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Thread: "No Predictive Theory in Biology or History" Carl

  1. #1 "No Predictive Theory in Biology or History" Carl 
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    PREDICTABILITY

    There is as yet no predictive theory of biology, just as there is not yet a predictive theory of history. These subjects are too complicated for us.
    -Carl Sagan, Cosmos, Futura, 1983, p.57.

    No suspicion, no theory, no expert,
    no Kremlinologist had the least idea
    that that vast superstructure was going
    to collapse. The best of academics were
    as ignorant as you and I. It would seem
    we are routinely unable to predict what
    will happen; our best seers are regularly
    humbled. What could The time for the
    destruction of the world and its people
    hath arrived1 possibly mean? Surely we
    are beginning to get some idea in a world
    which largely did not exist when these words
    were spoken with a tempest that keeps blowing
    and continues sweeping the face of the earth.

    Ron Price
    11 January 1998

    1 Baha’u’llah, The Promised Day Is Come, 1941, p.1.


    married for 37 years; teacher for 30; living in Australia for 33 years; Baha'i for 45 years. Writer of poetry for 25 years.
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    point is?


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  4. #3 The Point Is, Silylene 
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    I find it interesting as I listen to endless analysis of the current affairs in the world that analysts try to 'predict' what will happen next. It's natural really. I'm not critical of that. But history, like biology, possesses no predictive theory, it's all opinion. Even the so-called experts on 20th century Russian thought and life, to choose but one example, had no idea that the fall of the Berlin Wall would take place. Just an observation, man, just an observation. Poems are built on observations, among other things. If a point is found by readers, fine; in one is not found, fine too. -Over and out.-Ron Price, Tasmania.
    married for 37 years; teacher for 30; living in Australia for 33 years; Baha'i for 45 years. Writer of poetry for 25 years.
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    Biology has good models of how genes work, how neurons work, and how humans and other organisms work. The first is genetics, the second neurophysiology and the last, evolution. There are many, many other examples of this. Because no one knows everything about the science of biology, does not allow one to conclude that there are no good models in the field. There are in fact, many hundreds of such.

    There are quite a few predictive models and theories in biology. To compare a science to a non-science is simply a mistake in types. That you seem not to be aware of these facts is disturbing.
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    Just to anticipate a potential query from you Ron, here is an example of a biological prediction. This is hot off the presses of the Proceedings of the National Academy of Sciences.

    Jean-François Le Galliard, Patrick S. Fitze, Régis Ferrière, and Jean Clobert
    PNAS December 13, 2005 vol. 102 no. 50
    Sex ratio bias, male aggression, and population collapse in lizards
    The adult sex ratio (ASR) is a key parameter of the demography of human and other animal populations, yet the causes of variation in ASR, how individuals respond to this variation, and how their response feeds back into population dynamics remain poorly understood. A prevalent hypothesis is that ASR is regulated by intrasexual competition, which would cause more mortality or emigration in the sex of increasing frequency. Our experimental manipulation of populations of the common lizard (Lacerta vivipara) shows the opposite effect. Male mortality and emigration are not higher under male-biased ASR. Rather, an excess of adult males begets aggression toward adult females, whose survival and fecundity drop, along with their emigration rate. The ensuing prediction that adult male skew should be amplified and total population size should decline is supported by long-term data. Numerical projections show that this amplifying effect causes a major risk of population extinction. In general, such an "evolutionary trap" toward extinction threatens populations in which there is a substantial mating cost for females, and environmental changes or management practices skew the ASR toward males.

    The emphasis in the abstract is mine.
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    That article about lizards is quite interesting. There are indeed some analogies to human behavior and population statistics. I am particularly thinking of situations in China and India, where the M:F ratio is skewed in some regions as high as 1.25:1.....and in Arabic countires where polygamous marriages skew ratios and leave many men without a wife. In both cases, I have seen predictions in articles of increased violence as the individuals age to sexual maturity, which if taken to extreme can harm the viability of the population. (Already, single young males are being lured into Iraq to commit terrorism and insurrection because of promises of availability of willing women in Iraq, or promises of the 72 houri in heaven.)
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  8. #7 Predictive Theories and Predictive Theories 
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    When I introduced my poem at the beginning of this thread with a comment from Carl Sagan about 'predictive theories' I wanted to indicate a broad truth. Obviously, the sciences have predictive theories and use them all the time as we all do in our daily lives with the quotidian realities we all have to deal with. So, I have no problems with the existence of predictive theories.

    I would like to make one more point thought before I close and go off, as James Joyce says in his Portrait of the Artist As a Young Man, to forge my soul in the smithy of my experience--using predictive theories much of the time--it seems to me that science is basically "the systematic use of one's rational faculty." And 'faith' which we all use, is the (a) making of assumptions and (b) placing around these assumptions in various ways our emotional equipment. So, one can have a science of biology, a science of history, a science of virtually anything. I must run; I have some smithy work to do at yet another meeting here in Australia.-Ron Price, Tasmania.
    married for 37 years; teacher for 30; living in Australia for 33 years; Baha'i for 45 years. Writer of poetry for 25 years.
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    A science of biology exists. That of history does not, nor that of religions or faiths, which would fall within the purvue of sociology, which is not yet, formally, a science.

    What Sagan might have been referring to was within biology a broad kind of theory such as QM and Relativity in Physics, and plate tectonics in geology. However, evolutionary theory pretty much subsumes the same place in biology, altho it's of a different type. But there is no necessary, logical, or scientific reason why the general scientific model in one field necessarily hase to be of the same type found in physics.

    The medical field is one such. It's mostly verbal, not mathematical, yet it's a science, nonetheless. And it just might be that the enormous complexities seen in biology are too vast to be subsumed inside of a single, mathetical theory.

    To more or less quote Feynman, we cannot develop biology from quantum mechanics.
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  10. #9 Nicely Put 
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    I enjoyed reading your post, Steve. thanks. I may come back to this issue later.-Ron 8)
    married for 37 years; teacher for 30; living in Australia for 33 years; Baha'i for 45 years. Writer of poetry for 25 years.
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    I believe Sagan was saying that we must study the past in great detail in order to understand the present. And, while no predictive theory is available, a good understanding of the past and the present can allow us to make some educated guesses of the future. Perhaps enough that we can be alert to potential dangers.

    But the Sagan quote above was mostly in the context of the search for extraterrestrial life.
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    Forum Radioactive Isotope mitchellmckain's Avatar
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    I think steve has the right of it, but to put it in my own words. I think Sagan loves physics and was being pompous. As a physicist, myself, I shied away from this topic for this very reason. Instead I can come in at this late date and reap rewards of other people's embarassment and alleviate my own ignorance in (ego) safety.

    Furthermore, I would like to give additional thanks to steve for satisfying my desire (which I requested in another thread) to see some explanation towards the limits and definition of the science of biology.
    See my physics of spaceflight simulator at http://www.relspace.astahost.com

    I now have a blog too: http://astahost.blogspot.com/
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    Quote Originally Posted by mitchellmckain
    I think steve has the right of it, but to put it in my own words. I think Sagan loves physics and was being pompous.
    I think the correct tense of the verb would be loved, but I've read the passage in its context. There's no indication that Sagan was being "pompous." He really was speaking about extraterrestrial life. In the preceeding paragraphs, he discussed 'floaters, sinkers and hunters' of imagined gaseous planets in alien environments as a way of provoking the reader's imagination and illustrating that "life as we know it" is a self-limiting concept.

    The full paragraph the quote above come from is:
    Biology is more like history than it is like physics. You have to know the past to understand the present. And you have to know it in exquisite detail. There is as yet no predictive theory of biology, just as there is not yet a predictive theory of history. The reasons are the same: both subjects are still too complicated for us. But we can know ourselves better by understanding other cases. The study of a single instance of extraterrestrial life, no matter how humble, will deprovincialize biology. For the first time, the biologists will know what other kinds of life are possible. When we say the search for life elsewhere is important, we are not guaranteeing that it will be easy to find -only that it is very much worth seeking.
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    Do I get an overall sense (in this thread) of skepticism toward the potential eventual practical application of the predictablity of society as found in Asimov's Foundation Trilogy? (Mutants not withstanding.)
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    Well, let's be frank about Sagan. He was a great man, a good scientific thinker and fulfilled to the utmost degree the very laudable goal of promoting scientific education and thinking.

    He's gone now and one does not speak ill of the dead. One should let Poundstone's very fine biography of him, speak for itself.
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  16. #15 More On Carl Sagan 
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    LET THERE BE LIGHT

    In the third verse of the Book of Genesis we can read of God saying: "Let there be light!" Until the slow and complex evolution of the eye, and particularly the cornea, this light could not be the transmitting medium for any living thing to view the world. A convenient beginning point for the beginnings of sight is the Cambrian explosion of some 550 million years ago when the 'monopolizing grip of the algae was broken'
    -Ron Price, Textbook of Modern Biology, Atlas of Anatomy and Cosmos by Carl Sagan.


    We were blind until that great explosion
    when life's new burgeoning produced some
    of the earliest stages of the cornea's half mm
    thick, five-layered pack, humours and that
    marvellous mix of rods and cones after three
    billion years of darkness. Light finally transmitted
    to an inner being, the world seen at last, after
    endless bacteria, algae and granular protoplasm.
    Receptors in molluscs: squids and octopuses,
    arthropods with their mosaic of lenses and, then,
    breathtaking new adaptations in rapid succession,
    exquisite organic molecules in the elaborate machinery
    of the cell, its labyrinthine and subtle architecture and
    nucleic acids slowly refining that mixed-focus lens, cornea.

    Ron Price
    29 May 1998

    8)
    married for 37 years; teacher for 30; living in Australia for 33 years; Baha'i for 45 years. Writer of poetry for 25 years.
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    Evolution makes predictions, just not very specific ones about its own future course. Perhaps this reflects sublty different meanings of "prediction". For example I often say that evolution "predicts" that we are likely to find a fossil or genome with a given configuration within certain bounds at certain points in geological history. It also makes very broad predictions about how living things will react to change.
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    Quote Originally Posted by TheBiologista
    Evolution makes predictions, just not very specific ones about its own future course. Perhaps this reflects sublty different meanings of "prediction". For example I often say that evolution "predicts" that we are likely to find a fossil or genome with a given configuration within certain bounds at certain points in geological history. It also makes very broad predictions about how living things will react to change.
    Though there are, of course, specific examples of rather spectacular evolutionary predictions.

    As I recall the existence of naked mole rats was predicted rather beautifully. Here's talk.origins notes on how it happened, and it sems credible to me.

    Again, as you point out, this might be a subtly different use of the term 'prediction', but in evolutionary (rather than historical) timescales, it would be hard to make a prediction and see it come true. After all we've been thinking about evolution through natural selection for just 150 years, and evolution - or the dreaded "macro-evolution" - takes place over a timescales of thousands or tens of thousands of years at the very least. (Apropos - has anyone any references to something I recall reading a long time ago - that Polar Bears evolved from brown bears a mere 40,000 years or so ago?)
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    Every theory is predictive.

    Otherwise you can't test it.

    duh.
    "Kill them all and let God sort them out."

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    another example of a successful prediction (or in this case retrodiction) in paleontology:

    item #1: marsupials live in Australia
    item #2: marsupials live in South America
    item #3: Australia and South America were once both joined to Antartica

    prediction: fossil marsupials will be found in Antarctica

    validation: remains of Microbiotheriids are found on the Antarctican peninsula (NEW MARSUPIAL (MAMMALIA) FROM THE EOCENE OF ANTARCTICA, AND THE ORIGINS AND AFFINITIES OF THE MICROBIOTHERIA)

    and as icing on the cake, genetic analysis has shown that Microbiotheriids are closest related to Australian rather than South American marsupials
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    It is always possible to cherry pick and come up with low level predictions when the number of variables and influences are manageable. This is true for making predictions based on history or biology. But at the grand scale, where things really have an impact, predictions are impractical in both fields of study.
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    define grand scale or endure my ridicule.
    "Kill them all and let God sort them out."

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    can you predict specific historical events ?
    because, as the term "history of life" implies, that's what you seem to be asking of evolution, that it can spell out a specific path into the future

    remember that when we talk about evolution, the term can describe three different aspects :
    * the fact of evolution, as evidenced by the interrelatedness of all beings
    * the path of evolution, where paleontology and genetics attempts to trace HOW various lineages are related
    * the process of evolution, exploring the mechanisms behind the interrelatedness

    i'd say your demands of being able to predict are somewhat disingenious if you're just going to concentrate on the path of evolution, totally ignoring that the majority of successful predictions have happened in the areas of interrelatedness and its processes

    [edit]
    oh, and btw, are you going to play the creationist trick here, which is to belittle what you can't deny is true ? so every time someone comes up with an example that you can't deny is true, it will just be another "low level", meaningless item ?
    [/edit]
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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  24. #23  
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    The highest level of prediction you can make based on the theory of evolution is that all extant organisms are related.

    And evidence sincerely points this way. In the case of the genetic evidence it was in such a manner that it amazed the scientific community when they were confronted with it.
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    Quote Originally Posted by spuriousmonkey
    The highest level of prediction you can make based on the theory of evolution is that all extant organisms are related.

    And evidence sincerely points this way. In the case of the genetic evidence it was in such a manner that it amazed the scientific community when they were confronted with it.
    Yes but that is a not strictly a prediction, it is a tentative conclusion based on past evidence. It has no future tense. It does not make any informative future prediction other than the obvious that all future organisms will be related to current organisms (life begets life in other words).

    History is able to reach similar tentative conclusions about past events. The OP wonders if biology is able to make accurate (grand) predictions about the future.

    History can also be used to predict localized future events such as who is likely to win tomorrow's election, or what course of action a particular person or entity is likely to make in the short term. These predictions are similar to the predictions offered from biology.
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    Quote Originally Posted by marnixR

    remember that when we talk about evolution, the term can describe three different aspects :
    * the fact of evolution, as evidenced by the interrelatedness of all beings
    * the path of evolution, where paleontology and genetics attempts to trace HOW various lineages are related
    * the process of evolution, exploring the mechanisms behind the interrelatedness

    i'd say your demands of being able to predict are somewhat disingenious if you're just going to concentrate on the path of evolution, totally ignoring that the majority of successful predictions have happened in the areas of interrelatedness and its processes
    What you describe as the fact of evolution is actually the observation that many life forms have similar components. This may be evidence for common descent but it tells us nothing about evolution which is a process. At best you could say the possibility of common descent, as evidenced by similarity... (interrelatedness is not an established fact).

    btw I have only seconded the OP point that evolutionary biology, like history has relatively low predictive power. It's just a fact. Contrast it with biomedical research which reverse engineers biological function and has fairly strong predictive power.
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    WYSIWYG Moderator marnixR's Avatar
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    and where do you think biomedical sciences get their rationale for making predictions ?

    exactly, by starting with the assumption that evolution is the backbone of biology
    "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
    Quote Originally Posted by marnixR

    remember that when we talk about evolution, the term can describe three different aspects :
    * the fact of evolution, as evidenced by the interrelatedness of all beings
    * the path of evolution, where paleontology and genetics attempts to trace HOW various lineages are related
    * the process of evolution, exploring the mechanisms behind the interrelatedness

    i'd say your demands of being able to predict are somewhat disingenious if you're just going to concentrate on the path of evolution, totally ignoring that the majority of successful predictions have happened in the areas of interrelatedness and its processes
    What you describe as the fact of evolution is actually the observation that many life forms have similar components. This may be evidence for common descent but it tells us nothing about evolution which is a process. At best you could say the possibility of common descent, as evidenced by similarity... (interrelatedness is not an established fact).

    btw I have only seconded the OP point that evolutionary biology, like history has relatively low predictive power. It's just a fact. Contrast it with biomedical research which reverse engineers biological function and has fairly strong predictive power.
    The nature of similarity indicates evolution.

    This is done by the process of logic and rational analysis. I don't know how I would explain it to you.
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    Quote Originally Posted by marnixR
    and where do you think biomedical sciences get their rationale for making predictions ?

    exactly, by starting with the assumption that evolution is the backbone of biology
    Now that's just plain ridiculous. Biomedical researchers evaluate molecular function by understanding what each component is performing if operating normally. They approach the work by reverse engineering molecular function and then devise methods to get the system back to normal function. They do not use random chance to choose what molecular systems to investigate or to choose what formulations to try to treat the issue. Evolutionary theory may seem to help them make predictions, but it is sufficient to note that similar structures and areas of similar chemical affinities generally have similar function. This is true regardless how the differences came about. Biomedical research is interested in similarities and differences to understand function. The reasons for the differences are not very important.

    Here is what Jerry Coyne said about this.

    ... if truth be told, evolution hasn't yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably. But hasn't evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of 'like begets like'. Even now, as its practitioners admit, the field of quantitative genetics has been of little value in helping improve varieties. Future advances will almost certainly come from transgenics, which is not based on evolution at all

    Jerry Coyne, "Selling Darwin: Does it matter whether evolution has any commercial applications?," Nature Aug 2006
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    Quote Originally Posted by cypress
    Quote Originally Posted by marnixR
    and where do you think biomedical sciences get their rationale for making predictions ?

    exactly, by starting with the assumption that evolution is the backbone of biology
    Now that's just plain ridiculous.
    the mechanics of performing biomedical research may not depend on evolution, however, a lot of the research programme is inspired by evolutionary themes, and the relevance of research performed on plants and animals depends crucially on the fact that closely related organisms are usually the best predictor of behaviour in humans

    have a look at this book to see how evolutionary concepts help drive the research programme
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    I'll have a look at it, but I suspect that most of the predictive power is based on patterns of similarity without regard to how that similarity came to be. I agree that studies of patterns and similarity is a powerful research tool. It is the world I live in as a chemical engineer.
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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    The only reason we can use animal models is because they are related by history.

    They are even using Drosophila as a model for human biology. It would be bloody pointless unless they are related to each other in a very essential manner.

    And drosophila doesn't share similarities in function and appearance that warrant any study on them for the sake of being relevant for human biology.

    The only reason is that there is a deeper biological reason. Humans and fruitflies were longer together in the history of life than they they split ways.

    And that is all.

    And once you can start wrapping your limited thoughts around that you might appreciate life.
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    Quote Originally Posted by spuriousmonkey
    The only reason we can use animal models is because they are related by history.
    No, sorry we use them because the molecular components are similar and function similarly. Relatedness is not relevant. If it is true that all organisms are related, and relatedness is the only reason we can use them as models, then we could use any animal as a model. The reality is that we use animal with similar components and similar function because they function similarly regardless if they are closely related.

    They are even using Drosophila as a model for human biology. It would be bloody pointless unless they are related to each other in a very essential manner.
    No when fruit flies are used they are used because function is similar with respect to the purpose of the research.

    And once you can start wrapping your limited thoughts around that you might appreciate life.
    Unfortunately you are the one who is trapped by presupposition. Since these issues are unconfirmed, I keep an open mind to all reasonable alternatives. You prejudicially selected one and then construct straw man arguments like the one above to rationalize your prejudice.
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    Quote Originally Posted by cypress
    Quote Originally Posted by spuriousmonkey
    The only reason we can use animal models is because they are related by history.
    No, sorry we use them because the molecular components are similar and function similarly. Relatedness is not relevant. If it is true that all organisms are related, and relatedness is the only reason we can use them as models, then we could use any animal as a model. The reality is that we use animal with similar components and similar function because they function similarly regardless if they are closely related.

    They are even using Drosophila as a model for human biology. It would be bloody pointless unless they are related to each other in a very essential manner.
    No when fruit flies are used they are used because function is similar with respect to the purpose of the research.

    And once you can start wrapping your limited thoughts around that you might appreciate life.
    Unfortunately you are the one who is trapped by presupposition. Since these issues are unconfirmed, I keep an open mind to all reasonable alternatives. You prejudicially selected one and then construct straw man arguments like the one above to rationalize your prejudice.
    You deny facts.

    That's tragic.
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    If I do, then you are the classic case of the pot calling the kettle "black".
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    Quote Originally Posted by cypress
    Biomedical researchers evaluate molecular function by understanding what each component is performing if operating normally. They approach the work by reverse engineering molecular function and then devise methods to get the system back to normal function.
    Of all the billions of possiblities, how do you suppose they zero in on the one or two they need to check to establish what "normal" function is?
    Quote Originally Posted by cypress
    They do not use random chance to choose what molecular systems to investigate or to choose what formulations to try to treat the issue.
    Hold that thought -- -
    Quote Originally Posted by cypress
    Evolutionary theory may seem to help them make predictions,
    You mean, evolutionary theory helps them make predictions. There is no "seem" to it - they quite explicitly and deliberately use the theory to make predictions.
    Quote Originally Posted by cypress
    but it is sufficient to note that similar structures and areas of similar chemical affinities generally have similar function.
    In "similar" beings, the ones that are "related" in the relevant sense. Determining that state of relatedness is not easy, in biology, without a theory.

    Where would you look to find "related" drug metabolism and similar biochemistry between elephants and some more convenient lab animal, for example: rabbits, mice, hyraxes, rats, nematodes, cockroaches, pigs, fruit flies, dogs, cats, sheep, cows, chickens, frogs, or goldfish?

    If you had an outbreak of canine distemper along the Newfoundland coast, where would you first investigate its spread and reservoirs in the surrounding environment: among the skunks, cats, raccoons, otters, seals, beluga, perch, carp, crows, bears, deer, moose, squirrels, or voles?
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    Quote Originally Posted by iceaura
    If you had an outbreak of canine distemper along the Newfoundland coast, where would you first investigate its spread and reservoirs in the surrounding environment: among the skunks, cats, raccoons, otters, seals, beluga, perch, carp, crows, bears, deer, moose, squirrels, or voles?
    Humans are very good at finding patterns of similarity. We do not need evolutionary theory to classify similar forms, features, functions and molecular structures. I would look for these similarities and choose to look there. Why is this so difficult for you?

    Do you disagree with Jerry Coyne? I recently read an article on this subject. In it a preeminent medical researcher had surveyed 70 of his colleges. He asked them how their research approach would change if evolutionary theory were overturned. All seventy said it would make no difference.
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    Quote Originally Posted by cypress
    Quote Originally Posted by iceaura
    If you had an outbreak of canine distemper along the Newfoundland coast, where would you first investigate its spread and reservoirs in the surrounding environment: among the skunks, cats, raccoons, otters, seals, beluga, perch, carp, crows, bears, deer, moose, squirrels, or voles?
    Humans are very good at finding patterns of similarity. We do not need evolutionary theory to classify similar forms, features, functions and molecular structures. I would look for these similarities and choose to look there. Why is this so difficult for you?

    Do you disagree with Jerry Coyne? I recently read an article on this subject. In it a preeminent medical researcher had surveyed 70 of his colleges. He asked them how their research approach would change if evolutionary theory were overturned. All seventy said it would make no difference.
    Link us to the article please. The context of those results, the wording of the survey and the caveats provided by respondents would be pretty critical.
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    I provided a reverence to Jerry Coyne's statement earlier. I am unable to recall the name of the article or the source. It was linked from a link of a science blog. I don't recall who said it. The article indicated the survey was informal. There did not seem to be a specific question asked. The context seemed to be more of a sampling of his colleges thoughts on the topic.


    Can you demonstrate where Jerry is wrong in his statement? Do you doubt the response of the medical researchers? If so why? Can you provide a specific medical research topic that would have to be scrapped and restarted if it was determined that processes other than mutation and selection were involved in generating all observed biological diversity?
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    Quote Originally Posted by cypress
    I am unable to recall the name of the article or the source. It was linked from a link of a science blog. I don't recall who said it.
    How did I know you would fail to cite supporting evidence, even when directly requested? Pretty much every thread in which you participate has become shit.
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    Quote Originally Posted by marnixR
    Quote Originally Posted by cypress
    Quote Originally Posted by marnixR
    and where do you think biomedical sciences get their rationale for making predictions ?

    exactly, by starting with the assumption that evolution is the backbone of biology
    Now that's just plain ridiculous.
    the mechanics of performing biomedical research may not depend on evolution, however, a lot of the research programme is inspired by evolutionary themes, and the relevance of research performed on plants and animals depends crucially on the fact that closely related organisms are usually the best predictor of behaviour in humans

    have a look at this book to see how evolutionary concepts help drive the research programme
    Ok I looked at the book last night and this morning. What was most striking to me is that nearly all that we claim to know about common descent (presumably by known evolutionary processes) is because of pattern matching. The basis for this aspect of common descent and evolutionary theory is careful pattern matching and grouping of similarity and differences. It is almost as if it is a circular argument. Things are related based on similarities. The closer the similarities, the closer the relatedness. Therefore related organisms have greater similarities. It is not my point to disagree with this circular reasoning, but the facts presented in this book when stripped of the unnecessary inferences, seems to confirm my previous claim that it is sufficient to do research based on similarity and differences without making direct use of any causal reason for the differences or similarities.

    In fact to say that research relies on evolutionary theory is really nothing more than saying that biomedical research relies on patterns of similarity and differences observed in organisms.

    Now as to what may inspire a particular researcher might be interesting but not of interest here. When you say "closely related organisms" we can more accurately translate that to "organisms most similar". Let's call a spade a spade. No need to butter things up.
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    Quote Originally Posted by inow
    Quote Originally Posted by cypress
    I am unable to recall the name of the article or the source. It was linked from a link of a science blog. I don't recall who said it.
    How did I know you would fail to cite supporting evidence, even when directly requested? Pretty much every thread in which you participate has become shit.
    Im sorry that my memory is not as perfect as you want it to be. Google for it and you might find it, I just don't think it is that important to find that particular article I spent half an hour looking for it and didn't find it. It certainly does not lessen Jerry Coyne's remarks.

    However to overturn the substance of this argument you have to attack the argument not the presenter. If it is shit as you claim, you can show where Jerry Coyne (a reference I did provide) is wrong. You can cite a biomedical research program that would have to be redesigned if evolutionary theory regarding the mechanism of observed diversity is overturned.

    Oh but you didn't even attempt it. You are like the Emperor with no clothes, laughing at me because I have a hole in my jeans.
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    Quote Originally Posted by cypress
    Quote Originally Posted by inow
    Quote Originally Posted by cypress
    I am unable to recall the name of the article or the source. It was linked from a link of a science blog. I don't recall who said it.
    How did I know you would fail to cite supporting evidence, even when directly requested? Pretty much every thread in which you participate has become shit.
    Im sorry that my memory is not as perfect as you want it to be. Google for it and you might find it, I just don't think it is that important to find that particular article I spent half an hour looking for it and didn't find it.
    Listen. YOU made the claim, and YOU were asked to support it with a reference. The onus of providing evidence falls squarely on YOUR shoulders, and is not my responsibility.


    Quote Originally Posted by cypress
    It certainly does not lessen Jerry Coyne's remarks.
    It would, however, provided much needed context for your claims, as has already been explained to you repeatedly in this thread and others.


    I've essentially stopped reading any thread in which you participate since they are all filled with the same tiresome nonsense intended only to waste everyones time and annoy people.
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    Quote Originally Posted by inow
    Quote Originally Posted by cypress
    Quote Originally Posted by inow
    Quote Originally Posted by cypress
    I am unable to recall the name of the article or the source. It was linked from a link of a science blog. I don't recall who said it.
    How did I know you would fail to cite supporting evidence, even when directly requested? Pretty much every thread in which you participate has become shit.
    Im sorry that my memory is not as perfect as you want it to be. Google for it and you might find it, I just don't think it is that important to find that particular article I spent half an hour looking for it and didn't find it.
    Listen. YOU made the claim, and YOU were asked to support it with a reference. The onus of providing evidence falls squarely on YOUR shoulders, and is not my responsibility.
    Then disregard it completely. My argument does not depend on this reference. It was an interesting extension and something I recall running across in the not too distant past. Some readers, I suspect will find it useful even without reading it directly. However since you seem to take exception to the substance of my argument and since my argument is supported with fact and corroborated with a reference, unless you step up to the plate and address it directly you are still parading around with no clothes.

    Quote Originally Posted by cypress
    It certainly does not lessen Jerry Coyne's remarks.
    It would, however, provided much needed context for your claims, as has already been explained to you repeatedly in this thread and others.

    I've essentially stopped reading any thread in which you participate since they are all filled with the same tiresome nonsense intended only to waste everyones time and annoy people.
    Clearly you are still reading the thread. While I am sometimes forgetful, you seem to be a pathetic and very poor liar. I find myself repeating things because you and others consistently fail to address the points raised. Instead you just regurgitate presupposition or reframe the question to something easy, and answer it regardless of how unrelated it is. I can see how that works for people who are like minded as you are. I see how none of you complain when you repeat the same old tired canards about the ideas you are philosophically wedded to. I even understand why that is. I get comfort in the fact that readers who don't have a prior commitment to your world-view are contrasting your non-answers and they are making judgments about the explanatory power of the theory you advocate for.

    To your claim that this is nonsense, if that were the case, you could easily dispatch it with fact based evidence. I'll count this as another possible example of your tendency to stretch the truth.

    As i said before, disregard mention of the medical researcher completely and my argument remains intact.

    In other words, you can't address the argument. I suspected as much.
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    Quote Originally Posted by cypress
    While I am sometimes forgetful, you seem to be a pathetic and very poor liar. I find myself repeating things because you and others consistently fail to address the points raised. Instead you just regurgitate presupposition or reframe the question to something easy, and answer it regardless of how unrelated it is. I can see how that works for people who are like minded as you are. I see how none of you complain when you repeat the same old tired canards about the ideas you are philosophically wedded to. I even understand why that is. I get comfort in the fact that readers who don't have a prior commitment to your world-view are contrasting your non-answers and they are making judgments about the explanatory power of the theory you advocate for.
    Thanks for confirming for me that you are little more than a troll. You're right. I'll stop feeding you now. Carry on.
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    Quote Originally Posted by cypress
    Can you demonstrate where Jerry is wrong in his statement?
    No I cannot demonstrate this because you have...
    failed to provide the specific question that was asked?
    failed to describe the means by which the question was asked?
    failed to identify the age, religious affiliations and academic position of the responders
    failed to identify the range of answers received (were there any caveats to the 'Yes' or 'No' responses?)

    Quote Originally Posted by cypress
    Do you doubt the response of the medical researchers?
    Of course I do. Currently it is mere third hand, anecdotal evidence. That has no place in science. I am bemused that you would think it would.
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    Quote Originally Posted by cypress
    I provided a reverence to Jerry Coyne's statement earlier. I am unable to recall the name of the article or the source. It was linked from a link of a science blog. I don't recall who said it. The article indicated the survey was informal. There did not seem to be a specific question asked. The context seemed to be more of a sampling of his colleges thoughts on the topic.

    Can you demonstrate where Jerry is wrong in his statement? Do you doubt the response of the medical researchers? If so why? Can you provide a specific medical research topic that would have to be scrapped and restarted if it was determined that processes other than mutation and selection were involved in generating all observed biological diversity?
    I have no idea why I should have to do any of these things when you won't direct me to the source. The only way that argument could go is in circles based on guesswork and assumption. Give me the source or drop the point.
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    Once again and from page two of this thread is Jerry Coyne's words...


    ... if truth be told, evolution hasn't yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably. But hasn't evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of 'like begets like'. Even now, as its practitioners admit, the field of quantitative genetics has been of little value in helping improve varieties. Future advances will almost certainly come from transgenics, which is not based on evolution at all

    Jerry Coyne, "Selling Darwin: Does it matter whether evolution has any commercial applications?," Nature Aug 2006
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    Quote Originally Posted by Ophiolite
    Quote Originally Posted by cypress
    Can you demonstrate where Jerry is wrong in his statement?
    No I cannot demonstrate this because you have...
    failed to provide the specific question that was asked?
    failed to describe the means by which the question was asked?
    failed to identify the age, religious affiliations and academic position of the responders
    failed to identify the range of answers received (were there any caveats to the 'Yes' or 'No' responses?)
    Huh???? You can't respond to Jerry Coyne's words in the article from Nature referenced above.

    You are conflating the two points. You have mixed them into one.

    Quote Originally Posted by cypress
    Do you doubt the response of the medical researchers?
    Of course I do. Currently it is mere third hand, anecdotal evidence. That has no place in science. I am bemused that you would think it would.
    We have Coyne's statement and article. Will you reject that as well? The ancedotal reference to the article simply builds on an already valid point. The point stands without reference to the article I have lost.

    edit:

    I didn't find the news article I originally read (it must not be linked any longer) but I did find the article that the news writer was discussing in his column. The author, Dr. Philip Skell, a member of the National Acadamy of Science wrote this editorial in the Scientist several years ago. (I didn't remember it being this long ago).

    In that article among other points, he writes:

    "examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss."
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    Quote Originally Posted by cypress
    Humans are very good at finding patterns of similarity. We do not need evolutionary theory to classify similar forms, features, functions and molecular structures. I would look for these similarities and choose to look there. Why is this so difficult for you?
    So do it. Answer the questions. The very simple example is right there - find the similarities you think are relevant, draw your conclusion, and we can compare your guesswork with the conclusions standard theory provides.

    Here they are again: Where would you look to find "related" drug metabolism and similar biochemistry between elephants and some more convenient lab animal, for example: rabbits, mice, hyraxes, rats, nematodes, cockroaches, pigs, fruit flies, dogs, cats, sheep, cows, chickens, frogs, or goldfish?

    If you had an outbreak of canine distemper along the Newfoundland coast, where would you first investigate its spread and reservoirs in the surrounding environment: among the skunks, cats, raccoons, otters, seals, beluga, perch, carp, crows, bears, deer, moose, squirrels, or voles?

    Quote Originally Posted by cypress
    ... if truth be told, evolution hasn't yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say.
    A brief look at the fate of Soviet agricultural research under the guidance of an incorrect theory of evolution (Lysenko's) will demonstrate - fairly dramatically - the benefits of the better theory in guiding research etc.

    Quote Originally Posted by one of these guys
    Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably.
    Identifying the core genetic heritage - the features of the microbe that probably cannot easily evolve without trashing the capabilities of the organism to cause disease, say - can be a very important step in developing better countermeasures.

    Quote Originally Posted by cypress
    But hasn't evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of 'like begets like'.
    Why do you guys advance arguments like this? What difference does it make that breeding by good rules of thumb has produced major advances over the millenia?
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    Coyne's quote is taken from a single paragraph he wrote in the book review in Nature that cypress cited. This quote has often been tauted by creationists like cypress (whatever cypress pretends to be or not be, he's certainly a creationist. Probably from some southern fly-over state along the gulf) as a means of trying to introduce some imagined conflict or controversy within the ranks of science with regard to evolution.

    Conflicts and controversy certainly exist within the fact of evolution among scientists, but none of them who can genuinely call themselves scientists doubt that evolution occurred.

    And yet, creationist like cypress seem intent to sew seeds of imagined doubt with various quotes they are able to mine from reputable scientists. Interestingly enough, cypress omits Coyne's next paragraph.

    Allow me:
    As far as I know, there have been only two genuine commercial applications of evolutionary theory. One is the use of 'directed evolution' to produce commercial products (such as enzymes to protect crop plants from herbicides). The other is the clever use of insecticide-free 'pest refuges' to stop herbivorous insects evolving resistance to herbicides containing Bacillus thuringiensis (Bt) toxins, a strategy derived from principles of population genetics. There will certainly be more of these to come. And evolutionary algorithms are used in designing computer programs, and may have uses in engineering and economics.
    That was as far as he knew in 2006.

    The context of Coyne's larger point is that one doesn't generally do science with the hopes of having a direct monetary or commercial benefit. Those benefits arrive indirectly from people who gain knowledge and insight from the discoveries. Prior to Darwin, variation within species wasn't considered an important field of study -a distraction. After Darwin and his explanations of natural selection, heredity and the understanding of it became central to testing the theories.

    These theories have held time and again and evolution is directly observable in the fossil record of species like hominids. In spite of the doubt and disagreement about things like taxonomy or even the definition of species, here is no doubt among the rational and the educated that evolution occurred.
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    Quote Originally Posted by cypress
    Quote Originally Posted by marnixR
    Quote Originally Posted by cypress
    Quote Originally Posted by marnixR
    and where do you think biomedical sciences get their rationale for making predictions ?

    exactly, by starting with the assumption that evolution is the backbone of biology
    Now that's just plain ridiculous.
    the mechanics of performing biomedical research may not depend on evolution, however, a lot of the research programme is inspired by evolutionary themes, and the relevance of research performed on plants and animals depends crucially on the fact that closely related organisms are usually the best predictor of behaviour in humans

    have a look at this book to see how evolutionary concepts help drive the research programme
    Ok I looked at the book last night and this morning. What was most striking to me is that nearly all that we claim to know about common descent (presumably by known evolutionary processes) is because of pattern matching. The basis for this aspect of common descent and evolutionary theory is careful pattern matching and grouping of similarity and differences. It is almost as if it is a circular argument. Things are related based on similarities. The closer the similarities, the closer the relatedness. Therefore related organisms have greater similarities. It is not my point to disagree with this circular reasoning, but the facts presented in this book when stripped of the unnecessary inferences, seems to confirm my previous claim that it is sufficient to do research based on similarity and differences without making direct use of any causal reason for the differences or similarities.

    In fact to say that research relies on evolutionary theory is really nothing more than saying that biomedical research relies on patterns of similarity and differences observed in organisms.

    Now as to what may inspire a particular researcher might be interesting but not of interest here. When you say "closely related organisms" we can more accurately translate that to "organisms most similar". Let's call a spade a spade. No need to butter things up.
    Don't be so daft. I am one of these researchers and I know exactly what i write in a research grant, because I have written it.

    You reading a fictitious book isn't much of reassuring source.
    "Kill them all and let God sort them out."

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    In another thread cypress actually gave us a link to a paper which used another scientific and commercial application of evolution- SELEX. Though rather bizarrely at the time he was claiming that SELEX was some sort of abiogenesis experiment. There are many similar techniques based on mutation and selection which molecular biologists use to rapidly generate panels of oligonucleoties, larger nucleotide sequences, proteins and so forth with some sought-after traits. These techniques are used in all sorts of research and are a major source of new candidate therapeutic agents. So our understanding of evolution has in fact yielded major dividends for medicine and research in general.
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    Quote Originally Posted by cypress
    Ok I looked at the book last night and this morning. What was most striking to me is that nearly all that we claim to know about common descent (presumably by known evolutionary processes) is because of pattern matching. The basis for this aspect of common descent and evolutionary theory is careful pattern matching and grouping of similarity and differences. It is almost as if it is a circular argument. Things are related based on similarities. The closer the similarities, the closer the relatedness. Therefore related organisms have greater similarities. It is not my point to disagree with this circular reasoning, but the facts presented in this book when stripped of the unnecessary inferences, seems to confirm my previous claim that it is sufficient to do research based on similarity and differences without making direct use of any causal reason for the differences or similarities.

    In fact to say that research relies on evolutionary theory is really nothing more than saying that biomedical research relies on patterns of similarity and differences observed in organisms.

    Now as to what may inspire a particular researcher might be interesting but not of interest here. When you say "closely related organisms" we can more accurately translate that to "organisms most similar". Let's call a spade a spade. No need to butter things up.
    The "pattern matching" argument is garbage. If that were all there was to it, we would not be able to make any predictions about undiscovered species nor determine any underlying structure to the similarities. Again, the (imperfect) bifurcating phylogeny tells us that the similarities are more than mere similarities. If it's not due to relatedness by inheritance then by all means tell us what it is, but don't pretend that structure is not there because even the most sceptical biologists agree that it fundamentally exists even if it is compromised in places. That phylogeny is reinforced with every new discovery and the only exceptions we see are those that look exactly as we'd expect for HGT and similar events- monogenetic collisions or symbiosis. We don't see vertebrates with a coat of leaves or insects growing bony endoskeletons nor do we see countless other violations of the phylogeny that would require movement of genes outside of the capacity of HGT or endosymbiosis. The relationship between species is there, it is real and the only way to suggest otherwise is to ignore a vast body of evidence.
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    Quote Originally Posted by SkinWalker
    Coyne's quote is taken from a single paragraph he wrote in the book review in Nature that cypress cited. This quote has often been tauted by creationists like cypress (whatever cypress pretends to be or not be, he's certainly a creationist. Probably from some southern fly-over state along the gulf) as a means of trying to introduce some imagined conflict or controversy within the ranks of science with regard to evolution.

    Conflicts and controversy certainly exist within the fact of evolution among scientists, but none of them who can genuinely call themselves scientists doubt that evolution occurred.
    I don't doubt that evolution occures either. I am not a creationist. I am one who sees the conflict within the theory as an outsider without prejudice or a prior commitment. I note that we don't have an adequate answer to how the full process works. I also see it's limits and I am not willing to grant grander claims than it deserves.

    And yet, creationist like cypress seem intent to sew seeds of imagined doubt
    You see me the way you want to see me without any knowledge of what I actually believe. You see me as the enemy likely because you and many here have a prior commitment that causes you to see things in science the way you think they ought to be. It also causes you see me in a way that fits your prejudice that no thinking perso could possibly question aspects of modern evolutionary theory. It seems that anything that challenges your view of the world is wrong by definition.

    with various quotes they are able to mine from reputable scientists. Interestingly enough, cypress omits Coyne's next paragraph.

    Allow me:
    As far as I know, there have been only two genuine commercial applications of evolutionary theory. One is the use of 'directed evolution' to produce commercial products (such as enzymes to protect crop plants from herbicides). The other is the clever use of insecticide-free 'pest refuges' to stop herbivorous insects evolving resistance to herbicides containing Bacillus thuringiensis (Bt) toxins, a strategy derived from principles of population genetics. There will certainly be more of these to come. And evolutionary algorithms are used in designing computer programs, and may have uses in engineering and economics.
    That was as far as he knew in 2006.
    I have no problem with that paragraph either. I omitted it because directed evolution and evolutionary algorithms are designed and I didn't want to get into that.

    The context of Coyne's larger point is that one doesn't generally do science with the hopes of having a direct monetary or commercial benefit. Those benefits arrive indirectly from people who gain knowledge and insight from the discoveries. Prior to Darwin, variation within species wasn't considered an important field of study -a distraction. After Darwin and his explanations of natural selection, heredity and the understanding of it became central to testing the theories.
    Agreed.

    These theories have held time and again and evolution is directly observable in the fossil record of species like hominids. In spite of the doubt and disagreement about things like taxonomy or even the definition of species, here is no doubt among the rational and the educated that evolution occurred.
    Once again you, like the others before you are conflating evolution with common descent. We observe patterns of similarities that can lead to a conclusion of relatedness, yet these patterns do not tell us how the differences occured. Common descent can never confirm how or what process drove the differences. Evolutionary theory must explain the differences not the similarities. You use the term "rational and educated" to mean people who think the same as you, yet your prior commitment prevents you from recognizing that the full process is still not confirmed and other processes may well be involved.

    Yet this is not the point of this thread. the point of this thread is precisely what the original poster said namely, that biology does not provide good future predictions and what Coyne and Skell said. Namely that evolutionary theory is not a necessary component of most research programs.

    Again here is what Dr. Philip Skell, a member of the National Academy of Science wrote:

    "examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss."
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    Ok I looked at the book last night and this morning. What was most striking to me is that nearly all that we claim to know about common descent (presumably by known evolutionary processes) is because of pattern matching. The basis for this aspect of common descent and evolutionary theory is careful pattern matching and grouping of similarity and differences. It is almost as if it is a circular argument. Things are related based on similarities. The closer the similarities, the closer the relatedness. Therefore related organisms have greater similarities. It is not my point to disagree with this circular reasoning, but the facts presented in this book when stripped of the unnecessary inferences, seems to confirm my previous claim that it is sufficient to do research based on similarity and differences without making direct use of any causal reason for the differences or similarities.

    In fact to say that research relies on evolutionary theory is really nothing more than saying that biomedical research relies on patterns of similarity and differences observed in organisms.

    Now as to what may inspire a particular researcher might be interesting but not of interest here. When you say "closely related organisms" we can more accurately translate that to "organisms most similar". Let's call a spade a spade. No need to butter things up.
    The "pattern matching" argument is garbage. If that were all there was to it, we would not be able to make any predictions about undiscovered species nor determine any underlying structure to the similarities. Again, the (imperfect) bifurcating phylogeny tells us that the similarities are more than mere similarities. If it's not due to relatedness by inheritance then by all means tell us what it is, but don't pretend that structure is not there because even the most sceptical biologists agree that it fundamentally exists even if it is compromised in places. That phylogeny is reinforced with every new discovery and the only exceptions we see are those that look exactly as we'd expect for HGT and similar events- monogenetic collisions or symbiosis. We don't see vertebrates with a coat of leaves or insects growing bony endoskeletons nor do we see countless other violations of the phylogeny that would require movement of genes outside of the capacity of HGT or endosymbiosis. The relationship between species is there, it is real and the only way to suggest otherwise is to ignore a vast body of evidence.
    He's as blind as he can be, sees just what he wants to see, isn't he a bit like you and me? Oh but I digress...

    The point is, it is irelevant what the reason is for the similarities. It is sufficient for the research described by Dr. Skell that the similarities and patterns exist. Show me where we are wrong.

    Furthermore the patterns of similarities are sufficient to predict the range of forms we of undiscovered species.
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    The "pattern matching" argument is garbage. If that were all there was to it, we would not be able to make any predictions about undiscovered species nor determine any underlying structure to the similarities. Again, the (imperfect) bifurcating phylogeny tells us that the similarities are more than mere similarities. If it's not due to relatedness by inheritance then by all means tell us what it is, but don't pretend that structure is not there because even the most sceptical biologists agree that it fundamentally exists even if it is compromised in places. That phylogeny is reinforced with every new discovery and the only exceptions we see are those that look exactly as we'd expect for HGT and similar events- monogenetic collisions or symbiosis. We don't see vertebrates with a coat of leaves or insects growing bony endoskeletons nor do we see countless other violations of the phylogeny that would require movement of genes outside of the capacity of HGT or endosymbiosis. The relationship between species is there, it is real and the only way to suggest otherwise is to ignore a vast body of evidence.
    He's as blind as he can be, sees just what he wants to see, isn't he a bit like you and me? Oh but I digress...
    Thank you. I like the Beatles and I really like irony, so this made my day.

    Quote Originally Posted by cypress
    The point is, it is irelevant what the reason is for the similarities. It is sufficient for the research described by Dr. Skell that the similarities and patterns exist. Show me where we are wrong.
    Where you're wrong is in the assertion that "nearly all that we claim to know about common descent...is because of pattern matching". I have not read the source that you're on about, and perhaps it makes a similar assertion, but if it does, it is also wrong. Pattern matching alone tells us much but certainly not the full story, as I've already tried to explain. Analysis of the topology of the similarities and the determination of mechanisms are both major parts of what allows us to derive meaning from the similarities. I get that you're at great pains to suggest that meaning is speculative or just irrelevant to our modelling efforts but as I'll try to explain, that isn't so.

    We know of a variety of process by which living things may be similar, so what allows us to determine which, if any, of these process is involved in that similarity is what topolgy would be generated by the processes in combination and whether those processes are likely to occur under the conditions known. Hence we analyse the topology, make observations to determine whether the putative responsible processes actually occur and most critically we experiment by interfering with processes in order to distinquish causal relationships from correlations- so that we can say not only that they are happening but that they can account for our passive observations. The reasoning is not circular because we have gone to these other extents to confirm it. It is the results of all of these elements together which compel us to say "closely related organisms" rather than your conservative version "organisms most similar". If we were going by pattern matching alone, without consideration of any other factors, we might indeed view similarity as nothing more than similarity.

    Quote Originally Posted by cypress
    Furthermore the patterns of similarities are sufficient to predict the range of forms we of undiscovered species.
    Well, not really. Mere pattern matching will only tell us what combinations are possible, rather than what combinations are probable under this selective environment, that mutagenic environment and so forth. It would also not allow us to make any assumptions about rare exceptions to the pattern. We'd be able to see that sometimes a gene hops accross the phylogeny, but without a mechanism we'd be unable to say anything about how likely it is to happen again or what we'd expect it to look like if it did. In short, with more information our predictions become more accurate.

    Even putting all this aside, it would take a serious lack of imagination to be satisfied that a pattern exists and think it relevant to wonder why.
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    You want us to believe that the theory is intact and that organisms were once all the same and then evolutionary processes drove large differences by methods that can't explain even basic steps. All the while, symbiosis, convergent evolution and a host of other unexplained processes stirred the pot and masked the handiwork of evolution to make it appear somewhat out of sequence. This explanation was added after the fact to make the theory conform to the facts. Then you try to argue that the data is not actually out of sequence at all. The fact that these other processes are cited is the clearest evidence that the molecular data is out of sequence from expected. Meanwhile the data also fits patterns that would be produced by processes other than those cited by evolutionary theory, but most advocates of evolution won't admit it.

    The patterns fit best with the general observation that similar forms and similar functions are produced by similar molecular components and molecular processes. Differences are explained by differences in molecular shapes and patterns, differences in expression and developmental controls and many other related processing systems. Evolutionary theory has not been able to account for these differences.

    Putting all this aside, we are back to the reality that advocates of evolutionary theory oversell it's importance in driving research, and they oversell its predictive power. Just as you are hard selling it here. You point to similarity as evidence for the capability of evolution when evolution really must, but hasn't, explained how differences came to be. Evolution leads to differences not similarity. Yet biomedical research relies on understanding function which relies on similarity of components for experimental models.
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    What, no direct rebuttal of my argument? I fully explain why these other factors besides "pattern matching" are not merely relevant but essential and all you have for me is a broad dismissal of evolution?

    Quote Originally Posted by cypress
    You want us to believe that the theory is intact and that organisms were once all the same and then evolutionary processes drove large differences by methods that can't explain even basic steps.
    They can, but not to your satisfaction. There could be many reasons for that which do not relate to the quality of the science.

    Quote Originally Posted by cypress
    All the while, symbiosis, convergent evolution and a host of other unexplained processes stirred the pot and masked the handiwork of evolution to make it appear somewhat out of sequence. This explanation was added after the fact to make the theory conform to the facts.
    Imagine that. Modifying a theory to fit observations? Outrageous. Clear evidence of the dogmatic position of the establishment of course!

    Your definition of "unexplained" must be an odd one given that you yourself provided papers written by the very people who explained endosymbiosis and HGT and how they contribute to evolution. Those same people, despite your attempts to claim them in your support, will still agree that evolution is primarily driven by variation and selection and that the variety of life on Earth arose from a common ancestor.

    I have no idea why you would bring up convergence, it speaks against your position. If life is designed, it's rather baffling as to why the fin or the wing would be re-designed (at least twice in each case) so fundamentally and yet do an identical job to the original version. An analogous molecular example being the adaptive immune system in lampreys. And even more confusing as to why such re-designs would be exclusive to certain groups. Convergence and exclusivity support evolution by variation and selection.

    Quote Originally Posted by cypress
    Then you try to argue that the data is not actually out of sequence at all. The fact that these other processes are cited is the clearest evidence that the molecular data is out of sequence from expected.
    The data is out of sequence for what would be expected if natural selection and mutation were the only contributors. Nobody is denying that- I mentioned it the instant I brought up phylogeny. But the data looks correct for what would be expected if these two processes dominate evolution with infrequent contributions from some other processes. Perhaps we will one day find exceptions that defy this. Can you show me an example of a violation of the selection/mutation phylogeny that cannot be explained by the limited forms of natural HGT we have observed or by very rare cases of endosymbiosis?

    Quote Originally Posted by cypress
    Meanwhile the data also fits patterns that would be produced by processes other than those cited by evolutionary theory, but most advocates of evolution won't admit it.
    Who here is denying the influence of HGT and endosymbiosis in evolution? Who in the scientific community has done so in the last 10 years?

    Quote Originally Posted by cypress
    The patterns fit best with the general observation that similar forms and similar functions are produced by similar molecular components and molecular processes.
    Sure, except when they don't, as we see with convergence and exaptation. Making this general observation of yours so loose and full of exceptions as to be meaningless. It's also extremely narrow minded. All you've shown us is that you can't draw useful general conclusions if you cherry pick your evidence.

    Quote Originally Posted by cypress
    Differences are explained by differences in molecular shapes and patterns, differences in expression and developmental controls and many other related processing systems. Evolutionary theory has not been able to account for these differences.
    Again, not to your satisfaction. You're just making an appeal to ignorance.

    Quote Originally Posted by cypress
    Putting all this aside, we are back to the reality that advocates of evolutionary theory oversell it's importance in driving research, and they oversell its predictive power.
    The only time I see either point vigorously contested is when critics of evolution try to claim that the theory can't deliver on them. A bit like the old Hitler canard- not really relevant but worth contesting if only to expose the tactics of the opposition for what they are.

    The lack of practical applications for any piece of knowledge is not an indicator of its veracity- though the converse acts as sort of validation. So really, if true, this would be an appeal to ignorance rather than actual evidence. It just happens that evolution has actually had practical applications in research, one of which (SELEX) you yourself brought to the table in another display of wonderfully self-defeating citation. It is important to point out such examples when some try to make the claim that evolution does not have practical applications. Maybe it's an over-sell, but saying there have been no applications is simply incorrect.

    Predictive power is a good measure of the veracity of a theory. Nobody here has tried to claim the theory can predict more powerfully than it can- attempts by some futurist types to make projections about future evolution using the principles of the theory do not meet with broad support in the scientific community. The theory simply has not been demonstrated to have that power, though perhaps that is due to limitations how much information we can input into the function plus of course the issue of timescales- it's not really possible to judge that. But it can predict future discoveries of past events. That makes the theory useful as well as falsifiable for anyone who wishes to point out the relevant inexplicable species.

    Quote Originally Posted by cypress
    Just as you are hard selling it here. You point to similarity as evidence for the capability of evolution when evolution really must, but hasn't, explained how differences came to be.
    That explanation, along with testable implications, is built into the core of the modern synthesis. If the implications have been falsified then by all means provide the contradictory evidence. That's positive evidence rather than another gap, if you don't mind. We all know there are gaps, but they can't logically falsify the theory.

    Quote Originally Posted by cypress
    Evolution leads to differences not similarity. Yet biomedical research relies on understanding function which relies on similarity of components for experimental models.
    I have no idea what your point is meant to be here. Maybe you can explain it another way? Similarity and difference are not logically exclusive. They are by definition reciprocals of one another. Which means that measurement of one is the reciprocal measurement of the other. So really we are focusing on both with every experiment and observation. Biomedical research does not "rely" on understanding function. Function is relevant, just not all we are interested in.
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    I fear Cypress, that you may have reached the stage of 'If I say it three times that makes it true'. Science doesn't work that way.

    Here's a prediction: you will not respond substantively toThe Biologista's comprehensive post above, but will reiterate your past vagueries, and something you posted two pages back (comprehensively refuted by the professional biologists here), in the expectation that no one will bother to go back that far yet again and point this out.

    Also, the simple reason why natural selection cannot be predictive like, say, Newtonian physics is that life, being like society or the weather, is effectively self-referential and hence chaotic (in the mathematical sense). Just as meteorology constantly battles to create reliable predictions, and frequently fails, despite all the money riding on it, so also there are, in principle, limitations to predictions that can be made about interactive biological systems. And this is without even taking into account genuinely unpredictable events like the K-T meteor strike. (FWIW, even should you miraculously discover some further mechanism that has an important impact on evolution, these limitations will ensure that evolution will still never be as predictive as Newtonian physics.)

    If you still repeat yourself and fail to show the ability to learn from all the professional expertise, pro bono, being put at the service of this discussion, I will certainly be recommending to the other mods that you be treated as a troll, no matter how well you write.

    Regards

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    Quote Originally Posted by biologistica
    What, no direct rebuttal of my argument? I fully explain why these other factors besides "pattern matching" are not merely relevant but essential and all you have for me is a broad dismissal of evolution?
    Right. It was a side bar. It did not change the reality that evolutionary theory generally does not provide a very useful heuristic in biomedical research. While those other factors may be essential to evolutionary theory, that is not the debate. They do not change the reality that detailed knowledge of similar patterns and function are sufficient for biomedical research. Since it is not directly relevant and since you did not address the comments by Skell and Coyne, I saw no reason to address your points.

    Quote Originally Posted by sunshinewarrior
    I fear Cypress, that you may have reached the stage of 'If I say it three times that makes it true'. Science doesn't work that way.

    Here's a prediction: you will not respond substantively toThe Biologista's comprehensive post above, but will reiterate your past vagueries, and something you posted two pages back (comprehensively refuted by the professional biologists here), in the expectation that no one will bother to go back that far yet again and point this out.
    Here's the problem sunshine, biologista raises side issues and points that I don't dispute while consistently failing to address the actual topic of the thread. He is consistent on this point. He insisted that I search for an article that i had misplaced so he could respond and then after finding it he says nothing about it but then goes on to reiterate items I generally agree with and that I suspect he knows I agree with.

    He seems an expert at cherry picking positive snipits all while failing to address the substance and furthermore blaming the failure on me being overly critical.

    He also routinely mischaracterizes my position to try to reduce my credibility. He claims I am advocating for design when I am pointing out that evolution is not as robust in these areas as it made out to be. My entire point is that evolutionary theory is in need of some additional processes to shore it up. The first step is to be honest about what the theory explains and what it does not. It does nobody any good to oversell it. It has not been demonstrated that the basic steps required for new molecular components can be derived by known processes. It does not matter what can be shown. Earlier several posters disputed the OP's claim and I provided references that have been largely ignored that corroborate the position that evolutionary theory does not have much practical influence in biomedical research. Biologistica fails to address this point and instead launches off on a full court defense of evolutionary theory.

    Also, the simple reason why natural selection cannot be predictive like, say, Newtonian physics is that life, being like society or the weather, is effectively self-referential and hence chaotic (in the mathematical sense). Just as meteorology constantly battles to create reliable predictions, and frequently fails, despite all the money riding on it, so also there are, in principle, limitations to predictions that can be made about interactive biological systems. And this is without even taking into account genuinely unpredictable events like the K-T meteor strike. (FWIW, even should you miraculously discover some further mechanism that has an important impact on evolution, these limitations will ensure that evolution will still never be as predictive as Newtonian physics.)
    Good thanks finally someone admits the OP's point is correct .

    If you still repeat yourself and fail to show the ability to learn from all the professional expertise, pro bono, being put at the service of this discussion, I will certainly be recommending to the other mods that you be treated as a troll, no matter how well you write.
    The disturbing thing about all of this is that I agree with most of what bio and the others say. It is just that it often does not address the point.
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    Quote Originally Posted by cypress
    Quote Originally Posted by biologistica
    What, no direct rebuttal of my argument? I fully explain why these other factors besides "pattern matching" are not merely relevant but essential and all you have for me is a broad dismissal of evolution?
    Right. It was a side bar. It did not change the reality that evolutionary theory generally does not provide a very useful heuristic in biomedical research. While those other factors may be essential to evolutionary theory, that is not the debate. They do not change the reality that detailed knowledge of similar patterns and function are sufficient for biomedical research. Since it is not directly relevant and since you did not address the comments by Skell and Coyne, I saw no reason to address your points.
    They directly feed into the topic at hand! You're trying to argue that evolution is not useful or predictive by re-defining what it is and how we use it. By suggesting that pattern matching produces the same results as using the theory fully. I explained fully why I disagree and you've got nothing to say but that you think it's not central to what we're discussing here. What are you on about?

    Quote Originally Posted by sunshinewarrior
    I fear Cypress, that you may have reached the stage of 'If I say it three times that makes it true'. Science doesn't work that way.

    Here's a prediction: you will not respond substantively toThe Biologista's comprehensive post above, but will reiterate your past vagueries, and something you posted two pages back (comprehensively refuted by the professional biologists here), in the expectation that no one will bother to go back that far yet again and point this out.
    Here's the problem sunshine, biologista raises side issues and points that I don't dispute while consistently failing to address the actual topic of the thread.
    See above, I'm directly addressing the topic here.

    Quote Originally Posted by sunshinewarrior
    My entire point is that evolutionary theory is in need of some additional processes to shore it up.
    If that is your point then it is off topic. This is about whether evolution has predictive power. If you can show it does not then maybe invoking other processes would be relevant.

    Quote Originally Posted by sunshinewarrior
    The first step is to be honest about what the theory explains and what it does not. It does nobody any good to oversell it. It has not been demonstrated that the basic steps required for new molecular components can be derived by known processes. It does not matter what can be shown. Earlier several posters disputed the OP's claim and I provided references that have been largely ignored that corroborate the position that evolutionary theory does not have much practical influence in biomedical research. Biologistica fails to address this point and instead launches off on a full court defense of evolutionary theory.
    Those references that have been "largely ignored" consisted of several noteworthy papers which emphasise the relevance of HGT and endosymbiosis as well as a notoriously sensationalistic New Scientist article. The papers I had already pre-empted when talking about how evolution predicts phylogeny- I agree with them and have no argument to make against them. They also work against you. Yet again. You're trying to act like we don't know about these other processes within evolution or are trying to downplay them, but the research you're talking about is mainstream and broadly accepted. The papers- heavily cited and in good journals- are pretty clear evidence that biologists are certainly not ignoring this work. As are my repeated references to the significance of both processes to our use of the theory. I think you've been rather taken in by the New Scientist style take on the whole thing. A "maverick science versus the establishment" story sells much better than a "we accepted this stuff 20 years ago" story. And a "Darwin was wrong" cover gets people much more excited than "Darwin was right but didn't know about stuff discovered over a century after he died". New Scientist is fun to read- but it's tabloid science. They've also done a cover story on what was essentially a perpetual motion machine. They're fine for news, increasingly terrible for features.

    Quote Originally Posted by cypress
    Also, the simple reason why natural selection cannot be predictive like, say, Newtonian physics is that life, being like society or the weather, is effectively self-referential and hence chaotic (in the mathematical sense). Just as meteorology constantly battles to create reliable predictions, and frequently fails, despite all the money riding on it, so also there are, in principle, limitations to predictions that can be made about interactive biological systems. And this is without even taking into account genuinely unpredictable events like the K-T meteor strike. (FWIW, even should you miraculously discover some further mechanism that has an important impact on evolution, these limitations will ensure that evolution will still never be as predictive as Newtonian physics.)
    Good thanks finally someone admits the OP's point is correct .
    Finally? What was one of the the first things we brought up? The meaning of "predictive" in this case. If Sagan meant predictive in the same sense as relativity or Newtonian gravity is predictive, then we agree with him- evolution does not have the power to predict the specifics of the future course of any species. But "predictiveness" in science means more than just predicting future events. I means predicting unknowns of any sort. Like the equation of the line predicting a data point between already measured points. We can predict points in the phylogeny. Evolution can do that and has done that. Sagan probably meant the first sense, in which case he is probably right.

    Quote Originally Posted by cypress
    If you still repeat yourself and fail to show the ability to learn from all the professional expertise, pro bono, being put at the service of this discussion, I will certainly be recommending to the other mods that you be treated as a troll, no matter how well you write.
    The disturbing thing about all of this is that I agree with most of what bio and the others say. It is just that it often does not address the point.
    We're talking about various kinds of predictive power and my point about phylogeny is very much relevant to that.
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    if medical people had taken the predictive power of evolution more seriously then maybe we wouldn't have such a vast array of antibiotic-resistant bacteria around

    because, if anyone had bothered to listen to how natural selection works, you would have known that unless you kill all of them, only the hardiest will survive and take their resistance to the next generation
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Biologista, in another thread, one paper I provided described how over 1/3 of the genes studied were excluded from the results because they produced conflicting phylogenies. The process is nowhere as robust as you would have us believe. On the other hand biomedical research finds functional and structural similarity a useful study heuristic irrespective of the explanation.

    Quote Originally Posted by marnixR
    if medical people had taken the predictive power of evolution more seriously then maybe we wouldn't have such a vast array of antibiotic-resistant bacteria around

    because, if anyone had bothered to listen to how natural selection works, you would have known that unless you kill all of them, only the hardiest will survive and take their resistance to the next generation
    Both Coyne and Skell addressed this point.

    Coyne
    .. if truth be told, evolution hasn't yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably.

    Skell

    " I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss."
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    it all depends what level of prediction you want to insist on - to me the prediction that matters is that given half a chance life will find a way against your pesticides, insecticides, antibiotics etc.

    if medical people had understood this they wouldn't have been bragging how they were winning the war against diseases in the early 60s just when the first resistant strains were starting to rear their ugly little heads
    maybe you can't tell exactly what defences will arise, but you can tell with 100% certainty that some sort of defence will arise, so you'd better start making plans for when it does
    "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
    The disturbing thing about all of this is that I agree with most of what bio and the others say. It is just that it often does not address the point.
    Your point is that:

    because Darwinian evolutionary theory cannot be used to predict the exact future course of evolutionary development, the theory has been oversold and requires major modifications.

    This is about like saying that because the current thermodynamic theory fails to predict the weather, it requires major modification.
    Quote Originally Posted by cypress
    My entire point is that evolutionary theory is in need of some additional processes to shore it up. The first step is to be honest about what the theory explains and what it does not. It does nobody any good to oversell it. It has not been demonstrated that the basic steps required for new molecular components can be derived by known processes.
    So far, you have presented no evidence or argument supporting this point of yours. All of your examples and arguments have been irrelevant and/or invalid.

    You claim there is no evidence that Darwinian process is capable of producing certain structures, and therefore we must consider other processes. Both claims are wrong - we have plenty of evidence and argument that Darwinian process can produce such structures, and in fact has: if we didn't, that would still be no reason to take seriously other processes for which we have no support in evidence or argument.

    And you seem oblivious to this fact - at one point you were comparing symbiosis and other such sources of large-scale genetic change to Ptolemy's "epicycles"! You were, that is, comparing observed physical phenomena of verifiable importance and simplifying implication, with hypothetical abstractions elaborating a metaphysically based description of pattern, devoid of physical mechanism or explanation, and complicating the theory. That is fairly clueless.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    The disturbing thing about all of this is that I agree with most of what bio and the others say. It is just that it often does not address the point.
    Your point is that:

    because Darwinian evolutionary theory cannot be used to predict the exact future course of evolutionary development, the theory has been oversold and requires major modifications.

    This is about like saying that because the current thermodynamic theory fails to predict the weather, it requires major modification.
    No, you guys continuously change my point to something I agree with and something you can address. Here it is properly stated.

    Because evolutionary processes have not empirically been shown capable of producing even the most basic molecular events required to generate new protein function, it has been oversold. Science is empirical. It is not supposed to accept just so stories. Furthermore advocates of evolutionary theory oversell the theory on several other levels. They claim it is the backbone of all modern biological research when it clearly is not. They make sweeping claims about its future predictive ability when it is modest at best.

    So far, you have presented no evidence or argument supporting this point of yours. All of your examples and arguments have been irrelevant and/or invalid.

    You claim there is no evidence that Darwinian process is capable of producing certain structures, and therefore we must consider other processes. Both claims are wrong - we have plenty of evidence and argument that Darwinian process can produce such structures, and in fact has: if we didn't, that would still be no reason to take seriously other processes for which we have no support in evidence or argument.
    I am not asking for very much. Provide a real example of the generation of a new protein component of a multicomponent molecular machine with several well fitted components. Sudden appearance in the past of new components is evidence that some process generated the components but that tells us nothing about how it happened. You must demonstrate that a known process generated the component otherwise we may as well say it morphed by magic. If you can't demonstrate this, then demonstrate any of the other basic steps I previously described.

    And you seem oblivious to this fact -
    You all are cut from the same cloth... You have a prior commitment to Darwinian Evolutionary theory so to you, it must be true, therefore it is not a problem that it can't even produce the most basic events required to show that its fits the theory's sweeping claims.

    We will see if you can demonstrate any of these necessary basic steps ... We will see who is oblivious to the facts.

    Why over sell it? Why not just admit what can and cannot be demonstrated?
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    Quote Originally Posted by cypress
    Sudden appearance in the past of new components is evidence that some process generated the components but that tells us nothing about how it happened.
    So? No one ever claimed that the "sudden" (you don't know that) appearance of any such component was the evidence supporting Darwinian evolution. The evidence of Darwinian evolutionary process (the existence of phylogeny, the agreement of taxonomy and genetic relationships, the fossil record, the observations of the process in the lab, the modeling and simulation results, the mathematical underpinning's agreement with observation, etc etc etc) is detailed and extensive, but it is in other forms.
    Quote Originally Posted by cypress
    Because evolutionary processes have not empirically been shown capable of producing even the most basic molecular events required to generate new protein function, it has been oversold
    A false premise. Evolutionary processes have produced new protein functions under controlled conditions in the frigging lab, for pity's sake - antibiotic resistance involves new protein function, for one - let alone the empirical investigations into the natural world.
    Quote Originally Posted by cypress
    I am not asking for very much.
    You are making an invalid argument, and avoiding the issues you have raised.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Sudden appearance in the past of new components is evidence that some process generated the components but that tells us nothing about how it happened.
    So? No one ever claimed that the "sudden" (you don't know that) appearance of any such component was the evidence supporting Darwinian evolution. The evidence of Darwinian evolutionary process (the existence of phylogeny, the agreement of taxonomy and genetic relationships, the fossil record,
    Good evidence for common descent but not the Darwinian process of evolution. It is not because this evidence tells us nothing of how the differences occured. How many times are you going to repeat this error?

    the observations of the process in the lab, the modeling and simulation results, the mathematical underpinning's agreement with observation, etc etc etc) is detailed and extensive, but it is in other forms.
    These examples would be evidence for a process but you are overselling them. None of these examples deomonstrate how evoultionary processes might generate new function. They fall short because none of them show any sign generating the basic molecular level changes required to generate new protein structures, new protein binding sites or any of the control and transport mechanisms. Molecular and cell biology has shown that these features are necessary for new protein funtion. Models and simulations fail because the simulations use targeted search but the theory is that natural selection is not a targeted search. Show me where I am wrong.

    Quote Originally Posted by cypress
    Because evolutionary processes have not empirically been shown capable of producing even the most basic molecular events required to generate new protein function, it has been oversold
    A false premise. Evolutionary processes have produced new protein functions under controlled conditions in the frigging lab, for pity's sake - antibiotic resistance involves new protein function, for one - let alone the empirical investigations into the natural world.
    Please demonstrate that aquired drug resistence involves generation of new protein funtion. Describe the changes and the new funtion. My understanding is that every studied case of aquired drug resistence involves one and rarely two point mutations that break protein function thus preventing the drug from exploiting the protein to kill the pathogen. Breaking existing function is not the same as generating new function. Also provide an empirical investigation that confirms generation of any event I listed.
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    evolutionary theory is predictive as it can be.


    Give me several samples of DNA from different organisms and I will tell you without ever seen the organisms which ones are more closely related.

    There is a constant quest for missing links. And guess what. They keep finding them! Do you think anyone would bother to look for transitional fossils if the theory of evolution didn't predict that they would exist? Only a complete idiot would.

    My current project has two different sets of regulatory genes of interest. That is, I subdivided them in two categories based on the theory of evolution, and now I can test in another species whether my prediction will be valid. And I'll bet you 1000 that it will be.

    Anyone who calls biology not predictive is a full blown idiot. And carl sagan was probably the biggest moron around for a while.
    "Kill them all and let God sort them out."

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    Quote Originally Posted by cypress
    Biologista, in another thread, one paper I provided described how over 1/3 of the genes studied were excluded from the results because they produced conflicting phylogenies. The process is nowhere as robust as you would have us believe. On the other hand biomedical research finds functional and structural similarity a useful study heuristic irrespective of the explanation.
    Again you ignore most of my points.

    How robust have I claimed "the process" to be? How much, in some quantifiable sense, have I "sold" evolution? There are some issues in molecular cladistics that stem from a couple of points. The amount of information available to the guy doing the analysis and the statistics we use to make judgements on mutations. Both produce error, and as a result we often end up with multiple possible paths between sequences. By various statistical means, the optimum is chosen. Sometimes, the optimum for one gene contradicts the optimum for the other. Does this mean that the phylogeny is in fact broken, does it reflect a limitation to our method or does it reflect a lack of sufficient information? The scale of the error we're talking about here is not very large. As the authors of that very paper (actually an essay rather than a research paper) note, this is a limitation on the resolution of the phylogeny. Not a falsification of it. We can still see quite clearly enough to find signs of other processes at work, if they're there. Else we could not have come to understand the extent to which lateral transfer and symbiosis were at work.
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    Quote Originally Posted by spuriousmonkey
    evolutionary theory is predictive as it can be.


    Give me several samples of DNA from different organisms and I will tell you without ever seen the organisms which ones are more closely related.
    I don't see where this tells us anything about the process of evolution. I do see how it demnstrates that we are able to classify organisms based on similarity. I would fully expect similar molecular structures to generate similar function. I would also expect similar molecular components, similar gene control and developmental control sequences to produce similar forms.

    There is a constant quest for missing links. And guess what. They keep finding them! Do you think anyone would bother to look for transitional fossils if the theory of evolution didn't predict that they would exist? Only a complete idiot would.
    I have yet to see an example of a direct line missing link or transionary organism. every time I hear of a new "missing link" with much fanfare, several months later I quietly hear that it has been reclassified to a cut off branch some distance from where it was initially placed. But once again this is only evidence for common descent. Missing links tell us nothing about the process of evolution. The issue here is the process, not the outcome. The outcome is self evident.

    My current project has two different sets of regulatory genes of interest. That is, I subdivided them in two categories based on the theory of evolution, and now I can test in another species whether my prediction will be valid. And I'll bet you 1000 that it will be.

    Anyone who calls biology not predictive is a full blown idiot. And carl sagan was probably the biggest moron around for a while.
    I would imagine you will think you have demonstrated something profound too.
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    Quote Originally Posted by marnixR
    it all depends what level of prediction you want to insist on - to me the prediction that matters is that given half a chance life will find a way against your pesticides, insecticides, antibiotics etc.

    if medical people had understood this they wouldn't have been bragging how they were winning the war against diseases in the early 60s just when the first resistant strains were starting to rear their ugly little heads
    maybe you can't tell exactly what defences will arise, but you can tell with 100% certainty that some sort of defence will arise, so you'd better start making plans for when it does
    Maybe you should start a new thread on this. Back in the 60-80's. Predictions were that evolution moved too slowly to observe so it was unlikely that new function would arise to counter the effects of antibiotics anytime soon. Now we know that drug resistence occurs through a much more pragmatic mechanism whereby a key protein is damaged and therefore the drug can no longer use the protein to exploit that pathway to destroy the pathogen. Evolutionary theory predicts new funtion, not breaking or discarding existing funtion, in a sort of triage or bridge burning to prevent attack.

    Furthermore the damaged protein is best classified a case of adaptation of existing function. In these cases the adaptation is to damage or disable function.
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    [quote="cypress"]
    Quote Originally Posted by spuriousmonkey
    There is a constant quest for missing links. And guess what. They keep finding them! Do you think anyone would bother to look for transitional fossils if the theory of evolution didn't predict that they would exist? Only a complete idiot would.
    I have yet to see an example of a direct line missing link or transionary organism. every time I hear of a new "missing link" with much fanfare, several months later I quietly hear that it has been reclassified to a cut off branch some distance from where it was initially placed. But once again this is only evidence for common descent. Missing links tell us nothing about the process of evolution. The issue here is the process, not the outcome. The outcome is self evident.
    You dont pay any attention to paleontology at all then do you? please provide examples of NONnewsmedia papers that demonstrate your claim
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    Quote Originally Posted by Paleoichneum
    Quote Originally Posted by cypress
    Quote Originally Posted by spuriousmonkey
    There is a constant quest for missing links. And guess what. They keep finding them! Do you think anyone would bother to look for transitional fossils if the theory of evolution didn't predict that they would exist? Only a complete idiot would.
    I have yet to see an example of a direct line missing link or transionary organism. every time I hear of a new "missing link" with much fanfare, several months later I quietly hear that it has been reclassified to a cut off branch some distance from where it was initially placed. But once again this is only evidence for common descent. Missing links tell us nothing about the process of evolution. The issue here is the process, not the outcome. The outcome is self evident.
    You dont pay any attention to paleontology at all then do you? please provide examples of NONnewsmedia papers that demonstrate your claim
    What the claim that no transitory organism is in a direct evolutionary line between two others? In other words the later two organisms do not have morphologies that are completely consistent with and are therefore not direct descendents of the first? Do you say I am wrong about this? I don't find any cooroborated research articles that contradict my claim... Not one.

    However, the point here is that paleontology can never tell us how evolutionary processes might have generated the changes. The rest just emphasises consistency in the practice of overselling the theory.
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    Quote Originally Posted by TheBiologista
    How robust have I claimed "the process" to be? How much, in some quantifiable sense, have I "sold" evolution? There are some issues in molecular cladistics that stem from a couple of points. The amount of information available to the guy doing the analysis and the statistics we use to make judgements on mutations. Both produce error, and as a result we often end up with multiple possible paths between sequences. By various statistical means, the optimum is chosen. Sometimes, the optimum for one gene contradicts the optimum for the other. Does this mean that the phylogeny is in fact broken, does it reflect a limitation to our method or does it reflect a lack of sufficient information? The scale of the error we're talking about here is not very large. As the authors of that very paper (actually an essay rather than a research paper) note, this is a limitation on the resolution of the phylogeny. Not a falsification of it. We can still see quite clearly enough to find signs of other processes at work, if they're there. Else we could not have come to understand the extent to which lateral transfer and symbiosis were at work.
    Since you seem to have nothing further for me, I'll add to this. The authors point out that sometimes the optimal phylogeny for a gene is contradicted by the phylogeny for another gene in the same species- the 35% figure you mention. That doesn't mean that the set of phylogenies for both genes do not contain phylogenies that match up, but rather that the ones that match are statistically sub-optimal. A warning to anyone who would be short-sighted enough to derive a phylogeny from a single gene by picking the optimal tree.

    Since multiple possible phylogenies are generated even with the best available data (it's a probabilistic result), the real evidence that you are looking for is an example where the set of plausible phylogenies for gene A contradict the plausible set of phylogenies for gene B in species X. You want mutually exclusive sets. Find that example and you have a clear cut case of a phylogeny that cannot be explained by mutation and selection alone. Once you've got that, you need to show that the conflict cannot be explained by a lateral transfer or endosymbiosis. Both of which have known limitations and lots of tell-tale implications making them very much testable.

    Quote Originally Posted by cypress
    I have yet to see an example of a direct line missing link or transionary organism. every time I hear of a new "missing link" with much fanfare, several months later I quietly hear that it has been reclassified to a cut off branch some distance from where it was initially placed.
    An example being? Since you say "every", I assume you have multiple examples from the research literature of fossils being first given "missing link" status and then being relegated to a "cut off" branch?
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    Quote Originally Posted by TheBiologista

    Since you seem to have nothing further for me, ...
    You continue to detract and diverge from the topic of the thread. You might consider splitting your comments from this one.

    No amount of discussion about how nicely or in this case, not, the similarities in organisms line up, it does not provide any significant insight into how evolutionary processes might, or don't, account for the differences.

    Quote Originally Posted by cypress
    I have yet to see an example of a direct line missing link or transionary organism. every time I hear of a new "missing link" with much fanfare, several months later I quietly hear that it has been reclassified to a cut off branch some distance from where it was initially placed.
    An example being? Since you say "every", I assume you have multiple examples from the research literature of fossils being first given "missing link" status and then being relegated to a "cut off" branch?
    I don't recall saying I saw these mentioned in research papers. I suspect though, if I looked hard enough, I would have no trouble finding at least one, surly you agree there are at least a few overzelous researchers? The comment is not central to my point though and I have better things to do, forgive me for declining your request.
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista

    Since you seem to have nothing further for me, ...
    You continue to detract and diverge from the topic of the thread. You might consider splitting your comments from this one.
    We're talking about whether evolution is predictive. My points about phylogeny address that. Your arguments against that are also relevant to the topic. We're still on that topic, so this is still relevant. If I'm off topic and just not seeing it then I will welcome a split if paralith thinks it's appropriate.

    Quote Originally Posted by cypress
    No amount of discussion about how nicely or in this case, not, the similarities in organisms line up, it does not provide any significant insight into how evolutionary processes might, or don't, account for the differences.
    I'm sorry but that's a ridiculous statement. If similarities were all that we looked at there'd be no phylogeny at all, there'd just be one node with everything in it labelled "nucleic acids" or somesuch. Similarities make up nodes, differences generate branches. The two together make up a phylogeny and the topography of the phylogeny informs the nature of the relationship between nodes in terms both of similarities and differences.

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    I have yet to see an example of a direct line missing link or transionary organism. every time I hear of a new "missing link" with much fanfare, several months later I quietly hear that it has been reclassified to a cut off branch some distance from where it was initially placed.
    An example being? Since you say "every", I assume you have multiple examples from the research literature of fossils being first given "missing link" status and then being relegated to a "cut off" branch?
    I don't recall saying I saw these mentioned in research papers. I suspect though, if I looked hard enough, I would have no trouble finding at least one, surly you agree there are at least a few overzelous researchers? The comment is not central to my point though and I have better things to do, forgive me for declining your request.
    I'll certainly agree that there are researchers who have courted the media and overstated their findings. And the media have grotesquely misrepresented scientific findings across all fields since the media came into being. What matters to our argument is how the findings are dealt with by researchers.
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    Quote Originally Posted by cypress
    Good evidence for common descent but not the Darwinian process of evolution. It is not because this evidence tells us nothing of how the differences occured. How many times are you going to repeat this error?
    How many times are you going to overlook the fact that common descent is good evidence for Darwinian evolution?

    It's the theory's job to explain the evidence, not the other way around.
    Quote Originally Posted by cypress
    None of these examples deomonstrate how evoultionary processes might generate new function.
    But Darwinian theory does. And its predictions agree fully with observation.
    Quote Originally Posted by cypress
    Models and simulations fail because the simulations use targeted search but the theory is that natural selection is not a targeted search. Show me where I am wrong.
    Models and simulations of Darwinian evolution do not use targeted search. That would be a gross error in modeling or simulation.
    Quote Originally Posted by cypress
    My understanding is that every studied case of aquired drug resistence involves one and rarely two point mutations that break protein function thus preventing the drug from exploiting the protein to kill the pathogen.
    That's goofy. You need to quit getting your stuff from creationist PR, where people make idiotic claims about "no new information" and "mutations are damaging" and "the chances of so many simultaneous mutations are vanishingly small" and so forth. The world is full of easily obtained information about such matters, and the simplest of internet searches will hand you all kinds of stuff like this .
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    Quote Originally Posted by TheBiologista

    Quote Originally Posted by cypress
    No amount of discussion about how nicely or in this case, not, the similarities in organisms line up, it does not provide any significant insight into how evolutionary processes might, or don't, account for the differences.
    I'm sorry but that's a ridiculous statement. If similarities were all that we looked at there'd be no phylogeny at all, there'd just be one node with everything in it labelled "nucleic acids" or somesuch. Similarities make up nodes, differences generate branches. The two together make up a phylogeny and the topography of the phylogeny informs the nature of the relationship between nodes in terms both of similarities and differences.
    How do these relationships inform us about how the differences occured and what process generated the differences? It doesn't.

    How do these relationships inform us that known evolutionary processes are capable of generating these differences? It doesn't.

    How do these relationships inform us that other non-evolutionary processes that have been demonstrated and are capable of generating basic alterations required for molecular level differences were not involved? It doesn't
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Good evidence for common descent but not the Darwinian process of evolution. It is not because this evidence tells us nothing of how the differences occurred. How many times are you going to repeat this error?
    How many times are you going to overlook the fact that common descent is good evidence for Darwinian evolution?
    Endlessly. It simply is not because evolution is a process not an end state. See my last post.


    Quote Originally Posted by cypress
    None of these examples demonstrate how evolutionary processes might generate new function.
    But Darwinian theory does. And its predictions agree fully with observation.
    And yet you haven't provided even one example of new function involving multiple protein components. How odd that you can say the words so easily yet you can't support your claim.

    Quote Originally Posted by cypress
    Models and simulations fail because the simulations use targeted search but the theory is that natural selection is not a targeted search. Show me where I am wrong.
    Models and simulations of Darwinian evolution do not use targeted search. That would be a gross error in modeling or simulation.
    Please provide an example of a model that does not use a target or contrived search aids.

    Quote Originally Posted by cypress
    My understanding is that every studied case of acquired drug resistance involves one and rarely two point mutations that break protein function thus preventing the drug from exploiting the protein to kill the pathogen.
    That's goofy. You need to quit getting your stuff from creationist PR, where people make idiotic claims about "no new information" and "mutations are damaging" and "the chances of so many simultaneous mutations are vanishingly small" and so forth. The world is full of easily obtained information about such matters, and the simplest of internet searches will hand you all kinds of stuff like this .
    The first examples are of pre-existing antibiotic resistance. They do not arise from mutation and selection. They were in existence prior to introduction of modern antibiotics and I excluded them for that reason. Note that I used the term acquired to refer to mutation and selection. HGT is excluded unless you can demonstrate that evolutionary processes generated the B-Lactamase and the other enzymes in the first place. Let's talk about the other examples. The second involve damage to the one of the cell access and/or egress points. The third involves alteration of the site that the antibiotic exploits. These are clear cases of damaged protein function. The forth case is alteration of another enzyme causing it to bind the antibiotic. This is a clear case of damaging the previous enzyme function. These cases thus far are known only to weaken the pathogen as compared to its non-mutated form. Now you can argue that the weaker form has selective advantage in an antibiotic environment and that is true. However evolution predicts improved and new function while this is a case of damaged function.
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    Quote Originally Posted by cypress
    Endlessly. It simply is not because evolution is a process not an end state. See my last post.
    and YOU seem to totally disregard my post where i clearly stated that evolution is fact, path and process - in all 3 areas prediction is possible to a greater or lesser degree

    i just don't see why you should want a narrow definition of what evolution really is, unless you feel that you're on dodgier grounds with the other 2 ?
    "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
    Quote Originally Posted by Paleoichneum
    Quote Originally Posted by cypress
    Quote Originally Posted by spuriousmonkey
    There is a constant quest for missing links. And guess what. They keep finding them! Do you think anyone would bother to look for transitional fossils if the theory of evolution didn't predict that they would exist? Only a complete idiot would.
    I have yet to see an example of a direct line missing link or transionary organism. every time I hear of a new "missing link" with much fanfare, several months later I quietly hear that it has been reclassified to a cut off branch some distance from where it was initially placed. But once again this is only evidence for common descent. Missing links tell us nothing about the process of evolution. The issue here is the process, not the outcome. The outcome is self evident.
    You dont pay any attention to paleontology at all then do you? please provide examples of NONnewsmedia papers that demonstrate your claim
    What the claim that no transitory organism is in a direct evolutionary line between two others? In other words the later two organisms do not have morphologies that are completely consistent with and are therefore not direct descendents of the first? Do you say I am wrong about this? I don't find any cooroborated research articles that contradict my claim... Not one.

    However, the point here is that paleontology can never tell us how evolutionary processes might have generated the changes. The rest just emphasises consistency in the practice of overselling the theory.
    Check out the fossil records of Gerridae and Ginkgo biloba before claiming no morphological simiarities found. Both have apparent morph. stability extiending back over 48 million years.

    what exactly is not consistent within paleontology and modern evolutionary theory, why should not know the process generating negate the fact of well established lines of fossils from one taxon to another throughout the fossil record??

    and I'm still waiting for he non-newsmedia sources for your claim, not lust woowoo saying you couldn't find refutation of your claim you made in response to my request for sources
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista

    Quote Originally Posted by cypress
    No amount of discussion about how nicely or in this case, not, the similarities in organisms line up, it does not provide any significant insight into how evolutionary processes might, or don't, account for the differences.
    I'm sorry but that's a ridiculous statement. If similarities were all that we looked at there'd be no phylogeny at all, there'd just be one node with everything in it labelled "nucleic acids" or somesuch. Similarities make up nodes, differences generate branches. The two together make up a phylogeny and the topography of the phylogeny informs the nature of the relationship between nodes in terms both of similarities and differences.
    How do these relationships inform us about how the differences occured and what process generated the differences? It doesn't.
    Yes it does. The frequency at which branches derive from nodes tells us something about how the variation is being generated. It correlates with generation time, which is what we would expect if the variation were being generated by inherited mutations. It correlates with the size of the genome of the species at a given node, which is what we'd expect if the variation were based on random changes to that genome. In summary- variation correlates with the rate at which we have observed mutation to occur, so long as we also allow for HGT and similar rare event. So if something else is contributing to variation, it is either much less significant than the currently known processes, or it is substituting for them but only when we are not looking.

    Quote Originally Posted by cypress
    How do these relationships inform us that known evolutionary processes are capable of generating these differences? It doesn't.
    Again, it does. We expect a pure bifurcating topology if natural, artificial or sexual selection are at work. We expect a bifurcating topology with collisions at a low frequency if NS plus HGT are at work. We expect the same plus a few rather large collisions if these plus endosymbiosis are at work. If the process were HGT alone, we'd expect a loose web with no evidence of bifurcation. With endosymbioisis alone, we'd expect an even looser web. Both would also have very few nodes. If the main processes were genetic engineering- well that's a tricky one. We expect a web, but the density of the web, the frequency of branching events and the number of nodes depends strongly on the intent and nature of the agent using that technique. Similarly if an agent were changing the mutagenesis rate or biasing it in some way, we'd need to know some things about that agent in order to test that. If we have enough information about the agent, we can make judgements on both based on the topography of the phylogeny, though we can of course also refer to basic chemical laws to make some comparisons regarding mutation rates.

    Quote Originally Posted by cypress
    How do these relationships inform us that other non-evolutionary processes that have been demonstrated and are capable of generating basic alterations required for molecular level differences were not involved? It doesn't
    Well, as I've explained above- we can certainly make some judgement regarding the natural processes we've identified. I wouldn't rule out other contributors to evolution, but without defining those contributors, it's pretty hard to test for them. Which is why suggestions that there is more going on demand some sort of proposition, a hypothesis that we can test.
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    How do these relationships inform us about how the differences occured and what process generated the differences? It doesn't.
    Yes it does. The frequency at which branches derive from nodes tells us something about how the variation is being generated. It correlates with generation time, which is what we would expect if the variation were being generated by inherited mutations. It correlates with the size of the genome of the species at a given node, which is what we'd expect if the variation were based on random changes to that genome. In summary- variation correlates with the rate at which we have observed mutation to occur, so long as we also allow for HGT and similar rare event. So if something else is contributing to variation, it is either much less significant than the currently known processes, or it is substituting for them but only when we are not looking.
    How does frequency reveal whether the alterations are occuring stepwise or in multiple steps? How does it indicate the process by which a novel protein forms? How does it show us the process by which gene expression controls and developmental controls are modified to manage new function?

    Frequency and variation patterns are consistent with any number of processes. These observations are not exclusive to a theory that postulates stepwise modification. A pridiction that does not eliminate alternatives does not provide any new explanitory power.

    Since a long list of precursor molecular changes required to account for new cellular and protein function have not been generated by known evoultionary processes, why would we buck conventional wisdom and continue to presuppose that they do? Since we know of other processes that have generated these changes we can't properly throw up our hands and claim "what else could have?".

    Quote Originally Posted by cypress
    How do these relationships inform us that known evolutionary processes are capable of generating these differences? It doesn't.
    Again, it does. We expect a pure bifurcating topology if natural, artificial or sexual selection are at work. We expect a bifurcating topology with collisions at a low frequency if NS plus HGT are at work. We expect the same plus a few rather large collisions if these plus endosymbiosis are at work. If the process were HGT alone, we'd expect a loose web with no evidence of bifurcation. With endosymbioisis alone, we'd expect an even looser web. Both would also have very few nodes. If the main processes were genetic engineering- well that's a tricky one. We expect a web, but the density of the web, the frequency of branching events and the number of nodes depends strongly on the intent and nature of the agent using that technique. Similarly if an agent were changing the mutagenesis rate or biasing it in some way, we'd need to know some things about that agent in order to test that. If we have enough information about the agent, we can make judgements on both based on the topography of the phylogeny, though we can of course also refer to basic chemical laws to make some comparisons regarding mutation rates.
    But you didn't answer the question. You answered why one might suppose certain processes could be in play, but you did not address the question of capability. You passed over the question completely. Of course the reason is that this kind of evidence doesn't and can't answer the question posed.

    Quote Originally Posted by cypress
    How do these relationships inform us that other non-evolutionary processes that have been demonstrated and are capable of generating basic alterations required for molecular level differences were not involved? It doesn't
    Well, as I've explained above- we can certainly make some judgement regarding the natural processes we've identified. I wouldn't rule out other contributors to evolution, but without defining those contributors, it's pretty hard to test for them. Which is why suggestions that there is more going on demand some sort of proposition, a hypothesis that we can test.
    Agreed. The first step is recognizing the need to look at alternatives.
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    Quote Originally Posted by marnixR
    Quote Originally Posted by cypress
    Endlessly. It simply is not because evolution is a process not an end state. See my last post.
    and YOU seem to totally disregard my post where i clearly stated that evolution is fact, path and process - in all 3 areas prediction is possible to a greater or lesser degree

    i just don't see why you should want a narrow definition of what evolution really is, unless you feel that you're on dodgier grounds with the other 2 ?
    Start another post on that topic and I will be happy to discuss it. Here I only need to show that the process has an issue so I considered the other two areas a distraction.

    However, if you feel the theory is supported by extension of what it can explain to areas that it hasn't then let's have a look.
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    Quote Originally Posted by cypress
    And yet you haven't provided even one example of new function involving multiple protein components.
    Antibiotic resistance. Herbicide resistance. New species emergence ( in various places, recently).

    And that's ignoring the large visible record of such emergent new functions, in the current functions of many proteins in living beings.

    You have been presented with these examples many times now.

    Quote Originally Posted by cypress
    Please provide an example of a model that does not use a target or contrived search aids.
    What is a "contrived search aid"? What is a "target", other than the selection criteria of a Darwinian system?

    Any model that used a target other than a selection criterion would of course not be Darwinian.

    Anyway: Many neural net trainng programs employ Darwinian procedures. Toys like this or this . And so forth .
    Quote Originally Posted by cypress
    Let's talk about the other examples. The second involve damage to the one of the cell access and/or egress points. The third involves alteration of the site that the antibiotic exploits. These are clear cases of damaged protein function. The forth case is alteration of another enzyme causing it to bind the antibiotic. This is a clear case of damaging the previous enzyme function.
    Why do you confuse effective new function with "damage"?
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    And yet you haven't provided even one example of new function involving multiple protein components.
    Antibiotic resistance. Herbicide resistance. New species emergence ( in various places, recently).

    And that's ignoring the large visible record of such emergent new functions, in the current functions of many proteins in living beings.

    You have been presented with these examples many times now.
    They are interesting but they are not examples of what I asked for. You know this but you stubbornly continue to offer them. let's drill down to the molecular level on any one that you think answers the question. Provide the molecular details of the modification and show how a known evolutionary process accomplished the molecular modifications. Demonstrate each step. Demonstrate that the modified protein is part of a structure of many protein components.

    Quote Originally Posted by cypress
    Please provide an example of a model that does not use a target or contrived search aids.
    What is a "contrived search aid"? What is a "target", other than the selection criteria of a Darwinian system?

    Any model that used a target other than a selection criterion would of course not be Darwinian.

    Anyway: Many neural net trainng programs employ Darwinian procedures. Toys like this or this . And so forth .
    I started a new thread for this. Take one of these examples with you. The best one, if you think it accurately reflects the capability of Darwinian processes.

    Quote Originally Posted by cypress
    Let's talk about the other examples. The second involve damage to the one of the cell access and/or egress points. The third involves alteration of the site that the antibiotic exploits. These are clear cases of damaged protein function. The forth case is alteration of another enzyme causing it to bind the antibiotic. This is a clear case of damaging the previous enzyme function.
    Why do you confuse effective new function with "damage"?
    I don't . The alterations damages and weakens previous function and does not add any new biologically significant activity. Are you trying to redefine what new function means?
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    How do these relationships inform us about how the differences occured and what process generated the differences? It doesn't.
    Yes it does. The frequency at which branches derive from nodes tells us something about how the variation is being generated. It correlates with generation time, which is what we would expect if the variation were being generated by inherited mutations. It correlates with the size of the genome of the species at a given node, which is what we'd expect if the variation were based on random changes to that genome. In summary- variation correlates with the rate at which we have observed mutation to occur, so long as we also allow for HGT and similar rare event. So if something else is contributing to variation, it is either much less significant than the currently known processes, or it is substituting for them but only when we are not looking.
    How does frequency reveal whether the alterations are occuring stepwise or in multiple steps? How does it indicate the process by which a novel protein forms? How does it show us the process by which gene expression controls and developmental controls are modified to manage new function?

    Frequency and variation patterns are consistent with any number of processes. These observations are not exclusive to a theory that postulates stepwise modification. A pridiction that does not eliminate alternatives does not provide any new explanitory power.
    It does if we can't find plausible alternatives which would produce the same topology. If you know of some, please let us know.

    Quote Originally Posted by cypress
    Since a long list of precursor molecular changes required to account for new cellular and protein function have not been generated by known evoultionary processes, why would we buck conventional wisdom and continue to presuppose that they do? Since we know of other processes that have generated these changes we can't properly throw up our hands and claim "what else could have?".
    Always comes back to the same topic with you, doesn't it?

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    How do these relationships inform us that known evolutionary processes are capable of generating these differences? It doesn't.
    Again, it does. We expect a pure bifurcating topology if natural, artificial or sexual selection are at work. We expect a bifurcating topology with collisions at a low frequency if NS plus HGT are at work. We expect the same plus a few rather large collisions if these plus endosymbiosis are at work. If the process were HGT alone, we'd expect a loose web with no evidence of bifurcation. With endosymbioisis alone, we'd expect an even looser web. Both would also have very few nodes. If the main processes were genetic engineering- well that's a tricky one. We expect a web, but the density of the web, the frequency of branching events and the number of nodes depends strongly on the intent and nature of the agent using that technique. Similarly if an agent were changing the mutagenesis rate or biasing it in some way, we'd need to know some things about that agent in order to test that. If we have enough information about the agent, we can make judgements on both based on the topography of the phylogeny, though we can of course also refer to basic chemical laws to make some comparisons regarding mutation rates.
    But you didn't answer the question. You answered why one might suppose certain processes could be in play, but you did not address the question of capability. You passed over the question completely. Of course the reason is that this kind of evidence doesn't and can't answer the question posed.
    Actually I agree with you on that- I didn't read your question properly. Phylogeny alone doesn't tell us that the processes cited are capable of producing the phylogeny. Directed mutagenesis, artificial selection and other experiments tell us that mutation/selection can plausibly do it. The phylogeny is itself a prediction of the hypothesis that the relationship is based on mutation and selection, rather than the other way around. It supports the hypothesis, rather than predicting the capacity. But that means that the theory- which states that evolution occurs by mutation and selection- is predictive. It predicts a phylogeny of a specific topology, which we see.

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    How do these relationships inform us that other non-evolutionary processes that have been demonstrated and are capable of generating basic alterations required for molecular level differences were not involved? It doesn't
    Well, as I've explained above- we can certainly make some judgement regarding the natural processes we've identified. I wouldn't rule out other contributors to evolution, but without defining those contributors, it's pretty hard to test for them. Which is why suggestions that there is more going on demand some sort of proposition, a hypothesis that we can test.
    Agreed. The first step is recognizing the need to look at alternatives.
    But I would contend that we see no such need right now. We have in the past. But in those cases, a specific need for an extra process was identified positively, not by an appeal to ignorance. Those scientists you quoted before who did so much work on HGT and endosymbioisis did not start out by contending that mutation and selection couldn't do the most basic tasks required of them. They identified specific cases where the phylogeny seemed to have been broken, hypothesised as to how this might have occurred and then went about testing that hypothesis. Your negative position doesn't really moving things forward in this way.
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  90. #89 Fed up with this trolling 
    Forum Professor sunshinewarrior's Avatar
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    Dear (Sad?) Cypress

    1. The topic of this thread is whether or not modern evolutionary models have predictive power. Many posters here (including I) have provided examples of successful predictions based upon evolutionary theory that no other theory makes. The OP is, therefore, answered. For you to keep on about your particular hobby-horse (which appears not greatly distinct from Michael Behe's discredited nonsense about molecular machines) is a non sequitur, therefore, and a sign of trolling.

    2. You keep trying to imply that evolution must be limited to random genetic mutation rather than, as the theory has always said, whatever it is that causes variation upon which selection can work (mutation, horizontal genetic transfer, endosymbiosis et al). This is an example of the Strawman fallacy in logic and a clear sign of trolling.

    3. When I pointed out that the self-referential nature of biological systems would mathematically preclude (in terms of mathematical Chaos) perfectly Newtonian predictability, no matter what model was used, you smugly claimed that as a vindication of your position regarding evolutionary theory: an egregious misunderstanding that is yet another sign of trolling.

    If it waddles like a troll and quacks like a troll...

    I'm sorry but I have recommended that you be banned: you are wasting bandwidth for which you haven't paid and to which you are not contributing intellectually. Your posts show up a lack of a professional scientific background, a bee in your bonnet, and an inability to learn when genuine learning is presented to you.

    Please go away before you are sent, or as my USian friends might say 'shape up or ship out'.

    cheer

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    Quote Originally Posted by cypress
    I don't . The alterations damages and weakens previous function and does not add any new biologically significant activity. Are you trying to redefine what new function means?
    Actually, I suspect you may not understand how we think about function in biology or rather don't. We think about adaptation and exaptation, which I suppose could be said to be the same thing as function. Anything that undergoes positive selection, and is therefore increasing fitness under the current selective context, has "function" of some sort. It doesn't have to be engaging in a complex reaction or forming a vital point in a signal chain to be functional. For example, a normally membrane-bound receptor might undergo a mutation which renders it a secreted protein. This would be considered a loss of function under most contexts. But if that receptor is normally an entry point for a virus which is very common, the secreted receptor now has a function as a decoy. It is performing a neutralising function, somewhat like that of immunoglobulin. It's also an active function, rather than a passive function such as we see with examples such as the CCR5d32 mutation which loses us a receptor function and provides an HIV protective function but does so by failing to express the HIV binding site on the cell surface, rather than doing something as in the first example.

    Both are kinds of function though, or more correctly are kinds of adaptation. Actually both are exaptation, I think.
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  92. #91  
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    I don't . The alterations damages and weakens previous function and does not add any new biologically significant activity. Are you trying to redefine what new function means?
    Actually, I suspect you may not understand how we think about function in biology or rather don't. We think about adaptation and exaptation, which I suppose could be said to be the same thing as function. Anything that undergoes positive selection, and is therefore increasing fitness under the current selective context, has "function" of some sort. It doesn't have to be engaging in a complex reaction or forming a vital point in a signal chain to be functional. For example, a normally membrane-bound receptor might undergo a mutation which renders it a secreted protein. This would be considered a loss of function under most contexts. But if that receptor is normally an entry point for a virus which is very common, the secreted receptor now has a function as a decoy. It is performing a neutralising function, somewhat like that of immunoglobulin. It's also an active function, rather than a passive function such as we see with examples such as the CCR5d32 mutation which loses us a receptor function and provides an HIV protective function but does so by failing to express the HIV binding site on the cell surface, rather than doing something as in the first example.

    Both are kinds of function though, or more correctly are kinds of adaptation. Actually both are exaptation, I think.
    Lovely explanation. Am betting Sad Cypress misinterprets this as function meaning 'anything that happens' or circular reasoning or some other such ludicrousness.
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress

    How does frequency reveal whether the alterations are occuring stepwise or in multiple steps? How does it indicate the process by which a novel protein forms? How does it show us the process by which gene expression controls and developmental controls are modified to manage new function?

    Frequency and variation patterns are consistent with any number of processes. These observations are not exclusive to a theory that postulates stepwise modification. A pridiction that does not eliminate alternatives does not provide any new explanitory power.
    It does if we can't find plausible alternatives which would produce the same topology. If you know of some, please let us know.
    Alternative explanations are not welcome on this portion of the site according to the rules. Alternatives must be brought up in "alternative theories". Of course you realize that. You can't find what you don't look for. However there are indeed a number of plausible alternatives that would produce the same topology, and I suspect even you know this. This is why frequency and patterns are insufficient. This is why one also must show that the process is capable of producing the effect. It is only then that you can eliminate the alternatives.

    Quote Originally Posted by cypress
    Since a long list of precursor molecular changes required to account for new cellular and protein function have not been generated by known evoultionary processes, why would we buck conventional wisdom and continue to presuppose that they do? Since we know of other processes that have generated these changes we can't properly throw up our hands and claim "what else could have?".
    Always comes back to the same topic with you, doesn't it?
    I think you should admit that it is the crux of the issue; that the inability to explain the curious absence of observations keeps alternative explanations in play. In QM, inability to explain singularities and inability to identify universal equations of force are what causes them to treat many aspects of QM as tentative. Refusal to do the same here raises questions. It makes it seem like you are defending an ideology rather than discussing the facts. If you admit that then we can move on.

    Actually I agree with you on that- I didn't read your question properly. Phylogeny alone doesn't tell us that the processes cited are capable of producing the phylogeny. Directed mutagenesis, artificial selection and other experiments tell us that mutation/selection can plausibly do it. The phylogeny is itself a prediction of the hypothesis that the relationship is based on mutation and selection, rather than the other way around. It supports the hypothesis, rather than predicting the capacity. But that means that the theory- which states that evolution occurs by mutation and selection- is predictive. It predicts a phylogeny of a specific topology, which we see.
    Right, except in the many cases (roughly 30% of the time) when we don't see a phylogeny consistent with the predicted topology. With respect to the basic aspects of DNA replication and establishment of a phylogeny between prokaryotes and eukaryotes we have a disconnect:

    It is therefore surprising that the protein sequences of several central components of the DNA replication machinery, above all the principal replicative polymerases, show very little or no sequence similarity between bacteria and archaea/eukaryotes. (a)

    In particular, and counter-intuitively, given the central role of DNA in all cells and the mechanistic uniformity of replication, the core enzymes of the replication systems of bacteria and archaea (as well as eukaryotes) are unrelated or extremely distantly related. Viruses and plasmids, in addition, possess at least two unique DNA replication systems, namely, the protein-primed and rolling circle modalities of replication. This unexpected diversity makes the origin and evolution of DNA replication systems a particularly challenging and intriguing problem in evolutionary biology. (b)

    If the prokaryote-to-eukaryote transition came about by normal evolutionary mechanisms, then given the enormity of the structural and molecular differences between these two cell types, this transformation must have occurred over a very long period involving numerous intermediate species, each developing limited selective advantages and evolving certain eukaryotic characteristics. However, there is no evidence (living or fossil) for the existence of any such intermediate organisms, despite the great diversity of the prokaryotic and eukaryotic organisms that preceded or followed this major change.(c)

    a. D. Leipe, L. Aravind, E. V. Koonin, Did DNA replication evolve twice independently?, Nucleic Acids Research 27 (1999): 3389-3401.

    b. E. V. Koonin, Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases, Biology Direct 18 (2006): 1-39.

    c. R. S. Gupta, Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes, Microbiology and Molecular Biology Reviews 62 (1998): 1435-1491.

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    How do these relationships inform us that other non-evolutionary processes that have been demonstrated and are capable of generating basic alterations required for molecular level differences were not involved? It doesn't
    Well, as I've explained above- we can certainly make some judgement regarding the natural processes we've identified. I wouldn't rule out other contributors to evolution, but without defining those contributors, it's pretty hard to test for them. Which is why suggestions that there is more going on demand some sort of proposition, a hypothesis that we can test.
    Agreed. The first step is recognizing the need to look at alternatives.
    But I would contend that we see no such need right now. We have in the past. But in those cases, a specific need for an extra process was identified positively, not by an appeal to ignorance. Those scientists you quoted before who did so much work on HGT and endosymbioisis did not start out by contending that mutation and selection couldn't do the most basic tasks required of them. They identified specific cases where the phylogeny seemed to have been broken, hypothesised as to how this might have occurred and then went about testing that hypothesis. Your negative position doesn't really moving things forward in this way.
    Right, they passed over a difficult but critical aspect of the theory to to partially address an easier but entirely different issue. Clearly though HGT and the far less certain endosymbiosis only address a few of the difficulties. There is an endless set of examples including the one above that are unanserable by these processes.
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    Quote Originally Posted by cypress
    Alternative explanations are not welcome on this portion of the site according to the rules.
    False. If you had an alternative explanation, it would be welcome.

    Mind you, it would have to explain something.
    Quote Originally Posted by cypress
    However there are indeed a number of plausible alternatives that would produce the same topology,
    No, there aren't. Standard evolutionary theory handled an absence of plausible explanation that had dogged biology for hundreds of years, and nothing has come along since except refinements of it.
    Quote Originally Posted by cypress
    Right, except in the many cases (roughly 30% of the time) when we don't see a phylogeny consistent with the predicted topology.
    Standard evolutionary theory and the geological history of the planet predict that - if you mean by " predicted topology" what one assumes you mean. You seem unfamiliar with these big words and technical terms.
    Quote Originally Posted by cypress
    This is why one also must show that the process is capable of producing the effect. It is only then that you can eliminate the alternatives.
    There are no alternatives, at present. And the process of Darwinian evolution has been shown (it's pretty easy) capable of producing almost anything in the way of complexity, variation, etc. It's capability is not in serious question. That's one of the occasional criticisms of it - it's too easy to cook up Just So Stories to explain anything, within it.
    Quote Originally Posted by cypress
    With respect to the basic aspects of DNA replication and establishment of a phylogeny between prokaryotes and eukaryotes we have a disconnect:
    - - -
    Clearly though HGT and the far less certain endosymbiosis only address a few of the difficulties. There is an endless set of examples including the one above that are unanserable by these processes.
    Failures of imagination and easy claims of incredulity are not serious arguments.

    For one thing, if there were shown to have been two or more "origins of life", with evolutionary descendants from them all alive today, so what? We note that accepting the evolutionary explanation of any given major phylogeny of any of the Eukaryotes alone dismisses your claims of impossibility regarding the evolution of complex proteins.
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    I would love to hear an alternative plausible scientific theory.

    Give it to me. I am just dying to hear it. PLEASE!
    "Kill them all and let God sort them out."

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    Quote Originally Posted by spuriousmonkey
    I would love to hear an alternative plausible scientific theory.

    Give it to me. I am just dying to hear it. PLEASE!
    Start a new thread on it, but all of the previous threads on this topic were removed from the science section.
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  97. #96  
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    Quote Originally Posted by cypress
    Quote Originally Posted by spuriousmonkey
    I would love to hear an alternative plausible scientific theory.

    Give it to me. I am just dying to hear it. PLEASE!
    Start a new thread on it, but all of the previous threads on this topic were removed from the science section.
    Why don't you start it in the New Hypothesis and Ideas section? That is what it is for.
    Disclaimer: I do not declare myself to be an expert on ANY subject. If I state something as fact that is obviously wrong, please don't hesitate to correct me. I welcome such corrections in an attempt to be as truthful and accurate as possible.

    "Gullibility kills" - Carl Sagan
    "All people know the same truth. Our lives consist of how we chose to distort it." - Harry Block
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Alternative explanations are not welcome on this portion of the site according to the rules.
    False. If you had an alternative explanation, it would be welcome.
    Sorry, that's not true. Past moderator practices provide good heuristics on this point.

    Mind you, it would have to explain something.
    Actually I have previously learned it would only have to conform to the prior commitments of the moderators or conform to the opinions of talkorigns. Whether or not it had explanatory power is secondary.

    Quote Originally Posted by cypress
    However there are indeed a number of plausible alternatives that would produce the same topology,
    No, there aren't. Standard evolutionary theory handled an absence of plausible explanation that had dogged biology for hundreds of years, and nothing has come along since except refinements of it.
    I'm not suggesting that biology be completely overturned either. Regardless, there are plausible alternatives to mutation and selection being actively researched that would produce the same diversity and molecular configurations we observe.

    Quote Originally Posted by cypress
    Right, except in the many cases (roughly 30% of the time) when we don't see a phylogeny consistent with the predicted topology.
    Standard evolutionary theory and the geological history of the planet predict that - if you mean by " predicted topology" what one assumes you mean. You seem unfamiliar with these big words and technical terms.
    Topology in this case refers to the molecular landscape of observed organisms.

    Quote Originally Posted by cypress
    This is why one also must show that the process is capable of producing the effect. It is only then that you can eliminate the alternatives.
    There are no alternatives, at present. [/quote]

    Correction, none you are willing to consider.

    And the process of Darwinian evolution has been shown (it's pretty easy) capable of producing almost anything in the way of complexity, variation, etc. It's capability is not in serious question. That's one of the occasional criticisms of it - it's too easy to cook up Just So Stories to explain anything, within it.
    The criticism is not of the capability to generate an actual event, it is the simple capability to make up a story that might explain an event. Mutation and selection has never been shown capable of generating a new protein to protein binding site or a new developmental control sequence. And yet there are many thousands of these differences between just two organisms considered closely related.


    Quote Originally Posted by cypress
    With respect to the basic aspects of DNA replication and establishment of a phylogeny between prokaryotes and eukaryotes we have a disconnect:
    - - -
    Clearly though HGT and the far less certain endosymbiosis only address a few of the difficulties. There is an endless set of examples including the one above that are unanserable by these processes.
    Failures of imagination and easy claims of incredulity are not serious arguments.
    No they are not, but if that is your conclusion, then you missed the point. Biologista, seems to think that evolutionary theory along with all of the recent gymnastics thrown in to prop up the predictions of a tree structured phylogeny solves all issues. He must cherry pick and bring in unobservable and counterintuitive events to claim that the predictions are intact. There are numerous serious instances like this where the data contradicts Bioligista's notion of a bifurcating phylogeny. A better explanation is that you and Biologista and many others have prior commitments to this particular theory. When new facts emerge that contradict the theory, new unobservable complexities are added rather than looking for alternative explanations. It is a practice driven by bias not a desire to follow the evidence wherever it takes us.

    For one thing, if there were shown to have been two or more "origins of life", with evolutionary descendants from them all alive today, so what? We note that accepting the evolutionary explanation of any given major phylogeny of any of the Eukaryotes alone dismisses your claims of impossibility regarding the evolution of complex proteins.
    I would urge you to think more deeply about the implications of two distinct derivations of DNA and its replication systems in context with the concept that mutation and selection has no target. Can a blind mechanism ever be expected converge on the same solution in face of the innumerable permutations available?
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    No time for the rest of your post.

    Quote Originally Posted by cypress
    Right, except in the many cases (roughly 30% of the time) when we don't see a phylogeny consistent with the predicted topology.
    That's not actually true. What you're seeing in 30% of cases are phylogenies for different genes in the same organism considered to be optimum which conflict with one another. The individual phylogenies still match prediction- ie they are mostly bifurcating with the occasional collision. Furthermore, we're not seeing cases where there is no plausible agreement between multiple trees, it's just that the monogenetic trees we would have chosen in ignorance of other genes may not be correct, which means that our means of highlighting optimum trees is in fact suboptimal. That doesn't contradict theory, nor do the authors of that paper contend that it does. It highlights a limitation in how well we can resolve the tree of life, based on current methods.

    The monogenetic trees themselves still look as predicted by theory.
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    Quote Originally Posted by cypress
    Topology in this case refers to the molecular landscape of observed organisms.
    You don't appear to know what any of those words mean.
    Quote Originally Posted by cypres
    Regardless, there are plausible alternatives to mutation and selection being actively researched that would produce the same diversity and molecular configurations we observe.
    When alternatives (sic) to Darwinian theory have accumulated some evidence or argument to support them, do let us know what they are.
    Quote Originally Posted by cypress
    Correction, none you are willing to consider.
    Try. Empty assertions of the existence of things unseen and undescribed are not persuasive.
    Quote Originally Posted by cypress
    Mutation and selection has never been shown capable of generating a new protein to protein binding site or a new developmental control sequence.
    I sort of thought you weren't reading any of the links and so forth provided you here - your vocabulary, for one thing, remains vague and slippery (what is a "protein to protein binding site"?), and seems to indicate a lack of familiarity with the physical reality involved. But in response to what you seem to be requesting, one practical example will do: antibiotic resistance.

    But the real issue is what you regard as "shown capable". The capability of Darwinian process to produce structures of arbitrary complexity - anything at all, as far as we can tell - has never been in question. What exactly are you talking about?
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    Quote Originally Posted by cypress
    Sorry, that's not true. Past moderator practices provide good heuristics on this point.

    ....

    Actually I have previously learned it would only have to conform to the prior commitments of the moderators or conform to the opinions of talkorigns. Whether or not it had explanatory power is secondary.
    i see that we've finally arrived at the point where most conspiracy theorists end up: the reason why no-one listens to me isn't because my point of view doesn't have any scientific merit, but because there's a worldwide conspiracy to suppress the truth
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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