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Thread: Microevolution and Macroevolution

  1. #1 Microevolution and Macroevolution 
    Universal Mind John Galt's Avatar
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    Microevolution and macroevolution are perfectly proper terms in biology yet many armchair evolutionists claim, with great vigour – and often with a disparaging tone – that they were invented by creationists. The alleged motive was to admit to some minor changes in organisms, microevolution, whilst maintaining that true evolution, macroevolution, – the emergence of species and higher taxa – did not occur.

    However, Goldschmidt certainly used the terms in his studies on gypsy moths in the late 1920s and 1930s. He had come to believe that the traditional Darwinian process of accumulation of small changes could account for variation within species, giving rise to variants, races, or sub-species. This he considered to be micro-evolution. Changes that gave rise to new species he considered to be examples of macroevolution. [He expanded on these ideas in The Material Basis of Evolution, a work not well received at the time.]

    Dhobzhansky, who was one of the founding fathers of the Modern Synthesis, was also happy to use the two terms, though in a different sense from Goldschmidt. He saw microevolution as being responsible for speciation and macroevolution for the origin of the larger taxonomic groupings, genera, families, etc. Thus the differences between the two terms were quantitative rather than, as was the case for Goldschmidt’s view, qualitative,. Yet Dhobzhansky was unable to demonstrate this identity because ‘the genetics of the isolating mechanisms remains almost a terra incognita, [and so] an adequate understanding ….of the process of species formation is unattainable.’

    (Ironically Goldscmidt’s arguments for systemic mutation being the mechanism responsible for macroevolution were based largely upon Dhobzhansky’s research on fruit flys.)

    George C. Williams, for example, publishing in the 1960s, thought a separation of the mechanism of microevolution and macroevolution (he used those terms) was essential. Just like Goldschmidt, Williams saw no way in which small adaptive changes, arising from variations in allele frequency and micromutations could account for speciation.

    In the 1970s onwards Stephen J. Gould was also perfectly content to refer to micro and macro evolution when promoting the theory of punctuated equilibria with Niles Eldridge, his colleague at Columbia.

    In short, the two terms are not the invention of creationists; they have a long history within the development of evolutionary theory; and they represent distinctive concepts, both in terms of probable mechanism and certainly of end result. Might it be that failure to acknowledge this allows creationists to make justifiable claims that ‘evolutionists’ are as capable of following dogma as any bible belt preacher.


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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    evolutionists claim, with great vigour – and often with a disparaging tone – that they were invented by creationists.
    I think that is that evolutionists claim with great vigour - and often with soft patronizing tones - that the terms micro- and macro evolution were abused by creationists.


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    Forum Cosmic Wizard i_feel_tiredsleepy's Avatar
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    I'd like to state that creationist often use micro and macro evolution in a form that is not congruent with the use by biologist. When a biologist speaks of macro-evolutionary processes, they are just speaking of stuff on a higher scale and time.

    The idea of macroevolution being a separate process that functions under different rules is obsolete.
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    Creationists babble without making sense anyway. They open their mouths and nonsense comes out.

    The 'dogma' they are trying to use to discredit anything proving them wrong is simply an evolutionists' (armchair or otherwise) adherence to what they think has actually happened given the evidence. When you use evidence, proof, and therefore SCIENCE how can it possibly be 'dogma'?

    Whether it is a question of micro misinterpreted as macro or instead other mechanisms, evolution happened. How it happened is simply a problem to be worked out given observation and evidence neither of which have to do with dogma.

    Dogma is the purview of religion idiots, who once again try to foist their brainless stupidity upon scientists; claiming it makes the scientists just as fallible and ignorant of reality as they are.
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  6. #5 Re: Microevolution and Macroevolution 
    Forum Professor sunshinewarrior's Avatar
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    Quote Originally Posted by John Galt
    Just like Goldschmidt, Williams saw no way in which small adaptive changes, arising from variations in allele frequency and micromutations could account for speciation.
    Do you have any references to this? I have read some of Williams' work and don't recall this, is why I'm asking.
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    WYSIWYG Moderator marnixR's Avatar
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    i'm sure that Gould made the distinction though
    personally i remain unconvinced that there is a qualitative difference between speciation and the arising of new higher order groups - the latter is merely the impression you may get with 20/20 hindsight
    e.g. in the jurassic archaeopteryx would have been just another dinosaur
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Quote Originally Posted by C_Sensei
    Creationists babble without making sense anyway. They open their mouths and nonsense comes out.

    The 'dogma' they are trying to use to discredit anything proving them wrong is simply an evolutionists' (armchair or otherwise) adherence to what they think has actually happened given the evidence. When you use evidence, proof, and therefore SCIENCE how can it possibly be 'dogma'?

    Whether it is a question of micro misinterpreted as macro or instead other mechanisms, evolution happened. How it happened is simply a problem to be worked out given observation and evidence neither of which have to do with dogma.
    Both sides use dogma to interpret the evidence to their viewpoint (instead of viewpoint, you used the term "what they think has actually happened"). When you dissect the commonality, the disagreement is in the meaning but not the evidence itself. When evolution is as you have defined it above, "change over time" there is even agreement on that. As you said, the disagreement is in how it happened, and on this point neither side has much advantage.

    Those who see large scale change as a continuation of the adaptive alterations to existing function accomplished by random mutation and selection have not even been modestly successful in demonstrating this idea. While design advocates are building a case to show how genetic engineering does accomplish sweeping changes consistent with observation, they are thus far not able to provide clear evidence that natural processes can't do the same.

    Dogma is the purview of religion idiots, who once again try to foist their brainless stupidity upon scientists; claiming it makes the scientists just as fallible and ignorant of reality as they are.
    Whether you agree with them or not, it only hurts your own side of this debate to shut them out of the discussion as this site attempts to do, or to belittle them as you do. It hurts because while those who agree with you may see little harm to your credibility, to someone like me who sits on the fence with both feet firmly on your side, I see clearly the bias, and the double standard, and I can't help but suspect your judgement and begin to doubt if any of your story makes sense.

    If your goal is to only debate with yourselves, then keep it up while the other side continues to win over the undecided by building more thoughtful and compelling arguments (unlike advocates of naturalism, they have already demonstrated a process supporting their case). However if you want to attract people like me, then you have got to deliver a natural process capable of producing the changes that are clearly evident. The claim that mutation and selection accomplishes everything is wearing very thin.

    Your threat is not from the creationists since they will not convince people like me by showing me a book and imploring me to pray. Your threat is from the molecular and genetic engineers who make a case that coherent systems require goal driven processes and then back it up by showing how they succeed at making the changes mutation and selection thus far does not.
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    cypress. Forgetting about who is spouting dogma and biased opinions for a moment: employing straightforward logic and forgetting what answer you would be more comfortable with, can you at least see the simple logic of macro evolution being micro evolution over time? I mean, how can anyone argue against that?

    Look how we have bread dogs in a few thousand years, with most breads being bread in the last few hundred. So when natural selection does the picking and choosing instead of humans, can't you see a species changing into another over time? If not, why?
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    Those who see large scale change as a continuation of the adaptive alterations to existing function accomplished by random mutation and selection have not even been modestly successful in demonstrating this idea
    Well, in the first place that is a misrepresentation of 'the idea" - nothing in standard evolutionary theory requires the adaptation to be an "alteration to existing function", or denies that small genetic changes can have large phenotypic consequences, or requires that the mutation be "random" in all technical senses, or that "selection" be the only culling mechanism.

    And in the second place, the "demonstration of this idea" - the elucidation of adaptive pathways and research demonstration of mechanism and documentation of evidence of residual effects of this pattern having operated in real life phylogenetic development - has been much more than 'modestly" successful. It's been overwhelmingly persuasive and useful - one of the best established theories in science, at the present time.
    Your threat is from the molecular and genetic engineers who make a case that coherent systems require goal driven processes
    So no threat so far - no such case has been even respectably attempted, AFAIK.

    We live in a world full of coherent systems that we can see developing without "goal driven processes", after all; everything from the carbon cycle and thunderstorms to viral replication in bacterial cells. And we have a mechanism the appears completely adequate to explain arbitrary levels of complexity in such non-goal-driven coherencies of system. So it's going to be a tough argument for the ID folks, whenever they get around to it.
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  11. #10  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Quote Originally Posted by marnixR
    i'm sure that Gould made the distinction though
    personally i remain unconvinced that there is a qualitative difference between speciation and the arising of new higher order groups - the latter is merely the impression you may get with 20/20 hindsight
    e.g. in the jurassic archaeopteryx would have been just another dinosaur
    Is a sparrow not just another dinosaur?
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  12. #11  
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    Quote Originally Posted by spuriousmonkey
    Quote Originally Posted by marnixR
    i'm sure that Gould made the distinction though
    personally i remain unconvinced that there is a qualitative difference between speciation and the arising of new higher order groups - the latter is merely the impression you may get with 20/20 hindsight
    e.g. in the jurassic archaeopteryx would have been just another dinosaur
    Is a sparrow not just another dinosaur?
    From the avian clade, yes.
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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Let's not forget that species is just a scientific classification used to facilitate scientific work.

    So is the higher hierarchy.

    If species really meant something, that is that it really determined something limited and specific, than evolution wouldn't be possible.

    Every population generation is a transition form from the previous generation to the next generation.

    And if we don't see obvious change for a while we call it species. It doesn't mean evolution suddenly stopped working on the species. It doesn't mean things are changing when looking more than skin deep. It doesn't mean that species is an entity that will last forever.

    Snap out of the discontinuous thinking, and start looking at the whole picture.

    That is: every generation is a transition form.

    C'est toute.
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    cypress, there are far better educators than me that you can learn evolution from. I am an aggressive disagreeable type to the religious.
    If you sit on the fence, then you need to go spend a few years learning alot of biology and a respectable amount of paleontology too.
    Then you will see that there is NO dogma, assuming your teachers are actual scientists themselves.

    Any self-respecting university (assuming it isn't a religious one) will ensure that their course content contains all the arguments against evolution and the proofs that shoot them down utterly. Once I completed that course I came across a hot chick - who it turned out was the daughter of a priest or something, and claimed that the religious side won those exact same arguments. THAT sure pulled the reins on a second date! So make sure you use critical thinking and questions as you spend the years it takes to learn the truth - through PROOF. Not DOGMA.

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    I repeat the assertion here that while we do not yet fully understand the mechanism of evolution, it has clearly happened. Continuing investigation and modelling over the decades to come should yield an answer sooner or later. In any event, it seems that computer models should give some insight into how evolution might happen.
    Does anyone know of any?

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    I wonder if evolution, while working on every generation, can manage to change any given generation. Isn't the goal of any animal to survive within its environment? Doesn't it "want" to preserve its own adaptations?

    (Will we gladly step aside and let 'Magneto's' "Homo Superior" take over the world and voluntarily drop dead ourselves? No. We are here on the planet and WE will ensure our survival, even when we know the next evolutionary step in our own species has arisen.)

    I make this point (a far less ridiculous example than 'gahhhhd') to say that species resists change - our instinct is a reflection of the 'goal' of our DNA - maintain the species. I submit that it is the BIG and DRASTIC alterations of the environment (which include isolation) that causes the fast evolutionary changes - so yes I think Gould was right - I think evolution proceeds by punctuated equilibrium. The evidence points this way. I ask why we think evolution acts upon every generation when species remain unchanged through diverse environments for a few million years on average. My favorite example is Apatosaurus - it is unchanged through several strata; in varying environments. (Robert Bakker)

    -No DOGMA here, cypress - simply a discussion of the mechanism, using proof. Spurious will answer using proof himself, and we will all advance our understanding of the overall mechanism or -ismS, even if the thread gets polarized into two 'camps'. We're using PROOF, NOT DOGMA.
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    Quote Originally Posted by sensei
    I submit that it is the BIG and DRASTIC alterations of the environment (which include isolation) that causes the fast evolutionary changes - so yes I think Gould was right - I think evolution proceeds by punctuated equilibrium.
    That is not exactly what Gould seems to have had in mind - he seems to have been arguing for the necessity of some other mechanism, not merely changed fields of opportunity for the operation of the same old Darwinian mechanism.

    It is Dennett and the like, arguing against Gould, who point out that his "punctuation" is a series of intervals of increased rates for observable reasons, not different mechanisms entirely.
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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    In any event, it seems that computer models should give some insight into how evolution might happen.
    Does anyone know of any?
    Evolution just happens in changing environment with self replicating machines whose phenotype is partially or entirely dictated by the coding of these machines, when certain codes give advantages in effective reproduction rates.

    It's not really a secret how or why evolution happens.

    It's a system that just works.
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    Well certainly we know why it happens.

    But we seem to have disagreement on how. Yes indeed, punctuated equilibrium will take place during an ice age, that has isolated pockets of population which will not mix again until the ice recedes.

    While it might indeed happen "out of nowhere" when a new island chain becomes habitable and finally capable of supporting finches that find their way there.

    Is there any evidence against the idea that more extreme offspring tend to get reabsorbed by the gene pool?
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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    But we seem to have disagreement on how.
    Not really.

    A new generation is created by the previous generation. Some individuals are more successful than others.

    That's evolution.

    You are thinking of a different problem. You want to explain specific historic phenomena that occurred during evolution. In this case the seemingly 'sudden' appearance of species, bauplans, etc. etc.

    It's a different thing.
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    It might not be different. Obviously evolution proceeds differently every time it does proceed. It seems that you think Slow Darwinian evolution predominates?

    While I think evolution is generally a case of extreme catastrophic change that spurs rapid adaptation over a short period of time; with much of the intervening millions of years without much change - most change being reabsorbed into the gene pool when it isn't really "needed".
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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    It seems that you think Slow Darwinian evolution predominates?
    I'm not that arrogant to presume that I understand all aspect of evolutionary history.

    I only know one thing. Evolutionary change is entirely dependent on each new generation. There is no evolution without progeny. And each generation of progeny is a step in evolution.

    Very darwinian. But I am not going to presume evolution has to be slow because I know of several examples in the literature where evolution occurred within my lifetime, or major events of evolutionary radiation in a few thousand years.

    We all know that 30 years, or 10.000 years is nothing on a geological timescale.

    The point is really that you don't need any fancy mechanisms for fast evolution to occur. Evolution cannot go faster than the single generation step. And it can't go slower.

    I think that people often make errors in judgement. They think gradualism means slow evolution, and punctuated equilibrium means that there must be something special going on, and that both cannot be reconciled.

    Luckily we have documented factual science at our disposal where we can see that gradualism, that is evolution with the unit of change defined as the single generation step, is quite capable of very fast events in morphological, behavioural change, and species radiation events.

    any opinion is worthless compared to the knowledge present in the current literature.
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    Yes I agree with that last line! And several others of yours!

    But each generation being a step in evolution - I think it isn't always necessarily so!
    I think evolution CAN go slower than the generation step!

    If we use the example of Apatasarus - it doesn't change through six million years of deposition...through several vastly differing environments. I agree that some changes, generation to generation might be too minute for current science to detect; but then again - there might not be changes at all! For at least some of those generations.

    While I'm sure that both flavors of evolution do occur; but in most case histories one likely predominates over the other.

    I ask what do fossils tell us and what do modern studies tell us? I think modern studies are pretty conclusive that change happens very fast in our yearly observation, let alone geological fossil deposits!

    Does this not support the idea that Punctuated Equilibrium seems to be the dominant mode of species change? What other rate of change can we demonstrate? I don't want to focus entirely on one case at the expense of the other.
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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    If we use the example of Apatasarus - it doesn't change through six million years of deposition...through several vastly differing environments. I agree that some changes, generation to generation might be too minute for current science to detect; but then again - there might not be changes at all! For at least some of those generations.
    Of course it changes.
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    Quote Originally Posted by KALSTER
    cypress. Forgetting about who is spouting dogma and biased opinions for a moment: employing straightforward logic and forgetting what answer you would be more comfortable with, can you at least see the simple logic of macro evolution being micro evolution over time? I mean, how can anyone argue against that?
    Absolutely I can. No argument at all against the concept.

    Look how we have bread dogs in a few thousand years, with most breads being bread in the last few hundred. So when natural selection does the picking and choosing instead of humans, can't you see a species changing into another over time? If not, why?
    I don't accept the premise of the question because it depends on how a species is defined. If you mean can I conceptually see a donkey and a horse having evolved from a horse-like progeny by mutation and selection, sure or a lion and a tiger, sure. Can I agree ramdom mutation of genes and selection accounts for a new organ or an entirely new body plan? No, I don't see good case for that at all.
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    Quote Originally Posted by C_Sensei
    cypress, there are far better educators than me that you can learn evolution from. I am an aggressive disagreeable type to the religious.
    If you sit on the fence, then you need to go spend a few years learning alot of biology and a respectable amount of paleontology too.
    Then you will see that there is NO dogma, assuming your teachers are actual scientists themselves.
    I have done this. 3 years as an undergraduate, then 25 years of reading updated textbooks, publications and Journals and attending presentations and discussions. A few debates. I have encountered dogma nearly every step of the way from all sides.

    Any self-respecting university (assuming it isn't a religious one) will ensure that their course content contains all the arguments against evolution and the proofs that shoot them down utterly. Once I completed that course I came across a hot chick - who it turned out was the daughter of a priest or something, and claimed that the religious side won those exact same arguments. THAT sure pulled the reins on a second date! So make sure you use critical thinking and questions as you spend the years it takes to learn the truth - through PROOF. Not DOGMA.
    Sorry no, I have not seen any courses or good presentation by those who support mutation and selection as the primary mechanism for macro changes where the challenges to that process are adequately addressed. I have seen a lot of hand waving. Nearly all the "evidence" offered is phylogenetic studies that demonstrate what differences and similarities exist and why we should suppose a common source, but nothing specific about the processes that could account for the changes. It is little more than a just so story. I do not dispute

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    I repeat the assertion here that while we do not yet fully understand the mechanism of evolution, it has clearly happened. Continuing investigation and modelling over the decades to come should yield an answer sooner or later.
    No argument with the assertion.

    In any event, it seems that computer models should give some insight into how evolution might happen.
    Does anyone know of any?
    I have been keeping up with this area of investigation as well. I don't know of any successful evolutionary algorithm or model that does not use some form of targeted search. I look forward to an example of this too.

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    I wonder if evolution, while working on every generation, can manage to change any given generation. Isn't the goal of any animal to survive within its environment? Doesn't it "want" to preserve its own adaptations?

    (Will we gladly step aside and let 'Magneto's' "Homo Superior" take over the world and voluntarily drop dead ourselves? No. We are here on the planet and WE will ensure our survival, even when we know the next evolutionary step in our own species has arisen.)

    I make this point (a far less ridiculous example than 'gahhhhd') to say that species resists change - our instinct is a reflection of the 'goal' of our DNA - maintain the species. I submit that it is the BIG and DRASTIC alterations of the environment (which include isolation) that causes the fast evolutionary changes - so yes I think Gould was right - I think evolution proceeds by punctuated equilibrium. The evidence points this way. I ask why we think evolution acts upon every generation when species remain unchanged through diverse environments for a few million years on average. My favorite example is Apatosaurus - it is unchanged through several strata; in varying environments. (Robert Bakker)
    I agree that this seems more realistic. This is also something that can and is being tested in the lab. So far nothing of significant interest has turned up. Perhaps more variation will help.

    -No DOGMA here, cypress - simply a discussion of the mechanism, using proof. Spurious will answer using proof himself, and we will all advance our understanding of the overall mechanism or -ismS, even if the thread gets polarized into two 'camps'. We're using PROOF, NOT DOGMA.
    Your post was largely dogma free. Not much balance though.
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    Quote Originally Posted by C_Sensei
    But each generation being a step in evolution - I think it isn't always necessarily so!
    I think evolution CAN go slower than the generation step!

    If we use the example of Apatasarus - it doesn't change through six million years of deposition...through several vastly differing environments. I agree that some changes, generation to generation might be too minute for current science to detect; but then again - there might not be changes at all! For at least some of those generations.
    You are looking at gross phylogenetic characters, Spurious is considering allele frequency. You are arguing at cross purposes.
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    I don't accept the premise of the question because it depends on how a species is defined. If you mean can I conceptually see a donkey and a horse having evolved from a horse-like progeny by mutation and selection, sure or a lion and a tiger, sure. Can I agree ramdom mutation of genes and selection accounts for a new organ or an entirely new body plan? No, I don't see good case for that at all.
    But you just said that you have no problem with the concept of macro evolution being micro evolution + time? It doesn't depend on how a species is defined. The point of the example is to show how big changes can occur in mere hundreds of years. Look at the relatively huge morphological differences between a Bulldog and a Wolf. Now apply that over thousands and hundreds of thousands of years. Then apply it over millions and billions. You still can't imagine one quadruped animal evolving into another?

    The question about organs is a bit different, as you should realize, since that is a question of cell differentiation, gene expression, etc. For that we have to study things like Volvox.

    But what are the differences that are too huge between, say, a horse and a lion? Their common ancestor necessarily goes back quite a while. Don't you see the multitude of similarities?
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  27. #26  
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    Quote Originally Posted by cypress
    [
    I don't accept the premise of the question because it depends on how a species is defined. If you mean can I conceptually see a donkey and a horse having evolved from a horse-like progeny by mutation and selection, sure or a lion and a tiger, sure. Can I agree ramdom mutation of genes and selection accounts for a new organ or an entirely new body plan? No, I don't see good case for that at all.
    new bodyplans or organs do not evolve that easily.

    Nowadays everything is just a modification.

    The swim bladder as present in most fish is a modified lung. It didn't use to be a lung before that. Existing structures are taken and given a new function.

    random mutation can not explain the emergence of evolutionary novelty. Arguing that it does is stupid. Natural selection of random mutations can explain the emergence of novelty.
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    Sorry - didn't realize we were talking about apples and oranges. I am looking at the species level. Guess I better read thru the entire posts before punching the keyboard D'OH!


    Maybe I'll search for a Punctuated Equilibrium thread later.
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    Quote Originally Posted by spuriousmonkey
    Quote Originally Posted by cypress
    [
    I don't accept the premise of the question because it depends on how a species is defined. If you mean can I conceptually see a donkey and a horse having evolved from a horse-like progeny by mutation and selection, sure or a lion and a tiger, sure. Can I agree ramdom mutation of genes and selection accounts for a new organ or an entirely new body plan? No, I don't see good case for that at all.
    new bodyplans or organs do not evolve that easily.

    Nowadays everything is just a modification.

    The swim bladder as present in most fish is a modified lung. It didn't use to be a lung before that. Existing structures are taken and given a new function.
    I understand the concept that this might have been what happened but we don't have solid evidence this is true. Some phylogenies are consistent with this supposition while others are wildly in conflict. We have to cherry pick to accept this as strong evidence.

    But let's go ahaed and suppose this is the case. We still have no indication of how this change occured. You assume it was the same micro-evolutionary proceses we observe presently in operation, but you can't offer demonstrable evidence to support this assertion.

    random mutation can not explain the emergence of evolutionary novelty. Arguing that it does is stupid. Natural selection of random mutations can explain the emergence of novelty.
    On the contrary, modern experimental biology is demonstrating the opposite, namely that genetic mutation and selection is unable to produce the necessary changes because the stepwise pathways with selective advantage don't seem to exist and without selection, the numer of neutral and degenerative pathways are too great for random processes to blindly search sample space.

    I would love for you to offer an actual multi-step pathway greater than 4 steps where each step offered selectable advantage.
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    Quote Originally Posted by KALSTER
    I don't accept the premise of the question because it depends on how a species is defined. If you mean can I conceptually see a donkey and a horse having evolved from a horse-like progeny by mutation and selection, sure or a lion and a tiger, sure. Can I agree ramdom mutation of genes and selection accounts for a new organ or an entirely new body plan? No, I don't see good case for that at all.
    But you just said that you have no problem with the concept of macro evolution being micro evolution + time?
    I have no problem with the concept, which was the premise of your first question. Your second asked about actualizing the concept. For this we require evidence. Animal breading provides evidence that as long as form and function are not altered, micro-evolutionary process are effective. To argue this as evidence for macro-change seems unwaranted and therefore, while still conceptually valid by supposition, it is not actuallized and therefore not demonstrated.

    It doesn't depend on how a species is defined. The point of the example is to show how big changes can occur in mere hundreds of years. Look at the relatively huge morphological differences between a Bulldog and a Wolf. Now apply that over thousands and hundreds of thousands of years. Then apply it over millions and billions. You still can't imagine one quadruped animal evolving into another?
    The problem with extending this is that the morphological changes have not added any novel features. No new functions, no new boday plans. It has just stirred the pot, or rotated the tires in a sense. Again I can see this in concept, but it is one thing to say I can imagine it and another to be able to say it absolutely happend through a particular process.

    Don't get me wrong. I am not saying it did not happen because clearly changes over time did occur. I am simply saying that to an unbiased observer, the evolutionists have not made their case on how it happened.

    The question about organs is a bit different, as you should realize, since that is a question of cell differentiation, gene expression, etc. For that we have to study things like Volvox.

    But what are the differences that are too huge between, say, a horse and a lion? Their common ancestor necessarily goes back quite a while. Don't you see the multitude of similarities?
    Equine and feline have numerous macro differences in form and function. The digestive system is quite different as are many of the sensory systems, most obviously sight. As I have stated in other posts (that site moderators seem to find too offensive to retain in this section), modern experimental results indicate that mutation with selection is thus far unable to derive novel protein shapes and binding sites and developmental control systems and gene expression control sytems required to generate new form and function in a reasonable timeframe. Genetic engineering does seem capable of making these kinds of changes and I wonder if there are other natural process also capable of explaining these changes.

    I do of course see the similarities. The challenge for the evolutionists is not to explain the similarities but to explain the differences. For that we need a process and thus far, the process offered is not clearing the bar. I think it may be time to look for a new process. I hope this better explains my previous responses.
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    ou can't offer demonstrable evidence to support this assertion.
    Of course I can.
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    Quote Originally Posted by cypress
    I would love for you to offer an actual multi-step pathway greater than 4 steps where each step offered selectable advantage.
    Courtesy of TalkOrigins, greater than four independent components in greater than four steps:

    1. A passive, nonspecific pore evolves into a more specific passive pore by addition of gating protein(s). Passive transport converts to active transport by addition of an ATPase that couples ATP hydrolysis to improved export capability. This complex forms a primitive type-III export system.

    2. The type-III export system is converted to a type-III secretion system (T3SS) by addition of outer membrane pore proteins (secretin and secretin chaperone) from the type-II secretion system. These eventually form the P- and L-rings, respectively, of modern flagella. The modern type-III secretory system forms a structure strikingly similar to the rod and ring structure of the flagellum (Hueck 1998; Blocker et al. 2003).

    3. The T3SS secretes several proteins, one of which is an adhesin (a protein that sticks the cell to other cells or to a substrate). Polymerization of this adhesin forms a primitive pilus, an extension that gives the cell improved adhesive capability. After the evolution of the T3SS pilus, the pilus diversifies for various more specialized tasks by duplication and subfunctionalization of the pilus proteins (pilins).

    4. An ion pump complex with another function in the cell fortuitously becomes associated with the base of the secretion system structure, converting the pilus into a primitive protoflagellum. The initial function of the protoflagellum is improved dispersal. Homologs of the motor proteins MotA and MotB are known to function in diverse prokaryotes independent of the flagellum.

    5. The binding of a signal transduction protein to the base of the secretion system regulates the speed of rotation depending on the metabolic health of the cell. This imposes a drift toward favorable regions and away from nutrient-poor regions, such as those found in overcrowded habitats. This is the beginning of chemotactic motility.

    6. Numerous improvements follow the origin of the crudely functioning flagellum. Notably, many of the different axial proteins (rod, hook, linkers, filament, caps) originate by duplication and subfunctionalization of pilins or the primitive flagellar axial structure. These proteins end up forming the axial protein family.
    I would love for you to specify a pathway or cascade you feel cannot have evolved and explain what the barrier is for that example.
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    I would love for you to offer an actual multi-step pathway greater than 4 steps where each step offered selectable advantage.
    Courtesy of TalkOrigins, greater than four independent components in greater than four steps:

    1. A passive, nonspecific pore evolves into a more specific passive pore by addition of gating protein(s). Passive transport converts to active transport by addition of an ATPase that couples ATP hydrolysis to improved export capability. This complex forms a primitive type-III export system.

    2. The type-III export system is converted to a type-III secretion system (T3SS) by addition of outer membrane pore proteins (secretin and secretin chaperone) from the type-II secretion system. These eventually form the P- and L-rings, respectively, of modern flagella. The modern type-III secretory system forms a structure strikingly similar to the rod and ring structure of the flagellum (Hueck 1998; Blocker et al. 2003).

    3. The T3SS secretes several proteins, one of which is an adhesin (a protein that sticks the cell to other cells or to a substrate). Polymerization of this adhesin forms a primitive pilus, an extension that gives the cell improved adhesive capability. After the evolution of the T3SS pilus, the pilus diversifies for various more specialized tasks by duplication and subfunctionalization of the pilus proteins (pilins).

    4. An ion pump complex with another function in the cell fortuitously becomes associated with the base of the secretion system structure, converting the pilus into a primitive protoflagellum. The initial function of the protoflagellum is improved dispersal. Homologs of the motor proteins MotA and MotB are known to function in diverse prokaryotes independent of the flagellum.

    5. The binding of a signal transduction protein to the base of the secretion system regulates the speed of rotation depending on the metabolic health of the cell. This imposes a drift toward favorable regions and away from nutrient-poor regions, such as those found in overcrowded habitats. This is the beginning of chemotactic motility.

    6. Numerous improvements follow the origin of the crudely functioning flagellum. Notably, many of the different axial proteins (rod, hook, linkers, filament, caps) originate by duplication and subfunctionalization of pilins or the primitive flagellar axial structure. These proteins end up forming the axial protein family.

    Hilariously speculative and incomplete. Huge gaps in the supposed steps described. No process suggested for any of the assumed steps. No specific stepwise mutations offered as I requested.

    Step one involves an unknown multiplicity of steps, congers up some unnamed and undescribed proteins and declares that they mutated into yet another set of undescribed proteins. Step two is only a little better than one in that it at least identifies a group of proteins but then describes that it acquires an outer membrane but once again fails to describe how it does so. Yet How it does is the actual question I asked. The remaining steps are equally poor as an example of what I asked for.

    I asked for an example of a specific four or greater step mutation pathway where each step offers selective advantage. I asked for this because a previous poster (spuriousmonkey) claimed that selective advantage overcomes the long odds of blind search by offering selection to cull the dead end pathways. If this is true, then we would be able to, by now, identify a large number of actualized multiple mutative pathways with selective advantage for each step. They would likely be short given the limited time we have had to study this (40 years). The problem is there don't seem to be any to be found.

    What has been done here in this misleading and horribly speculative example is nothing more than what I have already agreed to accept by stipulation (though even this is unwarranted). It is simply another way of saying "Here is another example of similarities of structural protein components between one and another bacterial organism. We don't know how the differences were obtained but we know they evolved one from another so we will make up some just so story about it and declare that we have performed scientifically valid analysis".

    See this is why I get so frustrated with those who continue to insist that macro-evolution by mutation and selection is a foregone conclusion. You are either blindly ignorant or purposefully deceitful. It is times like this that I understand why the western worldwide population favors by a two to one margin alternative theories to evolution (see the latest IPSOS survey). I'm still looking for an evolutionary process but geez you don't help at all. Please offer an example that I asked for or admit that there aren't any that we know of.

    I would love for you to specify a pathway or cascade you feel cannot have evolved and explain what the barrier is for that example.
    Even you should know that science cannot prove a negative. This is a sucker's game. You are begging the question.

    Instead I have already provided numerous examples of situations where ongoing experimental research has attempted to identify the capability of mutation and selection to generate novel protein shape, novel binding sites, novel gene expression control mechanisms and developmental control mechanisms and with only the rare exception within the expected range of probabilistic analysis, all of these seem to be a barrier for mutation and selection.

    It is one thing to fabricate just so stories like this pathetic example you offered and another to do the real work to show that the process has capability. There is either another natural way as I suspect, or the public's intuition is correct.
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    I would love for you to offer an actual multi-step pathway greater than 4 steps where each step offered selectable advantage.
    Courtesy of TalkOrigins, greater than four independent components in greater than four steps:

    1. A passive, nonspecific pore evolves into a more specific passive pore by addition of gating protein(s). Passive transport converts to active transport by addition of an ATPase that couples ATP hydrolysis to improved export capability. This complex forms a primitive type-III export system.

    2. The type-III export system is converted to a type-III secretion system (T3SS) by addition of outer membrane pore proteins (secretin and secretin chaperone) from the type-II secretion system. These eventually form the P- and L-rings, respectively, of modern flagella. The modern type-III secretory system forms a structure strikingly similar to the rod and ring structure of the flagellum (Hueck 1998; Blocker et al. 2003).

    3. The T3SS secretes several proteins, one of which is an adhesin (a protein that sticks the cell to other cells or to a substrate). Polymerization of this adhesin forms a primitive pilus, an extension that gives the cell improved adhesive capability. After the evolution of the T3SS pilus, the pilus diversifies for various more specialized tasks by duplication and subfunctionalization of the pilus proteins (pilins).

    4. An ion pump complex with another function in the cell fortuitously becomes associated with the base of the secretion system structure, converting the pilus into a primitive protoflagellum. The initial function of the protoflagellum is improved dispersal. Homologs of the motor proteins MotA and MotB are known to function in diverse prokaryotes independent of the flagellum.

    5. The binding of a signal transduction protein to the base of the secretion system regulates the speed of rotation depending on the metabolic health of the cell. This imposes a drift toward favorable regions and away from nutrient-poor regions, such as those found in overcrowded habitats. This is the beginning of chemotactic motility.

    6. Numerous improvements follow the origin of the crudely functioning flagellum. Notably, many of the different axial proteins (rod, hook, linkers, filament, caps) originate by duplication and subfunctionalization of pilins or the primitive flagellar axial structure. These proteins end up forming the axial protein family.
    Hilariously speculative and incomplete. Huge gaps in the supposed steps described. No process suggested for any of the assumed steps. No specific stepwise mutations offered as I requested.
    Well that's not really what you asked for in your original post, there was no mention of specific mutations. Very well, I'll see if I can dig up something more detailed.

    Perhaps you found it funny, but one thing this outline was not was speculative. There was nothing outrageous or unusual in there. Those missing steps you seem to dwell on would be considered trivial by anyone with a basic knowledge of molecular biology. You might as well say it's implausible or wildly speculative for me to say my friend went from London to New York simply because I didn't specify what exact steps he took. We know of several plausible mechanisms to explain this, our failure to specify them does not make the process suddenly implausible. That's just an appeal to ignorance.

    Quote Originally Posted by cypress
    Step one involves an unknown multiplicity of steps, congers up some unnamed and undescribed proteins and declares that they mutated into yet another set of undescribed proteins. Step two is only a little better than one in that it at least identifies a group of proteins but then describes that it acquires an outer membrane but once again fails to describe how it does so. Yet How it does is the actual question I asked. The remaining steps are equally poor as an example of what I asked for.
    If you're going to try and take apart this "hilariously speculative" outline I posted the least you could do is try to understand it. At no point does it claim the group of proteins acquires an outer membrane. Membrane proteins are not the same thing as a lipid membrane. How are we supposed to debate even this broad outline meaningfully if you don't understand that basic distinction? You seriously want us to go into greater detail?

    Quote Originally Posted by cypress
    See this is why I get so frustrated with those who continue to insist that macro-evolution by mutation and selection is a foregone conclusion. You are either blindly ignorant or purposefully deceitful. It is times like this that I understand why the western worldwide population favors by a two to one margin alternative theories to evolution (see the latest IPSOS survey). I'm still looking for an evolutionary process but geez you don't help at all. Please offer an example that I asked for or admit that there aren't any that we know of.
    Why should we bother when you don't understand the outline?

    Quote Originally Posted by cypress
    I would love for you to specify a pathway or cascade you feel cannot have evolved and explain what the barrier is for that example.
    Even you should know that science cannot prove a negative. This is a sucker's game. You are begging the question.
    Actually, by asking you to specify a pathway I'm trying to get around the very vague objections you have to evolution and get right down to the specifics. Your position is that evolution cannot account for complexity, so you've already adopted a negative stance. I'm trying to get you to make a positive proposition of some sort so that this debate can, for the first time in about 5 threads, move forward.

    Quote Originally Posted by cypress
    Instead I have already provided numerous examples of situations where ongoing experimental research has attempted to identify the capability of mutation and selection to generate novel protein shape, novel binding sites, novel gene expression control mechanisms and developmental control mechanisms and with only the rare exception within the expected range of probabilistic analysis, all of these seem to be a barrier for mutation and selection.
    You've done no such thing. You've badly misread a number of papers, including some reviews, and then presented them to us as supporting evidence for your negative assumption. The mistakes you have made have at times been so fundamental as to call into question your capacity to understand the very basic evidence for evolution. Which sort of makes this all feel a bit futile at times, especially in light of your demands for more specifics.

    Quote Originally Posted by cypress
    It is one thing to fabricate just so stories like this pathetic example you offered and another to do the real work to show that the process has capability.
    You asked for us "to offer an actual multi-step pathway greater than 4 steps where each step offered selectable advantage." I get that you'd now like some more detail, but please don't act as if what I provided did not fit what you asked for.

    Quote Originally Posted by cypress
    There is either another natural way as I suspect, or the public's intuition is correct.
    Until you're willing to consider the third option, that you may be wrong, all you're doing is spouting dogma dressed as science.

    I'll see about getting you some of that detailed information you're after...
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    I'm sort of wondering whether there is a subgroup of creationists wh deny the oak trees grow from acorns, all by themselves, without a deity's guiding each step.

    We see microgrowth, of course. We all agree that things can grow a little bit. But macrogrowth on the big oak level has never been observed.
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    Quote Originally Posted by iceaura
    I'm sort of wondering whether there is a subgroup of creationists wh deny the oak trees grow from acorns, all by themselves, without a deity's guiding each step.

    We see microgrowth, of course. We all agree that things can grow a little bit. But macrogrowth on the big oak level has never been observed.


    And don't get us started on Redwoods. Those have never been directly observed to grow from seed to fully grown. The theory of Tree Growth is based on mere inference.
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    Quote Originally Posted by iceaura
    I'm sort of wondering whether there is a subgroup of creationists wh deny the oak trees grow from acorns, all by themselves, without a deity's guiding each step.
    Not sure who you are refering to unless you are incorrectly labeling me.

    We see microgrowth, of course. We all agree that things can grow a little bit. But macrogrowth on the big oak level has never been observed.
    Oh please. I have not been asking for demonstration of a macro-event. Instead I point out that for mutation and selection to account for macro-events, they must be capable of accomplishing certain specific micro-events. I listed them above. I am being completely reasonable to request demonstration of a very short pathway of 4 specific mutations where each had selective advantage. This is something that could be accomplished in short order (a few months) in bacteria and other micro organisms if each step had selective advantage but could take unreasonabley long if two or more of the steps were neutral or deleterious, as research is suggesting.
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    Quote Originally Posted by cypress
    Instead I point out that for mutation and selection to account for macro-events, they must be capable of accomplishing certain specific micro-events. I listed them above.
    Your list and its presentation embody a number of false assumptions about the situation you claim to describe - assumptions of independence of event, assumptions about the possible events relevant, etc.
    Quote Originally Posted by cypress
    This is something that could be accomplished in short order (a few months) in bacteria and other micro organisms if each step had selective advantage but could take unreasonabley long if two or more of the steps were neutral or deleterious, as research is suggesting.
    You have not cited any research that "suggests" any such thing. You appear to be misinterpreting the implications of the research you do cite, in part by assuming a false context (mostly complete knowledge of the possible evolutionary pathways, etc).
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Instead I point out that for mutation and selection to account for macro-events, they must be capable of accomplishing certain specific micro-events. I listed them above.
    Your list and its presentation embody a number of false assumptions about the situation you claim to describe - assumptions of independence of event, assumptions about the possible events relevant, etc.
    Let's step through these "number of false assumptions". Please tell my why you claim they are false.

    Quote Originally Posted by cypress
    This is something that could be accomplished in short order (a few months) in bacteria and other micro organisms if each step had selective advantage but could take unreasonabley long if two or more of the steps were neutral or deleterious, as research is suggesting.
    You have not cited any research that "suggests" any such thing.
    I have cited several in past threads that you have read, unfortunately moderator bias seems to have relegated those topics to the non-science section despite the fact they were peer reviewed papers in Nature and Science and J. of MB and others and the posts violated none of the posted rules. I'm reluctant to repost them, but I bet you can find them easy enough.

    To what exactly are you taking exception? Are you questioning the assertion that biological changes could occur rapidly by mutation and selection if each step offered selectable advantage or that they would proceed too slowly if any modification required two or more neutral steps? Do you have research to support your opinion?

    You appear to be misinterpreting the implications of the research you do cite, in part by assuming a false context (mostly complete knowledge of the possible evolutionary pathways, etc).
    I am happy to talk through the implications of past references. What exactly is your concern? What exactly did I misinterpret? In the Thornton paper the researchers found that the GR steroid receptor could not evolve to the previously designed non-specific receptor version via the reverse pathway because several neutral steps puts this pathway out of reach to mutation in any reasonable period of time. If you are asserting there are likely other selectable pathways to a non-specific receptor versions, then the onus is on you to demonstrate that is true. Otherwise we simply don't know and this is exactly my point. We don't have any example of actualized stepwise pathways to novel protein shapes, binding sites, regulation controls and developmental controls. We don't know of any. Furthermore though the writers don't address this point, the Thornton paper offers a glimpse into why we might be having difficulty demonstrating mutation to novel function. I discussed this previously too. Nowhere in my discussion did I assume complete knowledge of all possible pathways.

    Again I am happy to have a detailed discussion on this and other concerns you might have.
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    I find discussing science with you as interactive as pissing against a rock.
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    I would love for you to specify a pathway or cascade you feel cannot have evolved and explain what the barrier is for that example.
    Even you should know that science cannot prove a negative. This is a sucker's game. You are begging the question.
    Actually, by asking you to specify a pathway I'm trying to get around the very vague objections you have to evolution and get right down to the specifics. Your position is that evolution cannot account for complexity, so you've already adopted a negative stance. I'm trying to get you to make a positive proposition of some sort so that this debate can, for the first time in about 5 threads, move forward.
    My position is that mutation and natural selection does not presently account for new form and function but does account for modification of present form and function. I also find it frustrating that you continually attempt to change my argument into something it is not.

    Thornton and his fellow researchers identify a specific pathway they say cannot be traversed by mutation ans selection. This was one of the examples I previously provided.

    Bridgham, J., Ortlund, E, and Thornton, J. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461.

    If you accuse me of ignoring other uninvestigated pathways, I will point out that you asked for a specific pathway and reference back to the fools game I claimed this was and then challenge you to produce the pathway you suppose exits (and of course you can't), Instead we should use this research to understand why some things are difficult for mutation and selection to accomplish.

    You asked for us "to offer an actual multi-step pathway greater than 4 steps where each step offered selectable advantage." I get that you'd now like some more detail, but please don't act as if what I provided did not fit what you asked for.
    No not more detail. I would simply like the original question answered rather than a changed question like you did above. the key to answering the question is to note that you must show each step is selectable which implies the steps must be specifically defined and you can't skip any steps in the explanation.

    Until you're willing to consider the third option, that you may be wrong, all you're doing is spouting dogma dressed as science.
    The fact that I am asking questions and searching for a way that mutation and selection does succeed should suffice. I think it is somewhat likely that I am wrong and that either the traditional evolutionists are correct or diversity occurred by other mechanisms entirely. When was the last time you thoughtfully researched and considered alternatives to your dogma? How likely is it that you are wrong?
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    Quote Originally Posted by cypress
    My position is that mutation and natural selection does not presently account for new form and function but does account for modification of present form and function. I also find it frustrating that you continually attempt to change my argument into something it is not.

    Thornton and his fellow researchers identify a specific pathway they say cannot be traversed by mutation ans selection. This was one of the examples I previously provided.

    Bridgham, J., Ortlund, E, and Thornton, J. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461.
    You have either misunderstood or are misrepresenting the source provided. It doesn't support your position and furthermore its authors do not claim it does so. They show that the evolutionary pathway taken to produce the glucocorticoid receptor is non-reversible (albeit not absolutely so), not that it is non-traversable by mutation and selection. They see no need for any mechanisms outside of normal evolutionary processes for the pathway to be traversed, rather they simply demonstrate how it is highly unlikely that the ancestral form would be re-acquired. The hint is in the title- it's a one-way movement, like that of a ratchet. This paper would only support your position if the authors had found the ancestral form in a species where it should not be and were unable to plot a path to that form. They didn't though.

    Cypress, this is at least the third time that you have cited to me papers which do not merely fail to support your point but actually demonstrate a very deep misunderstanding of the source on your part.

    Quote Originally Posted by cypress
    You asked for us "to offer an actual multi-step pathway greater than 4 steps where each step offered selectable advantage." I get that you'd now like some more detail, but please don't act as if what I provided did not fit what you asked for.
    No not more detail. I would simply like the original question answered rather than a changed question like you did above. the key to answering the question is to note that you must show each step is selectable which implies the steps must be specifically defined and you can't skip any steps in the explanation.
    Very well. Ironically enough I offer:

    Bridgham, J., Ortlund, E, and Thornton, J. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461.

    A 5 step pathway culminating in the glucocorticoid receptor. I'm not sure all of the steps would have a selectable advantage, but then that would be a silly requirement to ask for since I'm sure you're aware that selection is not binary, but probabilistic. Which means that even disadvantageous steps can persist over multiple generations.

    Quote Originally Posted by cypress
    Until you're willing to consider the third option, that you may be wrong, all you're doing is spouting dogma dressed as science.
    The fact that I am asking questions and searching for a way that mutation and selection does succeed should suffice. I think it is somewhat likely that I am wrong and that either the traditional evolutionists are correct or diversity occurred by other mechanisms entirely.
    Then you accept the possibility of option three. Glad we could clarify that.

    Quote Originally Posted by cypress
    When was the last time you thoughtfully researched and considered alternatives to your dogma?
    Today, when I read a paper that I assumed would argue that some receptor could not evolve via mutation and natural selection, but then realised it had nothing to do with that whatsoever. I've read quite a few such papers here and elsewhere. I've also read numerous websites making arguments either against evolution or for some alternative to it. Aside for reading for work, it's probably the topic I read about most.

    Quote Originally Posted by cypress
    How likely is it that you are wrong?
    Not very. Not impossible, but I've seen no evidence that leads me to have serious doubts.
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    My position is that mutation and natural selection does not presently account for new form and function but does account for modification of present form and function.
    You are a confused person.

    Modification of the present = new.

    Or are you suggesting evolution will start today? and only today?
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    Quote Originally Posted by TheBiologista

    You have either misunderstood or are misrepresenting the source provided. It doesn't support your position and furthermore its authors do not claim it does so. They show that the evolutionary pathway taken to produce the glucocorticoid receptor is non-reversible (albeit not absolutely so), not that it is non-traversable by mutation and selection.
    I submit it is you who are confused. If my english prose is not exactly the way you like it, please forgive me but "non-reversible" and a "non-traversable [reverse path]" are the same thing in my book.


    They see no need for any mechanisms outside of normal evolutionary processes for the pathway to be traversed, rather they simply demonstrate how it is highly unlikely that the ancestral form would be re-acquired. The hint is in the title- it's a one-way movement, like that of a ratchet.
    Precisely my point.

    This paper would only support your position if the authors had found the ancestral form in a species where it should not be and were unable to plot a path to that form. They didn't though.
    First off they did not find an ancestral form. They designed and constructed a specific presumed ancestral form. Second it does support my position that pathways involving several neutral and deleterious intermediates are "constrained"

    Cypress, this is at least the third time that you have cited to me papers which do not merely fail to support your point but actually demonstrate a very deep misunderstanding of the source on your part.
    Sorry Biologistica, NO this paper is as I claimed it is. I did once provide an unintended reference to you and I admitted it and apologized for the confusion and provided the intended one.


    Very well. Ironically enough I offer:

    Bridgham, J., Ortlund, E, and Thornton, J. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461.

    A 5 step pathway culminating in the glucocorticoid receptor. I'm not sure all of the steps would have a selectable advantage, but then that would be a silly requirement to ask for since I'm sure you're aware that selection is not binary, but probabilistic. Which means that even disadvantageous steps can persist over multiple generations.
    NO, sorry you are wrong again. The writers admit that the hypothetical pathways suggested include neutral and deleterious intermediates. The pathways offered were modeled. They were not obtained by random mutation and selection. They were not tested to verify the selective power. Finally the endpoint was designed and there is nothing to assure us it is biologically active (though it likely is). Surely you don't think I would miss such an easy example if it met the stated conditions?

    I am aware that selectable advantage is not binary. The question was asked to address a claim by speriousmonkey that selection is the driving force that accelerates blind search each step of the way. Clearly this seems not to be the case.


    Quote Originally Posted by cypress
    When was the last time you thoughtfully researched and considered alternatives to your dogma?
    Today, when I read a paper that I assumed would argue that some receptor could not evolve via mutation and natural selection, but then realised it had nothing to do with that whatsoever.
    Oh please. The paper confirms what I claimed it confirms. That stepwise pathways even for a very minor change from selective steroid receptor to a less restrictive receptor are difficult for evolutionary processes to navigate in a timely fashion. You and the authors of this paper seem to want to have it both ways. Here is what he says:

    "Selection for the ancestral function would therefore not be sufficient to drive AncGR2 back to the ancestral states of w and x, because passage through deleterious and/or neutral intermediates would be required; the probability of each required substitution would be low, and the probability of all in combination would be virtually zero."

    But here is the rub. You want to claim there is nothing that prevents the protein from being evolved through another path but here in the paper he addresses it by use of the very scientific "somehow" and "could" and "whether or not ... [they] exist"

    See here:

    "There may be other potentially permissive mutations, of unknown number, that could compensate for the restrictive effect of group W and allow the ancestral conformation to be restored. Reversal by such indirect pathways could be driven by selection, however, only if these other mutations, unlike those we studied, could somehow relieve the steric clashes and restore the lost stabilizing interactions "

    then:

    "and also independently restore the ancestral function when helix 7 is in its radically different derived conformation. Whether or not mutations that could achieve these dual ends exist, reversal to the ancestral conformation would require a considerably more complex pathway than was necessary before the ratchet effect of W evolved.

    You can't undo the conclusions of this paper by claiming somehow some other way evolutionary processes can succeed and then not demonstrate that supposed "somehow". You are gaming us. The purpose of this paper was to show exactly what I discussed.
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    you know cypress, i'm starting to get bored reading your rants
    any discussion on evolution that you take part in becomes a clone of an earlier thread where you bring out the same old tired tactics of claiming that everyone is wrong apart from yourself
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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  46. #45  
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    Quote Originally Posted by marnixR
    you know cypress, i'm starting to get bored reading your rants
    I'm rather disgusted that a poster for whom I have considerable admiration and respect chooses to describe a logically structured, objectively delivered, carefully reasoned series of posts as a 'rant'.
    Such a response is an exact example of the knee jerk dogmatic reaction that cypress has been complaining of.

    I have been following the discussions relating to cypress's viewpoints on this and other threads and find, so far, that no one has adequately addressed cypress's points. This may be a reflection of my miniscule knowledge of biology, primitive understanding of evolutionary processes, or some character defect that leads me to see dogma where none exists, but at present I doubt this.

    Cypress does not seem to me to be making an especially remarkable statement. He believes in evolution - he has no doubts about its reality. He has reservations about the way in which some of the higher orders of eukaryotes have emerged. He concedes that this may have happened through the slow process of cumulative change, but insists that until we have demonstrated a wholly plausible suite of detailed pathways to account for this in one order or phylum then application of Occam's Razor is inappropriate and we should entertain the possibility that an as yet unrecognised mechanism is at work. (Cypress, have I correctly represented your views?)

    All I see from his opposition are glib answers that gloss over his reservations and implicitly (perhaps even explicitly) treat him as if he were some kind of creationist. I don't find that useful and I don't find it edifying.
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  47. #46  
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    I still haven't seen a shred of evidence that he believes in evolution.

    Maybe you are just wrong.

    The fact that people bother to write long posts of nonsense, and keep repeating to do so, doesn't make them intelligent. It doesn't mean they believe in evolution. Moreover, I actually bothered to check the literature that supports his notions. Did you?

    It turns out these articles always were arguing the complete opposite viewpoint than Cypress. Yet he was using them as support. When confronted with this, he switched stories. The literature was now just there as some general background. How ironic it is then that he could have found the exact arguments that refuted his viewpoints in a scientific manner if he had read and understood the exact literature he used as a reference that supports his position.

    And then there is his general unwillingness to listen to any counter argument which he simply waves away by using the argument of incredulity. He doesn't believe it can have happened, so it hasn't.

    All of these tactics are straight from the creationist's handbook.

    Maybe he isn't a creationist. He certainly has the same level of critical thought as they have, and he certainly isn't worthy of any respect or admiration.

    There is no debate on dogma vs fresh thought here.

    It is just 'critical thinking' vs disbelief/belief.

    You are way out of line in attacking marnix when he just writes the simply truth. And if you believe that cypress describes a logically structure, objectively delivered, carefully reasoned series of posts, you have lost your marbles.
    "Kill them all and let God sort them out."

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  48. #47  
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    Quote Originally Posted by spuriousmonkey
    You are way out of line in attacking marnix when he just writes the simply truth. And if you believe that cypress describes a logically structure, objectively delivered, carefully reasoned series of posts, you have lost your marbles.
    Identify a single element of cypress's posts that constitute a rant.
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  49. #48  
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    Quote Originally Posted by Ophiolite
    Quote Originally Posted by spuriousmonkey
    You are way out of line in attacking marnix when he just writes the simply truth. And if you believe that cypress describes a logically structure, objectively delivered, carefully reasoned series of posts, you have lost your marbles.
    Identify a single element of cypress's posts that constitute a rant.
    A rant or harangue is a speech or text that does not present a well-researched and calm argument; rather, it is typically an attack on an idea, a person or an institution, and very often lacks proven claims.

    http://en.wikipedia.org/wiki/Rant

    The literature cited as in favour of rant is actually in favour of position ranted upon.
    When being criticized Cypress identifies the critic as one of 'those people'.
    His post are attacks on well established principles and ideas, and on scientists.
    Lacking proven claims.

    So basically everything.
    "Kill them all and let God sort them out."

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  50. #49  
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista

    You have either misunderstood or are misrepresenting the source provided. It doesn't support your position and furthermore its authors do not claim it does so. They show that the evolutionary pathway taken to produce the glucocorticoid receptor is non-reversible (albeit not absolutely so), not that it is non-traversable by mutation and selection.
    I submit it is you who are confused. If my english prose is not exactly the way you like it, please forgive me but "non-reversible" and a "non-traversable [reverse path]" are the same thing in my book.
    Then your book is wrong. Traversal suggests movement without specifying a direction. An inability to reverse is not an inability to traverse. They show the traversal to the observed form and show that the ancestral form is unlikely to be re-acquired. You've utterly misunderstood the conclusion of the paper or you are blatantly misrepresenting it. Either way you're being extremely silly, as your misrepresentation would be transparent to anyone with first year biology or perhaps a dictionary.

    Quote Originally Posted by cypress
    They see no need for any mechanisms outside of normal evolutionary processes for the pathway to be traversed, rather they simply demonstrate how it is highly unlikely that the ancestral form would be re-acquired. The hint is in the title- it's a one-way movement, like that of a ratchet.
    Precisely my point.
    No. Your point is that some observed forms cannot be reached via mutation and selection. For this paper to support your position, the ancestral form would have to be observed as present in some species that follows the later form. Then the low probability of traversal from present to ancestral would be highly relevant. But it is not observed, and that is entirely in line with what we expect if a) evolution is driven by mutation and selection and b) the reversal is unlikely.

    Quote Originally Posted by cypress
    This paper would only support your position if the authors had found the ancestral form in a species where it should not be and were unable to plot a path to that form. They didn't though.
    First off they did not find an ancestral form. They designed and constructed a specific presumed ancestral form. Second it does support my position that pathways involving several neutral and deleterious intermediates are "constrained"
    Only in a direction not actually observed in nature. Hence observation supports evolution by mutation and selection. Tell you what, the corresponding author's address is on the paper. Put your proposition to him and as him his opinion on it.

    Quote Originally Posted by cypress
    Cypress, this is at least the third time that you have cited to me papers which do not merely fail to support your point but actually demonstrate a very deep misunderstanding of the source on your part.
    Sorry Biologistica, NO this paper is as I claimed it is. I did once provide an unintended reference to you and I admitted it and apologized for the confusion and provided the intended one.
    Simply put, garbage. For the reasons already explained.

    Quote Originally Posted by cypress
    Very well. Ironically enough I offer:

    Bridgham, J., Ortlund, E, and Thornton, J. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461.

    A 5 step pathway culminating in the glucocorticoid receptor. I'm not sure all of the steps would have a selectable advantage, but then that would be a silly requirement to ask for since I'm sure you're aware that selection is not binary, but probabilistic. Which means that even disadvantageous steps can persist over multiple generations.
    NO, sorry you are wrong again. The writers admit that the hypothetical pathways suggested include neutral and deleterious intermediates.
    And what's the issue with that? That only matters if selection is binary.

    Quote Originally Posted by cypress
    The pathways offered were modeled. They were not obtained by random mutation and selection. They were not tested to verify the selective power. Finally the endpoint was designed and there is nothing to assure us it is biologically active (though it likely is).
    As much a criticism of your use of the reference as mine.

    Quote Originally Posted by cypress
    Surely you don't think I would miss such an easy example if it met the stated conditions?
    At this point I suspect your understanding of the relevant science is weak enough that this is very likely indeed. I'm sorry that I have to repeatedly point that out but at this stage I'm becoming embarrassed on your behalf.

    Quote Originally Posted by cypress
    I am aware that selectable advantage is not binary. The question was asked to address a claim by speriousmonkey that selection is the driving force that accelerates blind search each step of the way. Clearly this seems not to be the case.
    I thought your were trying to show that a certain path was utterly non-traversable by selection and mutation. You failed to show that. Can you show that selection was not a driving force in the path that was traversed in the paper?

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    When was the last time you thoughtfully researched and considered alternatives to your dogma?
    Today, when I read a paper that I assumed would argue that some receptor could not evolve via mutation and natural selection, but then realised it had nothing to do with that whatsoever.
    Oh please. The paper confirms what I claimed it confirms. That stepwise pathways even for a very minor change from selective steroid receptor to a less restrictive receptor are difficult for evolutionary processes to navigate in a timely fashion.
    Irrelevant unless the ancestral form is observed to exist "down-evolution" from the current form within an evolutionary time frame that is insufficient for the low probability to be overcome. I don't know how better to explain this to you.

    Quote Originally Posted by cypress
    You and the authors of this paper seem to want to have it both ways. Here is what he says:

    "Selection for the ancestral function would therefore not be sufficient to drive AncGR2 back to the ancestral states of w and x, because passage through deleterious and/or neutral intermediates would be required; the probability of each required substitution would be low, and the probability of all in combination would be virtually zero."

    But here is the rub. You want to claim there is nothing that prevents the protein from being evolved through another path but here in the paper he addresses it by use of the very scientific "somehow" and "could" and "whether or not ... [they] exist"

    See here:

    "There may be other potentially permissive mutations, of unknown number, that could compensate for the restrictive effect of group W and allow the ancestral conformation to be restored. Reversal by such indirect pathways could be driven by selection, however, only if these other mutations, unlike those we studied, could somehow relieve the steric clashes and restore the lost stabilizing interactions "

    then:

    "and also independently restore the ancestral function when helix 7 is in its radically different derived conformation. Whether or not mutations that could achieve these dual ends exist, reversal to the ancestral conformation would require a considerably more complex pathway than was necessary before the ratchet effect of W evolved.

    You can't undo the conclusions of this paper by claiming somehow some other way evolutionary processes can succeed and then not demonstrate that supposed "somehow". You are gaming us. The purpose of this paper was to show exactly what I discussed.
    No, it wasn't. The purpose of the paper was to show that all pathways are not equally traversable irrespective of the presence or absence of selection, even when one pathway may be the reversal of a probable pathway. This is something we've hypothesised to be the case for a long time and yet again I stress that it would be relevant to your position only if we actually observed forms in locations in the phylogeny that could only be explained by improbable traversals. We do not.
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  51. #50  
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    Quote Originally Posted by Ophiolite
    Cypress does not seem to me to be making an especially remarkable statement. He believes in evolution - he has no doubts about its reality. He has reservations about the way in which some of the higher orders of eukaryotes have emerged. He concedes that this may have happened through the slow process of cumulative change, but insists that until we have demonstrated a wholly plausible suite of detailed pathways to account for this in one order or phylum then application of Occam's Razor is inappropriate and we should entertain the possibility that an as yet unrecognised mechanism is at work. (Cypress, have I correctly represented your views?)
    In what way is the Razor served by substituting a known complex mechanism for an utterly unknown mechanism? Cypress has a negative position. A and B do not account for X. He has no proposition for us, be it simpler or more complex. And he has yet to demonstrate even one example in which A and B do not account for X. His best shot so far is a paper that contradicts his position. Even in the face of that, he budges not an inch. This is why we are increasingly dismissive of him.
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    Cypress' initial post wasn't wrong, there are many problems with the current model of evolution (synthetic theory) that can be effectively explained with epigenetics/epigenomics; not only do they provide a more profound understanding, they contradict ID, since it depicts the environmental context as the "designer" - but this occurs unconsciously -.
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  53. #52  
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    Quote Originally Posted by Ophiolite
    Quote Originally Posted by marnixR
    you know cypress, i'm starting to get bored reading your rants
    I'm rather disgusted that a poster for whom I have considerable admiration and respect chooses to describe a logically structured, objectively delivered, carefully reasoned series of posts as a 'rant'.
    Such a response is an exact example of the knee jerk dogmatic reaction that cypress has been complaining of.
    and i'm complaining of the fact that every single thread that cypress has contributed to is starting to sound like a carbon copy of each other
    tbh, if i was mod for this part of the forum i would have issues with how several threads have gone off the topic set by the OP and becomes a cypress-clone
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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  54. #53  
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    Quote Originally Posted by Chronman
    Cypress' initial post wasn't wrong, there are many problems with the current model of evolution (synthetic theory) that can be effectively explained with epigenetics/epigenomics; not only do they provide a more profound understanding, they contradict ID, since it depicts the environmental context as the "designer" - but this occurs unconsciously -.
    Epigenetics is not really relevant to evolution over the sorts of timescales we're discussing here. Epigenetic traits are lost within a few generations, or are not inherited at all in most cases. Now a caveat to this is that the impact of epigenetics on evolution is still something of an open question, perhaps there are more extreme cases we have not observed, but right now we certainly could not say with confidence that it's an important factor. More than likely it will emerge as a minor element of the modern synthesis rather like HGT in eukaryotes. An exception to the rules, rather than a fundemental element such as NS.
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    Quote Originally Posted by TheBiologista

    Epigenetics is not really relevant to evolution over the sorts of timescales we're discussing here. Epigenetic traits are lost within a few generations, or are not inherited at all in most cases. Now a caveat to this is that the impact of epigenetics on evolution is still something of an open question, perhaps there are more extreme cases we have not observed, but right now we certainly could not say with confidence that it's an important factor. More than likely it will emerge as a minor element of the modern synthesis rather like HGT in eukaryotes. An exception to the rules, rather than a fundemental element such as NS.
    I agree with much of what you said, but I also believe that the accumulation of epigenetic traits/modifications, due to extended exposure in a particular environment/pressure can account for macro-evolution.

    You do agree that when this is demonstrated conclusively, that it will debunk ID, correct?
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    You do agree that when this is demonstrated conclusively, that it will debunk ID, correct?
    ID needs no debunking. They will invent some reason to continue with their nonsense.
    Disclaimer: I do not declare myself to be an expert on ANY subject. If I state something as fact that is obviously wrong, please don't hesitate to correct me. I welcome such corrections in an attempt to be as truthful and accurate as possible.

    "Gullibility kills" - Carl Sagan
    "All people know the same truth. Our lives consist of how we chose to distort it." - Harry Block
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    Quote Originally Posted by Chronman
    Quote Originally Posted by TheBiologista

    Epigenetics is not really relevant to evolution over the sorts of timescales we're discussing here. Epigenetic traits are lost within a few generations, or are not inherited at all in most cases. Now a caveat to this is that the impact of epigenetics on evolution is still something of an open question, perhaps there are more extreme cases we have not observed, but right now we certainly could not say with confidence that it's an important factor. More than likely it will emerge as a minor element of the modern synthesis rather like HGT in eukaryotes. An exception to the rules, rather than a fundemental element such as NS.
    I agree with much of what you said, but I also believe that the accumulation of epigenetic traits/modifications, due to extended exposure in a particular environment/pressure can account for macro-evolution.

    You do agree that when this is demonstrated conclusively, that it will debunk ID, correct?
    Well no, because ID makes no sense either way. We don't need to invoke either ID or epigenetics to explain macroevolution. Mutation, normal inheritance and selection are quite sufficient to allow macroevolution to occur. That is not to say that other factors cannot come into play, but their absence would not be barriers to significant changes over time such a sepciation and the like.
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    Quote Originally Posted by TheBiologista

    Well no, because ID makes no sense either way. We don't need to invoke either ID or epigenetics to explain macroevolution. Mutation, normal inheritance and selection are quite sufficient to allow macroevolution to occur. That is not to say that other factors cannot come into play, but their absence would not be barriers to significant changes over time such a sepciation and the like.
    I know our current model can account for macro-evolution, but I presented epigenetics as another means by which it would occur.

    I think it would debunk, conclusively, the ID argument.

    That's not to say I believe the ID argument is actually reasonable, I'm simply saying, this would be a (not "THE") conclusive proof against.
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    Quote Originally Posted by cypress
    there actually is some evidence for directed (goal driven) change. Genetic engineers have and do add novel molecular alterations by goal driven processes and we observe these kind of differences in higher orders. Furthermore we have not observed non-goal directed processes achieve these same differences.
    Nor have we observed these kinds of changes (the kinds of genetic alterations that engineers produce, that breeders can't) in evolving entities - hence the rejection of these directed techniques as explaining the evolution of the beings on this planet.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    there actually is some evidence for directed (goal driven) change. Genetic engineers have and do add novel molecular alterations by goal driven processes and we observe these kind of differences in higher orders. Furthermore we have not observed non-goal directed processes achieve these same differences.
    Nor have we observed these kinds of changes (the kinds of genetic alterations that engineers produce, that breeders can't) in evolving entities - hence the rejection of these directed techniques as explaining the evolution of the beings on this planet.
    Perhaps i misunderstand, but I believe you are incorrect. We do observe the kind of differences ( you chose the word "changes" rather than "differences") in higher orders (families, orders etc.). We don't observe that known observed evolutionary processes produce these differences but we do note that genetic engineering is capable of producing these kinds of differences. Therefore logically we must say there is some evidence supporting goal driven processes producing macro differences but currently no evidence that known evolutionary processes produce macro differences.
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    Quote Originally Posted by inow
    The point is that the description we have works incredibly well without the need to posit direction or intentionality.
    The problem of course is that the current description of known evolutionary processes and the predictions of their capacity to drive large scale change and therefore observed diversity is not supported by experimental and observational results. It does not work well at all. One could say that on the basis of experimental results it fails.

    If you wish to suggest otherwise. Please offer a real demonstration of an observed success. Please do not claim that it takes too long. That excuse no longer works because we now know what kinds of molecular level alterations are required to account for new protein function and interaction and they generally require 5-10 focused substitutions. That level change must occur in fewer than a trillion organisms in order to account for macro changes observed by the fossil record in the time allowed (there have been fewer than an estimated 10^14 total mammals ever in existence). It is easy to produce trillions of microorganisms in a few months or less.
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  62. #61  
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    Quote Originally Posted by cypress
    Quote Originally Posted by inow
    The point is that the description we have works incredibly well without the need to posit direction or intentionality.
    The problem of course is that the current description of known evolutionary processes and the predictions of their capacity to drive large scale change and therefore observed diversity is not supported by experimental and observational results. It does not work well at all. One could say that on the basis of experimental results it fails.
    Is today opposite day, or something? Nothing you just said is accurate or true (except for the "people could say" comment... you know, because people say all kinds of really stupid things everyday).
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by Ophiolite
    Cypress does not seem to me to be making an especially remarkable statement. He believes in evolution - he has no doubts about its reality. He has reservations about the way in which some of the higher orders of eukaryotes have emerged. He concedes that this may have happened through the slow process of cumulative change, but insists that until we have demonstrated a wholly plausible suite of detailed pathways to account for this in one order or phylum then application of Occam's Razor is inappropriate and we should entertain the possibility that an as yet unrecognised mechanism is at work. (Cypress, have I correctly represented your views?)
    In what way is the Razor served by substituting a known complex mechanism for an utterly unknown mechanism? Cypress has a negative position. A and B do not account for X. He has no proposition for us, be it simpler or more complex. And he has yet to demonstrate even one example in which A and B do not account for X. His best shot so far is a paper that contradicts his position. Even in the face of that, he budges not an inch. This is why we are increasingly dismissive of him.
    Biologista and speriousmonky seem to be so wedded to their presuppositions that they choose not to see my questions properly framed. They seem to want so badly to believe instead that I am ignorant or misinformed. They spend 90% of their effort attacking me personally and almost no time addressing the substance of the argument.

    Here is my scientific challenge properly framed:

    Provide an observed verified mechanism/process that accounts for transformation of a functional protein into a different functional protein that has either new tertiary shape or new binding site(s) where more that 4 amino acid substitutions are required to accomplish the difference.

    I note that one known way to accomplish this is by genetic engineering. That is a positive and verified solution to this challenge. I also note that to date, known evolutionary processes have not provided a solution to this challenge. I have offered several research papers that provide insight to why researchers are finding it difficult for known evolutionary processes to account for these differences. I suggest that this insight is suggestive of the possibility that known processes are perhaps not able to accomplish these changes sufficiently quickly enough to account for observed biological diversity and therefore we should be investigating other processes that would account for these changes in a timeframe consistent with geologic time.

    I am unlikely to respond to each of Biologista's largely irrelevant responses contained in his previous post. I may draw out one or two of them later.
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    Quote Originally Posted by inow
    Quote Originally Posted by cypress
    Quote Originally Posted by inow
    The point is that the description we have works incredibly well without the need to posit direction or intentionality.
    The problem of course is that the current description of known evolutionary processes and the predictions of their capacity to drive large scale change and therefore observed diversity is not supported by experimental and observational results. It does not work well at all. One could say that on the basis of experimental results it fails.
    Is today opposite day, or something? Nothing you just said is accurate or true (except for the "people could say" comment... you know, because people say all kinds of really stupid things everyday).
    If I am wrong and you are correct you would be able to provide a real demonstration where the "description we have" actually accounts for new form and function at the molecular level regularly enough to account for observed diversity. I'll wait for your example.
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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Provide an observed verified mechanism/process that accounts for transformation of a functional protein into a different functional protein that has either new tertiary shape or new binding site(s) where more that 4 amino acid substitutions are required to accomplish the difference.
    They did demonstrate this for more than 4 aminoacid substitutions.

    Does it have to be 4 exactly?
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    Quote Originally Posted by cypress
    Biologista and speriousmonky seem to be so wedded to their presuppositions that they choose not to see my questions properly framed. They seem to want so badly to believe instead that I am ignorant or misinformed. They spend 90% of their effort attacking me personally and almost no time addressing the substance of the argument.
    Cypress, it's a question of priorities. If you were to go to the physics forum, announce that Einstein was wrong and present in support of this a paper that actually confirms his predictions regarding gravitational lensing or somesuch then it would be vital that the posters and moderators first point out to you that you have misunderstood the source material and may be labouring under a misconception. We are not engaging in ad hominem attacks here, we're trying to point out to you that you've revealed some significant shortcomings in your understanding which suggest that you are indeed labouring under some misconceptions. If we can move past that and actually get to some evidence that supports you, then perhaps this discussion can become more useful for both parties.

    Instead you've essentially demonstrated another misconception in posting that last source, compounded your error by insisting it supports your position when it contradicts it and have now decided to brush that awkward detail under the carpet and whilst suggesting we're unfairly attacking your credibility in lieu of dealing with your actual arguments. For us to go on to your actual arguments in detail would be rather like debating how many angels can fit on the head of a pin.

    Quote Originally Posted by cypress
    Here is my scientific challenge properly framed:

    Provide an observed verified mechanism/process that accounts for transformation of a functional protein into a different functional protein that has either new tertiary shape or new binding site(s) where more that 4 amino acid substitutions are required to accomplish the difference.
    The source your provided in support of your argument does this with one extra step. The intermediate steps are putative but since you've already stated that you have no issue with inferrence, this should actually fit the bill.

    Quote Originally Posted by cypress
    I note that one known way to accomplish this is by genetic engineering. That is a positive and verified solution to this challenge. I also note that to date, known evolutionary processes have not provided a solution to this challenge. I have offered several research papers that provide insight to why researchers are finding it difficult for known evolutionary processes to account for these differences. I suggest that this insight is suggestive of the possibility that known processes are perhaps not able to accomplish these changes sufficiently quickly enough to account for observed biological diversity and therefore we should be investigating other processes that would account for these changes in a timeframe consistent with geologic time.
    Again, a negative position. I really wish you'd quit beating around the bush and make a proposition. The hint at genetic engineering - are you hypothesising that genetic engineering might account for some significant part of evolution?

    Quote Originally Posted by cypress
    I am unlikely to respond to each of Biologista's largely irrelevant responses contained in his previous post. I may draw out one or two of them later.
    Irrelavant? Imagine I make some claims.

    1. White is black
    2. My source on this is Supriousmonkey et al. (2009) "White is white".
    3. White light is not composed of photons

    I'm reducing to absurdity here for illustrative purposes, but it seems you are suggesting we should address point 3 and ignore points 1 and 2. In fact, point 1 here is rather stronger than your point one, since it is actually a proposition rather than say "white is not x, y or z".

    You may ignore our "irrelevant" points all you like. They're not going to go away.
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    Quote Originally Posted by TheBiologista
    2. My source on this is Supriousmonkey et al. (2009) "White is white".
    I have had 6 papers with my name on it this year, but none with that title.
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    Quote Originally Posted by spuriousmonkey
    Quote Originally Posted by TheBiologista
    2. My source on this is Supriousmonkey et al. (2009) "White is white".
    I have had 6 papers with my name on it this year, but none with that title.
    If you look closely you'll note that the paper was actually writter by "Supriousmonkey" and his colleagues. Different monkey entirely. My apologies for any confusion.
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    Biologista, Spurious and Marnix here is a point you may wish to consider.

    I think I have established myself on this forum as being a reasonably well educated individual, with a passable layman's knowledge of biology complemented by some specific evolutionary knowledge based upon a formal education in geology. I think I have also demonstrated an intolerance of creationists, or those who 'have a theory', or think 'Einstein is wrong'. Indeed, if I recall correctly, I was stripped of my moderatorship here for expressing such intolerance in a vigorous manner.

    Despite this background I find cypress's questioning to be balanced and sound, while the responses are lacking in substance and amount to little more than saying "you are wrong, get better educated". If I view your responses in this way it concerns me that those who doubt evolution will find nothing in what you are saying to change their view. Now you may reasonably declare that this simply represents a weakness on my part. You will understand I find that possibility difficult to accept based on the observations made in the paragraph above.
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    Quote Originally Posted by cypress
    Let's step through these "number of false assumptions". Please tell my why you claim they are false.
    Already done.

    To repeat: In your argument establishing the theoretical inadequacy of standard evolutionary theory, you assume independence of events that need not be independent; you assume non-function in proteins whose possible environments and possible functions you or anyone know little about; you assume merely one of several possible mechanisms of alteration of a protein (single point mutation only, various means of larger block swapout and editing, etc, disallowed). And so forth.
    Quote Originally Posted by ophiolite
    All I see from his opposition are glib answers that gloss over his reservations and implicitly (perhaps even explicitly) treat him as if he were some kind of creationist.
    He's just cribbing from the Book of Behe, pretty much word for word. His reservations have been dealt with, in very starightforward and simple terms, he remains oblivious, there's no point in rehashing the already glibly - by him - dismissed.
    Quote Originally Posted by ophiolite
    Despite this background I find cypress's questioning to be balanced and sound, while the responses are lacking in substance and amount to little more than saying "you are wrong, get better educated"
    Some of the responses have been limited so, but not all. Cypress has been answered, in all his actual "reservations", sufficiently, by several posts.
    Quote Originally Posted by cypress
    I note that one known way to accomplish this is by genetic engineering. That is a positive and verified solution to this challenge.
    There is no remaining argument that it is necessary to explain the facts, and there is no evidence it ever happened.

    It involves, as well, an extraordinary postulation: a genetic engineer, operating on evolutionary scales of time and space. That would require extraordinary evidence.
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    Quote Originally Posted by inow
    The point is that the description we have works incredibly well without the need to posit direction or intentionality.
    The problem of course is that the current description of known evolutionary processes and the predictions of their capacity to drive large scale change and therefore observed diversity is not supported by experimental and observational results. It does not work well at all. One could say that on the basis of experimental results it fails.

    If you wish to suggest otherwise. Please offer a real demonstration of an observed success. Please do not claim that it takes too long. That excuse no longer works because we now know what kinds of molecular level alterations are required to account for new protein function and interaction and they generally require 5-10 focused substitutions. That level change must occur in fewer than a trillion organisms in order to account for macro changes observed by the fossil record in the time allowed (there have been fewer than an estimated 10^14 total mammals ever in existence). It is easy to produce trillions of microorganisms in a few months or less.
    Cypress, you keep on bringing up the same topic up in multiple threads. Those threads get derailed and end up just another Cypress-says-evolution-can't-work-by-mutation-and-selection-alone thread. There's actually a fairly decent debate going on here so if you persist with this, I'll have to start merging your comments into the macro/mirco thread.
    Actually you and other posers keep overselling the known capacity of evolutionary processes and make it seem to have more capability than has been demonstrated. I simply correct them. The thread gets derailed when the poster takes exception to the correction. If you and the others leave the correction alone, the thread will continue uninterrupted with the correction noted.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    - - We do observe the kind of differences ( you chose the word "changes" rather than "differences") in higher orders (families, orders etc.). We don't observe that known observed evolutionary processes produce these differences but we do note that genetic engineering is capable of producing these kinds of differences.
    This is false. The kinds of differences we see between families, orders, etc, are not at all like the differences created by genetic engineers - instead, they form genealogical trees of relationships closely corresponding to expected relationships of inheritance and similarity by descent from common ancestor.

    And we do have a theory of evolutionary change that not only accounts for the relationship patterns we see, but predicted, the subsequently discovered mirroring of genealogical relationships in the content of inheritance - what was later identified as the genetic code of DNA. That was the Darwinian Theory of Evolution.
    Good post, and very true. If genetic engineering or some other intelligently-driven intervention were at play in evolution, we shouldn't be able to build bifurcating phylogenies without seeing significant and otherwise inexplicable exceptions. Rather like if we were to try and build a nested tree of relatedness between cars, we could only maintain the tree structure if we started to ignore traits. Designed objects inherit from multiple branches, the branches of the tree converge and we end up with a web structure instead.

    Whilst we do see a web structure in the relatedness of prokatyotic life, it's all on the scale expected for horizontal gene transfer. We don't see large scale multigenetic relationships that break the tree. In eukaryotes, there are pretty much no deviations from the tree structure at all, aside from some occasional HGT and some endosymbiosis. Aside from that, it all looks exactly as would be expected if the main driving forces were mutation, inheritence, drift and selection.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    - - We do observe the kind of differences ( you chose the word "changes" rather than "differences") in higher orders (families, orders etc.). We don't observe that known observed evolutionary processes produce these differences but we do note that genetic engineering is capable of producing these kinds of differences.
    This is false. The kinds of differences we see between families, orders, etc, are not at all like the differences created by genetic engineers -
    The molecular level changes required for new form and function can and are successfully accomplished by genetic engineering. In higher orders the numbers of these individual molecular changes becomes large and highly coordinated to form wholesale novel forms and functions but at the low level, genetic engineers are succeeding with the requisite differences. So when you reduce them to the molecular level they are like.

    To preserve the context of this thread, this is significant because it provides a basis to say there are some indications that diversity of life required goal directed activity. To date, we have not been able to demonstrate that the required molecular level changes can be obtained by non-goal directed processes.

    instead, they form genealogical trees of relationships closely corresponding to expected relationships of inheritance and similarity by descent from common ancestor.
    Evidence for common descent does not demonstrate in any way whether or not the process that caused common descent to proceed was a specific process or another. Goal driven processes are quite capable of generating a pattern consistent with common descent. The question is how do we know that the actual process that generated the pattern and thus diversity of life is not goal directed? I presently do not have an answer to that question.

    Common descent does not help in this question at all.

    And we do have a theory of evolutionary change that not only accounts for the relationship patterns we see, but predicted, the subsequently discovered mirroring of genealogical relationships in the content of inheritance - what was later identified as the genetic code of DNA. That was the Darwinian Theory of Evolution.
    The problem is that the theory fits in some ways but many of the predictions it has made were and remain incorrect. Furthermore the observed process invoked by the theory have not been able to produce modest molecular level alterations that would be required to "account" for observed diversity. Therefore it does not. The only process at this time known to be capable of generating the low level differences required is goal driven. This brings us back to the original question. How can we know that evolutionary change proceeded by random and deterministic processes with no goal driven processes involved?
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    Quote Originally Posted by cypress
    Actually you and other posers keep overselling the known capacity of evolutionary processes and make it seem to have more capability than has been demonstrated. I simply correct them. The thread gets derailed when the poster takes exception to the correction. If you and the others leave the correction alone, the thread will continue uninterrupted with the correction noted.
    The capacity of evolutionary processes and the veracity of the modern synthesis theory are not the topic here. The topic is, assuming evolution has occured by some process or other, how we go about discerning between directed and undirected change. Your point was not relevant.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Let's step through these "number of false assumptions". Please tell my why you claim they are false.
    Already done.

    To repeat: In your argument establishing the theoretical inadequacy of standard evolutionary theory, you assume independence of events that need not be independent;
    How so? Exactly what events am I treating as independent? What evidence can you offer that they are in fact not independent?

    you assume non-function in proteins whose possible environments and possible functions you or anyone know little about;
    No I disagree.

    First off I am asking for current experimental results not speculation about what might have happened previously. Second, I accept selection as described by the theory and therefore note that by definition, selection cannot select for future or past function. It only deals in the present.

    Are you suggesting that natural selection is preferential to future or past function? If you are not, then it should be obvious that I need not and do not make any assumption about possible function; I need only deal with current function, which is directly measurable.

    you assume merely one of several possible mechanisms of alteration of a protein (single point mutation only, various means of larger block swapout and editing, etc, disallowed). And so forth.
    I did not put any restriction on mechanisms. All known mechanisms are on the table. I asked for examples in 4 or more steps. These other mechanisms also progress in steps. Any mix of known mechanisms is allowed.

    Quote Originally Posted by ophiolite
    All I see from his opposition are glib answers that gloss over his reservations and implicitly (perhaps even explicitly) treat him as if he were some kind of creationist.
    He's just cribbing from the Book of Behe, pretty much word for word. His reservations have been dealt with, in very starightforward and simple terms, he remains oblivious, there's no point in rehashing the already glibly - by him - dismissed.
    Behe is not the only research biologist who recognizes these issues. This past spring there was a large event of prominent evolutionary biologists who met to address this issue and who called for research into alternative processes since they believe traditional evolutionary theory was not keeping up with the challenges. As ophiolite has noted on several occasions, you and your team here have not provided an adequate response. If you were to offer a direct solution to the challenge offered I would treat it fairly. The problem is you give non-answers that support your presuppositions but don’t address the question.

    Anyone can easily claim to "deal with" a challenge by brushing it off as you and biologista do, but it is much harder to provide a known case where evolutionary processes actually accomplish what I have requested. The Thornton team did not "evolve" the pathways by natural processes, they modeled them and explicitly designed them. Furthermore it is not an example of new function or a new binding site nor is it a case of selective advantage for each consecutive step. Thornton is on record acknowledging this. It is a very modest example of modified selectivity of existing function, something that known processes should easily accomplish, but as it turns out, it seems to be very difficult in some cases. I provided that example as a demonstration of why known evolutionary processes seem to be so impotent when faced with the kinds of obstacles I mention.

    Quote Originally Posted by ophiolite
    Despite this background I find cypress's questioning to be balanced and sound, while the responses are lacking in substance and amount to little more than saying "you are wrong, get better educated"
    Some of the responses have been limited so, but not all. Cypress has been answered, in all his actual "reservations", sufficiently, by several posts.

    Oh please, see above. If an answer is as easy as you claim you would be able to provide an endless list of experimental results confirming the events I listed. The criteria I require are not difficult to understand and traditional evolutionary theory predicts there should be hundreds of millions of examples of these low level changes occurring regularly, but we don’t observe them. Why not? The most reasonable answer is because they don’t happen this way.
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    Quote Originally Posted by cypress
    Goal driven processes are quite capable of generating a pattern consistent with common descent
    With reasonable probability, only if that were their goal. Are you postulating a genetic engineering effort devoted to imitating standard evolutionary processes?

    When you have common descent visible as a cause and sufficient as an explanation, and you have goal driven genetic engineers invisible as a cause and unnecessary an explanation, why would you go with the invisible and unnecessary?
    Quote Originally Posted by cypress
    To date, we have not been able to demonstrate that the required molecular level changes can be obtained by non-goal directed processes.
    We have evidence that it was so obtained. We have no valid argument that it could not have been.
    Quote Originally Posted by cypress
    The problem is that the theory fits in some ways but many of the predictions it has made were and remain incorrect.
    That is false. No necessary prediction of Darwinian Theory has ever been falsified.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Goal driven processes are quite capable of generating a pattern consistent with common descent
    With reasonable probability, only if that were their goal. Are you postulating a genetic engineering effort devoted to imitating standard evolutionary processes?
    No. I am making a comparison. Based on experimental results, we can say that there is evidence that known goal driven processes are likely capable of generating the kinds of differences required to explain observed biological diversity. On the other hand we cannot currently say the same thing about processes that are not goal driven. We can't because we don't observe that these other processes are capable of the requisite changes at the molecular level in a timeframe consistent with the fossil record.

    When you have common descent visible as a cause and sufficient as an explanation, and you have goal driven genetic engineers invisible as a cause and unnecessary an explanation, why would you go with the invisible and unnecessary?
    Common descent is consistent with both directed and undirected processes. It does not favor one over the other and since it does not, it does not strengthen the relative case for either one. Furthermore Common descent is not a process. It may tell us what happened but it does not tell us how it happened. Therefore it cannot be used to validate any particular process.

    The primary question in this thread is how can we know that [biological diversity] occurred by undirected (as previously defined) causes. If there was a necessary and sufficient undirected process offered that is observed and in operation today (there is not) then I would agree that invoking design would be unnecessary, but today we cannot say that. Recognize also that absence of an observed process is not the only issue against undirected processes.

    Quote Originally Posted by cypress
    To date, we have not been able to demonstrate that the required molecular level changes can be obtained by non-goal directed processes.
    We have evidence that it was so obtained. We have no valid argument that it could not have been.
    Most of the evidence is simply evidence that one form has components similar to another. But similarity does tell us how the difference came to be. Therefore that evidence is interesting for establishing relationships but it is not useful in this question about by what kind of process the differences occurred.

    It is a logical fallacy to claim that someone is wrong because they have failed to prove a negative. If one side is required to show the other could not have been, then the other side is also required to do the same.

    Quote Originally Posted by cypress
    The problem is that the theory fits in some ways but many of the predictions it has made were and remain incorrect.
    That is false. No necessary prediction of Darwinian Theory has ever been falsified.
    That's laughable. The theory has undergone regular adjustments (as many do) over the years as certain predictions were falsified (this does not necessarily make the theory entirely wrong). Darwin's theory made strong predictions about development that were falsified by embryology some time ago. Our inability to produce direct fossil transitions and the observations of stasis in the fossil record are also contradictions to predictions. It is possible to provide a long list of falsified predictions including two very recent ones regarding Junk DNA and vestigial organs. I'm sure there are numerous people who prefer to explain these away as misunderstandings and that's fine, I don't care to debate the reasons. Let's at least be honest. We can't easily determine the truth if we continually deny the facts.

    Returning to the main point, as far as I know, currently there is no way to scientifically establish that biodiversity proceeded purely by unguided processes.
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    Quote Originally Posted by cypress
    The primary question in this thread is how can we know that [biological diversity] occurred by undirected (as previously defined) causes. If there was a necessary and sufficient undirected process offered that is observed and in operation today (there is not) then I would agree that invoking design would be unnecessary, but today we cannot say that.
    This (in bold) is a misleading statement. As noted in this and other threads I do not currently believe we have identified all the important mechanisms by which macroevolution occurs. However, my strong suspicion is that this mechanism is available today, though it may be dormant.

    While that is apparently the same as your statment that it is not in operation today there is a significant difference. Your statement seems to me to imply that we could not identify this mechanism today because it is not present. Was that your intent
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    Quote Originally Posted by Ophiolite
    Quote Originally Posted by cypress
    The primary question in this thread is how can we know that [biological diversity] occurred by undirected (as previously defined) causes. If there was a necessary and sufficient undirected process offered that is observed and in operation today (there is not) then I would agree that invoking design would be unnecessary, but today we cannot say that.
    This (in bold) is a misleading statement. As noted in this and other threads I do not currently believe we have identified all the important mechanisms by which macroevolution occurs. However, my strong suspicion is that this mechanism is available today, though it may be dormant.

    While that is apparently the same as your statment that it is not in operation today there is a significant difference. Your statement seems to me to imply that we could not identify this mechanism today because it is not present. Was that your intent
    Fair point, I should have said "it is not apparent" or something like that. I agree we should be looking for a process that can be teased out, but does not show when the experiments are designed to test mutation and selection.
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    Quote Originally Posted by TheBiologista

    Good post, and very true. If genetic engineering or some other intelligently-driven intervention were at play in evolution, we shouldn't be able to build bifurcating phylogenies without seeing significant and otherwise inexplicable exceptions. Rather like if we were to try and build a nested tree of relatedness between cars, we could only maintain the tree structure if we started to ignore traits. Designed objects inherit from multiple branches, the branches of the tree converge and we end up with a web structure instead.

    Whilst we do see a web structure in the relatedness of prokatyotic life, it's all on the scale expected for horizontal gene transfer. We don't see large scale multigenetic relationships that break the tree. In eukaryotes, there are pretty much no deviations from the tree structure at all, aside from some occasional HGT and some endosymbiosis. Aside from that, it all looks exactly as would be expected if the main driving forces were mutation, inheritence, drift and selection.
    Thank-you for another opportunity to set right another myth from Talk.Origins. The idea that there is a good correspondence or a nested hierarchy between molecular morphological trees is wrong. It is also incorrect to claim that molecular phylogenies based on various genes to others correspond well.

    Have a look at Phillip Ward’s presentation at last month’s Darwin Conference at University of Chicago where he argued that the large numbers of deviations indicates that perhaps convergent evolution is far more pervasive than predicted (he was understandably unwilling to consider other explanations). He offered many mind blowing examples where molecular dada contradicted long established clades and “distributed the groups all over the tree”.

    Also, have a look at this article: Lawton, G., (Jan, 2009) “Why Darwin was wrong about the tree of life”, New Scientist, 284.

    Here is what the paper says:

    “For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

    And in contradiction to your claim that this problem is only encountered in microorganisms that swap genes I offer this quote from the paper:

    Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts—also known as tunicates—are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says.

    The argument is not improved by repeating myths and half-truths that only confuse the situation.
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    Here is a response to that New Scientist article by actual evolutionary biologists.

    I tried to find this 1985 study by Syvanen, and I did find a 1985 paper by him but it was theoretical and had no data. That paper, in line with the letter above, suggests that horizontal gene transfer is more common that previously thought and must be taken into consideration when constructing phylogenies. If Syvanen did this study with 2000 genes he did not publish it, and I suspect I know why. You cannot use genes that are functional and subject to natural selection in order to build a correct phylogeny of relatedness of the organisms that have them. Organisms that are distantly related but living in similar environments are more likely to evolve similar traits which makes them seem artificially more closely related. Organisms that are closely related but that live in extremely different environments are more likely to evolve very different traits that makes them seem artificially less related. A good molecular phylogeny will also utilize data from not one but very many neutral loci, which can help to overcome the error introduced by issues like horizontal transfer. Using functional genes to understand evolutionary history are only useful if you're interested in the history of that gene by itself.

    Phylogenies correctly constructed with these factors in mind maintain the bifurcating pattern.
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    Quote Originally Posted by paralith
    Here is a response to that New Scientist article by actual evolutionary biologists.

    I tried to find this 1985 study by Syvanen, and I did find a 1985 paper by him but it was theoretical and had no data. That paper, in line with the letter above, suggests that horizontal gene transfer is more common that previously thought and must be taken into consideration when constructing phylogenies. If Syvanen did this study with 2000 genes he did not publish it, and I suspect I know why. You cannot use genes that are functional and subject to natural selection in order to build a correct phylogeny of relatedness of the organisms that have them. Organisms that are distantly related but living in similar environments are more likely to evolve similar traits which makes them seem artificially more closely related. Organisms that are closely related but that live in extremely different environments are more likely to evolve very different traits that makes them seem artificially less related. A good molecular phylogeny will also utilize data from not one but very many neutral loci, which can help to overcome the error introduced by issues like horizontal transfer. Using functional genes to understand evolutionary history are only useful if you're interested in the history of that gene by itself.

    Phylogenies correctly constructed with these factors in mind maintain the bifurcating pattern.
    How do we determine which Actual biologists are correct? Let's say for the moment that Syvanen did not publish his results. Does that make the unpublished letter more correct than Syvanen? Here are some more published papers that also take exception to the claims of Biologista.

    Antonis Rokas, Dirk Krueger, Sean Carroll, (Dec 2005) "Animal Evolution and the Molecular Signature of Radiations Compressed in Time," Science, 310

    "Despite the amount of data and breadth of taxa analyzed, relationships among most phyla remained unresolved."

    Carl Woese: "Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves."

    Carl Woese "The Universal Ancestor," Proceedings of the National Academy of Sciences, Vol. 95 (June, 1998)

    Biologist Lynn Margulis, a member of the National Academy of Sciences studies the field of molecular systematics. In "The Phylogenetic Tree Topples," she says that "many biologists claim they know for sure that random mutation (purposeless chance) is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk, dichotomously branching-phylogenetic-tree pattern!” But she dissents from that view and notes, “Especially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors."

    In the paper, “Bushes in the Tree of Life.” the writers say that "a large fraction of single genes produce phylogenies of poor quality," and note that one study "omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom."

    Antonis Rokas & Sean Carroll, "Bushes in the Tree of Life," PLOS Biology, Vol 4 (Nov 2006)

    Do we accept the letter or the many published papers and presentations? Or do we admit that there is indeed a lack of correspondence as I said earlier. We certainly don't cherry pick as the letter writer's suggest. If you wish to defend the letter writers then you need to address a much larger group of papers and researchers than I noted here. The reality is that Darwinian predictions have failed on this point too and adjustments are required.

    The relevence for this thread is that we can't say that molecular systematics favors non-directed processes over directed processes because the evidence does suggest "Bushes" and "Webs" and an incongruent tree.

    Edit: It is even more revealing that traditional evolutionary theory requires that the presence of webs and bushes be realigned to the predictions by adding complex explanations much like prior to Galeleo, when planet movements required complex "epicycles". The letter paralith offered provides one epicycle. biologista offered another by excluding what he considers to be "symbiotic" components. Convergent evolution is a third "epicycle" inserted to allow the prediction to better match facts.
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    Quote Originally Posted by Ophiolite
    Biologista, Spurious and Marnix here is a point you may wish to consider.

    I think I have established myself on this forum as being a reasonably well educated individual, with a passable layman's knowledge of biology complemented by some specific evolutionary knowledge based upon a formal education in geology. I think I have also demonstrated an intolerance of creationists, or those who 'have a theory', or think 'Einstein is wrong'. Indeed, if I recall correctly, I was stripped of my moderatorship here for expressing such intolerance in a vigorous manner.

    Despite this background I find cypress's questioning to be balanced and sound, while the responses are lacking in substance and amount to little more than saying "you are wrong, get better educated". If I view your responses in this way it concerns me that those who doubt evolution will find nothing in what you are saying to change their view. Now you may reasonably declare that this simply represents a weakness on my part. You will understand I find that possibility difficult to accept based on the observations made in the paragraph above.
    yeah nice, but I am actually a research biologist. I can see right through the crap.
    "Kill them all and let God sort them out."

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    The premise is tired and unjustifed.

    We've looked at the evidence, found it non-supportive.

    Time for this thread to be correctly filed.
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    Quote Originally Posted by spuriousmonkey
    yeah nice, but I am actually a research biologist. I can see right through the crap.
    My point is that if you are unable to clearly point that crap out to me in a convincing manner you have absolutely no chance of convincing a fence sitter, or an out and out creationist.

    Perhaps you have no interest in doing so (in which case I would wonder why you participate in the discussion), but my view is that it is important to counter arguments that give support directly or indirectly to creationists.

    Part and parcel of that is to acknowledge areas of uncertainty. I think cypress has highlighted some of these. You and the majority (probably all) of the informed individuals on this forum disagree.

    I hope in ten years time we are all still posters here and I can turn round and say either 'OK, now I believe the uncertainties are adequately resolved without recourse to another mechanism', or - and this is preferable for me - 'I told you so! '
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    Quote Originally Posted by TheBiologista

    The premise is tired and unjustifed.
    Translation: We are embarrassed that we first claimed the premise was wrong but having tried to refute it we can't.

    We've looked at the evidence, found it non-supportive.
    Translation: Since it does not conform to our presuppositions, we prejudicially declare it incorrect.

    Time for this thread to be correctly filed.
    Translation: Time to cut our losses and jettison this topic.

    I wonder, whom do you think you are fooling? It is getting very difficult to see who is more dogmatic, the creation advocates or this group.
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  87. #86  
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista

    The premise is tired and unjustifed.
    Translation: We are embarrassed that we first claimed the premise was wrong but having tried to refute it we can't.
    Not to your satisfaction, but that appears to be because you have not understood the replies. I can't do much about that. Your premise is ill-defined. You have not made a proposition, nor have you suggested a means to test it. You speak in negatives and instead try to place the burden of evidence on us.

    Quote Originally Posted by cypress
    We've looked at the evidence, found it non-supportive.
    Translation: Since it does not conform to our presuppositions, we prejudicially declare it incorrect.
    Actually, it did conform to our presuppositions. That was the problem with the evidence. It supported our position and contradicted yours. No amount of snide "translation" will change that.

    Quote Originally Posted by cypress
    Time for this thread to be correctly filed.
    Translation: Time to cut our losses and jettison this topic.
    It's not jettisoned, it's moved. If we decide to jettison a topic, you won't be able to post on it anymore. And we won't be able to argue against you anymore. Neither is the case. We're still here and if you ever get round to finding some evidence that doesn't shoot your own foot off, we'll be here to consider it.

    Quote Originally Posted by cypress
    I wonder, whom do you think you are fooling? It is getting very difficult to see who is more dogmatic, the creation advocates or this group.
    I'm not trying to fool anyone and given your tendency to misrepresent (or is it really misunderstand?) the conclusions of research papers and the positions of their authors I would not throw that suggestion about so lightly if I were you. Honestly, if you expect us to be open to your ideas based on what you've shown us so far then you are incredibly naive. It's on you to convince us. Do better. Or just go away. But stop whining that we're being sceptical. That's science. If you want credulousness or polite nodding there are plenty of other circles that will provide, but they won't be scientific ones.
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    Quote Originally Posted by cypress
    Most of the evidence is simply evidence that one form has components similar to another. But similarity does tell us how the difference came to be.
    Patterns of similarities do provide evidence for what kinds of mechanisms are possible, or likely.

    We do see, for example, that the invisible genetic engineer hypothesis is vanishingly unlikely - there is no evidence for it, and the patterns observed are unlike the apparent expectations for such an entity.
    Quote Originally Posted by cypress
    Edit: It is even more revealing that traditional evolutionary theory requires that the presence of webs and bushes be realigned to the predictions by adding complex explanations much like prior to Galeleo, when planet movements required complex "epicycles". The letter paralith offered provides one epicycle. biologista offered another by excluding what he considers to be "symbiotic" components. Convergent evolution is a third "epicycle" inserted to allow the prediction to better match facts.
    These are observed factors, not proposed abstractions. The only issue is their relative importance.
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    Cypress, I have prepared some refutations of your use of these sources which I'll post up when I get home today. To summarise though, you're once again using sources which contradict your position and framing the comments of the authors as if they cast doubt on evolution by variation and selection. Instead these sources all focus on various mechanisms by which genetic material is inherited laterally (Woese and Margulis) or simply describe shortcomings in our ability to construct trees based on limited evidence (the rapid radiation paper). Nowhere in these sources is there any evidence of direction and it is that factor which you need to support, not the exceptions to phylogeny which I had already brought up before you went off on your quote mining spree. One point I'll address right now:

    Quote Originally Posted by cypress
    Edit: It is even more revealing that traditional evolutionary theory requires that the presence of webs and bushes be realigned to the predictions by adding complex explanations much like prior to Galeleo, when planet movements required complex "epicycles". The letter paralith offered provides one epicycle. biologista offered another by excluding what he considers to be "symbiotic" components. Convergent evolution is a third "epicycle" inserted to allow the prediction to better match facts.
    This is a fallacy on the order of saying "they laughed at Einstein, ergo their skepticism of me is evidenc that I am right". By which I mean that you're trying to derive a general pattern from a very specific example that happens to match your assumptions. Galileo and indeed Newton after him did indeed feel the need to add layers of complexity onto their theories in order to make them match observations. However, there's a critical difference between these "fudge factors" and what we are adding to evolution. Galileo could not explain nor describe a mechanism for his additions, nor could those who tried to fix the orbit of Mercury following Newton. They made adjustments to the model but could not provide a mechanistic basis nor demonstrate them in action. Of course there were practical barriers to this, but that's a problem for physicists. These events were not at all the same as the changes to evolution proposed by Woese, Margulis and others and which were eventually accepted. First, these changes were strongly resisted (as is appropriate for major revisions) and in response they were then heavily investigated and eventually supported with observational evidence. Second, the mechanisms were experimentally verified. HGT was demonstrated, and indeed your precious genetic engineering would be impractical if not impossible had we not delinieated the mechanisms which underlie it. Endosymbiosis was also verified by detailed examination of the morphology and genetics of organelles such as the mitochondrion and chloroplasts.

    As an aside to this, the argument is rather irrelevant either way. If endosymbiosis and HGT do indeed represent epicycle-style fudge factors within evolution, then all that really implies is that evolution as a theory will one day be superceded by something more fundemental and unified. Just as Newton was superceded by Einstein. But here's the problem for you; Newton was not wrong. He was merely inaccurate. He'd made a critical advance and his equations are still used to this day for many applications where General Reletivity is not needed. If evolution is relegated to this status, it still won't at all be the grand fall that you and others would hope for and it will not mean that Darwin was wrong, just that he, like Newton, did not have the full story.

    I would argue that this revolution has already happened. It would be a mistake to assume that we must always have a Kuhnian paradigm shift to make progress in science. Even Kuhn recognised the value of incremental change. There was in evolution a softer revolution than Einstein's, or rather several soft revolutions. Darwinian inheritence was dismissed and replaced with Mendelian but natural selection remained. Population genetics was added. Mendelian genetics was dismantled and partially replaced with molecular genetics which gave us a mechanism for the origin of variation (mutation). The theory has been undergoing fundemental revisions and revolutions incrementally. Which is rather apt I suppose.

    If I had to bet, I'd bet rather strongly against any grand paradigm shift in the science of species origins. Where the really interesting stuff in life sciences will happen is in the origin of life question. That's still anyone's game.
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    Quote Originally Posted by TheBiologista
    Cypress, I have prepared some refutations of your use of these sources which I'll post up when I get home today. To summarise though, you're once again using sources which contradict your position and framing the comments of the authors as if they cast doubt on evolution by variation and selection.
    I am not certain why you continually miss the point. Do you do this intentionally? You and your sources will surely interpret the facts to support your position but that does not change the raw data and facts at all. The fact is that the data does present webs and bushes. My point is not diminished by the numerous explanations for the the webs and bushes because they can't undo the reality of the data.

    Nowhere in these sources is there any evidence of direction and it is that factor which you need to support, not the exceptions to phylogeny which I had already brought up before you went off on your quote mining spree.
    Nonsense. I have show that the data is consistent with one or more explanations besides the one you favor and in doing so, demonstrate that this evidence does not favor the undirected processes you propose. It makes no difference if the authors support goal directed processes or not, the data demonstrates existence of webs and bushes in contradiction to your claims and consistent with what you yourself claimed is required to indicate goal directed processes.

    Even if the data didn't indicate webbing, since goal directed processes are capable of producing nearly any pattern of similarity, it is presumptive of you to say it should follow a particular pattern. How is it that you are qualified to predict what pattern a designer would follow?

    In any case it is not my intent to argue that observed diversity was generated by goal directed processes. My only purpose is to show that one cannot demonstrate that it was generated by a combination chance and necessity.

    Quote Originally Posted by cypress
    Edit: It is even more revealing that traditional evolutionary theory requires that the presence of webs and bushes be realigned to the predictions by adding complex explanations much like prior to Galeleo, when planet movements required complex "epicycles". The letter paralith offered provides one epicycle. biologista offered another by excluding what he considers to be "symbiotic" components. Convergent evolution is a third "epicycle" inserted to allow the prediction to better match facts.
    This is a fallacy on the order of saying "they laughed at Einstein, ergo their skepticism of me is evidenc that I am right". By which I mean that you're trying to derive a general pattern from a very specific example that happens to match your assumptions.
    You missed my intent again, which was to demonstrate that when people wedded to an idea find that the facts contradict the model, they busy themselves fabricating elaborate explanations to remold the theory to the facts. It is entirely possible that the new complexity is correct, but the reality that these complex explanations are popping up is an excellent indication that the facts are as I describe.

    I don't think it will add anything to the discussion to offer more research supporting the complex explanations. They can't change the facts.
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    I don't misunderstand or misrepresent the conclusions of the research. In fact I sometimes do not rely on the interpretations and therefore the conclusion of the authors. I find many of the conclusions presumptive and often at odds with the data. That is certainly the case with Thornton's paper.

    I do provide references based on the quality of the data and facts. Just because the authors interpret the facts and data a particular way does not mean that is the only way to interpret the data. You seem unable or unwilling to accept this reality. Surely you realize that studies of past research indicate that over 50% of the conclusions presented in peer-reviewed work is ultimately discovered to be incorrect. If you were as critical as you claim you would not insist that I present research where the author's conclusion is supportive of or even addresses the point I am making.

    I stand by my previous note, it is you are preventing debate by casting threads into unpopular categories when you are unable or unwilling to address the topic effectively. If the premise were as unworthy as you claim you would easily be able to provide a clear example that answers the issue in your favor without having to resort to trashing the person and the facts presented. You have utterly failed in this thread. Clearly it is not lost on others what is going on here.
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    Quote Originally Posted by cypress
    Nonsense. I have show that the data is consistent with one or more explanations besides the one you favor and in doing so, demonstrate that this evidence does not favor the undirected processes you propose
    The data is "consistent with" thousands of ridiculous explanations, from an unseen supernatural genetic engineer carefully imitating the patterns of Darwinian evolution to special creation by squid beings from Alpha Centauri.

    Quote Originally Posted by cypress
    My only purpose is to show that one cannot demonstrate that it was generated by a combination chance and necessity.
    In science we go by evidence and argument, not proof.
    Quote Originally Posted by cypress
    It is entirely possible that the new complexity is correct, but the reality that these complex explanations are popping up is an excellent indication that the facts are as I describe.
    The complexities are not "new", merely their likely relative importance in actual events has been adjusted upwards in light of evidence. They aren't "popping up", they are being argued closely from the evidence and from observations of their mechanisms, both lab and world.
    Quote Originally Posted by cypress
    . The fact is that the data does present webs and bushes
    The data also presents phylogenetic trees of great length and long existence. The standard theory accounts for both, using observed mechanism.
    Quote Originally Posted by cypress
    but the reality that these complex explanations are popping up is an excellent indication that the facts are as I describe.
    You have presented no valid argument in support of your interpretation of the evidence, or against anyone else's. The simple errors of reasoning you have presented as arguments have been corrected for you, by volunteers. Gratitude is due.
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    i once heard a forensic pathologist make the following warning : be careful about coming to a verdict on the basis of the facts being "consistent with" rather than being "indicative of" a certain interpretation - only the latter has any likelihood of standing up in court
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    . The fact is that the data does present webs and bushes
    The data also presents phylogenetic trees of great length and long existence. The standard theory accounts for both, using observed mechanism.
    If this were true you could provide an observed example of the major molecular processes required to generate new form and function including formation of novel binding sites, new signal processing, new developmental controls, new gene expression controls, new protein and raw material transport, new assembly structures, etc. You would be able to demonstrate that these new forms occur with sufficient speed and frequency to account for observed diversity.

    We indeed observe these similarities, but the similarities do not tell us how the differences happened. How can we know they happened by undirected causes?

    Quote Originally Posted by cypress
    but the reality that these complex explanations are popping up is an excellent indication that the facts are as I describe.
    You have presented no valid argument in support of your interpretation of the evidence, or against anyone else's. The simple errors of reasoning you have presented as arguments have been corrected for you, by volunteers. Gratitude is due.[/quote]

    My only purpose in this thread was to present the facts. The task itself is to show that undirected causes do (not might) explain the facts. I have no interpretation of why the evidence is the way it is. I have made no claim about how the facts came to be. I only note that goal driven processes are capable of causing the kinds of patterns we observe, but I did not claim they did cause the patterns. I have said that so far I have not seen that undirected processes are capable of the same. Can you show that they are? Of course you can't. Game over.
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    Quote Originally Posted by cypress
    If this were true you could provide an observed example of the major molecular processes required to generate new form and function including formation of novel binding sites, new signal processing, new developmental controls, new gene expression controls, new protein and raw material transport, new assembly structures, etc.
    Yep. All that stuff is providable by mutation and selection amid symbiosis, sexual recombination and various "conjugations" etc, viral and parasitic and other forms of genetic transfer, and so forth. All these processes have been observed.
    Quote Originally Posted by cypress
    My only purpose in this thread was to present the facts.
    Your assertions are not of facts, but of non-standard interpretations of evidence: and they lack sound argument.
    Quote Originally Posted by cypress
    We indeed observe these similarities, but the similarities do not tell us how the differences happened.
    They provide evidence. We then reason from it.
    Quote Originally Posted by cypress
    How can we know they happened by undirected causes?
    We can't. We can, however, recognize that the standard evolutionary theory is adequate, extremely productive and useful, and supported by all the evidence we have while being contradicted by none - including evidence predicted by it and subsequently discovered, and major areas of discovery of evidence not imagined by anyone but found later to fit perfectly, which combination is the gold standard for a scientific theory. No other theory so far proposed can make that claim.
    Quote Originally Posted by cypress
    I have said that so far I have not seen that undirected processes are capable of the same.
    Your inability to "see" is not an argument for your assertions.
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  96. #95  
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    Quote Originally Posted by cypress
    I have said that so far I have not seen that undirected processes are capable of the same. Can you show that they are? Of course you can't. Game over.
    What? You yourself gave us a reference by this guy called Thornton which showed that is was possible to go from an ancestral form of a receptor to a modern form with a distinct function via 5 mutations all under selection. They also showed that it was improbable that the process could be reversed if we rely on mutation and selection to do the job. This shows us one pathway "forbidden" to that process, so if we were to find the ancestral form in some species descended from one possessing the modern form, then we'd be able to point at that and say "mutation and selection can't do that so something else is going on". But we haven't, and we can't. Now you're telling us that mutation and selection can't do this or that, so why not give us an example or two that shows this is the case?

    Game over? What because you say so?
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    You must just make this stuff up biologista. Thornton et. al designed their presumed ancestor. Then they modeled the presumed evolutionary steps. They did not test each for function and selective advantage and it only required two steps to acquire selectivity for GR. The next four steps were presumed to have occurred after GR selectivity was established.
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  98. #97  
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    I wish I had never started this.
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  99. #98  
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    No, Your intent was on the level and sincere, it was simply pounced upon by trolls...
    Wise men speak because they have something to say; Fools, because they have to say something.
    -Plato

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    Quote Originally Posted by cypress
    You must just make this stuff up biologista. Thornton et. al designed their presumed ancestor. Then they modeled the presumed evolutionary steps.
    Neither point which you seemed to think was a mark against the paper when you assumed it was supporting your position...
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    You must just make this stuff up biologista. Thornton et. al designed their presumed ancestor. Then they modeled the presumed evolutionary steps.
    Neither point which you seemed to think was a mark against the paper when you assumed it was supporting your position...
    Its not a mark against the paper, it is a contradiction to your mistaken version of the paper.

    edit: mistaken description rather than version
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