they came up with the narrative. “what can account for the differences in morphology?” – how about common design? We see that happening all the time. In addition, isn’t “convergent evolution” common design?
    10. Silly question? Anyway do you agree with claim 10 or not?
    11. Wikipedia: “phylogenetic tree or evolutionary tree” – why are you lying so blatantly?
    12. Antibiotic resistance is built in characteristic of all living – you have it and is called immunity. How does life not look like human design? Besides, you misunderstand the claim. The point is, if “natural selection” worked, we would apply the method to develop cars, computers, etc. We don’t apply it because it doesn’t work.

    Con: What about organic design? Isn’t that natural selection at work? http://www.nature.com/news/supercomputer-redesign-of-aeroplane-wing-mirrors-bird-anatomy-1.22759 and http://www.genetic-programming.org/sp2003/Marta.pdf.

    Pro: No. This is just iterative optimization of a given design. In this case, the wing shape, the material, the environmental forces and the optimization target are all given. The algorithm will not generate a new wing shape or material and it will stop converging as soon as the environment is less than perfectly defined. In addition, this design is radically different from the previous one, and the next iteration will certainly be radically different than this one (no gradualism).
    13. What metaphor? “Intermediate” presupposes evolution – don’t you understand? Whatever you’re trying to say, you’re not addressing my previous argument re fossils. And you deviate again from the original claim 13 above.

  15. Nonlin.org
    Ignored
    says:

    Corneel: Excellent example. I found us some common ground to start off a real discussion.

    You claim organisms are designed. So what is the function that organisms need to fulfill? I would say reproductive success.

    I agree that living organisms are very different from human-made devices, but remember that the argument from analogy comes from your side of the fence; Don’t blame me for its inadequacy.
    Still, I think the analogy holds reasonably well here; A car has plenty of moving parts, and its parts are subject to wear and tear. But you immediately see that it is silly to claim that in has an infinity of parts, just because you can observe those parts at infinitisemally small time intervals. This is exactly what you were claiming for organisms. There is limited change due to development and senescence, but that will not amount to an infinity of phenotypic traits.

    Dude, I am not proposing “natural selection”, you are …and I am not getting into the “purpose” discussion.

    Let’s just see if your “natural selection” mechanism model works or not. There is no analogy for the model – cars simply do not follow “natural selection” in any way. Yes, the car “phenotype” is infinite as well, but forget that infinity.

    I am only asking 4 simple questions about your model that you should know to justify said model. I am not asking for all infinite phenotype measures – just give the 80/20 pareto, so just reply with the 20% (or fewer) metrics that determine 80% of the answer for any biologic entity including populations:
    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

    Of all proponents of “natural selection”, not one is attempting to answer these basic questions? Are you kidding me? Something is seriously wrong with you guys.

  16. Nonlin.org
    Ignored
    says:

    Corneel: Yes, I understood that. But how can we recognise designed adaptations if the phenotype is unknowable? We need to somehow establish that it fulfills some function, right?

    It’s not clear what you’re asking.

    OMagain:
    Nonlin,
    If the only provable experience with new designs is human design, then is your claim that humans designed humans?

    Ants design too and so do beavers, bees, and many others. And we do recognize those entities as designed when we encounter them.

  17. Richardthughes Richardthughes
    Ignored
    says:

    tl;dr – has someone rolled out ERVs, broken vitamin C gene, chromosomal fusion etc?

  18. Corneel Corneel
    Ignored
    says:

    Nonlin.org: Dude, I am not proposing “natural selection”, you are

    Not at the moment, I am not. I don’t see any point to discussing that topic until we got that “infinite unstable phenotype” nonsense straightened out.

    Nonlin.org: and I am not getting into the “purpose” discussion.

    You are not? That is rather telling. How can you claim one design is “better” than another without specifying what it’s better at?

    Nonlin.org: Yes, the car “phenotype” is infinite as well, but forget that infinity.

    WHAT?!? A car has an infinity of parts?!? So now, by analogy to living organisms, we are unable to learn anything useful about the car “phenotype”? You might want to retract that statement.

    Nonlin.org: Of all proponents of “natural selection”, not one is attempting to answer these basic questions? Are you kidding me? Something is seriously wrong with you guys.

    Patent nonsense, it’s just that your bizarre definition of a phenotype got us stuck at #1.

  19. Corneel Corneel
    Ignored
    says:

    Nonlin.org: Corneel: Yes, I understood that. But how can we recognise designed adaptations if the phenotype is unknowable? We need to somehow establish that it fulfills some function, right?

    It’s not clear what you’re asking.

    You associate phenotypes exclusively with evolutionary theory, but the concept derives from studies on heredity (genetics) and has much broader application. I think you also need it in a design framework.

    Up till now, you have been pretending that the perceived inability to link an isolated phenotypic trait to survival is a problem that exclusively concerns evolutionary biology. But you seem to be oblivious of the fact that if you want to establish that some trait an is “exquisitely designed adaptation” you need to link it to survival (or some other function) as well!

  20. Entropy Entropy
    Ignored
    says:

    Corneel,

    I don’t think Nonlin can understand anything you’re saying. Nonlin is stuck in some mental state that makes her jump from one thing to another when confronted with things that contradict her stance, and an astounding inability to connect the dots. Nonlin doesn’t remember what she wrote, doesn’t understand when she’s given an answer, cannot focus, cannot consider that she might be wrong, and thinks that she’s the most amazing thinker in the planet. I think she’s unreachable.

  21. Entropy Entropy
    Ignored
    says:

    Richardthughes:
    tl;dr – has someone rolled out ERVs, broken vitamin C gene, chromosomal fusion etc?

    It would be pointless, We’ve been trying to talk to a person who thinks that if she finds a definition for natural selection using google, and then determines that the definition is not to her liking, then “natural selection failed its definition.” After other equally “substantial” claims, she concludes that natural selection doesn’t exist.

    I kid you not.

  22. colewd
    Ignored
    says:

    John Harshman,

    Why? It’s easy to evolve a new transcription factor binding site; they’re short, and there’s a lot of wiggle room in the sequence that will bind.

    The binding site is not the only problem. Another problem is the irreducibly complex protein structure that initiates transcription.

    The data show that very little morphological change would be needed to turn a small, flightless theropod into a flying one.

    What do you mean by very little morphological change? What about genetic change?

    Simply repeating your original assertion is not an argument, especially when the data have already shown it to be wrong. The existence of Archaeopteryx and other maniraptoran intermediates falsifies all that. What bone shape and structure? What muscle shape and structure?

    How do you define intermediate? The fossil evidence and your proposed mechanism are very different things. If you consistently had evidence of very small steps you would still have the problem of random changes to a sequence likely breaking down the sequence.

    Further, the point of WAIR and other pathways is that they show how precursors to flight could be advantageous and thus facilitate the evolution of structures later useful in flight. You, on the other hand, have no explanation at all for the existence of intermediates.

    Do you really think intermediates points to a specific mechanism of change? I understand this argument prior to the discovery of the transcription translation mechanism but not since.

    Again, simply repeating your assertion is not an argument and does not deal with the evidence. Have you ever looked at a fossil or at the paleontological literature?

    I have already argued that flight is irreducibly complex. I am just tying together conclusions from that argument. I agree that I have not yet properly argued that feather manufacturing is irreducibly complex, however the Venn diagram potentially contains supporting evidence.

    I have looked at both fossil and paleontological literature but I have very little competence here.

  23. keiths keiths
    Ignored
    says:

    colewd,

    I have looked at both fossil and paleontological literature but I have very little competence here.

    Wait — are you implying that you’re competent in other relevant areas?

  24. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    The binding site is not the only problem.Another problem is the irreducibly complex protein structure that initiates transcription.

    I have asked you many times to try harder to communicate. When you say “irreducibly complex protein structure that initiates transcription”, what are you referring to? And what did you mean by “new regulatory elements” if not transcription factor binding sites?

    What do you mean by very little morphological change? What about genetic change?

    We have no direct access to the genetic changes; we can only compare birds and crocodiles, and that isn’t a great window. But is it not reasonable to suppose that small morphological changes can be produced by small genetic changes? It is, after all, what we observe in living populations. Now what I mean by “very little morphological change” should not be unclear. Archaeopteryx closely resembles many other maniraptorans, ones that couldn’t fly, in any respect you care to mention.

    How do you define intermediate?

    Again, I don’t see how that could be unclear. I means “in between”, in this case morphologically between primitive theropods and modern birds. I refer both t a mixture of features (e.g. flight feathers and a long, bony tail) an the intermediate nature of some features (e.g. arms longerthan in the typical theropod, but not modified in any other way).

    The fossil evidence and your proposed mechanism are very different things. If you consistently had evidence of very small steps you would still have the problem of random changes to a sequence likely breaking down the sequence.

    Word salad again. Yes, evidence and mechanism are different things, but I don’t think that’s what you meant to say. Your second sentence shows that you have no understanding of natural selection or of DNA or protein sequence evolution. A great many random changes are neutral, many of the rest are deleterious, and a few are (given some selective regime) advantageous. Selection ignores the neutral ones, eliminates the deleterious ones, and promotes the advantageous ones. Deleterious mutations do not achieve high frequency in the population.

    Do you really think intermediates points to a specific mechanism of change? I understand this argument prior to the discovery of the transcription translation mechanism but not since.

    I don’t think you ever understood the argument, nor do you have any idea of what the “transcription translation mechanism” might have to do with it. Intermediates don’t point to a specific mechanism, but they do falsify your claims of IC, and they do suggest the plausibility of selection acting on small changes as a mechanism.

    I have already argued that flight is irreducibly complex.I am just tying together conclusions from that argument.I agree that I have not yet properly argued that feather manufacturing is irreducibly complex, however the Venn diagram potentially contains supporting evidence.

    No, you have claimed that flight is irreducibly complex, which is not arguing. And I have falsified your claim by pointing to intermediates. The Venn diagram contains no evidence at all for IC.

    I have looked at both fossil and paleontological literature but I have very little competence here.

    That doesn’t stop you when you pronounce on on the molecular and phylogenetics literature. What’s the difference?

  25. Adapa
    Ignored
    says:

    colewd:
    If you consistently had evidence of very small steps you would still have the problem of random changes to a sequence likely breaking down the sequence.

    Unless the large majority of those changes were neutral to reproductive fitness. And unless there was a mechanism like natural selection to weed out the changes that “broke down” the function.

    It really is like trying to teach a cinderblock.

    I have already argued that flight is irreducibly complex.

    You’ve already been reminded half a dozen times science already understands how natural processes can produce IC features. But you’re hunkered down in your Fortress of Invincible Ignorance, no science can ever seep in.

    I have looked at both fossil and paleontological literature but I have very little competence here.

    New leading candidate, Understatement of the Year.

  26. Nonlin.org
    Ignored
    says:

    Corneel: Not at the moment, I am not. I don’t see any point to discussing that topic until we got that “infinite unstable phenotype” nonsense straightened out.

    You are not? That is rather telling. How can you claim one design is “better” than another without specifying what it’s better at?

    WHAT?!? A car has an infinity of parts?!? So now, by analogy to living organisms, we are unable to learn anything useful about the car “phenotype”? You might want to retract that statement.

    Patent nonsense, it’s just that your bizarre definition of a phenotype got us stuck at #1.

    Not my definition. Google:
    “phe·no·type
    ˈfēnəˌtīp/Submit
    nounBIOLOGY
    the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment”

    I don’t claim a design is better than other. How would I know? Better how? But you guys claim “better adapted”. You’re badly confused.

    Not an infinity of parts, an infinity of set of observable characteristics because you can measure for ever and ever all the details. If you disagree, make your case for “phenotype is a finite set of parameters”. Your “analogy” doesn’t hold – that’s not what I said. Are you planting bombs now?

  27. Nonlin.org
    Ignored
    says:

    Corneel: Up till now, you have been pretending that the perceived inability to link an isolated phenotypic trait to survival is a problem that exclusively concerns evolutionary biology. But you seem to be oblivious of the fact that if you want to establish that some trait an is “exquisitely designed adaptation” you need to link it to survival (or some other function) as well!

    As said, in a car “phenotype” is static, so that’s a big deal right there. Beyond that, just as with organisms, the “survival” of that car line is based on many factors, not just “phenotype”. In other words, you can measure your car all you want – that won’t tell you that they will continue the model or scrap and redesign it next year. And small things no one knows about or measures can kill it – see VW diesel scandal.

  28. colewd
    Ignored
    says:

    Entropy,

    The only other option is random similarity, and the probability is infinitesimally small.

    I think there is a third possibility but for argument sake I will agree that gene duplication and variation is the cause of the similarity of all the keratin genes.

    Not at all. The proposal of a designer is very poor philosophy, which includes extreme cherry-picking (the only feature about actual designers that you take into account is the capacity to design,

    This is a legit point and a weakness of the argument however if we understand the weakness but don’t totally discount the argument there is lots of evidence pointing in this direction.

    The problem here is beyond the poor philosophy. It’s also your lack of understanding about how easily duplications can and do happen.

    Can you support this claim? I am aware of this happening once in the Lenski experiment with a transporter transcription factor gene. I have not seen experimental data on multicellular animals at this point.

    Not at all. The theory starts with random mutations causing variation across many individuals. Many individuals don’t make it. The ones that make it have variations, the variations might be beneficial. It has a huge cost in millions upon millions of life forms that just won’t make it. I would not call that serendipity.

    The Venn data tells that 63 transcription factors have been identified to build feathers. They need to be able to manufacture at least 2 types of feathers for flight.

    Primary feathers: These are the largest of the flight feathers and propel the bird through the air. They are the farthest away from the body, attached to the skin of the wing on the ‘hand’ of the bird. In most bird species, there are 10 primary feathers on each wing. If these flight feathers are damaged or lost, a bird cannot fly.
    Secondary feathers: These run along the ‘arm’ of the wing and sustain the bird in the air, giving it lift. The number of secondary feathers varies with different species. Experiments have shown that, if half of the secondaries are removed, a bird will still be able to fly, but some control will be lost.
    Tertiary feathers: These are on the ‘upper arm’ of the bird. They are the short, innermost flight feathers on the rear edge of a wing, close to the body of the bird. They are not as important for flight as the primary and secondary feathers.

    The design hypothesis is the argument that appears to match this irreducibly complex system. During embryo development the bird needs to express bones, skin and feathers which are expressed in such a way that the animal can create powered flight.

  29. Nonlin.org
    Ignored
    says:

    John Harshman: colewd:
    I have asked you many times to try harder to communicate.
    …Word salad again.
    …I don’t think you ever understood the argument,

    I have seen those before. The problem is that you speak New Astrology aka Evolutionary Phrenology while others speak Logic.

    John Harshman: You have no idea what I think DNA is.

    I do. You told me what you think, and it’s wrong. I sent you the link explaining why.

  30. Nonlin.org
    Ignored
    says:

    Entropy: We’ve been trying to talk to a person who thinks that if she finds a definition for natural selection using google, and then determines that the definition is not to her liking, then “natural selection failed its definition.”

    Probably a waste replying to you:
    Wikipedia, not Google: https://en.wikipedia.org/wiki/Natural_selection
    1. If Wikipedia is wrong, say so and quote a better definition.
    2. What if Wikipedia is right and your other definition is wrong? How would we know?
    3. In what sense is Wikipedia wrong?

    See? Your beef is with Wikipedia, not with “she”.

    Btw, Google is just as bad: “the process whereby organisms better adapted to their environment tend to survive and produce more offspring.” – a tautology relying on a “process”. And check out process = “steps taken in order to achieve a particular end”. Taken by who? What end?

    Slippery definitions are a huge problem in “evolution”. Maybe you should work on that next.

  31. John Harshman John Harshman
    Ignored
    says:

    Nonlin.org: I have seen those before. The problem is that you speak New Astrology aka Evolutionary Phrenology while others speak Logic.

    You think Bill speaks logic? Interesting.

    You told me what you think, and it’s wrong. I sent you the link explaining why.

    When did I tell you? What did I say? I think you’re mistaking something here. But OK, I’ll look at your link. Wait for me here.

    …Well, that was painful. It would take me many pages to explain all your misconceptions. But at base it was just an argument from personal incredulity: you don’t believe that the information in DNA could be enough to account for development and morphology, though you don’t have an alternative. Sorry, “I don’t believe it” isn’t a good argument. Now there is a sense in which DNA is not the basis of development, since it’s really the interactions among DNA and its environment (regulatory proteins and RNAs, physical features of cells, and such) that produces he phenotype. But then again, differences between species do ultimately result from differences in their genomes. There is no other significant factor. Sorry.

    I also can’t stop myself from pointing out that your human-chimp comparison and your human-rat comparison are commensurable: they report the mean site difference between aligned sequences. But the human-banana comparison is something else entirely: the percentage of human genes with recognizable homologs in banana. And your human-human comparison is still another thing, though I don’t know what it would be. It’s much too big for any comparison I can think of. If you were talking about the mean site difference, that would be around 0.1 percent.

    Now, perhaps you could read my link. It really is relevant. I’ll explain why it’s relevant if you want.

  32. colewd
    Ignored
    says:

    John Harshman,

    I have asked you many times to try harder to communicate. When you say “irreducibly complex protein structure that initiates transcription”, what are you referring to? And what did you mean by “new regulatory elements” if not transcription factor binding sites?

    I am referring to protein transcription factors.

    Transcription factors are a very diverse family of proteins and generally function in multi-subunit protein complexes. They may bind directly to special “promoter” regions of DNA, which lie upstream of the coding region in a gene, or directly to the RNA polymerase molecule.

    Harshman:

    Word salad again. Yes, evidence and mechanism are different things, but I don’t think that’s what you meant to say. Your second sentence shows that you have no understanding of natural selection or of DNA or protein sequence evolution

    This is just very different view of what mutations really do in biological systems based on experimental results. If a protein coding gene sequence of 240 nucleotides or 80 amino acids has 10^11 more unsuccessful ways of binding to ATP then successful binding, what do you think happens to it when its sequence starts changing randomly?

    Your claim is based on DNA that you hypothesize is 90% junk. If DNA is junk then lots of mutations can be neutral. The new genes that code for proteins we are observing according to current evolutionist thinking come from copied functional genes that code for proteins; not junk. These changes are rarely neutral or beneficial. With the size of non functional gene space we observe from experiments, mutations break down protein coding gene sequences.

    No, you have claimed that flight is irreducibly complex, which is not arguing. And I have falsified your claim by pointing to intermediates. The Venn diagram contains no evidence at all for IC.

    Intermediates are independent of the irreducible complexity argument. Irreducible complexity is challenging the Darwinian mechanism.

    Flight is irreducibly complex because components such as muscle structure, bone structure, skin that expresses the right genes that can produce the right flight feathers in the right location work together to enable flight. Take away any of these components and the bird will not fly.

    The Venn diagram contains no evidence at all for IC.

    It shows 56 new regulatory proteins that work together to build feathers. A simple set of knock out experiments could validate the hypothesis. If you take away components and the system no longer produces the right wing structure, then the regulatory system is irreducibly complex.

  33. Corneel Corneel
    Ignored
    says:

    Nonlin.org: I don’t claim a design is better than other. How would I know? Better how? But you guys claim “better adapted”. You’re badly confused.

    Confused? Indeed I am. I thought you accepted the existence of adaptations. Like here:

    Among the most common adaptations are body color/size/shape, hair type, antibiotic/chemical resistance, and behavior, and even these are limited in scope.

    and that you claimed that designs could be optimised to fit a certain environment, like here:

    Designs do not transform into better designs without crossing an inevitable optimization gap. Given a certain environment, once a design is optimized for a certain function, it becomes suboptimal as soon as the function, the structure, or the materials changes. Until the new design is optimized for that particular change, it remains inferior to an old design already optimized to that environment.

    But we can never learn this for organisms, because the phenotype is unstable and infinite, thus unknowable. If that is not what you meant to say, than you are communicating rather poorly.

  34. Corneel Corneel
    Ignored
    says:

    Nonlin.org: Not an infinity of parts, an infinity of set of observable characteristics because you can measure for ever and ever all the details. If you disagree, make your case for “phenotype is a finite set of parameters”. Your “analogy” doesn’t hold – that’s not what I said.

    Very well, then I misunderstood and your claim is that a car has an “infinity of set of observable characteristics”. I doesn’t change a thing: by analogy to living organisms, we are unable to learn anything useful about the car “phenotype”, right?

    Oh, and the analogy is yours, not mine:

    Witness the manufacturing of your own car. It is designed and manufactured just as you are.

    But if I understand correctly, we can never establish that cars are designed, because cars have an infinite set of observable characteristics, so we cannot learn anything useful about them.

  35. Corneel Corneel
    Ignored
    says:

    Nonlin.org: As said, in a car “phenotype” is static, so that’s a big deal right there. Beyond that, just as with organisms, the “survival” of that car line is based on many factors, not just “phenotype”. In other words, you can measure your car all you want – that won’t tell you that they will continue the model or scrap and redesign it next year. And small things no one knows about or measures can kill it – see VW diesel scandal.

    There are two things in here: the issue of whether the phenotype is knowable and whether fitness is a coherent concept. I am only focusing on the former, because discussing fitness is pointless without agreement on the phenotype.

    You are claiming now that organisms are completely unlike cars, because organisms and cars have a dynamic phenotype and a static phenotype, respectively. This flatly contradicts the statement you made to Entropy:

    Witness the manufacturing of your own car. It is designed and manufactured just as you are.

    Well no, apparently not, since you are now denying that the analogy is adequate. Moreover, since you claim that we cannot learn anything useful about the phenotype of organisms, as it is unstable and infinite, we cannot tell whether they are designed and manufactured. Even worse, since you have chosen to claim that cars have an infinite set of observable characteristics as well, we can only learn that a car is manufactured by witnessing its construction.

    Can we please agree that this is ridiculous?

  36. Entropy Entropy
    Ignored
    says:

    colewd:
    Can you support this claim?I am aware of this happening once in the Lenski experiment with a transporter transcription factor gene.I have not seen experimental data on multicellular animals at this point.

    I supported the claim. I told you, there’s plenty of copy number variations all over the place in healthy humans. I told you that you know only of harmful ones because those are the most intensely studied for obvious reasons (they are harmful!).

    colewd:
    The Venn data tells that 63 transcription factors have been identified to build feathers. They need to be able to manufacture at least 2 types of feathers for flight.

    The Venn diagram shows that 63 Tis are involved in regulating those genes they point to, but it doesn’t say that the TFs are new. So, the binding sites in DNA evolve easily, and Tis could be involved in other things, or also be the result of duplications. I still don’t see any problem, let alone a problem as large and unsurmountable, that we’d have to quit trying to explain it.

    colewd:
    The design hypothesis is the argument that appears to match this irreducibly complex system. During embryo development the bird needs to express bones, skin and feathers which are expressed in such a way that the animal can create powered flight.

    There’s nothing irreducibly compels about bird flight. I’ve witnessed myself the enormous variety in intermediate capacities to fly, and I can easily see how this could happen in steps. From embryo studies, we know that the bones and muscles develop initially as any other vertebrate’s bones and muscles, only their relative sizes and fibre composition starts differing until you get overdeveloped chest muscles, bones this long, bones that hollow, bones that short, etc, that makes a wing. Since the pieces are mostly the same as in flightless animals, an evolutionary scenario building on differences in developmental patterns fits perfectly.

    The design “hypothesis,” again, is so philosophically poor that I’d have a very hard time considering it. The evidence would have to be authentically extraordinary. It’s never enough to point to something that’s hard to explain. It has to be positive evidence, not negative. It’s not enough to say “as far as we understand nature, this could not happen by itself!” It has to be much more obvious. Once the problems with the “designer” “hypothesis” are clear enough, we’re left with the conclusion that the supposed “hypothesis” is just an attempt to justify religious beliefs by performing very poor science and philosophy. It’s people working towards their preconceived “conclusions.”

  37. OMagain
    Ignored
    says:

    colewd,

    The design hypothesis is the argument that appears to match this irreducibly complex system.

    If flight is an irreducibly complex system, how come bats can fly with fur not feathers?

  38. Corneel Corneel
    Ignored
    says:

    OMagain: If flight is an irreducibly complex system, how come bats can fly with fur not feathers?

    Because bats have a different irreducibly complex system, silly!

  39. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,
    I am referring to protein transcription factors.

    Then you should actually say so. Who says that feather evolution requires any novel transcription factors?

    This is just very different view of what mutations really do in biological systems based on experimental results.If a protein coding gene sequence of 240 nucleotides or 80 amino acids has 10^11 more unsuccessful ways of binding to ATP then successful binding, what do you think happens to it when its sequence starts changing randomly?

    So many problems with that. First, most of a protein doesn’t consist of active sites. Second, many mutations are silent. Third, many non-silent mutations are to similar amino acids that have no strong effect on activity. Fourth, most mutations do not get to high frequency or become fixed; once again you ignore natural selection.

    Intermediates are independent of the irreducible complexity argument.Irreducible complexity is challenging the Darwinian mechanism.

    Yes, and the existence of intermediates makes “the Darwinian mechanism” more credible while it simultaneously demolishes the notion of IC. By definition, there can be no functional intermediates in an IC system.

    Flight is irreducibly complex because components such as muscle structure, bone structure, skin that expresses the right genes that can produce the right flight feathers in the right location work together to enable flight. Take away any of these components and the bird will not fly.

    I see you’re keeping it all vague enough that you can ignore the evidence. I have asked you repeatedly what muscle/bone structure you are referring to, and you have always ignored me. And your own reference shows that you can take away the secondaries and a bird can still fly.

    It shows 56 new regulatory proteins that work together to build feathers.

    Where does it say “new”? I think you may be confused about what that paper says. Have you ever looked at the actual paper, rather than just that one figure?

  40. Nonlin.org
    Ignored
    says:

    John Harshman: But at base it was just an argument from personal incredulity: you don’t believe that the information in DNA could be enough to account for development and morphology, though you don’t have an alternative. Sorry, “I don’t believe it” isn’t a good argument. Now there is a sense in which DNA is not the basis of development, since it’s really the interactions among DNA and its environment (regulatory proteins and RNAs, physical features of cells, and such) that produces he phenotype. But then again, differences between species do ultimately result from differences in their genomes. There is no other significant factor. Sorry.

    What are you talking about? This is not even abut biology, chemistry, or philosophy, it’s about information. Do you have any Information Theory credentials? Well, I do. And I have demonstrated with clear evidence why DNA does not account for human and in fact any organism development from zygote.

    Everything is nonsense “argument from incredulity” with you guys. And the totally illogical “don’t have an alternative” so let’s keep a known wrong “explanation” because there is no “alternative”?!? How about “we don’t know yet, and maybe we’ll find out one day”? How can you utter with any confidence: “There is no other significant factor”? How the heck can you be certain? Did pope Dawkins say so?

    It seems I might have given you way too much intellectual credit.

  41. Nonlin.org
    Ignored
    says:

    Corneel:
    1. Confused? Indeed I am. I thought you accepted the existence of adaptations. Like here:
    2. and that you claimed that designs could be optimised to fit a certain environment, like here:
    3. But we can never learn this for organisms, because the phenotype is unstable and infinite, thus unknowable. If that is not what you meant to say, than you are communicating rather poorly.
    4. Very well, then I misunderstood and your claim is that a car has an “infinity of set of observable characteristics”. I doesn’t change a thing: by analogy to living organisms, we are unable to learn anything useful about the car “phenotype”, right?
    5. But if I understand correctly, we can never establish that cars are designed, because cars have an infinite set of observable characteristics, so we cannot learn anything useful about them.
    6. There are two things in here: the issue of whether the phenotype is knowable and whether fitness is a coherent concept. I am only focusing on the former, because discussing fitness is pointless without agreement on the phenotype.
    7. You are claiming now that organisms are completely unlike cars, because organisms and cars have a dynamic phenotype and a static phenotype, respectively. This flatly contradicts the statement you made to Entropy:
    8. Well no, apparently not, since you are now denying that the analogy is adequate. Moreover, since you claim that we cannot learn anything useful about the phenotype of organisms, as it is unstable and infinite, we cannot tell whether they are designed and manufactured. Even worse, since you have chosen to claim that cars have an infinite set of observable characteristics as well, we can only learn that a car is manufactured by witnessing its construction.

    1. Remember, NS is supposed to explain “evolution”, not adaptations. You focus on adaptations, but that’s not what we’re debating. Of course adaptations happen.
    2. Yes, optimizations happen
    3. This is the disconnect. Phenotypes show that a camel is adapted to desert and polar bear to the arctic, but phenotype is infinite, hence does not explain why the camel and why the polar bear instead of some other virtual organism. Phenotype also does not forecast when these two might go extinct and most certainly does not explain how both camel and polar bear came into being.
    4. No. Again, phenotype informs us of some things, but not enough to forecast survival of this or that organism or car line – see 1. target
    5. Doesn’t follow. Infinite phenotype does not inform on what might kill a car line or a species – has nothing to do with designed or not. – see 1. target.
    6. Ok
    7. Not “completely unlike cars”. Just much more complicated.
    8. Previous points should dispel your 8. claims.

  42. Nonlin.org
    Ignored
    says:

    To those that complained about the definition of “natural selection”, here are some immaterial follow up changes in the analysis:
    1. Natural Selection described as “the differential survival and reproduction of individuals due to differences in phenotype” or alternatively as “survival of the best adapted”.
    2. No. Natural Selection fails since survival is not directly tied to phenotype and “survival of the best adapted” is tautological. In a small farm, only organisms closely related to their wild cousins survive, but agribusinesses select for chickens with oversize breasts and research labs select for populations with specific genetic mutations requiring tight environments to survive. As shown, all these different organisms may or may not survive regardless of their phenotype. The only measure of “selection” is survival – we only know if and organism was selected if it survives and reproduces. “Best adapted” is also unknowable separate from survival.

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

    Again, if you have a better description of “natural selection” and think Wikipedia, Google and the others I checked are still wrong, let me know.

    Incredibly, to date no one attempted to 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

  43. dazz dazz
    Ignored
    says:

    Nonlin.org,

    Your links are being blocked (for a good reason). Why do you keep trying to spam the blog with your bullshit every fucking time you post?. Definition of stupidity comes to mind. Are you by any chance Otangelo’s brother? his uncle? or maybe both?

  44. John Harshman John Harshman
    Ignored
    says:

    Nonlin.org: What are you talking about? This is not even abut biology, chemistry, or philosophy, it’s about information. Do you have any Information Theory credentials? Well, I do. And I have demonstrated with clear evidence why DNA does not account for human and in fact any organism development from zygote.

    No, I have no credentials, but I see no evidence that you do either. What evidence? All I see is that you don’t think, based on your unsupported opinion, that there’s enough information in the genome to account for human morphology. It hardly requires expertise in information theory to have an unsupported opinion. And yes, this is about biology.

    Everything is nonsense “argument from incredulity” with you guys. And the totally illogical “don’t have an alternative” so let’s keep a known wrong “explanation” because there is no “alternative”?!? How about “we don’t know yet, and maybe we’ll find out one day”? How can you utter with any confidence: “There is no other significant factor”?

    Significant factors in the differences among species must be heritable, right? The genome is the only thing that’s inherited over a long enough period (more than a generation or two) to be a possible source of those differences. And yes, the fact that you have not even a hint of any alternative is telling. If there were something else, shouldn’t we have some evidence of its existence?

    It seems I might have given you way too much intellectual credit.

    Could be. Dunning-Kruger syndrome is also a possibility.

  45. John Harshman John Harshman
    Ignored
    says:

    Nonlin.org:
    To those that complained about the definition of “natural selection”, here are some immaterial follow up changes in the analysis:
    1.Natural Selection described as “the differential survival and reproduction of individuals due to differences in phenotype” or alternatively as “survival of the best adapted”.
    2.No. Natural Selection fails since survival is not directly tied to phenotype and “survival of the best adapted” is tautological. In a small farm, only organisms closely related to their wild cousins survive, but agribusinesses select for chickens with oversize breasts and research labs select for populations with specific genetic mutations requiring tight environments to survive. As shown, all these different organisms may or may not survive regardless of their phenotype. The only measure of “selection” is survival – we only know if and organism was selected if it survives and reproduces. “Best adapted” is also unknowable separate from survival.

    What does “Survival is not directly tied to phenotype” mean? I have guessed twice: 1) there is a stochastic element contributing to survival and 2) survival for a given phenotype also depends on environment., but apparently neither of those, or even a combination of the two, is correct. What do you mean?
    You can’t just repeat the same examples in the same words and suppose you’re explaining anything. People have guessed repeatedly at your meaning and been told that they’re wrong, but you have never managed to explain what you mean, just repeated what you said before.

    You also seem confused about the nature of studies of natural selection. They don’t just involve determining the number of surviving offspring of a single individual and declaring that to be the individuals fitness. They involve large numbers of individuals and generally compare the effects on reproductive success of some particular genetic and/or phenotypic character across a large number of individuals. This has the effect of averaging out individual differences in other characters, stochastic effects, and small environmental fluctuations. It also results in the ability to predict the results of future studies of the same characters. And that keeps it all from being tautological. I believe I’ve asked before if you have ever read a scientific paper on natural selection, and the reason is that if you had, you might have noticed that your ideas don’t fit.

    Incredibly, to date no one attempted to 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

    Let’s try Biston betularia, a popular example that I would imagine you’re familiar with.
    1. The portion of its phenotype relevant to the current question would be the two color morphs, gray and black.
    2. English forests.
    3. You have me there. I don’t know what you mean by “fitness function”.
    4. In an environment in which trees are covered by lichen, the gray morph is well camouflaged but the black morph is visible to predators. The gray morph thus has greater reproductive success and fairly quickly approaches fixation in the population. Then again, in an environment in which pollution has killed off the lichen, the black morph is well camouflaged but the gray morph is visible to predators. The black morph has greater reproductive success and fairly quickly approaches fixation in the population. Nope, no tautology.

  46. colewd
    Ignored
    says:

    Entropy,

    The Venn diagram shows that 63 Tis are involved in regulating those genes they point to, but it doesn’t say that the TFs are new. So, the binding sites in DNA evolve easily, and Tis could be involved in other things, or also be the result of duplications. I still don’t see any problem, let alone a problem as large and unsurmountable, that we’d have to quit trying to explain it.

    Binding sites can evolve easily. Can they evolve easily in the right location? Transcription requires protein to protein binding also. Although we don’t know the origin of the 63 TFs we do know that they had to evolve at some point during the origin of multicellular life.

    There’s nothing irreducibly compels about bird flight. I’ve witnessed myself the enormous variety in intermediate capacities to fly, and I can easily see how this could happen in steps. From embryo studies, we know that the bones and muscles develop initially as any other vertebrate’s bones and muscles, only their relative sizes and fibre composition starts differing until you get overdeveloped chest muscles, bones this long, bones that hollow, bones that short, etc, that makes a wing. Since the pieces are mostly the same as in flightless animals, an evolutionary scenario building on differences in developmental patterns fits perfectly.

    The definition of irreducible complexity is if you remove one of the components then the function will cease. This is certainly true in flight. This does not make the blind watchmaker impossible it just creates a formidable obstacle.

    Prior to flight the components can change but flight is not on their radar screen. Until you show flight occurred you don’t know if the proposed “precursor components” really can match together and fly even with slight modification. I don’t believe there is enough data from the fossil records to determine how close the earlier dinosaurs were to achieving flight.

    If we think about bird flight with the from a biological stand point it starts with flight feather expression in the right location along the birds skin covered bone. We know that this requires various types of keratin proteins along with regulation proteins around 100 in total. They have to be expressed in such a way as to create flight feathers of the right type and the right location in order for powered flight to occur.

    This process started with around 100 genes translates to around 100000 nucleotides. From a 4 bit DNA code of 100000 bits a flight feather is built from the ground up in somewhat the same way as a 3D printer. The flight feather has a very complex structure and the bird can reproduce the manufacturing process with incredible repeatability. If enough of these feathers are defective the bird cannot fly. This appears to be a very sophisticated manufacturing process. It originated how?

  47. Corneel Corneel
    Ignored
    says:

    Nonlin.org: 1. Remember, NS is supposed to explain “evolution”, not adaptations. You focus on adaptations, but that’s not what we’re debating. Of course adaptations happen.

    Correction: natural selection is a description of adaptive evolution, so yes it explains both evolutionary change (partly) and the existence of adaptations.

    Nonlin.org: 2. Yes, optimizations happen

    Optimizations of what? Not survival?

    Nonlin.org: 3. This is the disconnect. Phenotypes show that a camel is adapted to desert and polar bear to the arctic, but phenotype is infinite, hence does not explain why the camel and why the polar bear instead of some other virtual organism. Phenotype also does not forecast when these two might go extinct and most certainly does not explain how both camel and polar bear came into being.

    How is a camel adapted to desert? In what way is a polar bear adapted to the arctic? Please tell me how you know this without considering phenotypic traits.

  48. Corneel Corneel
    Ignored
    says:

    Nonlin.org,

    Regarding the miscellaneous points, here is how I understand the argument you have been making:

    i) Individual phenotypic traits are not in itself sufficient to tell us something useful about the phenotype; We need to know about ALL components. For example, we can measure height, but this is not the complete phenotype.

    but

    ii) Phenotypes are impossible to define and measure in entirety even for one individual and, in addition, phenotype changes constantly from birth to adult to old age.

    Hence, we can learn nothing about phenotypes.

    This line of reasoning is damning to any line of enquiry, not just biology. But most devastating to your position is that it rules out that we can ever establish that organisms are designed. Just try it: explain to me how you can tell that organisms are designed, without referring to phenotypic traits (not the phenotype) or the complete phenotype (unknowable).

  49. Nonlin.org
    Ignored
    says:

    dazz:
    Nonlin.org,

    Your links are being blocked (for a good reason). Why do you keep trying to spam the blog with your bullshit every fucking time you post?. Definition of stupidity comes to mind. Are you by any chance Otangelo’s brother? his uncle? or maybe both?

    What links? Some morons don’t know how to open links or are looking for links where there’s none – your name comes to mind. Are you by any chance an orangutan’s brother? Or are you just trying to help your Darwinist cause by demonstrating orangutan behavior?

  50. Nonlin.org
    Ignored
    says:

    John Harshman: No, I have no credentials, but I see no evidence that you do either. What evidence? All I see is that you don’t think, based on your unsupported opinion, that there’s enough information in the genome to account for human morphology. It hardly requires expertise in information theory to have an unsupported opinion. And yes, this is about biology.

    Significant factors in the differences among species must be heritable, right? The genome is the only thing that’s inherited over a long enough period (more than a generation or two) to be a possible source of those differences. And yes, the fact that you have not even a hint of any alternative is telling. If there were something else, shouldn’t we have some evidence of its existence?

    Could be. Dunning-Kruger syndrome is also a possibility.

    Not a matter of opinion. 1GB of memory is insufficient, and that’s a fact. It’s also a fact that the genotype is no more than 1GB long. If you think there’s more somewhere else, you need to show the quantifiable evidence.

    Just because you only know about the genome, doesn’t mean “the genome is the only thing”. Get it?

    You don’t have “an alternative” to anything. All you got is a stupid story that doesn’t make any sense whatsoever. This pig won’t fly for ever.

    For your education, here’s a Darwinist that agrees “natural selection” is BS. Maybe you understand him better – after all, he speaks New Astrology like you: https://www.huffingtonpost.com/entry/jerry-fodor-held-high-ground-to-evolutions-militant_us_5a3ec86ae4b0d86c803c722f

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