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Thread: Evolutionary Theory and the Development of the Whale

  1. #1 Evolutionary Theory and the Development of the Whale 
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    In another topic,

    Quote Originally Posted by TheBiologista

    That's not what inference is. It is not speculation, nor even hypothesis. It is a logical extension. That aside, our inferences have testable implications. If our tests are successful, then we can be satisfied that our inference was good.
    I had already mentioned an issue with the prediction being out of step with Whale evolution. Let's explore this further.

    On this particular point, the tests are failing and the inference is in doubt. Stepwise mutation and selection processes are not demonstrating any broad tendency to generate the new forms and functions observed by examining the observed diversity of life. We see this in the example of presumed whale evolution. Consensus has whales evolving from land mammals in 9 million years. Evolutionary theory predicts that all the alterations, all the new forms and functions were a result of mutation and selection. These new forms and functions are numerous (and despite biologista's protests, they are obviously new, they are not simply modifications of existing function). Examples are a process to removing salt and minerals from sea water to allow the whale to consume sea water rather than fresh water. A redesign of the vertebrae to allow for up and down movement of the tail rather than side to side. A completely different skin system. Muscle structures for the blow hole. A countercurrent heat exchange and temperature control system to allow the testes to be internalized. Forelimbs to flippers, tail to fin, etc. All of these changes had to coordinate with each other to allow for a successful sea dwelling mammal. Any one of these changes require multiples of proteins with new binding sites, fitted to other proteins plus the accompaning gene regulation controls and developmental controls. Recent studies indicate that changes like these require 2 to 10 key alterations in binding sites to significantly affect protein function or regulatory controls.

    Population Genetic Modeling (1) indicate the frequency for these kinds of alterations very slow when breeding populations are low, and required alterations are cumulative, etc. In the case of mammals that tend to remain near water, we can safely estimate the breeding population at 10,000 or less. When we look specifically at these changes listed above and consider that just one of these many changes involved a specific alteration to a gene expression control of a particular gene and then consider that nearly all gene regulation binding sites require two or more coordinated modifications to change regulation and then apply the math given in the paper, we get about 40 million years for just one two step binding site change of the multitudes of specific changes required to account for these specific new functions of existing systems. Clearly if just one change requires 4 times the 9 million years inferred by the fossil record, we have a serious problem with the prediction.

    Then when you return to the numerous examples of rapid appearance of new protein and control functions that have no plausible traditional evolutionary pathway (some of which I previously provided), together with the complete inability to provide even one example of a multistep evolutionary pathway leading to new protein or control function in a reasonable timeframe (the example above), indicates strongly a different process for generating new form and new function. Darwinian Evolution has wonderfully explained modification of existing function to generate adaptation and to account for altered traits, but it thus far has not lived up to its grand claim that it accounts for all observed diversity.

    1. “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution” (Durrett, R & Schmidt, D. 2008. Genetics 180: 1501-1509)

    Yet evolutionary biologists happily persist with the mantra that gradual change driven by selection accounts for all observed diversity. At some point someone is going to have to address the dichotomy.


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  3. #2 Re: Evolutionary Theory and the Development of the Whale 
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    Quote Originally Posted by cypress
    Evolutionary theory predicts that all the alterations, all the new forms and functions were a result of mutation and selection.
    again you're confusing evolutionary pathways with evolutionary process : the fossil record clearly displays a pattern of stepwise evolution, but it doesn't say anything about whether this pattern was achieved through mutation and selection
    all you can say from the fossil record is that it is consistent with what you could expect from mutation and selection, but the proof of the validity of that mechanism rests mostly on evolution observed in action in the here and now


    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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  4. #3 Re: Evolutionary Theory and the Development of the Whale 
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    Quote Originally Posted by marnixR
    Quote Originally Posted by cypress
    Evolutionary theory predicts that all the alterations, all the new forms and functions were a result of mutation and selection.
    again you're confusing evolutionary pathways with evolutionary process : the fossil record clearly displays a pattern of stepwise evolution, but it doesn't say anything about whether this pattern was achieved through mutation and selection
    all you can say from the fossil record is that it is consistent with what you could expect from mutation and selection, but the proof of the validity of that mechanism rests mostly on evolution observed in action in the here and now
    Not much of a response marnixR. I am not confused by the difference. Both are aspects of the theory. The fossil record provides the timeframe of 9 million years, that is pretty much the only relevant information it provides to this discussion.

    Modern biology tells us that new form and function requires new protein structures, new binding sites, new expression controls and new developmental controls. Molecular biology shows us that these new structures and binding sites require on average 5-8 specific modifications. Population genetics like the article provided provides a mechanism to estimate the amount of time required to generate the new binding sites even when we reduce the required number to just two. When you put it all together, the predictions that follow from modern evolutionary theory are failing yet again.
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    but why do you say "Evolutionary theory predicts that all the alterations, all the new forms and functions were a result of mutation and selection" when that is merely YOUR statement and your statement alone, and not one many evolutionists or paleontologist would endorse uncritically

    the word "strawman" springs to mind
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  6. #5  
    Time Lord Paleoichneum's Avatar
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    Where is the 9 million number coming from??
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    Quote Originally Posted by Paleoichneum
    Where is the 9 million number coming from??
    presumably that's the time from the start of the Eocene to the appearance of Basilosaurus ?
    "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 marnixR
    but why do you say "Evolutionary theory predicts that all the alterations, all the new forms and functions were a result of mutation and selection" when that is merely YOUR statement and your statement alone, and not one many evolutionists or paleontologist would endorse uncritically

    the word "strawman" springs to mind
    hmm... These post are brief for a reason. I can't imagine, though incomplete, my statement actually misrepresents Darwinian Theory to any great degree. Propose an alternate if you disagree as I don't intend to be building a strawman. Let me say though that these other processes such as LGT/HGT, or the more speculative symbiotic function transfer etc. don't generate new function but could move it from one organism to another. So let's stay focused on the processes that the theory identifies as sources of new molecular function.

    Surely you agree that new molecular function requires new structural shapes and/or new binding sites along with expression and developmental controls. This is the focus of my argument.

    I urge you to stay focused on the primary issue lest you be accused of traipsing off into red herring arguments.
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    Quote Originally Posted by Paleoichneum
    Where is the 9 million number coming from??
    Here is a reasonable timeline. 47 Mya - 38 Mya = 9 My

    http://skywalker.cochise.edu/wellerr...les/whales.htm
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    Time Lord Paleoichneum's Avatar
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    Quote Originally Posted by cypress
    Quote Originally Posted by Paleoichneum
    Where is the 9 million number coming from??
    Here is a reasonable timeline. 47 Mya - 38 Mya = 9 My

    http://skywalker.cochise.edu/wellerr...les/whales.htm
    Seems a rather arbitrary and non-sequitur of a number what are the dates indicating?

    and why the link to a community college student paper from '07?
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    Quote Originally Posted by Paleoichneum
    Quote Originally Posted by cypress
    Quote Originally Posted by Paleoichneum
    Where is the 9 million number coming from??
    Here is a reasonable timeline. 47 Mya - 38 Mya = 9 My

    http://skywalker.cochise.edu/wellerr...les/whales.htm
    Seems a rather arbitrary and non-sequitur of a number what are the dates indicating?
    Unless you are going to argue for a timeframe in the 200 million years range, it is not that important to have the dates accurately described. The range is certainly somewhere between 0 and 15 million, do you agree? Whether the duration is 5 million or 20 million, it makes no difference. Propose a number yourself. I am likely to accept it for this discussion.

    and why the link to a community college student paper from '07?
    I liked the pictures. Even you should be able to clearly understand the purpose of having an estimated timeframe and you should see that the precise value is not important unless it could be stretched out to the hundreds of millions of years.

    The primary point is that using evolutionary theory predictions and the models derived by it (Population Genetics), along with new understanding from molecular and cell biology about what kinds of protein and expression control shape and binding site changes are required for new function, and the relative abundance of variations, we can clearly see that the proposed process operates too slowly to correspond with the predictions. We should therefore reject this pathway, modify the prediction, and propose a mechanism that does account for these kinds of new shapes and new binding sites more quickly with lower populations.
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    Quote Originally Posted by cypress
    and required alterations are cumulative, etc. In the case of mammals that tend to remain near water, we can safely estimate the breeding population at 10,000 or less
    You say such silly, stupid things with such confidence.

    It's as if your ignorance reflected some kind of structure of the universe - things unknown to you don't exist, things incredible to you are improbable in reality, what you don't believe is therefore doubtful and unlikely, and all of this off the top of your head - you surely never thought for ten minutes about examples of "mammals that stay near the water", such as (for example) the tens of thousands of hippos living in Virunga National Park alone, or the millions of beaver pelts trapped out of the Great Lakes region in less than a century.

    I mean, damn it, pay attention. You waste people's time with this shit.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    and required alterations are cumulative, etc. In the case of mammals that tend to remain near water, we can safely estimate the breeding population at 10,000 or less
    You say such silly, stupid things with such confidence.

    It's as if your ignorance reflected some kind of structure of the universe - things unknown to you don't exist, things incredible to you are improbable in reality, what you don't believe is therefore doubtful and unlikely, and all of this off the top of your head - you surely never thought for ten minutes about examples of "mammals that stay near the water", such as (for example) the tens of thousands of hippos living in Virunga National Park alone, or the millions of beaver pelts trapped out of the Great Lakes region in less than a century.

    I mean, damn it, pay attention. You waste people's time with this shit.
    Give me a break, iceaura. Propose a proper breading population for whale ancestors 40Mya. back it up with a solid rationale. Let's take your hippo example. How large is an active breading population? For a particular hippo, how large is the pool of possible mates? The total population is not the same as the active breeding pool.

    Perhaps you just don't think through your objections.
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    Quote Originally Posted by cypress
    Give me a break, iceaura
    You are already getting more of a break than you deserve when people who actually have a clue bother to respond to your garbage here.

    You pulled this
    Quote Originally Posted by cypress
    In the case of mammals that tend to remain near water, we can safely estimate the breeding population at 10,000 or less.
    completely out of your ass.

    Tell you what: you come up with some kind of "rigorous" definition of what you are talking about when you decide this or that new feature is a "modification" rather than a "new function", and I will look up a solid estimate of the breeding population of the American beaver, muskrat, otter, capybara, or raccoon (your choice) in the year 1600.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Give me a break, iceaura
    You are already getting more of a break than you deserve when people who actually have a clue bother to respond to your garbage here.

    You pulled this
    Quote Originally Posted by cypress
    In the case of mammals that tend to remain near water, we can safely estimate the breeding population at 10,000 or less.
    completely out of your ass.

    Tell you what: you come up with some kind of "rigorous" definition of what you are talking about when you decide this or that new feature is a "modification" rather than a "new function", and I will look up a solid estimate of the breeding population of the American beaver, muskrat, otter, capybara, or raccoon (your choice) in the year 1600.
    Oh Im sorry, I reviewed my numbers. I used 100,000 in the generational breading population of whales. It is estimated at 10,000 but I multiplied it by 10 to be conservative. Btw I also see that the breading population of the house mouse today with its millions upon millions of members is estimated between 400,000 and 800,000. I'm satisfied with these numbers. No need to hurt yourself looking up information.

    Modification vs. New function my be difficult for you to understand in the case of an enzyme binding to and cleaving certain very similar chemical structures that have well defined binding affinities, but surely you don't see an issue with these features of a whale vs. its proposed ancestor that did not have a countercurrent heat exchanger or kidneys that process different water mineral content or a ball socket vertebra etc. etc.
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  16. #15 Re: Evolutionary Theory and the Development of the Whale 
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    Quote Originally Posted by cypress
    Population Genetic Modeling (1) indicate the frequency for these kinds of alterations very slow when breeding populations are low, and required alterations are cumulative, etc. In the case of mammals that tend to remain near water, we can safely estimate the breeding population at 10,000 or less. When we look specifically at these changes listed above and consider that just one of these many changes involved a specific alteration to a gene expression control of a particular gene and then consider that nearly all gene regulation binding sites require two or more coordinated modifications to change regulation and then apply the math given in the paper, we get about 40 million years for just one two step binding site change of the multitudes of specific changes required to account for these specific new functions of existing systems. Clearly if just one change requires 4 times the 9 million years inferred by the fossil record, we have a serious problem with the prediction.
    i see a serious problem with your method of estimation - you assume that there's only a single lineage of 10,000 individuals, whereas what you probably have is a multitude of populations who undergo different modifications that make them more suitable for a marine existence

    imo you grossly overestimate the time it takes for evolution (whether through natural selection or some other mechanism) to make any meaningful changes
    "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 cypress
    I used 100,000 in the generational breading population of whales. It is estimated at 10,000 but I multiplied it by 10 to be conservative.
    Bullshit. (The calculation is meaningless in the first place, because you make silly assumptions critical to the probabilities involved).
    Quote Originally Posted by cypress
    Btw I also see that the breading population of the house mouse today with its millions upon millions of members is estimated between 400,000 and 800,000.
    Bullshit.
    Quote Originally Posted by cypress
    Modification vs. New function my be difficult for you to understand in the case of an enzyme binding to and cleaving certain very similar chemical structures that have well defined binding affinities, but surely you don't see an issue with these features of a whale vs. its proposed ancestor that did not have a countercurrent heat exchanger or kidneys that process different water mineral content or a ball socket vertebra etc. etc.
    So no rigorous definition - which was obvious anyway.

    The population of beaver in North America was more than 100 million in the 1600s, btw. The breeding population of otters was sufficient to power an expansion of their range in the late 1900s, in the face of - from trapping alone - 50k killed per year for a while - so about 20 thousand breeding females if there was no other source of mortality. The breeding population of raccoons would be much, much larger, of course. And so forth.
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    In Population Genetics breading population is not the total number breading, rather it is the number properly considered in a genetic pool capable of distributing and incorporating genetic variants. I dont think you realize this.
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    Quote Originally Posted by cypress
    In Population Genetics breading population is not the total number breading, rather it is the number properly considered in a genetic pool capable of distributing and incorporating genetic variants. I dont think you realize this.
    The strategy of talking until you start to make relevant sense by accident is not going to work. Human culture does not evolve in a Darwinian manner.
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  20. #19 Re: Evolutionary Theory and the Development of the Whale 
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    Quote Originally Posted by marnixR
    Quote Originally Posted by cypress
    Population Genetic Modeling (1) indicate the frequency for these kinds of alterations very slow when breeding populations are low, and required alterations are cumulative, etc. In the case of mammals that tend to remain near water, we can safely estimate the breeding population at 10,000 or less. When we look specifically at these changes listed above and consider that just one of these many changes involved a specific alteration to a gene expression control of a particular gene and then consider that nearly all gene regulation binding sites require two or more coordinated modifications to change regulation and then apply the math given in the paper, we get about 40 million years for just one two step binding site change of the multitudes of specific changes required to account for these specific new functions of existing systems. Clearly if just one change requires 4 times the 9 million years inferred by the fossil record, we have a serious problem with the prediction.
    i see a serious problem with your method of estimation - you assume that there's only a single lineage of 10,000 individuals, whereas what you probably have is a multitude of populations who undergo different modifications that make them more suitable for a marine existence
    No actually the model provided by the artcle addresses that issue. Regardless of the number of available breeding pools, any one of them still requires a particular number of generations to make the alterations prescribed. when you take that into account and address it as prescibed by the model my results are valid.

    You used the word probably to describe your objection. Can you offer any support for that prediction of mutitudes of different modifications amongst different populations? Can you aplly population genetics to help me understand how many protein binding sites, gene expression controls and developmental controls are likely to be formed within each breeding pool and how these accumulate to form the functional systems unique to sea mammals?

    imo you grossly overestimate the time it takes for evolution (whether through natural selection or some other mechanism) to make any meaningful changes
    in your opinion? Is this hw science operates? I offered a model and provided input assumptions. Where is the error?
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    the error lies in the fact that the data from the fossil record don't match your prediction of v.v.slow change

    we know from the fossil record that evolution DID take place and modify a semi-aquatic mammal into a fully marine whale over the space of 9 million years, independent of what the driving force was, hence the inescapable conclusion is that there's something wrong with the method you've used to arrive at a prediction of extremely slow change - since i'm not a geneticist i can't point to the detail of where you're going wrong, but i suspect it has something to with how regulation expresses the genotype during development as well as an underestimate of the available genetic variability in populations

    after all, we know from the study of Galapagos finches that natural selection can noticeably change species over periods of years, never mind millions of years - it's just that in 99% of cases the environment doesn't cause directional change but rather oscillates which results in stabilising selection
    when, however, the environment does cause directional change, there's no reason to expect that natural selection would not be capable of rapid morphological change

    as far as 'imo' goes, no that's not how science operates - i'd be the first to admit i'm not a scientist but an interested layman and amateur philosopher of science
    but since this is a forum and not a peer-reviewed article, i've taken the presumption that i'm allowed an opinion based on some knowledge of how science and logic works
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    Whales you say?

    http://www.plosgenetics.org/article/...l.pgen.1000634

    Enamel is the hardest substance in the vertebrate body. One of the key proteins involved in enamel formation is enamelin. Most placental mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks, pygmy and dwarf sperm whales). All toothless and enamelless mammals are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin's theory of descent with modification.

    When all crown mysticete branches were treated as a separate category in dN/dS analyses (Methods), the result was in agreement with the null hypothesis that ENAM evolved as a pseudogene (i.e., ω = 1) based on a χ2 test (0.10<P<0.25). Thus, it appears that ENAM was released from selective constraints in crown mysticetes as predicted by the basal position of the archaic toothless mysticete, Eomysticetus whitmorei (Figure 5) [15]. If we assume that ENAM evolved as a pseudogene in crown-group mysticetes, which as a group are characterized by generation times and lifespans that equal or exceed those of most other mammals, then the neutral rate of nucleotide substitution is only 3.3×10−4 substitutions/site/myr, which is almost an order of magnitude lower than Kumar and Subramanian's [27] estimate of the average mammalian genome rate of 2.2×10−3 substitutions/site/myr based on an analysis of fourfold degenerate sites.
    Stem physeteroids (sperm whales) are known from the Miocene and had teeth with enamel [40]. Physeter and Kogia are the only living genera of sperm whales and the teeth in adults belonging to these genera lack enamel. A caveat is that thin, prismless enamel has been observed on the unerupted teeth of P. macrocephalus (giant sperm whale) [42]. Our results provide support for loss of the intact enamelin protein in both Kogia species, but not in P. macrocephalus (Figure 5, Text S1).

    For some reason cypress' estimates are way off from the scientifically determined ones. I wonder why?

    And do note this particular sentence in the article:

    The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin's theory.
    Carl Sagan was a moron. Could have posted this also in the other thread.

    Didn't take me long to find this article. It was on the first page of general search results in PubMed.

    Shows how little effort creationists and IDers want to put into their search for the truth. It's always easier to misquote articles and confuse.

    Note that in the article they tested the predictive power of evolution for all animals lacking enamel on their teeth or toothless animals altogether.
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    Quote Originally Posted by marnixR
    fully marine whale
    They're not there yet. Early whales got the bends, probably as they pushed their limits. Telltale damage is in the bones. Still, sperm whales suffer this. It's a chronic problem that is certainly painful and eventually debilitating in older whales.

    Given that sperm whales' probable M.O. involves killing squid by dragging those suckers to death by decompression, they have every reason to adapt further.
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    what i meant by fully marine is that they can no longer come on land and survive
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    I would define fully marine if they don't exit the marine environment for any reason anymore, especially for giving childbirth.

    Aerial jumps are not 'exiting the marine environment'.
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    Quote Originally Posted by marnixR
    the error lies in the fact that the data from the fossil record don't match your prediction of v.v.slow change

    we know from the fossil record that evolution DID take place and modify a semi-aquatic mammal into a fully marine whale over the space of 9 million years, independent of what the driving force was, hence the inescapable conclusion is that there's something wrong with the method you've used to arrive at a prediction of extremely slow change
    Actually thee are three possibilities that have not been confirmed or falsified.

    One is that I might be in error. If i made an error, that would be easy to discuss and confrim.

    Two is that whales did not evolve from dog-like land creatures in 9 million years. Fossil evidence is far from conclusive.

    Three the one I favor, is that new form and function is derived by processes different from the present suite of observed evolutionary processes.


    - since i'm not a geneticist i can't point to the detail of where you're going wrong, but i suspect it has something to with how regulation expresses the genotype during development as well as an underestimate of the available genetic variability in populations
    Only a prior commitement could lead you to focus your suspisions on one of the three possibilities since you have don't have direct evidence to support your suspicions.

    after all, we know from the study of Galapagos finches that natural selection can noticeably change species over periods of years,
    We do not need the example of adaptation of beak size to know that traits can be altered by adaptive processes. Animal breading provides a more vivid picture of adaptions due to trait expression. Surely you can see a difference between slight alteration of an existing set of traits and development of novel components.

    never mind millions of years - it's just that in 99% of cases the environment doesn't cause directional change but rather oscillates which results in stabilising selection
    when, however, the environment does cause directional change, there's no reason to expect that natural selection would not be capable of rapid morphological change
    It is a typical just so story, based on metaphysical prior commitements. In order to support this statement you have to understand exactly how morpological changes occur and how they are expressed. Then you need to show that the proceeses cited are capable of accomplishing these effects. We know what changes are required for new form and function. I described them above and also show why we don't observe these kinds of changes by known evolutionary processes.

    as far as 'imo' goes, no that's not how science operates - i'd be the first to admit i'm not a scientist but an interested layman and amateur philosopher of science
    but since this is a forum and not a peer-reviewed article, i've taken the presumption that i'm allowed an opinion based on some knowledge of how science and logic works
    Fair I should make more allowance, but I 've noticed that your tendency is to berate others for intorducing opinion and, belief and faith into the discussions, you even claim be confused by it, but you do the same.
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    Quote Originally Posted by spuriousmonkey
    Whales you say?

    http://www.plosgenetics.org/article/...l.pgen.1000634

    Enamel is the hardest substance in the vertebrate body. One of the key proteins involved in enamel formation is enamelin. Most placental mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks, pygmy and dwarf sperm whales). All toothless and enamelless mammals are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin's theory of descent with modification.

    When all crown mysticete branches were treated as a separate category in dN/dS analyses (Methods), the result was in agreement with the null hypothesis that ENAM evolved as a pseudogene (i.e., ω = 1) based on a χ2 test (0.10<P<0.25). Thus, it appears that ENAM was released from selective constraints in crown mysticetes as predicted by the basal position of the archaic toothless mysticete, Eomysticetus whitmorei (Figure 5) [15]. If we assume that ENAM evolved as a pseudogene in crown-group mysticetes, which as a group are characterized by generation times and lifespans that equal or exceed those of most other mammals, then the neutral rate of nucleotide substitution is only 3.3×10−4 substitutions/site/myr, which is almost an order of magnitude lower than Kumar and Subramanian's [27] estimate of the average mammalian genome rate of 2.2×10−3 substitutions/site/myr based on an analysis of fourfold degenerate sites.
    Stem physeteroids (sperm whales) are known from the Miocene and had teeth with enamel [40]. Physeter and Kogia are the only living genera of sperm whales and the teeth in adults belonging to these genera lack enamel. A caveat is that thin, prismless enamel has been observed on the unerupted teeth of P. macrocephalus (giant sperm whale) [42]. Our results provide support for loss of the intact enamelin protein in both Kogia species, but not in P. macrocephalus (Figure 5, Text S1).

    For some reason cypress' estimates are way off from the scientifically determined ones. I wonder why?
    Known evolutionary processes are well known for breaking function as described above. I have support this capablility all along. the argument here is in generating novel function in the examples described earlier in this thread. Your example is irelevant to these calculations.

    And do note this particular sentence in the article:

    The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin's theory.
    Carl Sagan was a moron. Could have posted this also in the other thread.

    Didn't take me long to find this article. It was on the first page of general search results in PubMed.

    Shows how little effort creationists and IDers want to put into their search for the truth. It's always easier to misquote articles and confuse.

    Note that in the article they tested the predictive power of evolution for all animals lacking enamel on their teeth or toothless animals altogether.
    Spurious you're guilty of your own complaint. Loss of function by disabling a gene or protein is not a difficult task for known evolutionary processes. You can't answer the issue I raise so you change it to one you can answer and then assign claims to me I do not make. My example was of generating a countercurrent heat exchanger and feedback control system for cooling the internalized testes of whales. You chose to discuss the trivial loss of enamel by disabling a gene, something we all knows happens very frequently. Please stay focused on the issue.
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  28. #27  
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    Quote Originally Posted by cypress
    Three the one I favor, is that new form and function is derived by processes different from the present suite of observed evolutionary processes.

    Only a prior commitement could lead you to focus your suspisions on one of the three possibilities since you have don't have direct evidence to support your suspicions.
    i'll only be able to evaluate the strength of your third alternative once you've described it - that's just why natural selection is currently seen by most biologists as the main drive behind evolution : (1) it describes the available evidence pretty well, and (2) no alternative has the same explanatory power, although some alternatives may have been contributing factors

    the thing i'm not going to do is throw away natural selection in favour of an as yet unknown explanation until said explanation has been brought forward and proves to be better at explaining the available evidence

    Quote Originally Posted by cypress
    Surely you can see a difference between slight alteration of an existing set of traits and development of novel components.
    no i don't : small deviations over time have the potential to become large deviations

    Quote Originally Posted by cypress
    never mind millions of years - it's just that in 99% of cases the environment doesn't cause directional change but rather oscillates which results in stabilising selection
    when, however, the environment does cause directional change, there's no reason to expect that natural selection would not be capable of rapid morphological change
    It is a typical just so story, based on metaphysical prior commitements. In order to support this statement you have to understand exactly how morpological changes occur and how they are expressed. Then you need to show that the proceeses cited are capable of accomplishing these effects.
    what's "just-so" about observing evolutionary change in real time and extrapolating from there ? if natural selection has been shown to produce a certain amount of change over a certain amount of time, that's all i need to know

    Quote Originally Posted by cypress
    Fair I should make more allowance, but I 've noticed that your tendency is to berate others for intorducing opinion and, belief and faith into the discussions, you even claim be confused by it, but you do the same.
    i merely point out inconsistencies in logic, or when beliefs / faith are contradicted by the available evidence
    i'm not saying that i'm not capable of not following my own rules, but i should hope that the main body of contributions are consistent with known facts
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Somewhat Off Topic but what puzzles me in whales is how the nostrils ended up on the back of the head?

    As for the generic shape it would not be surprizing to find similar shapes in marine animals on another planet with liquid water(that had multi-cellular animals), given that different animals (prehistoric reptile[Ichthyosaurs], peguin[farther], seal ) have ended up with somewhat similar shapes. I also wonder if, had there been no humans, penguins would eventually get a dolphin like shape and if flying fishes would have eventually evolve to fly completely (like bats).
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  30. #29 Re: Evolutionary Theory and the Development of the Whale 
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    Quote Originally Posted by cypress
    Quote Originally Posted by marnixR
    Quote Originally Posted by cypress
    Evolutionary theory predicts that all the alterations, all the new forms and functions were a result of mutation and selection.
    again you're confusing evolutionary pathways with evolutionary process : the fossil record clearly displays a pattern of stepwise evolution, but it doesn't say anything about whether this pattern was achieved through mutation and selection
    all you can say from the fossil record is that it is consistent with what you could expect from mutation and selection, but the proof of the validity of that mechanism rests mostly on evolution observed in action in the here and now
    Not much of a response marnixR. I am not confused by the difference. Both are aspects of the theory. The fossil record provides the timeframe of 9 million years, that is pretty much the only relevant information it provides to this discussion.

    Modern biology tells us that new form and function requires new protein structures, new binding sites, new expression controls and new developmental controls. Molecular biology shows us that these new structures and binding sites require on average 5-8 specific modifications. Population genetics like the article provided provides a mechanism to estimate the amount of time required to generate the new binding sites even when we reduce the required number to just two. When you put it all together, the predictions that follow from modern evolutionary theory are failing yet again.
    What if the cart comes before the horse? Maybe the function evolves before the genes really completely formed, so the function exists but is not genetically stable. Maybe at first, 1/3 of the pups born to a female are being born without the new trait, or with serious birth defects, but after a while the gene begins to stabilize.

    My point is: gene structures might become more elegant over time. Maybe the original version of a trait that now rests on cooperation between 2 or more genes might have only rested on one gene when it first appeared.

    Quote Originally Posted by Pong
    Quote Originally Posted by marnixR
    fully marine whale
    They're not there yet. Early whales got the bends, probably as they pushed their limits. Telltale damage is in the bones. Still, sperm whales suffer this. It's a chronic problem that is certainly painful and eventually debilitating in older whales.

    Given that sperm whales' probable M.O. involves killing squid by dragging those suckers to death by decompression, they have every reason to adapt further.
    I think that's a fine example of how a less than ideal genetic structure or evolution pattern can be functional.

    A survival strategy exists, but some the needed machinery hasn't appeared yet to support it. In the meantime, it's still a viable strategy.
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    Quote Originally Posted by marnixR
    Quote Originally Posted by cypress
    Three the one I favor, is that new form and function is derived by processes different from the present suite of observed evolutionary processes.

    Only a prior commitement could lead you to focus your suspisions on one of the three possibilities since you have don't have direct evidence to support your suspicions.
    i'll only be able to evaluate the strength of your third alternative once you've described it - that's just why natural selection is currently seen by most biologists as the main drive behind evolution : (1) it describes the available evidence pretty well, and (2) no alternative has the same explanatory power, although some alternatives may have been contributing factors
    Yes , it is unfortunate that alternatives to the moderators version of evolution is not alowed in this subforum. You might want to review the rules. while modification and selection paints an interesting picture, it is failing to live up to the predictions made of it.

    the thing i'm not going to do is throw away natural selection in favour of an as yet unknown explanation until said explanation has been brought forward and proves to be better at explaining the available evidence
    It makes little difference if an alternative is any better. Why favor an explanation that can't live up to its claim? Using evolutionary models and mutation rates we get over 40 million years to generate a specific new gene regulation site to regulate a gene differently than before. We also know that a typical complex trait (such as the countercurrent exchanger) requires tens and hundreds of genes. With this as a backdrop, how can you support that mechanism in a 9 million year window?

    Quote Originally Posted by cypress
    Surely you can see a difference between slight alteration of an existing set of traits and development of novel components.
    no i don't : small deviations over time have the potential to become large deviations
    Only if it can be experimentally confirmed that small deviations are the feedstock for novel protein shapes, binding sites and control sites. Otherwise they only serve to modify existing features.


    what's "just-so" about observing evolutionary change in real time and extrapolating from there ? if natural selection has been shown to produce a certain amount of change over a certain amount of time, that's all i need to know
    Nothing if the extrapolation is justified by knowledge that the observed changes also generate the kinds of molecular changes when combined allow for the novel functions required. The problem is that experimental biology has been investigating this and these real time alterations have not generated even one example of this.
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  32. #31  
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    Quote Originally Posted by cypress
    novel functions... The problem is that experimental biology has been investigating this and these real time alterations have not generated even one example of this.
    Just give us a
    Quote Originally Posted by cypress
    9 million year window
    I'm under the impression that novel traits never just appear. They gradually morph from something else. Like the nostrils of whales sliding back over their heads. Cypress you seem to demand the impossible.
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    Quote Originally Posted by Pong
    Quote Originally Posted by cypress
    novel functions... The problem is that experimental biology has been investigating this and these real time alterations have not generated even one example of this.
    Just give us a
    Quote Originally Posted by cypress
    9 million year window
    I'm under the impression that novel traits never just appear. They gradually morph from something else. Like the nostrils of whales sliding back over their heads. Cypress you seem to demand the impossible.
    You're making excuses. Excuses you would never accept from those who say "God did it a long time ago and you seem to want me to explain how he did it".

    But no, I am not asking for experimental evidence that is impossible to provide. I am asking for experimental evidence that is in every way consistent with what we should see if the predictions of evolution by mutation and selection are accurate. The prediction is that selectable modifications accumulate over time at a rate sufficient to generate observed diversity in the estimated timeframe. If this were true then the whale line would have to have generated many tens of thousands of new protein structures, gene expression controls, developmental controls, and cell functional controls. Molecular biology studies have provided us with an understanding of how these systems work and what is required to generate functional systems. We now know that they require molecular systems with the correct shape and binding sites. We also know that these binding sites generally require a sequence of 5-10 amino acids. From this we can estimate the rate that we should see generation or adaptation of new binding and shape sequences. What we get from the prediction is that we should see this scale of new shape structures and binding sites on the order of once ever 100 generations and every 10 billion or so organisms. However in the laboratory we don't even see one of these kinds of alterations in 30,000 generations and many trillions of organisms.

    So while I am not asking for anything more than what the predictions require, unfortunately the theory is repeatedly failing to live up to the predictions, and yet while many creationists cling to their prior commitment without having their predictions overturned, you cling to your failing predictions and complain that those who show how your predictions seem hollow ask too much.

    But wait, it gets worse. While observed processes of mutation and selection routinely fails in the lab to generate even the most basic steps required for new molecular function (the building blocks of large scale form and function) in any reasonable timeframe, we have an accumulating list of novel molecular systems generated quickly without the precursor steps that mutation and selection would predict. So while your favored path is failing, these systems have and are generated apparently by some other process. In addition, genetic engineers are now easily able to generate novel structures and binding sites by processes other than mutation and selection so we know of at least one alternate process in operation today. Event the ID advocates are therefore at least one step ahead of advocates of Darwinian Evolution in explaining how novel function might arise.
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    Sounds like you want faster, more detailed simulations. For analogy, you could explain land erosion, and I'd say yeah just show me one rock migrating through a stand of trees.

    And you're unsatisfied with wiener dogs why?
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  35. #34  
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    [quote="cypress"]
    What we get from the prediction is that we should see this scale of new shape structures and binding sites on the order of once ever 100 generations and every 10 billion or so organisms. However in the laboratory we don't even see one of these kinds of alterations in 30,000 generations and many trillions of organisms.

    This is the part that seems ridiculous to me. Not all environments introduce the same level of selection. A stronger force of selection will certainly yield results faster than a weaker selection.

    Think about it: the first time a new advantageous mutation emerges, there's a certain probability that its carrier will die despite it being beneficial. This probability is inversely linked to the likelihood of an organism without the mutation surviving. (It spreads more rapidly if the others are dying faster to make room for it.) With a stronger selection criteria, there are fewer "false starts". Fewer "false starts" means you're going to evolve more rapidly.

    A species that produces 10 pups per litter on average, and then sees an average of 6 of them dying before maturity is going to evolve more rapidly than a species that has 5 pups per litter and sees 1 die on average.
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    The mutations cypress says have not been observed are in fact observed everyday - including in humans. Point mutations, insertions, deletions and chromosomal rearrangements occur continually - some of which lead to major changes in morphology or biochemistry. Atavisms reveal how minor changes in things like transcription factors that are important in development can produce major alterations in body plan without requiring tens of thousands of sequential mutations over thousands of generations. Thousands of new proteins with new functions are not required - whales, for example, like us are still Chordata > Craniata > Vertebrata > Gnathostomata > Tetrapoda > Amniota > Mammalia i.e. they have pretty much the same the same set of biochemical functions to carry out as we do.

    From my limited understanding of whale evolution I simply don't see where the need for tens of thousands of new proteins with novel function arises.
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    Zwirko sets it straight, finally.
    A pong by any other name is still a pong. -williampinn
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    Quote Originally Posted by Zwirko
    The mutations cypress says have not been observed are in fact observed everyday - including in humans. Point mutations, insertions, deletions and chromosomal rearrangements occur continually - some of which lead to major changes in morphology or biochemistry. Atavisms reveal how minor changes in things like transcription factors that are important in development can produce major alterations in body plan without requiring tens of thousands of sequential mutations over thousands of generations. Thousands of new proteins with new functions are not required - whales, for example, like us are still Chordata > Craniata > Vertebrata > Gnathostomata > Tetrapoda > Amniota > Mammalia i.e. they have pretty much the same the same set of biochemical functions to carry out as we do.

    From my limited understanding of whale evolution I simply don't see where the need for tens of thousands of new proteins with novel function arises.
    Interesting description Zwirko, but can you substantiate it with verified examples? Is it real or a cute story? I have already granted the list of mutations you offered. Please provide a verified example of a major alteration in body plan that has selective advantage with just a minor change. Then describe the molecular path for that change. I am aware of minor changes producing deformities that can only survive in the lab but not selectable morphological changes. In addition you seem to be changing the theory from selection of altered of gene expression to something else. Are you suggesting the theory is wrong and should be altered? Because this is what I am suggesting. Also even with your concept there still remains the thousands of altered developmental and gene expression controls and the novel gene function you have not explained.
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    [quote="kojax"]
    Quote Originally Posted by cypress
    What we get from the prediction is that we should see this scale of new shape structures and binding sites on the order of once ever 100 generations and every 10 billion or so organisms. However in the laboratory we don't even see one of these kinds of alterations in 30,000 generations and many trillions of organisms.

    This is the part that seems ridiculous to me. Not all environments introduce the same level of selection. A stronger force of selection will certainly yield results faster than a weaker selection.
    Population genetics models allow for this. If every stepwise alteration were highly advantageous, the timeframes would be greatly reduced. Molecular biology studies indicate that they are very rare though estimates are fewer than 1 in 10^12 mutation for a specific gene or control. This is discussed in the paper I referenced.

    Think about it: the first time a new advantageous mutation emerges, there's a certain probability that its carrier will die despite it being beneficial. This probability is inversely linked to the likelihood of an organism without the mutation surviving. (It spreads more rapidly if the others are dying faster to make room for it.) With a stronger selection criteria, there are fewer "false starts". Fewer "false starts" means you're going to evolve more rapidly.
    Generally agree.

    A species that produces 10 pups per litter on average, and then sees an average of 6 of them dying before maturity is going to evolve more rapidly than a species that has 5 pups per litter and sees 1 die on average.
    All accounted for in the model. One aspect of the model that is perhaps a weakness is that it does not give much allowance for cooptation of unrelated genes and control functions. This allowance is currently not granted because we don't have objective evidence that this occurs.
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    cypress, nobody is changing anything. You said for a whale to evolve there needs to be "many tens of thousands of new protein structures, gene expression controls, developmental controls, and cell functional controls". You need to demonstrate that thousands of new proteins are indeed needed. Not variations on other proteins, but entirely novel functions as you have been labouring to point out. I'm disputing the validity of one of the very foundations of your argument. What evidence supports your assertion that so many new proteins are required? It's your argument in a thread created by you, so defend it with evidence please. Since you listed four main categories amongst the "tens of thousands" I'll let you off with just listing at least 500 from any one category of your own choosing. A silly request, to be sure, but one that is little different from you own.

    My point is simple: 1) the number of required changes to make a novel protein is nowhere near as great as you pretend; 2) thousands of such new proteins are not needed to "make a whale"; and 3) changes to genes controlling development can have major outcomes. Your request to see this happen live on CNN and see it selected for is simply naive and unnecessary.
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    Quote Originally Posted by Zwirko
    cypress, nobody is changing anything. You said for a whale to evolve there needs to be "many tens of thousands of new protein structures, gene expression controls, developmental controls, and cell functional controls". You need to demonstrate that thousands of new proteins are indeed needed. Not variations on other proteins, but entirely novel functions as you have been labouring to point out. I'm disputing the validity of one of the very foundations of your argument. What evidence supports your assertion that so many new proteins are required? It's your argument in a thread created by you, so defend it with evidence please. Since you listed four main categories amongst the "tens of thousands" I'll let you off with just listing at least 500 from any one category of your own choosing. A silly request, to be sure, but one that is little different from you own.
    Comparison of the whale genome to land mammals provides the basis for concluding that there are thousands and thousands of gene sequence differences even while on a percentage basis the total sequence is fairly similar. While most point diferences are inconsequential, we also know that 2-10 differences in key locations do significantly alter protein function so even minor differences at key locations in gene sequences have the potential for novel function. I contend that many of these differences define the difference we observe in form and function. do believe otherwise? If so, why?

    My point is simple: 1) the number of required changes to make a novel protein is nowhere near as great as you pretend;
    Earlier in the thread I indicated that novel proteins, gene expression controls and developmental controls generally require 4-10 point differences. The number I used in the example was just two point changes. I would hope you agree that two point changes is not a great number.

    2) thousands of such new proteins are not needed to "make a whale"; and
    Now you are speculating. Genome analysis reveals thousands and thousands of differences. Why should we say that only a few are needed?

    3) changes to genes controlling development can have major outcomes. Your request to see this happen live on CNN and see it selected for is simply naive and unnecessary.
    I have asked you to support your claim with empirical observation. I have little interest in witnessing it myself. Can you validate your claim? If you can't, how is that scientific?
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    Quote Originally Posted by cypress
    We now know that they require molecular systems with the correct shape and binding sites. We also know that these binding sites generally require a sequence of 5-10 amino acids. From this we can estimate the rate that we should see generation or adaptation of new binding and shape sequences. What we get from the prediction is that we should see this scale of new shape structures and binding sites on the order of once ever 100 generations and every 10 billion or so organisms.
    Your estimation methodology is garbage. Faster evolutionary changes than that are routinely observed in the lab and in the world. You appear to be making the standard creationist assumptions of independence of event, oversimplification of such processes as horizontal transfer and symbiosis, sexual recombination and large scale one step genetic changes, etc.
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    I'm well aware that there are major differences between the genomes of whales and humans. The point, as you well know, is that you keep shifting the definition of "novel".

    Here's the sperm whale myoglobin:

    Code:
    mvlsegewql vlhvwakvea dvaghgqdil irlfkshpet lekfdrfkhl kteaemkase dlkkhgvtvl talgailkkk ghheaelkpl aqshatkhki pikylefise aiihvlhsrh pgdfgadaqg amnkalelfr kdiaakykel gyqg
    and the human:

    Code:
    mglsdgewql vlnvwgkvea dipghgqevl irlfkghpet lekfdkfkhl ksedemkase dlkkhgatvl talggilkkk ghheaeikpl aqshatkhki pvkylefise ciiqvlqskh pgdfgadaqg amnkalelfr kdmasnykel gfqg
    Similar protein, same function, lots of amino acid differences. It's not novel (according to your very own definition). Obviously there are great differences between the proteomes as expressed by whales and humans - that's what makes whales what they are and us what we are; that was never disputed. What we don't see is tens of thousands of proteins with novel function. Recall that all beta-lactamases are the same, no matter their sequence or substrate? A new beta-lactamase is not novel - you said it. Where are the tens of thousands of novel whale proteins with novel function?

    I'd also add that the paper you cited in the first post of this thread doesn't even support your argument. It's discussing the odds of one transcription factor binding site being inactivated and another being formed in a two-step process. Their results are not at odds with mainstream evolutionary thought - they even say as much themselves in subsequent commentary with Behe.
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    Quote Originally Posted by cypress
    I have asked you to support your claim with empirical observation. I have little interest in witnessing it myself. Can you validate your claim? If you can't, how is that scientific?
    Do you plan to be finished trolling any time soon?

    Are you seriously asking for empirical observation of the evolution of whale genome from Eocene terrestrial mammals? Its enough that there is a clear progression through the fossil record or morphological changes. This is plenty support for the evolution of whales from terrestrial mammals or humans from rodent-like primates of the Cretaceous.

    Obviously evolution happened since whales and animals are here when they're completely absent in the fossil records of past epochs.

    What you seem to be arguing is that there isn't enough evidence to say evolution is a real process yet you claim to not be a creationist.

    Let me ask you this (and your continued participation on this board might just hinge on the answer): what, then, are you suggesting occurred to produce the whales and humans of the Holocene? What better explanation exists other than evolution -those gradual changes over time that are empirically observed in the fossil record. Please consolidate your arguments in the many threads you've hijacked, started, and abused in a post or set of posts that follows in this thread and no other.
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    Skinwalker, as I have explained several times now, I agree that the fossil record indicates a progression of change over time. I do not dispute that progression.

    I dispute the efficacy of selection acting on mutation of expressed genes to accomplish this change. I think other processes must be involved. This is not a fringe concept either. It is gaining traction in evolutionary biology. Search the publications and you will find many prominent biologists increasingly making this and similar claims.

    I am not certain that ther are "better" explanations. I do know that the explanation being discussed seems inadequate. Since this forum does not allow for alternative explanations in this section, I learned quickly that they are not welcome. I realize that you are the administrator and can suspend the rules or me or both, but I will attempt to follow the rules as stated.
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    Biology is not physics. Its systems are far more complex and lthe state of the art in terms of quantitative models is far less developed.

    Evolution is not as quantitative nor predictive a theory as one would like. That is simply the resut of the fact that biology is not yet a quantitative science, although progress in molecular biology is rapidly taking it in that direction.

    There is no predictive, and quantitative theory of evolution. But the basic priinciples are sound and are consistent with what is known of genetics on both a phenonemological and molecular level.

    It would be nice to have a more quantitative theory, a predictive model, and computer simulations of both past and continuiing changes in species. But that is far in the future. In the meantime Darwwin did offer a good explanation for speciation and that explanation is consistent with what is known at more baseic level. One could not reasonably ask for more given the current state of knowledge. There is certainly no rational competing theory.

    And for the "ID crowd" -- there is absolutely no conflict between evolution and religion unless you want to create one. If that is your objective, go argue with the Pope.
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    Quote Originally Posted by cypress
    Skinwalker, as I have explained several times now, I agree that the fossil record indicates a progression of change over time. I do not dispute that progression.
    The question, then, is what, if not evolution, explains this progression. Clearly we're looking at evolution -the morphological appearance and function of the fossils indicate the organisms evolved, that is they changed over time. There are four mechanisms of evolution: natural selection, gene flow, genetic drift, and mutation.

    I dispute the efficacy of selection acting on mutation of expressed genes to accomplish this change. I think other processes must be involved.
    Since the presence of mutation is a fact, it really, really happens; and since populations both share genes and become isolates; and since climates and environments consistently change over time as evident in the geologic record -why, then, can these mechanisms not be involved? It appears that you're arguing from ignorance since you seem to be stating that because we cannot directly observe such gradual changes that causes speciation in a laboratory, it, therefore, cannot happen.

    This is not a fringe concept either. It is gaining traction in evolutionary biology. Search the publications and you will find many prominent biologists increasingly making this and similar claims.
    Help us out. Cite the 5 most convincing alternate explanations to the four mechanisms of evolution listed above by the 5 most prominent biologists. You obviously have access to the material. Give us an idea where you're basing your assumptions and/or opinions.

    I am not certain that ther are "better" explanations. I do know that the explanation being discussed seems inadequate.
    You've stated over and over that you think its "inadequate." And your preface that you're not sure better explanations exist seem disingenuous. You come across like an ID proponent or someone who's familiar to pseudoscience organizations like the Discovery Institute but pretending to fit in on a science forum just enough to test this argument or that. Clearly, your own personal agenda isn't revealed. What you haven't done is demonstrate the explanations of evolution to be inadequate. You've exploited the many questions that still remain to be explored by biological sciences, but have yet to show why current mechanisms of evolution are truly inadequate. Several members have successfully refuted several of your "questions" and assertions, yet you keep repeating them over and over as if no one wrote a word.

    So here are the questions for you:

    Who are the 5 most prominent authors of the 5 most convincing alternative explanations in modern biological journals?

    What better explanations exist than the four mechanisms of evolution? (ostensibly based on the preceding 5 authors/alternative explanations)
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    Quote Originally Posted by Cypress
    Examples are:

    1) a process to removing salt and minerals from sea water to allow the whale to consume sea water rather than fresh water.
    The first whales were consumers of fresh-water. Oxygen isotope analysis of the phosphates in the bones and teeth of these early Cetacea clearly show the transition (Thewissen, et al 1996). There's no good reason to think that 1) this couldn't have evolved from mutation in the time alloted, or 2) that the gene allowing for the processing of salt water wasn't already present but dormant until selected for by the environment. Not to mention it is entirely likely that early whales received their fresh water from prey.

    Quote Originally Posted by Cypress
    2) A redesign of the vertebrae to allow for up and down movement of the tail rather than side to side.
    Utter nonsense. Mammals already posses the capability to move their tails up and down. Haven't you ever watched a modern ungulate swat flies with a tail? A dog curl its tail under its legs? This is evidence that you are simply regurgitating some creationist BS probably from the 90s. Did you even try to think this through or read it before you so obviously copy/pasted it from "Discovery" Institute or ICR?

    Quote Originally Posted by Cypress
    3) A completely different skin system.
    Again, there's no reason to believe that 1) this couldn't have evolved from mutation in the time alloted, or 2) that existing characters aren't being selected for via natural selection.

    Quote Originally Posted by Cypress
    4) Muscle structures for the blow Hole.
    Again, there's no reason to believe that 1) this couldn't have evolved in the time alloted, or 2) that existing characters aren't being selected for via natural selection.

    Quote Originally Posted by Cypress
    5) A countercurrent heat exchange and temperature control system to allow the testes to be internalized.
    This is an example of paedomorphic development of existing arteries and veins and actually good evidence for Artiodactyla being the ancestral species since it would be just the sort of derived embryonic character states that evolution would carried into adults through natural selection (Pabst, et al 1998).

    6) Forelimbs to flippers, tail to fin, etc.[/quote]

    This is just evolutionary adaptation of existing skeletal structure but, again, there's no reason to believe that 1) this couldn't have evolved in the time alloted, or 2) that existing characters aren't being selected for via natural selection.

    Quote Originally Posted by Cypress
    Population Genetic Modeling (Durrett and Schmidt 2008) indicate the frequency for these kinds of alterations very slow when breeding populations are low, and required alterations are cumulative, etc.
    Did you even read the article you cited? They're discussing a single gene pair of Drosphila not the entire genome of a breeding population of Cetacea!

    Quote Originally Posted by Cypress
    In the case of mammals that tend to remain near water, we can safely estimate the breeding population at 10,000 or less.
    Why is that safe to assume? What citation have you?

    To use this article, you'll also have to assume that the Drosphila mutation rate is the same as that of Cetacea. Why should this be the case? The Drosphila genome has 13,601 genes. The human genome has at least 20,000 genes. I don't know the number of genes present in the whale genome, but I do know that there are some whale species with 22 chromosomes and some with 21. Humans have 23 so it stands to reason that there could be a comparable number of genes. This is relevant because the very citation you provided refutes your assertion that it would be mathematically improbable for enough mutations to have occurred from an ungulate to a proto-whale in just 9 million years. The figures you're working with is a for a single gene-pair and clearly not for all the pairs in a breeding population.

    Durrett and Schmidt state: " there are at least 20,000 genes in the human genome and for each gene tens if not hundreds of pairs of mutations that can occur in each one. Our results show that the waiting time for one pair of mutations is well approximated by an exponential distribution. If there are k nonoverlapping possibilities for double mutations, then by an elementary result in probability, the waiting time for the first occurrence is the minimum of k independent exponentials and hence has an exponential distribution with a mean that is divided by k. From this we see that, in the case in which the first mutant is neutral or mildy deleterious, double mutations can easily have caused a large number of changes in the human genome since our divergence from chimpanzees. Of course, if the first mutant already confers an advantage, then such changes are easier."

    Quote Originally Posted by Cypress
    Actually thee are three possibilities that have not been confirmed or falsified.

    One is that I might be in error. If i made an error, that would be easy to discuss and confrim.
    You have made several errors. I've confirmed them above.

    Quote Originally Posted by Cypress
    Two is that whales did not evolve from dog-like land creatures in 9 million years. Fossil evidence is far from conclusive.
    I don't know of anyone suggesting whales evolved from dog-like land creatures. The most likely candidate for a terrestrial ancestor is Artiodactyla, an even-toed ungulate that eventually began taking refuge in an aquatic environment.

    Quote Originally Posted by Cypress
    Three the one I favor, is that new form and function is derived by processes different from the present suite of observed evolutionary processes.
    What's interesting is that 1) you don't say what this "new form and function is" and that 2) you favor it.

    The reason this is interesting is because I believe it exposes you for what you've been claiming yourself not to be: a creationist. You clearly favor 'Intelligent' Design over natural explanations -your arguments come from the ID playbook. Your whale argument is an only slightly updated version of Frank Sherwin's 1996 essay on the ICR creationist site.

    References

    Pabst, D.A., Rommel, S.A., McLellan, W.A. (1998) Evolution of the Thermoregulatory Function in Cetacean Reproductive Systems: in The Emergence of Whales, Thewissen, J.G.M. (ed.). New York: Plenum Press

    Thewissen, J.G.M., Roe L.J., O'Neill J.R., Hussain S.T., Sahni A, Bajpal S.(1996) Evolution of cetacean osmoregulation. Nature 381: 379-380
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    Quote Originally Posted by SkinWalker
    Quote Originally Posted by Cypress
    Examples are:

    1) a process to removing salt and minerals from sea water to allow the whale to consume sea water rather than fresh water.
    The first whales were consumers of fresh-water. Oxygen isotope analysis of the phosphates in the bones and teeth of these early Cetacea clearly show the transition (Thewissen, et al 1996). There's no good reason to think that 1) this couldn't have evolved from mutation in the time alloted, or 2) that the gene allowing for the processing of salt water wasn't already present but dormant until selected for by the environment. Not to mention it is entirely likely that early whales received their fresh water from prey.
    I think you are missing the point. I have previously stipulated that the changes occured. But I demonstrate by Population genetics and knowledge of mutation rates that the uniform processes subscribed to mutation and selection operate too slowly to explain the changes we both accept.

    Quote Originally Posted by Cypress
    2) A redesign of the vertebrae to allow for up and down movement of the tail rather than side to side.
    Utter nonsense. Mammals already posses the capability to move their tails up and down. Haven't you ever watched a modern ungulate swat flies with a tail? A dog curl its tail under its legs? This is evidence that you are simply regurgitating some creationist BS probably from the 90s. Did you even try to think this through or read it before you so obviously copy/pasted it from "Discovery" Institute or ICR?
    Have you investigate the changes to the vertebrea? It is a different design. It has clearly been altered.

    More later.
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    Quote Originally Posted by SkinWalker
    it exposes you for what you've been claiming yourself not to be: a creationist. You clearly favor 'Intelligent' Design
    Quote Originally Posted by cypress
    It is a different design. It has clearly been altered.
    Take that as a confession.
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    Take it as you will, but you would be wrong. I'm an engineer and was using that word frequently today. I keep forgetting how careful one must be to choose words on this site. Again the vertebrae is clearly different in form and function.
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    Quote Originally Posted by cypress
    I think you are missing the point. I have previously stipulated that the changes occured. But I demonstrate by Population genetics and knowledge of mutation rates that the uniform processes subscribed to mutation and selection operate too slowly to explain the changes we both accept.
    According to you and a handful of other creationists who keep arguing for 'intelligent' design. However, I've yet to see a good argument why natural selection cannot account for the changes. It happened. It really, really happened. We have the evidence before us in the form of the genetic and fossil records.

    There is simply no good reason not to accept that the time alloted was insufficient for change. You haven't excluded that the features aren't the result of new expressions of genes already present; nor have you demonstrated that the rate of mutation cannot be accounted for. You cited a paper dealing with a single gene pair of a completely different Order, Drosphila, and attempted to impose that mutation rate on a new Order, Cetacea, with an apparent assumption that only one gene pair in the whole Cetacea genome will ever mutate rather than the tens of thousands (exponentially increasing the rate for the population); you assume that Drosphila mutate at the same rate as Cetacea; and you apparently pulled some breeding population numbers out of a hat.

    Tip for you: when you mine creationist websites for data, quotes, and arguments, it might pay to actually read the papers they cite and synthesize the information for yourself.

    Have you investigate the changes to the vertebrea? It is a different design. It has clearly been altered.
    It doesn't appear to be a design at all. Clearly you think so. There is no reason at all that natural selection, mutation, genetic drift, and gene flow cannot account for the changes we see in the the evolution of terrestrial mammals to whales. The fossil record shows it. Isotope evidence reveals it. It happened.

    What you're saying is that you agree it happened, but you just don't agree that it evolved. You keep pointing at some as yet unknown mechanism of evolution, but you refuse to suggest what it might be. Regardless, there is no reason to believe that the current mechanisms aren't sufficient to result in the evolution we see.

    In an earlier post, you stated that your "alternative mechanism" speculation "is not a fringe concept either. It is gaining traction in evolutionary biology."

    I challenged you to list the top 5 prominent authors of the 5 most convincing papers that discuss this mystery alternative.

    You said, "Search the publications and you will find many prominent biologists increasingly making this and similar claims." I looked at several publications and searched several databases. No one seems to be seriously discussing any alternative mechanism of evolution except Behe. In each publication that I saw his name mentioned, it was followed by real scientists ripping his "work" to shreds. Like the paper you cited in the OP, ironically enough.
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    Quote Originally Posted by SkinWalker
    Quote Originally Posted by cypress
    I think you are missing the point. I have previously stipulated that the changes occured. But I demonstrate by Population genetics and knowledge of mutation rates that the uniform processes subscribed to mutation and selection operate too slowly to explain the changes we both accept.
    According to you and a handful of other creationists who keep arguing for 'intelligent' design. However, I've yet to see a good argument why natural selection cannot account for the changes. It happened. It really, really happened. We have the evidence before us in the form of the genetic and fossil records.
    I suppose to you, anyone who does not agree with you is a creationist and that's fine, I don't mind being improperly included in that group. I am coming to learn that your clique is far more dogmatic, so I have little intrest in joining it.

    However. while the evidence does confirm that changes occurred over time, the evidence does not provide any indication of how thoese changes happened. I completely agree with you that the changes really, really happened. But you cannot provide any observation, or any repeatable test that can confirm that natural selection acting on random mutation is capable of explaining the change we both agree happened. This example from whale evolution is just one way your predicted mechanism fails by showing how this proposed mechanism operates too slowly. The challenge for you and others who want to revive this prediction is to show by verified tests how this mechanism operates orders of magatudes faster that we have ever observed in the 50 years it has been studied.

    There is simply no good reason not to accept that the time alloted was insufficient for change. You haven't excluded that the features aren't the result of new expressions of genes already present; nor have you demonstrated that the rate of mutation cannot be accounted for. You cited a paper dealing with a single gene pair of a completely different Order, Drosphila, and attempted to impose that mutation rate on a new Order, Cetacea, with an apparent assumption that only one gene pair in the whole Cetacea genome will ever mutate rather than the tens of thousands (exponentially increasing the rate for the population); you assume that Drosphila mutate at the same rate as Cetacea; and you apparently pulled some breeding population numbers out of a hat.
    No skinwalker. I used mution rates for land and sea mammals, and population sizes for cetecea and shoreline dwelling mammals. I would be happy to include all genes in the calculations if you can confirm that cooptation is a valid mechanism in operation today. Were that the case, then the peer-reviewed article I provided would have included that mechanism in the formulas. You insist that thoes who challenge your prior commitement use validated scientific methods but you seem to think you are exempted.


    Tip for you: when you mine creationist websites for data, quotes, and arguments, it might pay to actually read the papers they cite and synthesize the information for yourself.
    Nice diversion.

    Have you investigate the changes to the vertebrea? It is a different design. It has clearly been altered.
    It doesn't appear to be a design at all. Clearly you think so. There is no reason at all that natural selection, mutation, genetic drift, and gene flow cannot account for the changes we see in the the evolution of terrestrial mammals to whales. The fossil record shows it. Isotope evidence reveals it. It happened.
    I agree that given enough time significant changes are theoreticaly possible. I also agree that diversification occurred. I don't know why you keep raising this straw man argument other than to mask the failure to address the substance of the argument.

    What you're saying is that you agree it happened, but you just don't agree that it evolved. You keep pointing at some as yet unknown mechanism of evolution, but you refuse to suggest what it might be.
    Site rules don't allow for alternative theories. Alternatives go in a different areas. My early experience confirmed this. Change the rules and I will happily discuss them.

    Regardless, there is no reason to believe that the current mechanisms aren't sufficient to result in the evolution we see.
    Sure but it is a prior commitment, a metaphysical belief. It is not supported by the scientific method. I have no issue with beliefs. I do have an issue when people try to smuggle their prior commitements into science.


    In an earlier post, you stated that your "alternative mechanism" speculation "is not a fringe concept either. It is gaining traction in evolutionary biology."

    I challenged you to list the top 5 prominent authors of the 5 most convincing papers that discuss this mystery alternative.

    You said, "Search the publications and you will find many prominent biologists increasingly making this and similar claims." I looked at several publications and searched several databases. No one seems to be seriously discussing any alternative mechanism of evolution except Behe. In each publication that I saw his name mentioned, it was followed by real scientists ripping his "work" to shreds. Like the paper you cited in the OP, ironically enough.
    I'm sorry you were unsuccessful. I assure you they are out there. I will continue to follow the rules of this posting category and refrain from offering alternatives. By all means ban me if you like. You don't mean to imply that the paper I offered has been ripped to shreds do you?
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    Quote Originally Posted by cypress
    Again the vertebrae is [sic] clearly different in form and function.
    The vertebrae of whales do not have a different function from those found in other members of the Vertebrata. They protect the spinal column, provide attachment for ligaments, muscles and tendons, provide structural support, protection to internal organs, have biochemical functions and enable movement of the organism itself and movement of the organism within its environment. What exactly are the different functions of whale vertebrae that you say exist?

    The vertebrae of whales are different from those found in birds, snakes, frogs and humans - just as they are all different from each other. It's not of a different "design", it's a modification of the ancestral form - these bones are a shared characteristic of the entire lineage of Vertebrata. It's a difference of morphology, not of design. Sure it's different (or "altered" as you describe it). Who ever declared otherwise? Differences in overall size, or in the shape of the various elements or by the fusion of neighbouring vertebra are just variations on the same "design".

    The form of the whale vertebra is constrained by its evolutionary history and is precisely the reason why whales and other marine mammals move the way that they do and not the way fish do. Mammalian vertebral columns are constructed using common developmental pathways and don't require the evolution of a myriad new proteins and controls - they are literally stuck with more or less the same set of tools as all other mammals. Human vertebrae are not even all the same - they have different morphology at different points along the spinal column.

    Just why you are pointing out that the vertebrae of whales have evolved differences since their last common ancestor with land-dwelling mammals is something of a mystery, since it lends no support at all to your argument unless you can demonstrate it to be statistically unlikely.
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    Quote Originally Posted by Zwirko
    Quote Originally Posted by cypress
    Again the vertebrae is [sic] clearly different in form and function.
    The vertebrae of whales do not have a different function from those found in other members of the Vertebrata. They protect the spinal column, provide attachment for ligaments, muscles and tendons, provide structural support, protection to internal organs, have biochemical functions and enable movement of the organism itself and movement of the organism within its environment. What exactly are the different functions of whale vertebrae that you say exist?

    The vertebrae of whales are different from those found in birds, snakes, frogs and humans - just as they are all different from each other. It's not of a different "design", it's a modification of the ancestral form - these bones are a shared characteristic of the entire lineage of Vertebrata. It's a difference of morphology, not of design. Sure it's different (or "altered" as you describe it). Who ever declared otherwise? Differences in overall size, or in the shape of the various elements or by the fusion of neighbouring vertebra are just variations on the same "design".

    The form of the whale vertebra is constrained by its evolutionary history and is precisely the reason why whales and other marine mammals move the way that they do and not the way fish do. Mammalian vertebral columns are constructed using common developmental pathways and don't require the evolution of a myriad new proteins and controls - they are literally stuck with more or less the same set of tools as all other mammals. Human vertebrae are not even all the same - they have different morphology at different points along the spinal column.

    Just why you are pointing out that the vertebrae of whales have evolved differences since their last common ancestor with land-dwelling mammals is something of a mystery, since it lends no support at all to your argument unless you can demonstrate it to be statistically unlikely.
    My example was of the countercurrent heat exchanger and flow contoller for maintaining internal testes temperature. I mentioned the vertebrea as one of several modifications noted in the presumed progression of whale evolution. My argument does not depend on these modifications, if you don't consider them new form, I won't dispute it any further. This argument over vertebrea is an interesting diversion.
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    Cypress, if, as you claim, these "alternatives" are accepted and suggested by prominent biologists, then there should be no reason you cannot list the 5 most prominent authors of the 5 most convincing papers. The only thing this sub-forum restricts is pseudoscience and you've implied that what you're suggesting is not pseudoscience in your statements -indeed, you said "[these are not] fringe concept[s]."

    I used mution (sic) rates for land and sea mammals, and population sizes for cetecea and shoreline dwelling mammals.
    My bad. I only saw the citation for Drosphila. Could you cite your sources of data so that I might revise my statements?
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    Quote Originally Posted by cypress
    My example was of the countercurrent heat exchanger and flow contoller for maintaining internal testes temperature. I mentioned the vertebrea as one of several modifications noted in the presumed progression of whale evolution. My argument does not depend on these modifications, if you don't consider them new form, I won't dispute it any further. This argument over vertebrea is an interesting diversion.
    It's at times like this that I wonder if the last common ancestor between humans and eels is a lot closer than is currently estimated.

    Lying doesn't make your argument any more convincing.
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    Just read from the beginning of the thread. I don't see any reason to go off on a straw man argument about vertebrae since there are plenty of clear examples of novel form and function to discuss.

    I'll get the sources I used for population estimates and mutation rates in a bit. Perhaps you have a better calculated result than the 40 million years I derived?
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    Would you see any reason why you you cannot list the 5 most prominent authors of the 5 most convincing papers that detail this alleged and mysterious "alternate mechanism" of evolution?
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    yes I tried to raise alternate mechanisms on other occasions and was told by moderators they belong in the alternate theories sub forum. I don't care to post there. I know you can make exceptions but don't want an exception. My case here is against the predictions of natural selection acting on random mutation. I don't need an alternate to demonstrate how this prediction is not working and should be altered and not extended beyond what it can explain.
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    First, you haven't demonstrated that natural selection isn't at work. Not by a long shot. Second, you said the notions you have "aren't fringe" and that there are "prominent researchers" who are doing the work. The only thing that might be off-limits here is pseudoscience, which would, naturally, be moved to the pseudoscience sub-forum. However, this clearly isn't the case with the work you're discussing, since it isn't "fringe" (that is, not pseudoscience) and the research is conducted by "prominent researchers." Also, I'm only asking for the citations, not your synthesis and explanations of the research.

    Clearly, there is no conflict. Unless you're lying to us.

    In addition, I'm still interested in the sources for data regarding "[mutation] rates for land and sea mammals, and population sizes for cetecea and shoreline dwelling mammals."
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    cypress, an adminestrator is directly asking you for those sources. If they are not fringe, why not provide them? Stop sidestepping and please cough them up already.
    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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    In defense of cypress, challenging a theory should not require alternate explanations.

    Conflicting data though is fair call.
    A pong by any other name is still a pong. -williampinn
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    Quote Originally Posted by cypress
    Just read from the beginning of the thread. I don't see any reason to go off on a straw man argument about vertebrae since there are plenty of clear examples of novel form and function to discuss.

    See, that's the thing. I did go back through the thread. You've brought whale bones into the discussion several times of your own accord. Pretending that you've been focusing on whale thermoregulatory systems and have merely mentioned whale vertebrae in passing is an outright lie. You've given both equal prominence.

    Why can't you just admit that you've made multiple statements about whale vertebrae that are flat out wrong? Learning new things needn't be painful and there is no shame in having your mistakes pointed out. Instead you choose to distance yourself from your own statements, reduce them to an irrelevancy so that you can accuse anybody that questions them of wasting everybody's time.

    Yes, the whale spinal column has evolved since the last common ancestor between whales and land-dwelling mammals. Yes, it requires changes in gene expression. Just quit saying that whale vertebrae have novel function and that the whale had to evolve an "up and down" movement from it's pre-existing "side to side" movement.
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    Quote Originally Posted by Zwirko
    Quote Originally Posted by cypress
    Just read from the beginning of the thread. I don't see any reason to go off on a straw man argument about vertebrae since there are plenty of clear examples of novel form and function to discuss.

    See, that's the thing. I did go back through the thread. You've brought whale bones into the discussion several times of your own accord. Pretending that you've been focusing on whale thermoregulatory systems and have merely mentioned whale vertebrae in passing is an outright lie. You've given both equal prominence.
    Sure because other posters raised questions about them just as you have.

    Why can't you just admit that you've made multiple statements about whale vertebrae that are flat out wrong? Learning new things needn't be painful and there is no shame in having your mistakes pointed out.
    I often make mistakes. If you want to say that the vertebrae is modified and not new, fine. I don't need that point to make my argument, and though I disagree I will accept your view. There is an abundance of novel features to focus on.
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    Here is the material I used to estimate population size and mutation rates.

    http://www.sciencemag.org/cgi/conten...284/5423/2055a

    http://mbe.oxfordjournals.org/cgi/content/full/25/1/120

    http://www3.interscience.wiley.com/j...TRY=1&SRETRY=0


    To bring us back to the subject, granting that whales evolved from land mammals to sea creatures in roughly 9 million years (based on fossil evidence), using Population genetics, estimated mutation rates and population sizes, along with recent information from molecular and experimental cell biology regarding the kinds of molecular alterations needed to produce novel protein structures and binding sites, geene expression controls, developmental controls and cell function controls, I estimate it would take far far more than 9 million years to evolve whales by natural selection acting on random mutation. I argue that some other mechanism is in play.

    So far, nobody has offered better calculations or shown how my estimates are incorrect. This is just one of many examples of how predictions from traditional evolutionary theory are failing to live up to the claims.
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    The problem arises because simple mutations of the type that are normally envisaged in calculations such as yours are quite possibly not enough to bring about any major changes at all. I've always thought about these sorts of changes as a "fine-tuning" mechanism myself, playing a minor role in the grand scheme of things. Indeed, it's an area of great activity in evolutionary biology - just which of all the varied mechanisms of generating diversity are the most important? Simple random mutation is quite possibly not that important, or maybe it is - time will tell.

    Are these other known mechanisms accounted for in your calculation? What about mutation that is not random? Did you factor that in?
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    Quote Originally Posted by Zwirko
    The problem arises because simple mutations of the type that are normally envisaged in calculations such as yours are quite possibly not enough to bring about any major changes at all. I've always thought about these sorts of changes as a "fine-tuning" mechanism myself, playing a minor role in the grand scheme of things.
    Interesting that you say this. The evidence shows rather clearly that mutation and selection serves to fine-tune. For quite a while given experimental limitations, it was reasonable to extend this process to all observed changes. these days it no longer seems warranted.

    Indeed, it's an area of great activity in evolutionary biology - just which of all the varied mechanisms of generating diversity are the most important? Simple random mutation is quite possibly not that important, or maybe it is - time will tell.
    There are cases of new molecular level structures and function that arise very quickly without the kind of progression the selection of random mutation would predict. These examples seem like a area ripe for investigation.

    Are these other known mechanisms accounted for in your calculation? What about mutation that is not random? Did you factor that in?
    No they are not. Neither is non-random mutation. I have seen a couple papers postulating non-random mexhanisms. I think they show potential.
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    Quote Originally Posted by cypress
    Here is the material I used to estimate population size and mutation rates.
    - - - -
    So far, nobody has offered better calculations or shown how my estimates are incorrect.
    None of those links enables anyone to estimate population size or mutation rates in ancestral whales.

    You keep making silly assumptions (we can safely assume a breeding population of ten thousand) and claiming to reason from them in obscure manners involving invalid probabilistic and statistical approaches (independence of event in mutations and combinations). You then conclude that the apparently obvious has not happened, or does not exist.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Here is the material I used to estimate population size and mutation rates.
    - - - -
    So far, nobody has offered better calculations or shown how my estimates are incorrect.
    None of those links enables anyone to estimate population size or mutation rates in ancestral whales.

    You keep making silly assumptions (we can safely assume a breeding population of ten thousand) and claiming to reason from them in obscure manners involving invalid probabilistic and statistical approaches (independence of event in mutations and combinations). You then conclude that the apparently obvious has not happened, or does not exist.
    Two of those papers provide the basis for my estimates. I compared them to others. I will try to dig them up. Do you know my estimates are wrong? You must since you call them silly assumptions. So let's have the correct numbers please.
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    I haven't yet had the opportunity to review the sources as iceaura has, but I'm assuming these are speaking to the breeding populations of the Eocene and not the Holocene, yes?
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    Quote Originally Posted by cypress
    No skinwalker. I used mution rates for land and sea mammals, and population sizes for cetecea and shoreline dwelling mammals.
    You assumed independence of event and adoption for the mutations, and your estimates of the breeding population size for shoreline dwelling mammals were ridiculously low.

    Ten thousand is a population bottleneck, not a safe assumption for the breeding population a a successful lineage of mammals.
    Quote Originally Posted by cypress
    Do you know my estimates are wrong?
    I know they have no visible support in reason or evidence.
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    Over the last decade it has been becoming apparent that evolution taking place at a level above that of the gene sequence (if I can phrase it that way) is also very important. Specifically, evolution at the chromosomal level may be of major importance. Two main strands of thought include chromosomal recombination and mobile DNA elements.

    Mobile elements such as DNA transposons, retrotransposons, retroelements, endogenous retroviruses and even retroviruses have shaped our genomes in profound ways - just think, retroelements alone comprise some 40% of the human genome. Now, while capable of wreaking havoc within a host genome, these elements have been shaping their host genomes in profound ways and not without trivial effect.

    The recombination and disruptive events promoted by such elements can: delete or duplicate gene sequences; delete, duplicate or create exons and introns; create poly-adenylation signals; create alternative splice sites; move, create, delete, duplicate or disrupt promoter and enhancer sequences; move transcriptional signals into non-coding regions; they can also trigger large scale recombinations between chromosomes. Some elements, like the Alu element, also have CpG sites. This means that their insertions can create CpG islands, and thus have important regulatory consequences at both the epigenetic and gene expression levels. The small transcripts produced off the human Alu element are even used to regulate gene expression at the post-transcriptional and translational level. There's also a whole crazy world of small RNA's to contend with, that seem to have major roles to play in development, but that's a story for another day.

    Waiting millions of years for a new regulatory sequence to appear is simply not the way it works. Waiting for multiple and consecutive sequence mutations to occur and be selected for to produce a new protein is not the way it works. Evolution is too often seen as a very slow, gradual accumulation of mutation over time. The fossil record indicates that evolution proceeds rapidly and often in great leaps separated by periods of quiescence.

    Calculations such as that presented at the very start of this thread are discussing one particular type of mutational event, namely point mutations. The mistake comes when people extend this reasoning to cover all of the myriad tools that evolution has at its disposal, using the calculations in a way that they were never intended to be used. The calculations are meaningless when used in this manner.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    No skinwalker. I used mution rates for land and sea mammals, and population sizes for cetecea and shoreline dwelling mammals.
    You assumed independence of event and adoption for the mutations, and your estimates of the breeding population size for shoreline dwelling mammals were ridiculously low.
    Ten thousand was the estimated based on research, but I multiplied by 10 and used 100,000 to be conservative. Suggest a better number. Eocene correct Skinwalker.

    Ten thousand is a population bottleneck, not a safe assumption for the breeding population a a successful lineage of mammals.
    Quote Originally Posted by cypress
    Do you know my estimates are wrong?
    I know they have no visible support in reason or evidence.
    I'm willing to admit an error if you have a more accurate number. I used 100,000 in the formula.
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    Quote Originally Posted by Zwirko
    Over the last decade it has been becoming apparent that evolution taking place at a level above that of the gene sequence (if I can phrase it that way) is also very important. Specifically, evolution at the chromosomal level may be of major importance. Two main strands of thought include chromosomal recombination and mobile DNA elements.

    Mobile elements such as DNA transposons, retrotransposons, retroelements, endogenous retroviruses and even retroviruses have shaped our genomes in profound ways - just think, retroelements alone comprise some 40% of the human genome.
    I don't doubt the role of mobile elements in altering DNA sequence, and I have not yet seen direct evidence of new gene sequences or regulatory controls, by the processes you mention. Do you know of any examples? Where can I find information on supporting the 40% retroelement number?

    Now, while capable of wreaking havoc within a host genome, these elements have been shaping their host genomes in profound ways and not without trivial effect.

    The recombination and disruptive events promoted by such elements can: delete or duplicate gene sequences; delete, duplicate or create exons and introns; create poly-adenylation signals; create alternative splice sites; move, create, delete, duplicate or disrupt promoter and enhancer sequences; move transcriptional signals into non-coding regions; they can also trigger large scale recombinations between chromosomes. Some elements, like the Alu element, also have CpG sites. This means that their insertions can create CpG islands, and thus have important regulatory consequences at both the epigenetic and gene expression levels.
    What are some examples of important regulatory consequences? Are any constructive or are they generally destructive or neutral?


    The small transcripts produced off the human Alu element are even used to regulate gene expression at the post-transcriptional and translational level. There's also a whole crazy world of small RNA's to contend with, that seem to have major roles to play in development, but that's a story for another day.
    I've read about this as well. this raises another interesting point in that yet another traditional evolutionary prediction is failing and that is this notion of Junk DNA. With the possible exception of retro elements, it seems the non-gene coding portion of DNA has important function after all.

    Waiting millions of years for a new regulatory sequence to appear is simply not the way it works. Waiting for multiple and consecutive sequence mutations to occur and be selected for to produce a new protein is not the way it works. Evolution is too often seen as a very slow, gradual accumulation of mutation over time. The fossil record indicates that evolution proceeds rapidly and often in great leaps separated by periods of quiescence.
    Agreed, it is time to throw out that outdated model in my opinion. It seems to be coming clearer that macro changes are not a cumulation of gradual stepwise changes driven by random mutation and selection.

    Calculations such as that presented at the very start of this thread are discussing one particular type of mutational event, namely point mutations. The mistake comes when people extend this reasoning to cover all of the myriad tools that evolution has at its disposal, using the calculations in a way that they were never intended to be used. The calculations are meaningless when used in this manner.
    Yes, thanks for the explanation. Though not just point mutations. It includes the full suite of observed mutational processes except the retroinsertions. The popular theory still holds to these processes as the primary driver for change so most will object to your statement that they are meaningless. The processes you describe have not been delineated so frequencies and results are largely unknown. therefore they can't be figured into population genetics just yet. As far as I know, it has not been shown that these processes produce the genes and controls needed either but it logically appears more fruitful.
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    Quote Originally Posted by cypress
    Ten thousand was the estimated based on research, but I multiplied by 10 and used 100,000 to be conservative. Suggest a better number.
    How about ten million? A number that matches observed physical reality - including the successful evolution of whales - would be a reasonable beginning. Keep ramping up until you get there. There were millions of breeding beavers in North America in 1500. There were more than 100,000 breeding fur seals on South Georgia island alone, once upon a time. There were at least 100,000 breeding blue whales before steam power - a single, uncommon, very large and long-lived species.

    btw: Your calculations are of little use regardless of your "breeding population" estimate, because they begin with too many unlikely assumptions (of independence, etc). "A proof teaches us where to concentrate our doubts".
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    Not that it has much to do with the progression which this thread has taken, but I thought (as per the subject) that some people would be interested in this article about whale evolution which I read recently. Enjoy.


    http://news.nationalgeographic.com/n...er-fossil.html
    The fossil whale, thought to be between 25 and 28 million years old, hints that mud sucking might have been a precursor to the filter feeding used by today's baleen whales.

    Many modern whale species use hair-like structures called baleen to filter tiny prey such as krill from seawater. Baleen species include the humpback, the minke, and the largest animal ever to have lived on Earth, the blue whale.

    The newfound fossil whale, which measures just nine feet (three meters) long, shares the same distinct jaw and skull structures as today's baleens.

    But the tiny whale also had teeth, said study author Erich Fitzgerald, a paleontologist at Museum Victoria in Melbourne, Australia.

    The odd combination suggests that the dwarf whale might have been adept at feeding on larger, chewier prey from the seafloor, using its tongue and facial muscles to "vacuum" along the sandy bottom, the study authors say.
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    Quote Originally Posted by cypress
    Here is the material I used to estimate population size and mutation rates.

    http://www.sciencemag.org/cgi/conten...284/5423/2055a

    http://mbe.oxfordjournals.org/cgi/content/full/25/1/120

    http://www3.interscience.wiley.com/j...TRY=1&SRETRY=0


    To bring us back to the subject, granting that whales evolved from land mammals to sea creatures in roughly 9 million years (based on fossil evidence), using Population genetics, estimated mutation rates and population sizes, along with recent information from molecular and experimental cell biology regarding the kinds of molecular alterations needed to produce novel protein structures and binding sites, geene expression controls, developmental controls and cell function controls, I estimate it would take far far more than 9 million years to evolve whales by natural selection acting on random mutation. I argue that some other mechanism is in play.

    So far, nobody has offered better calculations or shown how my estimates are incorrect. This is just one of many examples of how predictions from traditional evolutionary theory are failing to live up to the claims.
    What is this insistence on "novel protein structures"? Who says you need novel protein structures or binding sites? Why can't you develop a trait first, and then afterward form the needed DNA structures? The first manifestation of a trait doesn't need to be streamlined and perfect.

    People were buying Model T Fords back when they could only do about 20 mph, and broke down constantly. Why? Because they filled a necessary function. They didn't need to fill it well. Something was better than nothing.

    Quote Originally Posted by cypress

    Waiting millions of years for a new regulatory sequence to appear is simply not the way it works. Waiting for multiple and consecutive sequence mutations to occur and be selected for to produce a new protein is not the way it works. Evolution is too often seen as a very slow, gradual accumulation of mutation over time. The fossil record indicates that evolution proceeds rapidly and often in great leaps separated by periods of quiescence.
    Agreed, it is time to throw out that outdated model in my opinion. It seems to be coming clearer that macro changes are not a cumulation of gradual stepwise changes driven by random mutation and selection.
    So this is what you're really getting at. You're not into ID, you're just saying that sometimes things happen fast?

    It brings to mind something like the "Dumbo" situation. (Not referring to anyone's intelligence. I mean the Disney movie.) A single mutant is born with a trait that seems like a genuine abberation at first, but ultimately proves useful, so every female in the herd wants to mate with this guy in the hope that their kids will have big wing ears too.

    Is it possible to articulate this sort of situation into standard evolution theory?
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Ten thousand was the estimated based on research, but I multiplied by 10 and used 100,000 to be conservative. Suggest a better number.
    How about ten million? A number that matches observed physical reality - including the successful evolution of whales - would be a reasonable beginning. Keep ramping up until you get there. There were millions of breeding beavers in North America in 1500. There were more than 100,000 breeding fur seals on South Georgia island alone, once upon a time. There were at least 100,000 breeding blue whales before steam power - a single, uncommon, very large and long-lived species.

    btw: Your calculations are of little use regardless of your "breeding population" estimate, because they begin with too many unlikely assumptions (of independence, etc). "A proof teaches us where to concentrate our doubts".
    Perhaps you should study up of population genetics modeling and then answer the question. We are looking for the number in a contiguous group of interbreeding organisms in a single generation. the number is not the entire population or even the population of a single species. Sorry Iceaura.
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    Quote Originally Posted by kojax
    Quote Originally Posted by cypress
    To bring us back to the subject, granting that whales evolved from land mammals to sea creatures in roughly 9 million years (based on fossil evidence), using Population genetics, estimated mutation rates and population sizes, along with recent information from molecular and experimental cell biology regarding the kinds of molecular alterations needed to produce novel protein structures and binding sites, geene expression controls, developmental controls and cell function controls, I estimate it would take far far more than 9 million years to evolve whales by natural selection acting on random mutation. I argue that some other mechanism is in play.

    So far, nobody has offered better calculations or shown how my estimates are incorrect. This is just one of many examples of how predictions from traditional evolutionary theory are failing to live up to the claims.
    What is this insistence on "novel protein structures"? Who says you need novel protein structures or binding sites? Why can't you develop a trait first, and then afterward form the needed DNA structures? The first manifestation of a trait doesn't need to be streamlined and perfect.
    It does however need to be functional in order to have selectable advantage which is the prediction based on the theory. Studies show that different function requires different structures and binding sites.


    Quote Originally Posted by cypress

    Agreed, it is time to throw out that outdated model in my opinion. It seems to be coming clearer that macro changes are not a cumulation of gradual stepwise changes driven by random mutation and selection.
    So this is what you're really getting at. You're not into ID, you're just saying that sometimes things happen fast?
    That these changes have to have happened much faster than predictions based on selection of random mutations. Right, that some other process(es) had to be involved.
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    Why would random mutations have to be selected? Evolution is not necessarily about the fixation of advantageous mutations by positive selection (al la Darwin). Deleterious mutations can become fixed within a population as well, particularly at low population levels. What if natural selection wasn't that important? How important are non-adaptive mechanisms? Some might even argue that the genome sequence itself is only one part of the story. No offence intended, but you're really arguing against evolutionary theory as it stood 40 years ago or more.
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    Quote Originally Posted by cypress
    It does however need to be functional in order to have selectable advantage which is the prediction based on the theory. Studies show that different function requires different structures and binding sites.
    But there are differing degrees of functionality... Proteins with parts missing can still function to a varying amount but as long as it is near enough the right shape and size it can half do it's job. evolution can then perfect that making it better and better...
    Come see some of my art work at http://nevyn-pendragon.deviantart.com/
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    Quote Originally Posted by cypress
    Quote Originally Posted by kojax
    Quote Originally Posted by cypress
    To bring us back to the subject, granting that whales evolved from land mammals to sea creatures in roughly 9 million years (based on fossil evidence), using Population genetics, estimated mutation rates and population sizes, along with recent information from molecular and experimental cell biology regarding the kinds of molecular alterations needed to produce novel protein structures and binding sites, geene expression controls, developmental controls and cell function controls, I estimate it would take far far more than 9 million years to evolve whales by natural selection acting on random mutation. I argue that some other mechanism is in play.

    So far, nobody has offered better calculations or shown how my estimates are incorrect. This is just one of many examples of how predictions from traditional evolutionary theory are failing to live up to the claims.
    What is this insistence on "novel protein structures"? Who says you need novel protein structures or binding sites? Why can't you develop a trait first, and then afterward form the needed DNA structures? The first manifestation of a trait doesn't need to be streamlined and perfect.
    It does however need to be functional in order to have selectable advantage which is the prediction based on the theory. Studies show that different function requires different structures and binding sites.
    It needs to result in a functional organism, but the DNA strand itself doesn't need to be streamlined and beautiful. When the trait first emerges, it might be highly unstable, so maybe only half the offspring born with it are so badly mutated they can't even function on a basic level, but the other half will be highly successful, and finding easy access to mates.

    Think of autism, which sometimes emerges at a low enough level that a person is able to function in society, but keeps the massive super-computer-for-a-brain part. Bill Gates has Aspergers syndrome, which is low level autism, but the data-head side of his brain enabled him to do some fairly impressive things.

    What I'm saying is: over time, after an unstable mutant trait has managed to assert itself, and a community of creatures emerge that possess the trait, then it can start stabilizing its DNA by gradually selecting out all the screwed up versions. You seem to be assuming that traits have to be streamlined, and perfectly packaged, in order to ever present themselves in the first place.
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    Quote Originally Posted by Nevyn
    Quote Originally Posted by cypress
    It does however need to be functional in order to have selectable advantage which is the prediction based on the theory. Studies show that different function requires different structures and binding sites.
    But there are differing degrees of functionality... Proteins with parts missing can still function to a varying amount but as long as it is near enough the right shape and size it can half do it's job. evolution can then perfect that making it better and better...
    Im not sure its true that proteins with (I'll assume significant) parts missing can still function. Recent studies indicate this is not correct. But even if it were the primary challenge is getting it near enough the right shape and size with the right binding sites. Here the studies indicate that fewer than 1 in 10^78 possible combinations derive a protein with a functional shape and binding sites. this relative scarcity makes it difficult to maintain a model of stepwise gene evolution, by mutation and selection.

    I think Zwirko may be on the right track by postulating mechanisms that might be more likely to produce these kinds of systems . Currently though they have not been observed to any degree and the principle of uniforitarianism demands that we only cite processes that are known and in operation today. As it stands today,leaving out genetic engineering, there is no known process. Lot's of speculation though.
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    Quote Originally Posted by kojax

    It needs to result in a functional organism, but the DNA strand itself doesn't need to be streamlined and beautiful. When the trait first emerges, it might be highly unstable, so maybe only half the offspring born with it are so badly mutated they can't even function on a basic level, but the other half will be highly successful, and finding easy access to mates.

    Think of autism, which sometimes emerges at a low enough level that a person is able to function in society, but keeps the massive super-computer-for-a-brain part. Bill Gates has Aspergers syndrome, which is low level autism, but the data-head side of his brain enabled him to do some fairly impressive things.

    What I'm saying is: over time, after an unstable mutant trait has managed to assert itself, and a community of creatures emerge that possess the trait, then it can start stabilizing its DNA by gradually selecting out all the screwed up versions. You seem to be assuming that traits have to be streamlined, and perfectly packaged, in order to ever present themselves in the first place.
    Not exactly what I'm saying. The story-line you offer sounds very plausible and elegant, however when you put it to the test by looking at known rates that this model progresses and the known ratios of successes to failures along with the working gene pool size you get a process that would proceed too slowly by many orders of magnitudes. An objective look at this should convince the unbiased person to look for other avenues of explanation. Kwirko and myself are taking that step to looking elsewhere. The ID advocates are looking elsewhere, too.
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    I wouldn't describe myself as sailing in the same boat as yourself, cypress. I don't think, for example, that there are unknown mechanisms at work as such. All the mechanisms of generating new proteins that I have previously listed are becoming increasingly well documented with many examples. I think that what we do know needs to be shaken-up and re-evaluated; a re-interpretation of the existing evidence, as opposed to requiring the need for radically new observations of currently unknown processes. I also think that the knowledge gained from recent studies in molecular evolution and from theoretical biology have yet to fully filter down to the popular science level and even to much of the academic world. The focus on the slow accumulation of mutation and natural selection will likely shift so that other evolutionary forces such as mutation, recombination and drift will come to be seen as equally important and that some new fundamentals in the relationship between genome architecture and phenotype will be revealed. New layers of complexity as opposed to new mechanisms. New understandings of the complex goings on at the interface between genome and phenotype will come to light.

    For example you maintain that the evolution of new proteins and their control networks evolve slowly and at low probability, such that there is not enough time to account for the diversity that we see. You see regulatory sites arising de novo as an important step. You see regulatory networks as complex entities that require to be constructed step by step, each one with presumable selectable advantage. You see these changes as either being preserved or eliminated by natural selection and that low population sizes effectively means that the generation of such diversity can't be accounted for and thus requires new mechanisms. This, I think, is the opposite to how I see things.

    I see new proteins evolving primarily from pre-existing proteins by the recombination of existing sequences and by the addition and removal of sequences. Processes I favour include those such as gene duplication and subsequent subfunctionalisation and neofunctionalisation, exon-shuffling, alternative splicing, large scale mutations etc - all things that can arise either as a direct consequence of mobile element proliferation or by the very nature of large complex genomes. I don't discount the importance of many small mutations over long periods of time either. I see deleterious mutations as important. I see random drift as important. I see complex regulatory networks as being built in an ad hoc fashion on top of pre-existing controls, and only later does the system become dependent upon them. I see known mutation rates as being more than adequate to generate the diversity that we see today. I see small population sizes as being a necessary requirement for the generation of diversity and that large complex genomes just can't help themselves from evolving diversity rapidly and that they probably spend considerable effort trying to minimise the potential effects of it - i.e. prevent their mutation in to random noise.

    Where we do seem to agree is in the idea that many biologists seem to have become complacent over the years when it comes to evolutionary biology and that the standard of evidence used is often not as rigorous as it could (should?) be. And, for the record, I'd like to make clear that I think that ID has absolutely nothing constructive to offer biology.
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    Quote Originally Posted by cypress
    Perhaps you should study up of population genetics modeling and then answer the question. We are looking for the number in a contiguous group of interbreeding organisms in a single generation.
    No, we aren't. We are talking about every member of the worldwide population that bequeathed at least one copy of at least some of its genetic heritage unto one or more progeny at some time during its life. That's the genetic material available for Darwinian selection in the next generation, in that species.
    Quote Originally Posted by cypress
    It does however need to be functional in order to have selectable advantage which is the prediction based on the theory.
    It doesn't, and that is not "the prediction based on the theory".
    Quote Originally Posted by cypress
    Studies show that different function requires different structures and binding sites.
    Just different structure, will often do. Or the same structure, better established. Or some new context of functioning - as in symbiosis, etc.
    Quote Originally Posted by cypress
    That these changes have to have happened much faster than predictions based on selection of random mutations.
    So make predictions based on your idea of selection of "non-random" mutations - nobody will care. You are arguing against your own personal version of Darwinian theory, based on your own personal version of "random" and your own application of mathematical probability etc.
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    Quote Originally Posted by cypress
    Quote Originally Posted by kojax

    It needs to result in a functional organism, but the DNA strand itself doesn't need to be streamlined and beautiful. When the trait first emerges, it might be highly unstable, so maybe only half the offspring born with it are so badly mutated they can't even function on a basic level, but the other half will be highly successful, and finding easy access to mates.

    Think of autism, which sometimes emerges at a low enough level that a person is able to function in society, but keeps the massive super-computer-for-a-brain part. Bill Gates has Aspergers syndrome, which is low level autism, but the data-head side of his brain enabled him to do some fairly impressive things.

    What I'm saying is: over time, after an unstable mutant trait has managed to assert itself, and a community of creatures emerge that possess the trait, then it can start stabilizing its DNA by gradually selecting out all the screwed up versions. You seem to be assuming that traits have to be streamlined, and perfectly packaged, in order to ever present themselves in the first place.
    Not exactly what I'm saying. The story-line you offer sounds very plausible and elegant, however when you put it to the test by looking at known rates that this model progresses and the known ratios of successes to failures along with the working gene pool size you get a process that would proceed too slowly by many orders of magnitudes. An objective look at this should convince the unbiased person to look for other avenues of explanation. Kwirko and myself are taking that step to looking elsewhere. The ID advocates are looking elsewhere, too.
    I don't know what "known rates" you are talking about. This whole thread started on the basis of your perception that whale evolution had progressed more rapidly than you think it should. That's the "known rate" I'm thinking of.

    To me, the simplest explanation is that genetic stability is always the last thing to evolve. The first thing is function. Nature doesn't care if there's a rubber band holding it together with some duct tape and a few popsicle sticks. If the new flipper is functionally more effective than its predecessor, it will be selected for over a less functional flipper that has a shiny smooth finish, polished, and professionally crafted.
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    Quote Originally Posted by kojax
    Quote Originally Posted by cypress
    Quote Originally Posted by kojax

    It needs to result in a functional organism, but the DNA strand itself doesn't need to be streamlined and beautiful. When the trait first emerges, it might be highly unstable, so maybe only half the offspring born with it are so badly mutated they can't even function on a basic level, but the other half will be highly successful, and finding easy access to mates.

    Think of autism, which sometimes emerges at a low enough level that a person is able to function in society, but keeps the massive super-computer-for-a-brain part. Bill Gates has Aspergers syndrome, which is low level autism, but the data-head side of his brain enabled him to do some fairly impressive things.

    What I'm saying is: over time, after an unstable mutant trait has managed to assert itself, and a community of creatures emerge that possess the trait, then it can start stabilizing its DNA by gradually selecting out all the screwed up versions. You seem to be assuming that traits have to be streamlined, and perfectly packaged, in order to ever present themselves in the first place.
    Not exactly what I'm saying. The story-line you offer sounds very plausible and elegant, however when you put it to the test by looking at known rates that this model progresses and the known ratios of successes to failures along with the working gene pool size you get a process that would proceed too slowly by many orders of magnitudes. An objective look at this should convince the unbiased person to look for other avenues of explanation. Kwirko and myself are taking that step to looking elsewhere. The ID advocates are looking elsewhere, too.
    I don't know what "known rates" you are talking about. This whole thread started on the basis of your perception that whale evolution had progressed more rapidly than you think it should. That's the "known rate" I'm thinking of.
    Mutation rates, birth, death and mean generation times.

    It seems to have progressed more rapidly than the current evolutionary model, observed natural processes, and the resulting predictions would tell us it should. The unavoidable conclusion is that it must have proceeded by processes other than those included in the current model. Zwirko proposed several other processes that may show more promise but thus far that have not been confirmed by experimental biology and repeated tests that the scientific process requires. Much of the evidence is indirect, having been based on unobserved past events. Principles of Uniformatarianism requires process operating today. Currently the only confirmed process operating today capable of proceeding this rapidly involves genetic engineering. Therefore, advocates of natural processes have work ahead of them. I think Zwirko seems to be heading in a reasonable direction.

    To me, the simplest explanation is that genetic stability is always the last thing to evolve. The first thing is function. Nature doesn't care if there's a rubber band holding it together with some duct tape and a few popsicle sticks. If the new flipper is functionally more effective than its predecessor, it will be selected for over a less functional flipper that has a shiny smooth finish, polished, and professionally crafted.
    Sure, this is the narrative, and it is elegant. HOwever the narrative lacks an effective, timely process. Natural selection acting on random mutation is very effective at sifting out failures and enabling adaptation of existing function. Thus far it provides no evidence that as a process it can generate anything novel in any reasonable timeframe other than the very rare accident based on probability.
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  90. #89  
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    Quote Originally Posted by cypress
    Mutation rates, birth, death and mean generation times.

    It seems to have progressed more rapidly than the current evolutionary model, observed natural processes, and the resulting predictions would tell us it should.
    Can you quantify the difference between the observed and expected values please?
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    Quote Originally Posted by cypress

    To me, the simplest explanation is that genetic stability is always the last thing to evolve. The first thing is function. Nature doesn't care if there's a rubber band holding it together with some duct tape and a few popsicle sticks. If the new flipper is functionally more effective than its predecessor, it will be selected for over a less functional flipper that has a shiny smooth finish, polished, and professionally crafted.
    Sure, this is the narrative, and it is elegant. HOwever the narrative lacks an effective, timely process. Natural selection acting on random mutation is very effective at sifting out failures and enabling adaptation of existing function. Thus far it provides no evidence that as a process it can generate anything novel in any reasonable timeframe other than the very rare accident based on probability.
    But in the long run, those very rare accidents happen with a predictable frequency. They just can't be factored in to experiments in real time, unless you want to expose the creatures to radiation in order to increase their likelihood of having birth defects.

    I think what bothers you is that the wild cards are not supported by experimentation, which is always the ID peoples' complaint. They want a smoking gun.
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    Quote Originally Posted by kojax
    Quote Originally Posted by cypress

    To me, the simplest explanation is that genetic stability is always the last thing to evolve. The first thing is function. Nature doesn't care if there's a rubber band holding it together with some duct tape and a few popsicle sticks. If the new flipper is functionally more effective than its predecessor, it will be selected for over a less functional flipper that has a shiny smooth finish, polished, and professionally crafted.
    Sure, this is the narrative, and it is elegant. HOwever the narrative lacks an effective, timely process. Natural selection acting on random mutation is very effective at sifting out failures and enabling adaptation of existing function. Thus far it provides no evidence that as a process it can generate anything novel in any reasonable timeframe other than the very rare accident based on probability.
    But in the long run, those very rare accidents happen with a predictable frequency. They just can't be factored in to experiments in real time, unless you want to expose the creatures to radiation in order to increase their likelihood of having birth defects.

    I think what bothers you is that the wild cards are not supported by experimentation, which is always the ID peoples' complaint. They want a smoking gun.
    They happen with predictable frequency but since the predictable frequency is several orders of magnitude longer than the time available, we should conclude that the observed changes did not happen by the presumed mechanism. The idea that probability cannot be factored into this, that wild cards trump uniform experience, is dismissal of scientific principles. It is metaphysics.

    Proponents of the current evolutionary theory claim to be following reasoned scientific principles, but when you drill down to these kinds of issues, in the end, when the proponents lay down their final card, invariably the card is a metaphysical argument. Go figure.

    I think a more sensible response should be to recognize the issue and agree that other processes not yet understood are involved.

    To say we don't know exactly how, but we know it happened a particular way, or that we know it did not happen some other particular way is also not scientific.
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    Quote Originally Posted by cypress
    Quote Originally Posted by kojax

    But in the long run, those very rare accidents happen with a predictable frequency. They just can't be factored in to experiments in real time, unless you want to expose the creatures to radiation in order to increase their likelihood of having birth defects.

    I think what bothers you is that the wild cards are not supported by experimentation, which is always the ID peoples' complaint. They want a smoking gun.
    They happen with predictable frequency but since the predictable frequency is several orders of magnitude longer than the time available, we should conclude that the observed changes did not happen by the presumed mechanism. The idea that probability cannot be factored into this, that wild cards trump uniform experience, is dismissal of scientific principles. It is metaphysics.

    Proponents of the current evolutionary theory claim to be following reasoned scientific principles, but when you drill down to these kinds of issues, in the end, when the proponents lay down their final card, invariably the card is a metaphysical argument. Go figure.

    I think a more sensible response should be to recognize the issue and agree that other processes not yet understood are involved.

    To say we don't know exactly how, but we know it happened a particular way, or that we know it did not happen some other particular way is also not scientific.
    You have yet to provide any reasonable argument against the current time line as accepted by science until you do this topic cant proceed.
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    Quote Originally Posted by Paleoichneum
    You have yet to provide any reasonable argument against the current time line as accepted by science until you do this topic cant proceed.
    You must be confused. I do not claim the accepted timeline is in error, I claim that if, as presumed, the whale evoled within this timeline, then some process other than the observed evolutionary processes was involved because the observed processes would proceed too slowly.

    Since I do not question the timeline, there is no need to make an argumet against it.
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    You have yet to adequately demonstrate that existing processes of evolution (as they are understood) are not sufficient for evolution to occur. Perhaps there are as yet unknown processes of evolution. So far, however, the current understood processes are adequate in their explanatory power.

    The only people who seem to be making spurious claims otherwise appear to be creationists who use pseudoscience to make their case(s).
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    Of course what you are asking of me is to prove a negative, which you should know, requires a nearly impossible exhaustive search. You would never accept such an argument from me. Actually, skinwalker evolutionary biologists have thus far failed to show that observed evolutionary processes are capable of generating the alterations we now know are required to generate new cell functions. Scientific study of course is expected to not only show that the premises are correct it is expected to repeat these results with observable processes in the lab repeatedly.

    It is a metaphysical belief you hold that current processes are adequate. It is metaphysical because you can't point to a single scientific demonstration that observed processes do generate the required subcomponents, for example a new protein binding site, or a new gene expression control.

    Here is an article by a materialist who agrees and has a book coming out next week that covers this topic quite thoroughly it is called "What Darwin Got Wrong".

    Here is what the publisher's comments say:

    "This is not a book about God, or about intelligent design. Rather, here is a remarkable book, one that dares to challenge natural selection—not in the name of religion but in the name of good science. Most scientists are so terrified of religious attacks on the theory of evolution that it is never examined critically. "

    The author if this paper describes the popular view of evolution as "untenable in light of recent observations from genomic sequencing and population-genetic theory" He goes onto describe the goal of his paper thus:

    "The goal here is to dispel a number of myths regarding the evolution of organismal complexity. Given that life originated from inorganic matter, it is clear that there has been an increase in phenotypic complexity over the past 3.5 billion years, although long-term stasis has been the predominant pattern in most lineages. What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms."
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    Quote Originally Posted by cypress
    Of course what you are asking of me is to prove a negative, which you should know, requires a nearly impossible exhaustive search. You would never accept such an argument from me.
    I'm asking only that you support your claim that evolutionary processes that are currently known are inadequate to explain speciation.

    Actually, skinwalker evolutionary biologists have thus far failed to show that observed evolutionary processes are capable of generating the alterations we now know are required to generate new cell functions.
    How many examples of new cell functions that are demonstrably evolved would suffice for you to retract this bold statement?

    Scientific study of course is expected to not only show that the premises are correct it is expected to repeat these results with observable processes in the lab repeatedly.
    Not only are you attempting to obfuscate the issue with a typical creationist approach, believing that since evolutionary processes take millions of years your argument is won simply because no scientist has a hope of making the observation; you also tripping over your own argument. Evolutionary premises are shown to be observable in laboratory experiments such that they are both repeatable and predictable. Again, I ask how many of these sorts of experiments would suffice for you to admit your own attempt to obfuscate and mischaracterize?

    The answer to both questions above should, of course, be one each.

    It is a metaphysical belief you hold that current processes are adequate. It is metaphysical because you can't point to a single scientific demonstration that observed processes do generate the required subcomponents, for example a new protein binding site, or a new gene expression control.
    If I point to just a single of these experiments, which demonstrate what you are claiming do not exist, will you finally admit you are a creationist or at least depart this forum?

    Here is an article by a materialist who agrees and has a book coming out next week that covers this topic quite thoroughly it is called "What Darwin Got Wrong".
    The Fodor and Piattelli-Palmarini book is already out as of Feb 16. I'm not sure why you think it isn't yet. And it received a bit criticism leveled at the sensationalist title, the poor science it employed at times, and an oft mischaracterization of evolution that Fodor and Piattelli-Palmarini used in their text.
    http://network.nature.com/people/bob...tion-101-again
    http://www.amazon.com/review/R1W37QW...cm_cr_rdp_perm

    But very telling were the letters that follow the article you link to above from some very preeminent scientists and authors of their own right who so effectively demolished Fodor's first attempt one can only assume he's a gluten for punishment in writing a new book. At least he had the foresight to take on a co-author to share the abuse he will undoubtedly, and deservedly receive.

    Here are those letters:
    Simon Blackburn, Daniel Dennett, Jerry Coyne, et al
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    Quote Originally Posted by SkinWalker

    I'm asking only that you support your claim that evolutionary processes that are currently known are inadequate to explain speciation.
    Several examples have previously been offered. There are a number of very basic sub-steps required to build new functional cell processes. These represent the smallest basic step that any process that ultimately generates new biological diversity would require. Currently observed evolutionary processes have not been observed to accomplish these sub steps except for the very rare exception allowed for by probability and fall well within the bounds of what would be expected.

    How many examples of new cell functions that are demonstrably evolved would suffice for you to retract this bold statement?
    Advocates of the observed processes employ evidence from similarity to supposedly demonstrate that a particular process accomplished the changes the similarities indicate. But pointing to similarities does not tell us what processes actually accomplished the changes. You will undoubtedly employ this same technique to "demonstrate" evolution. I don't dispute that x changed into y and therefore you will only succeed at demonstrating what I have already accepted, but you will fail to show what process accomplished the change. This approach is tiresome and unscientific. It begins with a presumption that observed processes are responsible and then uses similarities to build a metaphysical argument to support the prior commitment.

    Not only are you attempting to obfuscate the issue with a typical creationist approach, believing that since evolutionary processes take millions of years your argument is won simply because no scientist has a hope of making the observation; you also tripping over your own argument.
    Nonsense. These days we have observed over 30,000 generations 10^18 individual bacteria organisms attempt to navigate just one of these basic steps under extreme selection pressure. Contrast that to the estimate of all humans and our primate like ancestors <10^14 who collectively have accomplished tens of thousands of these basic steps and it should be easy to see the issue.

    Evolutionary premises are shown to be observable in laboratory experiments such that they are both repeatable and predictable. Again, I ask how many of these sorts of experiments would suffice for you to admit your own attempt to obfuscate and mischaracterize?
    You are moving the goal post. I fully admit these observable processes effect changes in gene sequences but they have not generated the kinds of changes that would lead to novel cell function, except of course for the occasional lucky hit based on probability. We now know what it takes to generate novel function and the known evolutionary processes don't make the grade with sufficient regularity to account for observed diversity.

    The answer to both questions above should, of course, be one each.
    And of course, if you offer one each, they will undoubtedly be examples of an answer to a different question or the occasional one that falls within the probability bounds. With 10^18 organisms we should have observed tens of thousands of them by now. This thread is about explaining how observed processes would regularly and repeatably generate the sub steps. In the case of Whale evolution employing many orders of magnitude fewer organisms we have many thousands of these steps over the course of 5-10 million years. Something is not adding up. I suspect there must be other far more capable processes involved.

    In the beginning of this thread I offered research that indicates a single one of these thousands should be expected every 10-40 million years based on observed processes indicating that biological change occurred many orders of magnitudes faster than would be expected by observed processes. So even I am admitting these should happen rarely, so why should we be surprised if you offer one of the rare examples? I even know of a few. The challenge facing you is to show that observed processes are capable of generating these steps consistently and repeatedly with sufficient frequency to evolve a land animal into a whale in 5-10 million as the geologic record seems to indicate.


    But very telling were the letters that follow the article you link to above from some very preeminent scientists and authors of their own right who so effectively demolished Fodor's first attempt one can only assume he's a gluten for punishment in writing a new book. At least he had the foresight to take on a co-author to share the abuse he will undoubtedly, and deservedly receive.

    Here are those letters:
    Simon Blackburn, Daniel Dennett, Jerry Coyne, et al
    Why should we expect any different from these critics? They are completely wedded to their prior commitments and stand ready to defend it. I don't find their counter arguments particularly strong. If I had, I would have used a different example. I notice you said nothing about the other article.
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    Quote Originally Posted by cypress
    And of course, if you offer one each, they will undoubtedly be examples of an answer to a different question or the occasional one that falls within the probability bounds. With 10^18 organisms we should have observed tens of thousands of them by now. This thread is about explaining how observed processes would regularly and repeatably generate the sub steps. In the case of Whale evolution employing many orders of magnitude fewer organisms we have many thousands of these steps over the course of 5-10 million years. Something is not adding up.
    My guess is that you aren't counting "substeps" correctly, and you are not estimating probabilities correctly, and you are not reasoning solidly from the research you reference.

    i predict that if you count better, estimate probabilities better, and reason correctly from the available research, things will add up.

    In science, when physical evidence conflicts with one's theoretical calculations the theoretical calculations are what is doubted first. We have quite a bit of evidence that whales evolved according to standard Darwinian theory. We have no evidence of any other influence. If your theory forbids the one, and demands the other, it's time to take a closer look at that theory, with the presumption that some changes are in order.

    I know, for one, that you are multiplying probabilities without attending to the independence of the events described.
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