Intelligent Design

Metaphors, Design Recognition, and the Design Matrix

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Here are excerpts from The Design Matrix by Mike Gene:

Metaphors such as “fear”, “cost”, “abhor” and “angry”, commonly share the projection of consciousness onto the world. Metaphors such as these represent the human tendency to view the world through anthropomorphic glasses. However, the metaphors employed by molecular biologists are not of this type.
….
Metaphors typically break down when we begin to take them literally.

[but] The design terminology that is used in the language of molecular biology does not break down when interpreted literally
….

there is a basic and literal truth to the use of design terminology in molecular biology–these technological concepts are just too useful. Metaphors are certainly useful when explaining concepts to other human beings, yet the design terminology often goes beyond pedagogy–it provides true insight into the molecular and cellular processes. An understanding of our own designed artifacts, along with the principles required to make them, can guide the practice of molecular biology.

Why is it that some metaphors are no where near as effective for describing biology as well other metaphors, especially design metaphors?

Mike Gene recognizes qualitatively the enigma that others recognize quantitatively. There is an improbable coincidence between the architecture of human-made systems and the architecture of biological systems. Recognition of these coincidences is the recognition of specified complexity, and recognition of specified complexity is the recognition of design. Outside of biotic reality, there are no other assemblages of matter in the universe which fit design metaphors more exactly than those found in biology.

I liked Mike’s book, but I especially liked Chapter 3. Chapter 3 suggests the fact that biology is well described by design metaphors is a clue that biological systems (like birds, plants, and bunnies) are intelligently designed. UD readers are invited to read about the other clues which Mike outlines in his book, and the consilience of these clues constitutes The Design Matrix.

Notes:

From wiki:

Metaphor (from the from Latin metaphora; see the Greek origin below) is language that directly compares seemingly unrelated subjects. It is a figure of speech that compares two or more things without using the words “like” or “as.” More generally, a metaphor describes a first subject as being or equal to a second object in some way. This device is known for usage in literature, especially in poetry, where with few words, emotions and associations from one context are associated with objects and entities in a different context. A simpler definition is the comparison of two unrelated things without using the words “like” or “as”, the use of these words would create a simile. For example,she is a button.(as cute as a button)

124 Replies to “Metaphors, Design Recognition, and the Design Matrix

  1. 1
    scordova says:

    Mike Gene’s website is:

    http://designmatrix.wordpress.com/

  2. 2
    Jerad says:

    “There is an improbable coincidence between the architecture of human-made systems and the architecture of biological systems.”

    Improbable coincidence . . . I think you’re going to invoke cries of “God of the gaps” with that kind of language. Aside from the logical difficulty of trying to prove a negative. And I wonder if any engineer would design a motor this way really . . . .

  3. 3
    Mapou says:

    Nice post. As an aside, here’s what Aristotle wrote about metaphors:

    The greatest thing by far is to be a master of metaphor. It is a sign of genius, since a good metaphor implies an intuitive perception of the similarity in dissimilars.

    Metaphor is the application of an alien name by transference either from genus to species, or from species to genus, or from species to species, or by analogy, that is, proportion.

    Aristotle, Poetics.

    It is interesting to note that Sir Isaac Newton and his nemesis Gottfried Leibniz were convinced that almost all ancient myths were intended as metaphors for other things, especially the myths that are too strange to be litterally true.

  4. 4
    David Kellogg says:

    I find the view of metaphor here rather simplistic.

    A more sophisticated understanding of metaphor is found contemporary scholarship. I would recommend especially the work of the linguist George Lakoff and colleagues (Mark Johnson, Mark Turner, and others). In studies beginning with Metaphors we Live By and continuing through more recent work, Lakoff’s way of thinking has introduced the notion that metaphors are conceptual relationships rather than rhetorical figures. This work transformed the simplistic view of metaphor we all got in high school (the kind presented above).

    In actuality, metaphors are not linguistic equations but ways of understanding that are more or less one-directional and depend on an inequality between the things compared. In metaphor, we understand what Lakoff calls the “target domain” in terms of what Lakoff calls the “source domain,” and not the other way round. We don’t understand the source in terms of the target.

    An example. When Emily Dickinson writes

    Because I could not stop for death
    He kindly stopped for me

    the metaphor is
    LIFE IS A JOURNEY
    where the target domain is life and the source domain is journey. The thing to be understood is “life,” and “journey” maps onto it because we’ve all been on journeys, but nobody I know has lived a complete life.

    It is because we don’t understand “life” that Dickinson’s poem works. It doesn’t help us understand “journeys” — we already know what a journey is.

    To the point at hand, the metaphor

    BIOLOGICAL LIFE IS DESIGNED

    works not because there is something “real” about the relationship but because the person who uses it doesn’t understand “biological life.” The source domain can cast light on the target domain, but it doesn’t provide “knowledge” of it. In fact, there’s a sense in which it depends on ignorance of the target domain — because the more we know about the target domain in any metaphor, the more we can find ways in which the metaphor breaks down.

  5. 5

    Metaphors are a special case of analogies (the other being similes). I have written extensively on the subject of the application of analogies and metaphors in science, and especially in the evolution/design debate:

    http://evolutionlist.blogspot......gical.html

    http://evolutionlist.blogspot......ience.html

    http://evolutionlist.blogspot......ience.html

    The fundamental question in this ongoing debate is, how do we know an analogy really exists? For example, do we have any objective way to determine if one rock is analogous with another? Or whether an anatomical feature (or a protein/substrate binding site) is analogous to another?

    As in the case of agency detection, we think we can do this very easily (just as we can easily identify what looks like design), but I would argue that this is because both “finding” analogies and “finding” design and purpose are capabilities of the human mind (and the nervous system that supports it) that have conferred enormous adaptive value on our ancestors. As in the case of our hypothesized “innate agency/design/purpose detector” (which first becomes active in very early infancy), our “analogy detector” also appears to become active at a very early age, and operates entirely in the background. That is to say, we are almost totally unaware of its operation, and concentrate only on its output.

    Our ability to detect (and construct) analogies is, IMO, the core of our intelligence, as demonstrated by the fact that identifying analogies has been traditionally used as one of the most sensitive gauges of general intelligence in intelligence tests (such as the Miller Analogies Test).

    And, as Sal and others have pointed out in other venues, doing engineering, and especially mathematics, is essentially the construction of highly compact analogies, in which numerical (and sometimes physical) relationships are expressed in the form of abstract symbols. Indeed, many mathematical relationships (especially in the natural sciences) are expressed as equations, which are quite literally metaphors expressed in symbolic form. For example, Newton’s equation for force:

    F = ma

    is a metaphor linking the concept of force with the concepts of mass and acceleration.

    In molecular biology we encounter once again the concept of metaphors, for what is the genome of an organism but a highly abstract metaphor for the fully embodied and operating organism itself? I agree with those (and I expect Sal would number himself among them) who assert that the encoding of “life” into a string of nucleotides is indeed the crucial difference between biological “metaphors” and physical “direct necessities”. Gravity isn’t “encoded” in anything, but proteins are, and so are cells, tissues, organs, organ systems, organisms, and (at least at some level) their behaviors.

    So, is there a way to verify if an analogy or metaphor is “real”? In the case of some analogies in biological systems we have an independent double-check on our identification of analogies. This is based on the evolutionary concept of homology, or derivation from a common ancestor. If two structures on two different organisms (say a small bone of the jaw of a reptile and the even smaller bone in the middle ear of a mammal) appear to be analogous (on the basis of size, location, relationship to other bones, etc.) there are at least two different, though related, methods of verifying that these structures are indeed analogous (and not just accidentally similar).

    One way is by means of comparative paleoanatomy, in which a series of fossils of known age are compared to determine if there is a connection between the evolutionary pathways of derivation of the structures. If such a pathway can be empirically shown to exist, this would be strong evidence for both the analogous and homologous nature of the objects.

    Alternatively one could compare the nucleotide sequences that code for the structures to determine if they are sufficiently similar to warrant a conclusion of homologous derivation. In both cases, evidence for homology, combined with our intuitive “identification” of analogous structure and/or function, both point to the same conclusion: that the two structures are both analogous and homologous.

    This is why structures that appear to be analogous, but for which there is no convincing evidence of homology (as in the wings of birds and insects) can present a serious problem to evolutionary biologists, and especially those engaged in biological classification. Such apparent similarities (technically called homoplasies) can either be the result of “true” (i.e. partial) analogy at the functional (and/or structural) level (and therefore assumed to be the result of convergent evolution) or they can be completely accidental. Simple inspection is often insufficient to separate these two hypotheses, and lacking either fossil or genomic evidence, conclusions about the validity of such analogies can be extremely difficult to draw. However, if there is fossil and/or genomic evidence and it points away from homology (i.e. descent from a common ancestor), then the structures can be considered to be analogous, but not homologous.

    One of the dangers in invoking analogies and metaphors is overusing the concept of analogy to mean almost anything. Indeed, it is essential in discussions such as these that we be as precise as possible about our definitions, as imprecision can only lead to confusion (at best) and unsupportable conclusions (at worst).

    Perhaps the most essential distinction to be made in this regard is between “analogies of description” (which could also be called “semantic analogies”) and “analogies of function/structure” (which could also be called “natural analogies”). The former (i.e. “semantic analogies”) are merely artifacts of the structure of human cognition and language, as happens whenever we describe an analogy that we have perceived.

    By contrast, the latter (i.e. “natural analogies”) are the actual similarities in function/structure that we are describing (i.e. that resulted in our identification and description in the first place). As in the Zen koan about the roshi and the novice in the moonlit garden, much of the confusion about which of the two types of analogies we are discussing seems to stem from confusion between the moon that illuminates the garden and the finger pointing at the moon.

    In the brief example that Sal posted at the head of this thread, the implication is that the analogies we perceive between biological systems and those engineered by humans are “natural analogies”; that is, they are real analogies, and not simply a form of linguistic convenience. However, there is nothing about the finding of an analogy that necessarily verifies that the analogy is “natural” (i.e. “real”), as opposed to “semantic” (i.e. “imaginary”).

    To verify that an analogy is “natural” requires an independent source of validation for the assertion that the analogy is “real” and not merely “semantic”. At this stage in my reasoning about this subject I am not at all sure how one would go about this.

    However, one thing I am sure of is that simply asserting over and over again that one has perceived an analogy, and that this is all that is necessary to validate the analogy, is not sufficient. Even I am but mad north-north-west: when the wind is southerly I know a hawk from a handsaw.

  6. 6
    Freelurker says:

    There is an improbable coincidence between the architecture of human-made systems and the architecture of biological systems.

    So who are these people who think it’s an improbable coincidence? Doesn’t everyone agree that the architectures of human-made systems and the architectures of biological systems are all selected?

  7. 7
    Frost122585 says:

    Very nice post Cordova, and nice fallow up as well Mapou.

  8. 8
    Frost122585 says:

    Though I would add that the argument for design is not for metaphorical design but for actual or literal design- that is that terms like “molecular machine” are not metaphor’s but what actually exists with subjects like the cell.

  9. 9

    Just a quick note to say that I have apparently once again been “moderated” off of the threads at Uncommon Descent. Apparently my comments were cutting a little too close to the bone. One could almost say I’d been Expelled (No Intelligence Allowed)

    And to Timaeus and others from UD: I will be indirectly responding to some of the posts at Uncommon Descent at The Evolution List (time and weather permitting, of course).

  10. 10

    Just Another One of the Boyz in the Banned…

    A quick note to say that I have apparently once again been “moderated” off of the threads at Uncommon Descent. Apparently my comments were cutting a little too close to the bone. One could almost say I’d been Expelled (No intelligence Allowed)

    And to Timaeus and others from UD: I will be indirectly responding to some of the posts at Uncommon Descent at The Evolution List (time and weather permitting, of course).

  11. 11
    scordova says:

    Dear Allen, David, (and other gentlemen),

    If it is any consolation, even some of my comments are being trapped in the spam buffer (on other threads at UD).

    I can release some of the comments, but not all of them. It appears, the comments posting to my threads can be released by me.

    I can’t release comments on other threads.

    I try to monitor the spam queue (which has 190,000 comments). Please save your fine work before posting. I will do my best, but sometimes things slip through the cracks.

    If you are posting on my thread, I’ll try to make sure your comments are released.

    Thank you for your comments. Sorry for the delays and technical problems.

    PS
    Nice to see you again Allen!

  12. 12

    Nice to hear from you, too, Sal. We’ve had this conversation on analogies and metaphors before, and it pleases me to take it up again. That’s what these debates are for, IMHO; clarifying our own thoughts on where we stand on these issues.

  13. 13
    scordova says:

    David wrote:

    In fact, there’s a sense in which it depends on ignorance of the target domain

    Thank you for your comment.

    We may be ignorant of most of the characteristics of the target domain, but this still may not decrease the applicability of a metaphor:

    Here are source descriptions of the target domain of “a cell”. The metaphors do not have to be a comprehensive descriptor of the cell, but they can still be completely accurate:

    1. a computer
    2. a software processor
    3. an information processing system
    4. an energy consumer
    5. a language processor
    6. a signal processor
    7. an inegrated system
    8. a self-replicating Turing machine
    9. a parallel processor

    or the parts of the cell:

    1. decoders
    2. encoders
    3. sensors
    4. feedback control systems
    5. memory

    etc.

    I don’t think a metaphor has to completely describe something to be totally accurate. To say someone is a human being is completely accurate, even though that description does not totally describe that person.

  14. 14
    scordova says:

    Doesn’t everyone agree that the architectures of human-made systems and the architectures of biological systems are all selected?

    I mention here are some systems (redunant systems) which would evade selection: Airplane magnetos, contingency designs, and reasons ID will prevail

    So that’s one problem. Other systems might resist selection because they are irreducibly complex.

    Third, even if all the above problems were solved, there are the issues of population resources. One may not have the population resources for natural selection to work. There are: Speed Limits to Evolution.

    The list goes on.

    Doesn’t everyone agree that the architectures of human-made systems and the architectures of biological systems are all selected?

    No. Not every thing will be selected for the reasons listed above and more.

    Not to mention, random selection often over-rides natural selection. See: Gambler’s Ruin is Darwin’s Ruin.

  15. 15
    scordova says:

    Allen wrote:

    To verify that an analogy is “natural” requires an independent source of validation for the assertion that the analogy is “real” and not merely “semantic”. At this stage in my reasoning about this subject I am not at all sure how one would go about this.

    I agree that we cannot prove the analogy is “real”. As far as the ID/EB debate goes, what might be feasible is determining what mechanims (like random mutation) are unlikely to create such an analogy.

    For example, with Genetically Modified Organisms (GMOs) when a company like Genetic-ID discovers a sequence in an organism that matches a signature in their database, there is an undeniable analogy. They can rule out certain mechanisms which created that analogy.

    [For the reader’s benefit, here is my post on genetic-ID: Genetic-ID,an instance of design detection.]

    I believe the very powerful impression that biological systems are analogous to human engineered artifacts cannot be achieved via:

    1. natural selection (for the reasons I cited above)
    2. neutral evolution
    3. any variety of mutation except maybe pre-programmed mutations

    I think #1 and #2 are correct. I think #3 is not conclusive. I looked at your rather daunting list of mutational mechanisms, and it would be unfair to dismiss the list your presented outrightly. But you are aware of my biases on the matter. 🙂

    That is my current view, anyway.

    regards,
    Sal

  16. 16

    I have a problem with the division of the content of analogies and metaphors into “sources” and “targets”. While that may be the case in at least some linguistic analogies, it is clearly not the case in “natural” analogies.

    The whole “source”/”target” terminology seems to me to be analogous to Batesian mimicry. For example, in the famous monarch/viceroy butterfly example, the monarch butterfly is the “model” and the viceroy butterfly is the “mimic”, in much the same way as Lakoff’s et al “source” and “target” are related to each other. That is, we say the viceroy butterfly “looks like” the monarch butterfly because it is the viceroy that has converged on the monarch prototype, and not the other way around.

    However, there is another kind of mimicry: Müllerian mimicry, in which equally repellent “models” all converge on each other’s phenotypes (or, to be more precise, they all converge on an “average” phenotype). This kind of mimicry is “equidirectional”, and there is no “source” or “target” involved (or, each convergent butterfly species is both “model” and “mimic” simultaneously).

    I believe the same thing is true for the analogies we perceive between similar objects. For example, we would find a “natural” analogy between green apples, green oranges, green pears, green plums, etc., but we would be hard-pressed to say which of these were the “source” and which the “target”.

    In the same way, it seems difficult (indeed, perhaps impossible) to say which is the “source”/”model” and which the “target”/”mimic”: biological complexity or humanly engineered complexity. And if one can’t determine which direction the analogy is being made, then it would appear to me that Mike Gene’s argument falls apart.

  17. 17

    And here is my response to Sal’s post on Genetic ID and design detection:

    http://evolutionlist.blogspot......ilter.html

  18. 18
    David Kellogg says:

    Allen [16], let me follow up in a slightly tangential way. Without going too deeply into the source/target issue, I want to critique Sal’s claim that “the fact that biology is well described by design metaphors is a clue that biological systems (like birds, plants, and bunnies) are intelligently designed.” I want to say, No, it’s not. In fact, Gene’s characterization of such metaphors as “just too useful: suggests that we should avoid the temptation to conflate the metaphor with the reality.

    Consider the following pair of metaphors:

    LIFE IS PRESENCE
    DEATH IS ABSENCE

    We use these metaphors when we send a card saying “Congratulations on your new arrival” or when we speak of someone having “passed away,” when we say that people have “left this earth” or “come into the world.” Such metaphors may be useful theologically, but scientifically, they fundamentally misrepresent life and death. They make it easier for us to come to grips with death, personally and within our tradition; they don’t, however, do much else. In fact, they may lead to outlandish attempts to “prove” that a soul leaves the body at the moment of death — it would have to, if death meant absence, because the body is still there.

    My point is this: that a metaphor is tempting is a reason to avoid embracing it scientifically. It’s a reason to be suspicious.

  19. 19
    Joseph says:

    Evolutionists don’t like analogies because they do not have any.

    What would they say?

    “Hey look at that pile of twisted metal and broken glass- yeah just like biological organisms!”

    LoL!!!

    As a matter of fact all evolutionists can do is hide behind father time and invoke magical mystery mutations.

    Oh well…

  20. 20
    scordova says:

    My point is this: that a metaphor is tempting is a reason to avoid embracing it scientifically. It’s a reason to be suspicious.

    Dr. Kellogg,

    Thank you for you comment. I agree that wrong metaphors will hinder scientific advancement. For example, here are some wrong metaphors which have been damaging to exploration:

    “junk DNA”
    “junk RNA”
    certain “vestigial” organs.

    In contrast, there are some metaphors that have been extraordinarily useful. As Mapou pointed out, even the notion of Genus and Species is useful. The most powerful metaphors, imho, have been the machine metaphors for biology, especially the cell being called a Turing machine.

    I think using metaphors as a scientific hypothesis is legitimate. When we say DNA is “transcribed” or “translated”, this seems like the correct description. It seems awfully hard to argue that these metaphors are wrong.

    I recognize the problem of subjectivity, and subjectivity is something that seems loathesome in the scientific enterprise.

    However, subjectivity is the order of the day when characterizing both human-made and naturally existing machines. For example, when we say something is a “sensor”, or “amplifier”, or “decoder”, or “error correction mechanism”, we can’t justify that claim in terms physics and chemistry. Does that make the application of a metaphor scientifically illegitimate?

    The moment we begin to characterize something in terms of teleology and purpose in science, we have stepped over into the subjective. I do not believe this is wrong. It’s very much par for the course in engineering, especially in Information Technology, where we frequently ascribe subjective interpretations to inanimate matter.

    Pure reductionism and objectivity does not apply in the world of information processing. An image is not reducible to the Cartesian coordinates and color properties of the pixels. A sentence is more than the letters which compose it. A sentence is meaningful because of how the observer perceives it. A computer program is meaningless without a machine to interpret it. Bits inside of a computer are meaningless without the interpretive machinery surrounding it. Context is important!

    The momement we begin to describe biology in terms of information and engineering metaphors, we have crossed over into the subjective. Nevertheless, from an engineering standpoint, this seems correct. Avoiding this subjectivity seems deeply awkward, if not wrong.

    To quote Allen (from something he wrote in 2006), the fact biology seems to be so amenable to being described by engineering metaphors is “The Paradox of Purpose”.

  21. 21
    scordova says:

    Teleological concepts seem to be abundant in biology.

    However there was at least one notable application of teleological concepts in physics, namely, least action principles.

    For reference here is some info on teleology in physics from some of my prior posts at UD:

    Teleology and ID in physics, ID-inspired least action principles

    and

    Cosmological ID in 1744?.

  22. 22
    Joseph says:

    Yes it is true we should not confuse analogies and metaphors with reality.

    However when analogies and metaphors fit the bill, so to speak, then it would be very unscientific to not investigate whether or not they have any merit.

    IOW if something has the appearance of design then it would be a mistake not to investigate whether or not that design is real.

    I say that because experience has taught us that it matters a great deal to an investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely.

    Therefor to refute the design inference all one has to do is to demonstrate that nature, operating freely, can account for it.

  23. 23
    ab says:

    BTW, Allen MacNeill, John A. Davison has much to say to you about your Darwinian mechanism/s (especially about natural selection), would you go ahead already and get the show started while John is still alive or would you rather prefer to continue and hide behind your UD friends here?

  24. 24
    jerry says:

    There are many in evolutionary biology that question most of Darwin’s ideas but never the naturalistic origin of evolution or that natural selection works once something new appears. The essence of the discussion is always what causes new things to appear.

    Once the new thing appears. natural selection can work with it if in fact the new thing affects reproduction. It is just that the natural selection process cannot create what is not there in the first place.

    So as the old saying goes, It is not the selection of the fittest that is under scrutiny but the arrival of the fittest.

    So we have to be careful when we criticize Darwinian mechanisms as to exactly what is meant.

  25. 25
    Rude says:

    The mystery of apprehending an infinitude of reality with a finite set of symbols has long perplexed logicians and linguists. Most every theory is an atomic theory, i.e., words are defined by semantic features (elemental units of meaning). The trouble is that these features generally wind up as idiosyncratic and nonuniversal as the words they supposedly define.

    One way to constrain the set of features is to look to grammar. Language is a combination of symbols (words) and grammar, with the former coding the more specific meanings and the latter the more general features of consciousness, intention, cause and effect, time and perspective. Also, as it turns out, those very features are the ones that become grammaticalized across all human languages.

    George Lakoff’s main contribution was to show that some metaphors are universal (such as life equals a journey) and others more culture specific (time equals money), and that metaphors are not just memorized memes but also on the spot creations based on these relationships. And, as various linguists (T. Givón, Joan Bybee, …) have shown, it is a relatively small set of universal metaphors that effect grammaticalization in the world’s languages. For example, if a language has a future tense and we know its origin, it is always based on the sense that time is motion (thus the English gonna) or that volition is toward the future (e.g., the Eng. will future).

    Another helpful contribution has been the prototype semantics of Eleanor Rosch. Some features of a word are more salient than others—values are not simply plus or minus. Grammatical categories are also prototypes with more central and more extended applications.

    Now the question (as I think all this might apply here): Just as the cosmos was designed for discovery, might our minds also have been designed for the same?

    Much has been made of the counterintuitive findings of physics. Let me make a prediction. Someday the physicist’s counterintuitive Block Time and antipathy to free will will be discarded and some of the aspects of quantum theory that materialists find counterintuitive will be seen as both intuitive and the best theory.

  26. 26

    Re #23 by ab:

    Greetings, Jon. I have already posted my response to your offer at my blog. As I stated there,

    “As you can clearly see, you haven’t been banned from this blog. On the contrary, I am ready to discuss with you whatever you want to discuss, and agree to abide by your stated rules of civility and full disclosure. So , what would you like to discuss first?”

    We will have to take up the conversation at The Evolution List. I have not been able to register for your site, despite following the instructions listed.

  27. 27

    In #24 jerry wrote:

    “Once the new thing appears. natural selection can work with it if in fact the new thing affects reproduction. It is just that the natural selection process cannot create what is not there in the first place.”

    This was precisely my point in the post I made on the subject of the “engines of variation” at The Evolution List:

    http://evolutionlist.blogspot......ution.html

    and

    http://evolutionlist.blogspot......awman.html

    As I pointed out, natural selection isn’t a mechanism, it’s an outcome. Furthermore, natural selection doesn’t (indeed, cannot) create anything new at all. On the contrary, natural selection simply removes some of the inter-individual variations that are produced by the “engines of variation”.

    So, I basically agree that we shouldn’t be focussing our attention on natural selection as the source of innovations in phenotypes. Rather, we should be focussing our attention on the various mechanisms by which phenotypic variations are generated. This will, of course, require us to become informed about them, which is quite a task (there are over 50 mechanisms already known, ranging in scope from single point mutations to whole genome fusion). If I were interested in forwarding the agenda of ID, this is what I would spend my time and energy investigating, rather than posting the same old negative arguments that “RM + NS can’t do it”. Nobody is now saying they can, nor do they need to.

    To kick off this discussion, let me pose a question: since the “engines of variation” are what produce new, and therefore presumably adaptive phenotypic variations, it seems reasonable to expect that, if there is anything to ID, one should be able to show empirically that the appearance of new variations is not random. Furthermore, if ID is to actually have any ontological force, it should be possible to show empirically that a particular new phenotypic variant would qualify as a “foresighted” variation, thereby biasing natural selection toward favoring it.

    Has anyone attempted to approach the question of variation from this viewpoint?

  28. 28
    JohnADavison says:

    If Allen MacNeill has been “moderated off,” just who is sending these enormously long messages under his name?

    On the outside chance that it is really Allen MacNeill, let me remind him that there is absolutely nothing in the Darwinian model that ever had anything whatsoever to do with the formation of true species or with the appearance of any other taxonomic category. All that has ever been demonstrated through selection, natural or artificial, is the production of intraspecific varieties and largely unverified subspecies. Darwinism in all its guises is the most persistent hoax in the history of science. To continue to support the Darwinian myth here or anywhere is no longer acceptable and all such attempts should be summarily rejected as pseudoscience.

    Furthermore, there is no place for “debate” in science. There is only “discovery.”

    “A past evolution is undeniable, a present evolution undemonstrable.”

  29. 29
    jerry says:

    JohnADaviison,

    Nearly all of Darwin’s ideas have been discarded by evolutionary biology. What is left is natural selection and they still worship common descent. But natural selection that is left is an empty shell of its former self.

    There are all types of selection but the real game is in the origin of variation such as proposed by Lynch and the punctuated equilibrium crowd. Darwin’s form of gradualism is dead but Gould’s latent gradualism is starting to rule the kingdom. Only when the new appears can any of the selection models step in. They are powerless without novel input.

  30. 30
    jerry says:

    Allen,

    I answered John Davison’s comment without seeing yours above it. I wrote about this at length the other day but did not express it as well as you did here.

    I made the point that to take a fairly large family of species that have a fossil history of several million years and to map the genomes of all the species to see the differences and that you would find two types of changes that led to differences between the individual species.

    1) changes that could arise strictly from the genetic side of evolution including natural selection, drift, epigenetic factors etc. due to simple variation arising from any of your engines of variation or from variation already in the gene pool with the boundary conditions that the environment provides. ID would have no quarrel with any of these. These are changes that do not produce novel complex capabilities, the issue at hand. Each change should be visible in the genome as a result of gradual changes and should be discernible by analyzing the various species in the families and when in time they separated.

    2) changes that are novel, complex and represent new capabilities for a particular species. The argument is that these changes would not arise from the processes outlined in 1). In other words there would be no gradual set of changes leading up to the capability. So the question is how did such changes arise. This supposes that there are no changes in 2) that can be traced to some form of gradual process.

    The Darwin crowd and the Gould crowd both espouse some form of gradualism. But what if some change can not be seen as arising from such a process. What is the explanation. Some form of evo devo or is it that begging the question by assuming that these capabilities lie within the original gene pool and just needs some trigger to get them out. Or is another very different paradigm necessary?

    There is another possibility. Namely, that all the changes in most species are of type 1. And the question is then, why? With all these reproductive events, why didn’t the forces of nature produce at least one such new capability. Which is why there should be a lot of work done on echo location and flight with bats and the blood pressure system of giraffes. You can probably think of other novel capabilities.

    This debate will rage till the genomes are mapped, analyzed and understood and it is determined how all significant changes arose. And if it is still a mystery after this, is it time to move to a new paradigm. Or possibly support the 8000 pound gorilla that is not allowed in the door that predicted it would be impossible to generate the information to get to these new capabilities.

    It should be an interesting next 30-40 years to find the answers to all this. I personally believe it is all in the genomes and it will eventually support ID at some point that will be hard to deny.

  31. 31
    JohnADavison says:

    Natural Selection is very real and very important. It prevents change. Just as Nature abhors a vacuum so does She abhor change right to the bitter end of extinction. That is the undeniable testimony of the fossil record.

    “The struggle for existence and natural selection are not progressive agencies, but being, on the contrary, conservative, maintain the standard.”
    Leo Berg, Nomogenesis, page 406

    We are now witnessing the extinction of the climax biota which was planned probably millions of years ago. Chance has never played a role in either ontogeny or phylogeny.

    “Neither in the one nor in the other is there room for chance.”
    Leo Berg, Nomogenesis, page 134.

    The origin of every taxon from Phylum to species was an instantaneous event without any continuous transformations whatsoever. Gradualism in ANY form is without verification. That is why, with no exceptions, every species representing an orthogenetic series is so different from its presumed predecessor that it must be assigned to a separate genus.

    “We might as well stop looking for the missing links as they never existed…The first bird hatched from a reptilian egg.”
    Otto Schindewolf

    “Any system that purports to account for evolution must invoke a mechanism not mutational and aleatory.”
    Pierre Grasse, Evolution of Living Organisms, page 245

    Every aspect of the Darwinian model is an experimental and descriptive disaster. My conclusions and my Prescribed Evolutionary Hypothesis are based on the independent findings of a handful of the finest minds of the post Darwinian era not one of whom was either a professed atheist or a religious fanatic.

    I didn’t come here to “debate.” I came to offer an antidote to the Godless Darwinism that still is allowed here for reasons I fail to understand. An evolution driven by chance and selection is the most ridiculous notion ever proposed by an overactive human imagination. It dwarfs the Phlogiston of Chemistry and the Ether of Physics.

    It is hard to believe isn’t it?

  32. 32
    jerry says:

    “An evolution driven by chance and selection is the most ridiculous notion ever proposed by an overactive human imagination. It dwarfs the Phlogiston of Chemistry and the Ether of Physics.”

    John, we agree. That is those who support ID agree. It is just the specific mechanism used to enable how the various species came into being that is under debate.

    However, how the first bird arrived and how all the rest of the birds arrived seem to be a separate issue. Or is it?

  33. 33
    JohnADavison says:

    Jerry

    Of course the mechanism of the origin of new life forms has always been the crucial question. It may never be answered. First causes are like that. The important point is to emhasize that chance could never have played any role in that event or events. The Darwinians believe that it is intrinsic in the nature of matter to self assemble into a living, metabolizing, evolving organism at least once. I cannot accept that perspective and I cannot understand how any serious student of the living world can. As I have explained in my essays, there is no more reason to believe in a monophyletic evolution than there is in a monotheistic God. There is very little that is known with certainty about the origins of ontogeny and phylogeny.

    Leo Berg proposed that there were tens of thousands of primary forms. There is nothing that we know for certain that is at variance with that remarkable summary and much with which it is in accord.

    Any honest appraisal of that which is certain must conclude that it is a very short list indeed.

    As for Darwinism with all its necessary assumptions I quote Bertrand Russell –

    “It is undesirable to believe a proposition when there is no ground whatsoever for believing it to be true.”

  34. 34
    Joseph says:

    Allen MacNeill:

    As I pointed out, natural selection isn’t a mechanism, it’s an outcome. Furthermore, natural selection doesn’t (indeed, cannot) create anything new at all. On the contrary, natural selection simply removes some of the inter-individual variations that are produced by the “engines of variation”.

    If it isn’t a mechanism- and I agree that it isn’t- how can it remove anything?

    The mechanisms of “sh!t happens” and “ooops shouldn’t have done that”, are good at removing things.

  35. 35

    In #34 joseph asked:

    “If [natural selection] isn’t a mechanism- and I agree that it isn’t- how can it remove anything?”

    Natural selection can’t “remove” anything, because natural selection doesn’t “do” anything. As I pointed out above, it’s an outcome, not a mechanism. The “engines of variation” are what “do” things in evolution, and it is those mechanisms (see the list here: http://evolutionlist.blogspot......awman.html ) that produce the new variations that drive the changes we see in the fossil record, the genomic record, and the world around us. We are only just beginning to appreciate how extensive and how powerful these sources of phenotypic variation are, and how they work. I fully expect that, as we learn more about them, we will change our models of how evolution happens. That’s where all the open questions in evolutionary biology are, and what makes it such a fascinating discipline to me.

  36. 36
    jerry says:

    “If it isn’t a mechanism- and I agree that it isn’t- how can it remove anything?”

    Two things. I think it is a process. Allen called it the summation of about 3 processes some time ago so I think it is a process but arguing over that is pointless. It happens.

    It removes variation because the processes favor some elements of the gene pool over others. And these processes will send some of the genetic elements into fixation. If an allele becomes fixed then variation has been removed from the gene pool. Other variations of that gene are not gone. Genetic drift also removes variation. A new environment will probably reduce variation as certain alleles will not be appropriate for it. Allen can probably say it better.

  37. 37
    jerry says:

    The previous should say

    “Other variations of that gene are now gone.”

    which has a completely different meaning.

  38. 38
    scordova says:

    Allen suggested:

    To kick off this discussion, let me pose a question: since the “engines of variation” are what produce new, and therefore presumably adaptive phenotypic variations, it seems reasonable to expect that, if there is anything to ID, one should be able to show empirically that the appearance of new variations is not random.

    I think the way that a variation is suggested to not be of random origins is when it conforms to design metaphors, and does so in a way that defies probability. In fact this idea is consistent with the idea of specified complexity.

    We can’t project very specific design metaphors (like decoder, computer, sensor) to rocks, rivers or any other kind of natural phenomenon, except biological organisms. When matter starts to conform to recognizable patterns associated with human design, it begins to suggests the variation had premeditation.

    Variation in and of itself cannot be what prods objects to look exquisitely designed. Neither do I think the sieve of “natural selection” will help the process along.

    A rock dropping on a car will cause variation in the car, but these aren’t the sort of variations (accidents) that we would consider as the source of the car’s designs.

    As far as I can tell, the sort of mutational change that we have direct knowledge of has very limited ability to create certain levels of designs. There is no question variation and mutation are engines of change, but it is the kinds of changes that are important.

    Improbable conformance to a design metaphor seems like a good standard for deciding if the source of variation is random (in the sense of mindless origins).

    As an example, protein interactions can be analogous to the lock-and-key or login-password metaphor. The strength of the metaphor is the strength of the improbability of the interaction. I thought that the exploration of binding site evolution could be a fruitful area of research.

    I was pleased that Durrett and Schmidt (very fine scientists at Allen’s school) explored the issue Behe raised up regarding proteins. I felt their critique was one of the most well-reasoned, although I don’t count Behe’s hypothesis out. The numbers Durret and Schmidt came up with still appear pretty daunting for mindless origins of design.

    Finally, I don’t insist that the conformance of biology to design metaphors constitutes an absolute proof of intelligent origins, but I would argue it makes the case compelling. If the designs in biology were not so compelling, if they were as common place as the air we breathe, we probably wouldn’t be debating the topic.

  39. 39

    Greetings, Jon:
    Good to see you here. Sorry about the misunderstanding about my abilities to post comments here. My comments are apparently always held in moderation for periods lasting from an hour to more than a day, and so I assumed that they would never appear (indeed, some of them did disappear while awaiting moderation, only to reappear later).

    So, can we agree that natural selection is not a creative force in evolution? I think we can, and having gotten over that particular speed bump, can we go on to discuss the mechanisms by which you think phenotypic variation is generated, and why you think such mechanisms are no longer operative? I’m particularly interested in your semi-meiotic hypothesis for the origin of species; how exactly does it work? Yes, I’ve read your papers, but I’m not a cell biologist. Could you explain it in such a way that a reasonably well-educated undergraduate might understand it? I’d appreciate it, and think it might lead to some interesting discussions.

    BTW, I expect you are aware that, rather than completely rejecting Goldschmidt, Shindewolf, and the other macromutationists, Stephen Jay Gould believed that they were on the right track, so much so that his version of the theory of punctuated equilibrium depended on arguments that were quite similar to theirs. Indeed, he caught a lot of flack from the “modern synthesis” crowd for doing so, but time has vindicated some of his views, and may vindicate others as well.

  40. 40

    As for the problems involved with delayed appearance of comments due to long moderation queues, it’s a little like corresponding via pen & paper mail. You just write what you want to write, not attempting to keep up with the flow or fit into the sequence, and trust your correspondence to figure out where your comment goes. I’ve been doing that with my friend and colleague, Hannah Maxson, for almost three years, and the time lag in our letters to each other runs about three weeks to a month and a half.

  41. 41
    Freelurker says:

    I wasn’t clear in my last comment. You said:

    There is an improbable coincidence between the architecture of human-made systems and the architecture of biological systems.

    The statement didn’t make sense to me, because neither IDists nor evolutionists think that this is an improbable coincidence.

    (My comment about selection was not limited to natural selection. IDists, too, say that biological architectures were selected — by a designer.)

    However, your subsequent comments indicate that what you meant was that you see an improbable coincidence absent a designer.

    Evolutionists, of course, don’t see this as improbable; human designers select efficient structures and processes, and so does natural selection. One would therefore expect to see similar structures and processes between the two domains.

  42. 42
    skeech says:

    Salvador,

    I think the mistake that you and Mike are making is to conflate design terminology and metaphors with functional terminology and metaphors.

    To see this, look at this passage from chapter 3 of Mike’s book:

    Your body maintains an average internal temperature of 98.6 degrees Fahrenheit. When you are in a cold environment, without layers of clothing, your body quickly begins to lose heat and your core body temperature begins to decrease. Thermal sensors are activated to signal your brain that your body temperature is decreasing. In response, your brain attempts to compensate by signalling your muscles to begin short bursts of contractions which cause you to shiver. As you shiver, the muscle contractions work to generate heat, which in turn warms the blood that travels through them, increasing the body’s core temperature. In essence, it’s as if your body is activating a program to solve a problem posed by the environment… Biologists do not teach homeostasis to students by drawing from the fundamentals of chemistry and physics. Instead biology textbooks often introduce the concept of homeostasis by using a furnace and thermostat as an analogy for how such constant internal states can be maintained.

    Mike would presumably agree with the standard ID argument that the complexity alone of the homeostatic system implies design, but here he is arguing for something more: that each system — the biological system and its artificial counterpart — contains a thermal sensor and a controllable heat source, and that the fact that the biological system can be so readily described in these “design terms”, in Mike’s view, should heighten our suspicion that it is, in fact, designed.

    In reality, though, these terms are not design terms — they are functional terms. By this I mean that any system that performs the function in question — maintaining a constant warm temperature in a variably cold environment, despite a lack of insulation — must contain a part that plays the role of a temperature sensor and another part that plays the role of a controllable heat source. This is true whether the system is designed or not. You simply cannot have thermal homeostasis under these conditions without components that play these roles.

    If any successful system of thermal homeostasis must contain such components, then the fact that it can be described in terms of such components is inevitable. It therefore loses any significance, and you are left falling back on the standard ID argument: the system is complicated, so it must be designed.

  43. 43
    JohnADavison says:

    Natural selection is anti-evolutionary and always was. It has always been a losing battle ending in extinction.

    “Here I stand. I can do no otherwise.”
    Martin Luther

  44. 44
    jerry says:

    John,

    “Natural selection is anti-evolutionary and always was. It has always been a losing battle ending in extinction.”

    I agree generally, but yet we have, you name it, several million species, mostly bugs etc. Where did all the variation come from for these guys? You say the first bird came out of a reptile egg but where did his cousins come from and where did the variation to fuel all the aves species come from? I find it hard to fathom that all of a sudden that reptiles are giving birth to birds or that a small colony of primitive birds generated the variation for all the bird species.

    Allen would say the variation came from his engines of variation but somehow I doubt all of it came that way because it seems the trend is to less variation within species over time, not more because of natural selection.

  45. 45

    Greetings, Sal:
    Once again it is extremely demoralizing to put time and energy into formulating reasoned responses to other peoples comments, only to find that one’s own responses have vanished into “moderation limbo”. Until yesterday I could at least see the comments I had attempted to post, headed by the phrase “Your comment is awaiting moderation”. That at least allowed me to copy and paste them someplace else, so that my work would not be entirely wasted. Now, even that is no longer happening. My comments simply vanish as soon as I click on “Submit Comment”, with no explanation as to why.

    Sal, I have always treated you as a colleague and a gentleman. At the very least, please explain what it was about my comments that caused them to be removed, so that I can avoid making such mistakes in the future. That’s only fair, IMHO.

  46. 46
    Joseph says:

    Some organisms die and some live.

    Sometimes they die just because they were in the wrong place at the worng time.

    Sometimes they live not because they have better genes but that have better behavioral patterns.

    IOW acquired traits can and do outweigh genetically inherited traits.

    There is no way to predict what will be selected for at any point in time.

    So when people say “natural selection has been observed” all they really mean is we have seen some die and some live and we “think” we know why.

  47. 47
    scordova says:

    Dr. Kellogg wrote:

    My point is this: that a metaphor is tempting is a reason to avoid embracing it scientifically. It’s a reason to be suspicious.

    But then on those grounds, one might then argue that the metaphor “natural selection” should be exorcised from science.

    “Natural Selection” as Darwin conceived of it is not what really happens in nature.

    Natural Selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good.

    C.DARWIN sixth edition Origin of Species — Ch#4 Natural Selection

    This doesn’t happen in nature, in fact Darwin refuted this claim even in the subsequent pages of Origins when he effectively pointed out the success of random selection over natural selection. Natural selection has been unwittingly refuted by some of it’s proponents such as Fisher and Haldane. The notion of “Haldane’s Dilemma” has been used by ID proponents and neutral evolutionists to great effect.

    “Natural Selection” can select defective organism over healthy ones (such as blind cave fish, wingless beetles, etc. etc.). This is not consitent with Darwin’s notion of “good”. In fact, “good” and “bad” are deeply metaphorical.

  48. 48
    JohnADavison says:

    https://www.blogger.com/comment.g?blogID=22102663&postID=8651024580496088104&page=1

    I offer the above sequence from Allen MacNeill’s “The Evolution List” as an answer to some of the questions that have been posed here.

  49. 49
    GSV says:

    scordova
    “Natural Selection” can select defective organism over healthy ones (such as blind cave fish, wingless beetles, etc. etc.). This is not consitent with Darwin’s notion of “good”. In fact, “good” and “bad” are deeply metaphorical.

    Can you elaborate on Darwin’s notion of ‘good’?

    I thought one of the points of his book is that fitness is defined by the evolutionary niche the creature finds itself in hence ‘good’ or ‘bad’ depends on the environment.

  50. 50
    GSV says:

    Can someone let me know why all my comments are being moderated? Have I broken a rule?

  51. 51
    jerry says:

    Joseph,

    I think in the short term there are random events that may determine who survives or not but in the long term, animals and plants seem to be adapted to their environment. You see different animals and plants at the equator then you do in the mountains or on the plains or at the poles. This wasn’t random.

  52. 52
    iconofid says:

    scordova says: “There is an improbable coincidence between the architecture of human-made systems and the architecture of biological systems.”

    There’s no “improbable coincidence” at all. Both human designs and biological systems must function in the same environment, with the same physical restraints, and often solve the same or similar problems. We see similarities for the same reason that we see convergent evolution.

    Indeed, there are examples of convergence in the evolution of human technology, when the same or similar solutions are invented separately (bows and arrows, the automobile).

    We can even see it in the “designs” of very different species. Termites do complex buildings, air conditioning and agriculture.

  53. 53

    Having now appealed to Sal Cordova’s sense of fair play several times at Uncommon Descent and despite this having my comments deleted without explanation on multiple occasions, I must conclude that either Sal is being over-ruled by his UD overlords or he agrees with them that reasoned argument is not the point and that unanimity of propaganda is. How sad; I would have thought that becoming a graduate student in a legitimate science might have given Sal a somewhat different perspective on the value of differing viewpoints in the advancement of science. Clearly, that is not the case.

    Given that I have only limited time to prepare and research the posts and comments I make online, I will no longer be posting comments at Uncommon Descent.

  54. 54
    scordova says:

    iconofid,

    There’s no “improbable coincidence” at all. Both human designs and biological systems must function in the same environment, with the same physical restraints, and often solve the same or similar problems. We see similarities for the same reason that we see convergent evolution.

    Thank you for your comment.

    Needing a solution to a problem is different from finding a solution to a problem. The need of a solution is no guarantee a solution will be found.

    The presumption in your argument is that if a creature needs to solve a problem, somehow it will (without any inelligent guidance) through mechanisms of selection. We know experimentally and observationally and theoretically this is not true.

    I have provided links that explain some of the reasons why above.

    “Natural Selection” exists, but it works more along the lines of Blyth’s conception (preservation of species) versus Darwin’s conception (origin of species).

    We see similarities for the same reason that we see convergent evolution.

    Convergent architectures make just as much sense under a design paradigm as they do under a mindeless paradigm.

    Convergent evolution cannot be used as an argument against intelligent design.

    For mindless processes to create convergence, one would have to show mutation and/or selection can converge on the same complex solutions. We know experimentally this is unlikely. We knockout enough genes in an organism, and the organism seems unable to coverge back on the solution that once made the organism functional.

    Thus converegent evolution via mindless mechanisms is still highly improbable. Convergent evolution via intelligent design is possible, imho. Long-time professor of biology, John A. Davison, used convergence arguments in his peer-reviewed paper to argue that convergence is an evidence of Intelligent Design:

    Prescribed Evolutionary Hypothesis

    The so-called phenomenon of convergent evolution may not be that at all, but simply the expression of the same preformed “blueprints” by unrelated organisms.

    Example include marsupial “moles”, “wolves”, “anteaters”, “rabbits” (bandicoots), “squirrels”,
    including flying forms (phalangers), “woodchucks” (wombat), ”bears”, (koala), “mice”
    (Coenolestes) and most remarkable of all, saber-toothed cats. In Figure 1 Schindewolf presented
    pictures of the skulls of the marsupial Thylacosmilus atrox ( left) opposite that of the placental
    Eusmilus sicarius (right), the former from the Pleistocene of Patagonia, the latter from the
    Oligocene of South Dakota. The two forms are separated by thousands of miles spatially and
    millions of years temporally. Schindewolf’s legend beneath the figure is of special significance
    as it bears, not only on the questions raised here, but also, on the whole issue of Intelligent
    Design
    with which those questions are clearly related.

  55. 55
    scordova says:

    How sad; I would have thought that becoming a graduate student in a legitimate science might have given Sal a somewhat different perspective on the value of differing viewpoints in the advancement of science. Clearly, that is not the case.

    Dear Allen,

    I have no jurisdiciton over who gets moderated into a “pending approval” queue. This queue is operated via computer, and I cannot add or remove the names that get automatically put in that queue.

    However, once you are in the queue, and you are commenting on a thread I author, I can release your comment from the queue.

    It was my fault for not seeing your comments in the “pending approval” queue earlier (I do not check it every hour). I check the queue only when I remember to. Sorry for the delay.

    Some of my comments on another thread are still not released, so I have to endure this as much as you.

    I have nothing against you, and I hope our history of interaction will assure you that I personally have no intent to suppress what you have to say.

    I’m sorry for the misunderstanding and I hope you can extend a little forebearance.

    regards,
    Sal

  56. 56
    scordova says:

    Allen,

    UD is not my weblog, I am a guest here, I am under obligation to be supportive of those who have been kind enough to host my offerings.

    I am delighted you are here, but since I am a guest at UD, I must defer to those kind enough to grant me the privilege of being an author here.

    I’m appreciative of your comments. I hope you will not interpret the events of today as any sort of systematic attempt to suppress your valuable input to a dicsussion I started.

    Sal

  57. 57
    JayM says:

    scordova @56

    I am delighted you are here, but since I am a guest at UD, I must defer to those kind enough to grant me the privilege of being an author here.

    Alternatively, you could interact with Allen in a forum where neither of you are subject to “moderation” by third parties. I, for one, would like to follow your discussion. Is there an open venue agreeable to both of you?

    JayM

  58. 58
    jerry says:

    I hope Allen’s comments get posted immediately. I personally have learned a lot from Allen in the last couple years through what he has said and what he has recommended.

  59. 59
    scordova says:

    Can you elaborate on Darwin’s notion of ‘good’?

    I thought one of the points of his book is that fitness is defined by the evolutionary niche the creature finds itself in hence ‘good’ or ‘bad’ depends on the environment.

    Darwin’s notion of fit is more in line with the notion of inherent good (somewhat independent of context). Darwin regarded “Good” in the sense of what a designer would consider “good”. He seemed to suggest nature would somehow nurture the exploration of “good” patterns.

    The modern notion of “fit” is nebulous and situationally defined, contrary to Darwin’s notion. “Fit” is also poorly defined.

    See Lewontin in the Santa Fe Bulletin Winter 2003

    Darwin took the metaphorical sense of fitness literally. The natural properties of different types resulted in their differential
    “fit” into the environment in which they lived.

    The better the fit to the environment the more likely
    they were to survive and the greater their rate of reproduction. This differential rate of reproduction would then result in a change of abundance of the different
    types.

    In modern evolutionary theory, however, “fitness” is no longer a characterization of the relation of the organism to the environment that leads to reproductive consequences, but is meant to be a quantitative expression of the differential reproductive schedules themselves.

    Darwin’s sense of fit has been completely bypassed.

    So the popular notion of what is fit (Darwin’s notion) is not consistent with the notion of “fit” as defined by modern theory. In modern theory, when selection acts to destroy vision (such as blind cave fish), then that is in contrast to Darwin’s notion that nature somehow nurtures into existence, and therefore would tend to preserve rather than destroy an eye.

    Darwin’s metaphorical notions were literally wrong according to modern evolutionary theory.

    Lewontin notes it is hard to reconcile Darwin’s notion of “fit” (inherently good characteristics) with the notion of “fit” in practice:

    How, then, are we to assign relative
    fitnesses of types based solely on their properties of reproduction? But if we cannot do that, what does it mean to say that a type with one set of natural properties is more reproductively fit than another? This problem has led some theorists to equate fitness with outcome.

    If a type increases in a population then it is, by definition, more fit. But this suffers from two difficulties. First, it does not distinguish random changes in
    frequencies in finite populations from changes that are
    a consequence of different biological properties.

    Finally, it destroys any use of differential fitness as an
    explanation of change. It simply affirms that types change in frequency. But we already knew that.

    Andreas Wagner notes that fitness is illegitimate in charcaterizing biological function. Wagner unwtingly supports Behe:

    However, fitness is hard to define rigorously and even more difficult to measure….An examination of fitness and its robustness alone would thus not yield much insight into the opening questions. Instead, it is necessary to analyze, on all levels of organization, the systems that constitute an organism, and that sustain its life. I define such systems loosely as assemblies of parts that carry out well-defined biological functions.

    “assemblies of parts that carry out well-defined functions”? As in Irreducible complexity. 🙂 Function, rather than fitness, is a better characterization of biology. But “function” is a design metphor.

    I pointed out in the link that some functional systems elude any measures of fitness since they are not visible to selection: Airplane magnetos, contingency designs.

  60. 60
    JohnADavison says:

    I came here to Uncommon Descent specifically to offer an antidote to the atheist inspired Darwinian mysticism being presented by Allen MacNeill. So what does MacNeill do? He promptly disappears. I will let others interpret his departure as they choose. I ssy he didn’t have the stomach for a confrontation. I will continue my pursuit of Allen MacNeill at his weblog – “The Evolution List” as I recently linked.

    I thank Uncommon Descent for giving me the opportunity to evoke this expected reaction.

    Why don’t you now invite P.Z. Myers or Richard Dawkins to present their versions of the great mystery of phylogeny? I am itching to take them on as well. Only by inviting them can you have the pleasure of seeing them decline.

    It doesn’t get any better than this.

  61. 61
    jerry says:

    “It doesn’t get any better than this.”

    Yes, it would if you were able to debate Dawkins or Myers.

  62. 62
    JohnADavison says:

    Scordova

    Thanks for the plug of my 2005 paper – “A Prescribed Evolutionary Hypothesis”

    It is unfortunate that you did not include Schindewolf’s text commenting on the similarities shared by the placental and marsupial Saber toothed cats. That commentary ends as follows –

    “The similarities of form are present in such details as the structure of the large flange on the lower jaw, DESIGNED TO GUIDE AND PROTECT THE UPPER CANINES.”
    (Caps in italics in the original).

    I mention this to remind IDists that Schindewolf wrote those words in 1950 when many of you were not yet born. I was a mere 22 myself!

    Let’s give credit to those who were the original IDists, Otto Schindewolf, Robert Broom, Leo Berg, Reginald C. Punnett and William Bateson.

    “There is nothing new under the sun.”

  63. 63
    JohnADavison says:

    Thank you jerry but I do not “debate.” I confront and expose.

  64. 64

    Here is a direct quote from post #60 at Uncommon Descent:

    (http://www.uncommondescent.com...../#comments):

    “I came here to Uncommon Descent specifically to offer an antidote to the atheist inspired Darwinian mysticism being presented by Allen MacNeill. So what does MacNeill do? He promptly disappears. I will let others interpret his departure as they choose. I ssy he didn’t have the stomach for a confrontation. I will continue my pursuit of Allen MacNeill at his weblog – “The Evolution List” as I recently linked.”

    This is such a gross mis-characterization of what happened at UD that I can only assume that you are either demented or just plain despicable. I have at all times treated you with the utmost in courtesy, and this is how you respond. You are hereby banned from THE EVOLUTION LIST permanently, and all of your comments there have been removed.

  65. 65

    I would like to say thanks to all of the commentators here who have valued my participation in our discussions. Yes, we have had our disagreements, and yes they have been heated at times, but I have never attacked a person’s character, nor their motives in criticizing my positions. Indeed, as should be clear by now, I value your criticisms, as they have made me think about these issues in ways that I would not have without the opportunity to defend them in this forum.

    I have attempted at all times to maintain as civil and courteous a tone as possible, while at the same time criticizing those ideas with which I disagree. Sal has explained the situation that has caused my comments to be withheld from posting, and I understand. Indeed, I have had the same problem at THE EVOLUTION LIST, and have had to revert to full-time moderation.

    Ergo, I will be returning here and posting comments from time to time, as the opportunity presents itself and my time permits. I understand that there will be a lag time between posting my comments and their appearance here, and recommend that you all take that into account when soliciting responses from me.

    As to any further responses to Dr. Davison, I will not be making any, not to any of his comments, not here, nor anywhere else under any circumstances, ever. To those of you who value civility, courtesy, and the ancient and honorable traditions of the academy, I recommend that you do the same.

  66. 66
    JohnADavison says:

    Dear Allen MacNeill.

    Since you have now deleted all my comments at your own blog, I am not surprised that you would refuse to recognize my existence here or anywhere else for that matter.

    Apparently I cannot characterize the Darwinian fairy tale as an experimental and descriptive disaster without damaging your precious sensibilities and launching you into a veritable petit mal seizure.

    I have said nothing incivil either here or at The Evolution List and you know it. I have simply challenged the biggest hoax in the history of science. So did every one of my distinguished sources.

    If you choose to refuse to respond to my critique of the Darwinian model it will make my task that much easier. That suits me just fine.

    So you go right on influencing undergraduate minds at Cornell with the most tested, the most failed, and the most persistent flight of human imagination ever generated in the history of rational discourse.

    It doesn’t get any better than this.

    I love it so!

  67. 67
    Pendulum says:

    Dr. Davidson, I’m having a hard time understanding your position. There have been many many posts recently about Weasel, and Dr. Elsberry was nice enough to help out with some code that has been posted. Is it your position that in a “pocket universe” like a GA that evolution happens, or doesn’t happen? In the history of life on Earth, has evolution happened in the past, but stopped recently? Is it possible that life is at this moment evolving on other planets? I’m trying to understand what exactly it is that you are fulminating against.

  68. 68
    bFast says:

    Allen_MacNeill:

    As to any further responses to Dr. Davison, I will not be making any, not to any of his comments, not here, nor anywhere else under any circumstances, ever. To those of you who value civility, courtesy, and the ancient and honorable traditions of the academy, I recommend that you do the same.

    I know of where you speak. I have toyed around with starting my own blog. One of the few people who would be banned would be the good doctor of which you speak.

    I’m sorry to hear that you are getting too busy for this website. I rarely agree with you, but do value your learned perspective.

    JohnADavison:

    Thank you jerry but I do not “debate.” I confront and expose.

    That would be the problem. Dr. Davison, your theories have a lot of merit, but they need civil debate. Civil debate needs to be richer than siting what another expert has said. I am sorry to see you reinvigorated on this site, as I watched you crumble the ISCID brainstorms site with a flood of frequently very ungracious comments that usually had little information in them.

  69. 69

    For what it’s worth (and because I have been rather sneeringly referred to as an atheist by persons who shall remain unnamed, here is some information that some here may find interesting.

    I am a Quaker; that is, a member of the Ithaca Monthly Meeting of the Religious Society of Friends. The actual name for “Quakers” is Friends. When they started out (in England in the 17th century) they tended to refer to themselves (rather grandly, IMHO) as the “children of the light” and/or “the publishers of truth”. However, by the time they had come to America they had settled on the Society of Friends. “Quakers” was a somewhat derogatory name given to them by their opponents in Cromwell’s England.

    It is important to note that there are two different kinds of Friends, known as “programmed” and “unprogrammed” (sometimes referred to as “evangelical” and “traditional”, respectively). The programmed/evangelical friends are a lot like Methodists: they meet on Sundays in buildings that look like churches (but generally without steeples), there is a minister who gives a sermon, there is often a choir, and the congregation sits auditorium-style facing the front of the “church” where the pastor speaks. Following the service there is generally “fellowship time”, with coffee and snacks in the fellowship room, etc. Herbert Hoover and Richard Nixon were both brought up in “programmed” Friends meetings.

    The other kind (the original kind, the kind invented by the founder of the Friends, George Fox, and the kind of meeting that I belong to) meets in silence in a simple (often very plain) meeting house, with no minister, no choir, no hymns, no sermons, indeed no “program” at all. Everybody waits in silence for the “gathering of the spirit”, usually all facing each other in a roughly circular (or square) arrangement of chairs or short pews. Sometimes a person in meeting is “moved” to stand up and speak (or, much more rarely, to sing). This almost never happens until at least a half hour of silence has gone by. No one comments while they speak, although people sometimes join in with a familiar song. When they have finished speaking, they sit back down and all wait for the silence to “settle”. I’ve never been at a meeting at which more than a half dozen people spoke, and I’ve been at plenty at which nobody spoke for the entire hour (and sometimes much longer than that, as some special meetings have no set time limit).

    In an unprogrammed/traditional meeting such as the one in Ithaca there are no officials except for the Clerk of the Meeting, whose responsibility it is to keep people informed of when and where meetings are happening, and to take notes at “meetings for worship with attention to business”, which generally happen once a month. The Clerk also “breaks” meeting by catching people’s eyes and turning to the people next to them to shake hands. At the “rise of meeting” the Clerk makes announcements and invites members of the meeting to share concerns. There is also a Treasurer, who keeps accounts, but is not considered to be an “officer” and is not elected. Both the Clerk and the Treasurer have assistants, and are usually chosen annually by the committee for ministry and oversight (which used to be referred to as the elders, a now archaic term). I was for many years a member of this committee.

    Probably not surprisingly to some at this website, I am generally known among the Ithaca Meeting as a “minister”; that is, someone who is often moved to speak. I haven’t done so in about a year, but that’s not unusual, especially for our meeting. Some meetings have a tradition of recording and drawing attention to ministers, but this is rare and becoming more so among “traditional” Friends meetings.

    Although as one might expect there are a number of Cornell and Ithaca College professors in our meeting, the overwhelming majority of our members are not professional academics. Rather, they are working people from the town; everything from secretaries to lumberjacks to farmers (quite a few of these, as it turns out; Ithaca is “centrally isolated”).

    Membership in a traditional Friends meeting is gained by petition to the committee on ministry and oversight, who appoints a “clearness committee” for the prospective member. Clearness committees work together with members to “come to clearness” on particular issues. People can ask for a “clearness committee” to join the meeting, get married “under the care of the meeting” (FWIW, the Ithaca meeting has been recognizing marriages between same-sex couples “under the care of the meeting” for almost thirty years), decide on taking a particular job, pursue a particular academic degree, get divorced (yes, it happens, although not often) or whatever is of concern to them. Anyone can ask to join a meeting, and there is no prohibition against people becoming members of a Friends meeting while remaining full members of other churches or religions. Indeed, there are a number of agnostics and atheists in our meeting (but, as I stated earlier, I’m not one of them). Because of this process, we say that a person becomes a Friend by “convincement”, not conversion, and that “convincement” must come from within, not from a minister or the group.

    Perhaps the most noticeable difference between “traditional” Friends and other religious groups is the total lack of a creed or “confession of faith”. Instead, we maintain a collection of written “Queries and Advises”, which are periodically read and revised by clearness committees. We feel that it is each person’s responsibility to come to whatever “measure of the light” we can. All decisions (and I mean ALL decisions) are made by pure consensus. There are no votes taken at any Friends meetings, including those held with attention to business. This means that some decisions take a generation or more to be reached, but when they are finally arrived at, everyone in the meeting has agreed to the decision and will back it wholeheartedly.

    Friends are one of the three historic “peace churches” (along with the Brethren and Mennonites). To be a Friend means never to participate in war or the preparation for war in any form whatsoever. I was a conscientious objector during the Vietnam War, and remain one to this day.

    This doesn’t mean that Friends are pacifists, however. Quite far from it; Friends are very active in our “peace witness”, often placing ourselves between combatants and doing humanitarian work around the world. The Friends service group, the American Friends Service Committee, received the 1947 Nobel Peace Prize on behalf of Friends worldwide, for our corporate work for peace and reconciliation.

    Friends also don’t proselytize (indeed, there is a heavy but unspoken prohibition against doing so), and so the foregoing should be considered to be informational only. If you would like to learn more about the Society of Friends, I recommend this website:

    http://www.quaker.org/

    Here is the website for the meeting I attend:

    http://ithacamonthlymeeting.or

    “Dearly beloved Friends, These things we do not lay upon you as a rule or form to walk by, but that all, with the measure of light which is pure and holy, may be guided: and so in the light, walking and abiding, these may be fulfilled in the Spirit, not from the letter, for the letter killeth, but the Spirit giveth life.”

    – Given forth at a General Meeting of Friends in the Truth at Balby in Yorkshire, in the ninth month 1656, from the Spirit of Truth to the Children of Light

  70. 70
    iconofid says:

    scordova: “Thank you for your comment.”

    And thankyou for your reply.

    “Needing a solution to a problem is different from finding a solution to a problem. The need of a solution is no guarantee a solution will be found.”

    I agree entirely.

    “The presumption in your argument is that if a creature needs to solve a problem, somehow it will (without any inelligent guidance) through mechanisms of selection. We know experimentally and observationally and theoretically this is not true.”

    No, that’s not what I would presume, and the fact that the overwhelming majority of species are extinct illustrates that we do not get exactly what we need. The other thing is obvious imperfections amongst those lineages still around. We could have used resistance to the Black Death when it killed half the population of Europe, but there weren’t mutant immune systems to cope with it, and the cetaceans could arguably use a new breathing system that draws oxygen from water, but they haven’t evolved it yet!

    What I meant was that our machines have to function under the restraints of the laws of physics, and so does evolution, so there will be (often superficial) similarities like the use of wings, but there are massive differences as well.

    As for experiments asking for organisms to solve specific problems, they certainly will sometimes. It must be remembered that, if the only possible route to the solution is complex, evolution has a lot more time than we do, and the quantity of organisms in a laboratory is nothing compared to what’s in the wild!

    Convergent evolution finding the same blueprint? We should be able to tell by looking at genomes. I know of one example in fish where the same solution was arrived at by completely different routes.

  71. 71

    Flight (defined as “locomotion through the air”), has evolved independently dozens of times, in taxa that are hardly related at all (indeed, are in at least three different kingdoms):

    KINGDOM ANIMALIA:
    Bats
    Fruit Bats (very different from insectivorous bats)
    Flying Squirrels
    Phalangers
    Birds
    Dromaeosaurs
    Pterosaurs
    Amphibians (there are 3,400 species of frogs from both New World (Hyla) and Old World (Rhacophoridae) that have independently evolved gliding flight)
    Flying Fish
    Insects
    Spiders (babies, who “balloon”)

    KINGDOM PLANTAE:
    Plants that reproduce using winged seeds, called samaras:
    Ash Trees
    Elms
    Hop Trees
    Maples
    Basswoods
    Plants that reproduce using seeds carried in balls of drifting fluff:
    Cattails
    Dandelions (and many other Compositae)
    Milkweeds
    Thistles

    KINGDOM FUNGI:
    Many widely separated taxa of fungi have a spore-producing stage in which the spores are transported by drifting in air currents

    And if one broadens one’s definition of “flight” to include “locomotion through a gaseous or liquid medium, without regular contact with a solid substrate”, then this would include most aquatic metazoa. This is why some “fish” (such as rays) look surprisingly like birds and bats, as they “fly” through the water, and why some winged animals, such as penguins, “fly” only in the water.

    “Flight-like movement”, in other words, is strongly constrained by the mechanics of flight, and so all “flying” entities (including imaginary ones, like dragons, and man-made ones, like airplanes) have structural features in common. This is the sense in which “convergence” is used in evolutionary biology, and clearly it is not necessarily the result of “related genetic pre-programming”.

  72. 72
    iconofid says:

    JohnADavison: I didn’t come here to “debate.” I came to offer an antidote to the Godless Darwinism that still is allowed here for reasons I fail to understand.

    I thought you might have come here to give us all a good laugh. Either that, or to demonstrate a new method of doing science by quotes and assertions.

  73. 73
    scordova says:

    Convergent evolution finding the same blueprint? We should be able to tell by looking at genomes. I know of one example in fish where the same solution was arrived at by completely different routes.

    I would agree that recognition of a common theme is important. Convergences in biology converge to metaphors. Some of the most notable metaphorical concepts seem so real that we don’t give them a second thought because to our thinking, that’s what they are.

    An eye is an eye. A male is a male, a female is a female. These seem so obvious, but if we step back we will realize these convergent features are organized and grouped together under metaphors we created or accepted “naturally”. There is nothing in physics in chemistry that compels us to lump certain characteristics in a certain way.

    A powerful example of convergence? Eyes.

    Another example of convergence, sexual reproduction. From Dr. Davison’s evoutionary manifesto:

    In the Darwinian or sexual model, one might anticipate some universal sex-determining mechanism operating throughout evolutionary history. If, as I believe, the role of sexual reproduction is to limit
    evolution, one would anticipate a wide variety of sex-determining devices evolving independently. Such is the actual case. I found that the idea of an independent sexual evolution had already been
    expressed. The Russian cytologist N.N. Vorontsov was one of the first to call attention to the independent evolution of sex determination.

    Just as the transition from isogamy to anisogamy and to oogamy took place independently of each other in the various phyla of plants so the formation of mechanisms of the cytogenetical sex
    determination with differentiated heterochromosomes follows the same pattern in various kingdoms and phyla and results in an independent occurrence of the XX-XY system in Melandrium as well as in many Insects and Mammals, whereas the ZW-ZZ system evolved independently in Trichoptera,
    Lepidoptera, Serpentes and Aves. Against the background of these facts it is unclear whether the male species of different groups are homologous to each other or not; they appear to be nonhomologous.

    “The evolution of the sex chromosomes”
    (1973), page 646

    From Evolutionary Manifesto

  74. 74
    JohnADavison says:

    bfast

    Since you would ban me summarily, please do not get a weblog. I have enough enemies already. You are of course welcome at my weblog provided you use your full name of Bruce Fast.

    As for “debate” in any form, I challenge anyone to cite a single example in which “debate” has served to resolve any problem, scientific or otherwise. “Debate” is for politicians, lawyers, referees and certain weblog “debating teams” whose names I am hesitant to mention but who are already well known.

    Now if I am going to be banished once again from participation here, (which seems to be the goal of Bruce Fast and perhaps others), I recommend that it be for good cause.

    I have but one goal which is to discover “The Truth” which often requires responding to those who are convinced they have already found it.

    “Truth is incontrovertible, malice may attack it, ignorance may deride it, but in the end, there it is.”
    Winston Churchill

  75. 75
    JohnADavison says:

    Bruce Fast in #68.

    If I have “crumbled” brainstorms as you claim, why am I still allowed to comment there, one of the few venues from which I have not been banished.

    I do not have “theories” either. I have proposed a couple of hypotheses which are in complete accord with everything we now know about the fossil record as well as all the findings of molecular biology. To be candid, I regard my hypotheses as already largely verified and accordingly well on their way to theory status. Of course history will be the final arbiter. It has already relegated the Darwinian fairy tale to the trash bin of evolutionary science.

    The Truth lies elsewhere and I think I know where that is. It is summarized in my Prescribed Evolutionary Hypothesis and in the closely related Universal Genome Hypothesis, neither of which can ever be reconciled with Godless, aimless, purposeless Darwinism.

  76. 76
    hazel says:

    Allen, thank you very much for your description of being an unprogrammed Friend. That was both fascinating and inspiring.

    hazel.

  77. 77
    Joseph says:

    Allen MacNeill:
    Flight (defined as “locomotion through the air”), has evolved independently dozens of times, in taxa that are hardly related at all (indeed, are in at least three different kingdoms):

    How can we test the premise that flight “evolved” from the flight-less?

    That is the issue.

    Saying X evolved is meaningless unless it can be demonstrated that such evolution is even possible.

  78. 78

    In #77 joseph asked:

    “How can we test the premise that flight “evolved” from the flight-less?”

    The same way one tests any hypothesis about evolutionary derivations: look at comparative anatomy, comparative genomes, and the fossil record. Here’s a place to look on the web:

    http://www.ucmp.berkeley.edu/v.....volve.html

    and here’s another:

    http://www.nurseminerva.co.uk/adapt/evolutio.htm

    and another:

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

    There are many technical references on this subject as well. I would start with the first link, and then follow up the references listed in the second and third links (the Wikipedia link also has links to the evolution of flight in groups other than birds).

    For plant seed dispersal mechanisms via the air, check this link:

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

    and this one:

    http://en.wikipedia.org/wiki/Samara_(fruit)

    and this one:

    http://plantbiology.msu.edu/fi.....lution.pdf

    You can also read the last link online here:

    http://74.125.93.104/search?q=.....#038;gl=us

  79. 79

    Here’s the abstract for the reference on the evolution of seed dispersal in flowering plants:

    Evolution of fruit types and seed dispersal: A phylogenetic and ecological snapshot.

    Claire M. Lorts, Trevor Briggeman, and Tao Sang

    (Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA)

    Abstract: Success of flowering plants is greatly dependent on effective seed dispersal. Specific fruit types aid
    different mechanisms of seed dispersal. However, little is known about what evolutionary forces have driven the diversification of fruit types and whether there were phylogenetic constraints on fruit evolution among angiosperm lineages. To address these questions, we first surveyed the orders and families of angiosperms for fruit types and found no clear association between fruit types and major angiosperm lineages, suggesting there was
    little phylogenetic constraint on fruit evolution at this level. We then surveyed fruit types found in two contrasting habitats: an open habitat including the Indian desert and North American plains and prairies, and a closed forest
    habitat of Australian tropical forest. The majority of genera in the survey of tropical forests in Australia were fleshy fruit trees, whereas the majority of genera in the survey of prairies and plains in central North America were herbs with capsules and achenes. Both capsules and achenes are frequently dispersed by wind in the open,
    arid habitat, whereas fleshy fruits are generally dispersed by animals. Since desert and plains tend to provide continuous wind to aid dispersal and there are more abundant mammal and bird dispersers in the closed forest, this survey suggests that fruit evolution was driven at least in part by dispersal agents abundant in particular habitats.

    In other words, the evolution of similar air-borne fruit and seed dispersal mechanisms in flowering plants (like the evolution of flight in animals) is more likely to have evolved via convergence than homology. Again, movement through the air clearly involves stringent constraints on physical structure, which is why all “flying things” have many structural features in common, despite having come from very different, non-flying ancestors.

  80. 80
    jerry says:

    Joseph,

    The four indispensable friends of the natural evolutionist are

    It evolved
    It was selected for
    it emerged
    it was exapted

    There may be others but the lack of these would leave them speechless on most discussions of evolution. And from my recent readings, the last one is the most in favor at the moment.

  81. 81
    scordova says:

    I like to salute Allen for his patience and persistence here.

    I consider myself honored to have him lend his expertise here.

    He was extraodinarly kind to my fellow IDEA students at Cornell at some risk to himself. I feel a debt of gratitude on behalf of those in IDEA (the ID organization I was affiliated with).

    I will try to release any of his moderated comments on this thread as quickly as I can, but I cannot monitor the moderation and spam queues continuously. If I inadvertently delete a comment, I hope he will bring it to my attention by reposting.

    There are other threads by other authors at UD. I have no jurisdiction there whatsover, in fact I have to wait for my comments to be released there. These measures evolved at UD because of the intense traffic that attempts to enter this website. This has also led to technical and logistic issues.

    I appreciate everyone’s patience with the process, and if it is any consolation, I have to wait for some of my comments at UD to appear as well.

  82. 82
    jerry says:

    Allen,

    By the timing of your post, I assume they are not being held up anymore or is it just on this thread?

    An interesting list of species that move either by air or water.

    I assume the term convergence which has been used here would require different genomic combinations for specification and if the same proteins, systems are used then the term convergence would be inappropriate.

  83. 83
    iconofid says:

    JohnADavidson: “Of course history will be the final arbiter. It has already relegated the Darwinian fairy tale to the trash bin of evolutionary science.”

    Eberhard Dennert: “Today, at the dawn of the new century, nothing is more certain than that Darwinism has lost its prestige among men of science. It has seen its day and will soon be reckoned a thing of the past. A few decades hence when people will look back upon the history of the doctrine of Descent, they will confess that the years between 1860 and 1880 were in many respects a time of carnival; and the enthusiasm which at that time took possession of the devotees of natural science will appear to them as the excitement attending some mad revel.” Eberhard Dennert, At the Deathbed of Darwinism, 1904,

    Plus ca change…..:)

  84. 84
    scordova says:

    How can we test the premise that flight “evolved” from the flight-less?

    That is the issue.

    Saying X evolved is meaningless unless it can be demonstrated that such evolution is even possible

    Joseph,

    I understand you are a retired airline pilot. Perhaps you might elaborate to our readers the effect of on an aircraft of a malformed airfoil. What may not be evident to someone looking at an flying system is how sensitive the system is to unwelcome variation.

    For a bird to fly it must coordinate a large number of surfaces simultaneously. In aircraft with many control surfaces a computer is needed to coordinate the surfaces because a human would not be able to do this.

    I would expect evolution of flight to be rather costly since the intermediate stages would usually be fatal!

    Anyone in the aerospace industry knows how difficult it is to create a system capable of controlled flight. The functional constraints are extremely narrow.

    It may appear an airplane is tolerant of change (such as damage to a warplane’s wings), but this tolerance is a design feature.

    The problem with the evolution of flight is as Walter Brown said, “an arm will become a bad arm before it becomes a good with”. The conceptual intermediates would appear to be selected against not selected for.

    An airplane that can’t fly makes a bad car.

    I deeply appreciate Allen’s providing info that attempts to explain evolution through cladistic analysis. But this illustrates that radically different thought process between the communities of EBers and IDers. The physilogical and mechanical details are often the questions my side of the aisle are insterested in.

    As Leo Berg pointed out, it appears all the required parts appeared suddenly and in the right location morphologically. This makes sense to an engineer, the intermediates wouldn’t make much mechanical sense. A car will become a bad car before becoming a good airplane. For people on my side of the ailes, there is similar principle at issue in the evolution of flight.

  85. 85
    scordova says:

    By the way, it is my understanding one of Dr. Davison’s specialties was physiology.

  86. 86
    Pendulum says:

    Allen,

    Is there something about flight that encourages speciation? I was always struck by the large numbers of species in flying groups.

  87. 87
    iconofid says:

    Jerry: “I assume the term convergence which has been used here would require different genomic combinations for specification and if the same proteins, systems are used then the term convergence would be inappropriate.”

    Yes, Jerry. If the same route, it’s parallel. Here’s a neat example of convergent rather than parallel.

    Two different designers, perhaps.

  88. 88
    iconofid says:

    Sorry, missing link above. HTML didn’t work. How do I put in a link, someone?

  89. 89
    Tom MH says:

    iconofid:
    You can use this syntax:
    [a href=”http://google.com”]Interesting Link[/a]
    except replace [ and ] with .

    This will generate the following hyperlink: Interesting Link.

  90. 90
    iconofid says:

    Cheers, Tom. I thought that was what I did, but I must’ve missed something out.

    Convergent frozen fish

    (Missing link from a few posts up, with apologies).

  91. 91
    JohnADavison says:

    Iconofid

    It is Davison not Davidson and it has been Dr. Davison since 1954.

    As for the death of Darwinism, that occurred in 1871, twelve years after the publication of the Origin of Species when St. George Mivart asked the question in his book Genesis of Species –

    How can natural selection have been involved in a structure which had not yet appeared?

    Mivart dedicated all of chapter II to it –

    THE INCOMPETENCY OF “NATURAL SELECTION” TO ACCOUNT FOR THE INCIPIENT STAGES OF USEFUL STRUCTURES, pages 35-75.

  92. 92
    iconofid says:

    JohnADavison: Iconofid

    It is Davison not Davidson and it has been Dr. Davison since 1954.

    My sincere apologies.

    As for the death of Darwinism, that occurred in 1871, twelve years after the publication of the Origin of Species when St. George Mivart asked the question in his book Genesis of Species –

    How can natural selection have been involved in a structure which had not yet appeared?

    It certainly couldn’t, Dr. Davison. I should imagine that that’s one thing that everyone on this blog would agree on.

    I think that all theories depending on the clairvoyance of natural selection should be abandoned immediately.

  93. 93

    In #86 Pendulum asked:

    “Is there something about flight that encourages speciation?”

    Indeed, there is: organisms that can locomote through the air (either by active flight or passive drifting) can move from place to place more often and over farther distances than organisms that swim, and especially organisms that are either constrained to locomotion on the ground surface or fixed to the ground (like plants). This is because organisms that can move relatively long distances can become geographically isolated much more easily, and geographic isolation (technically referred to as “vicariance” in evolutionary theory) is the most common process that leads to genetic divergence and reproductive isolation. See:

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

  94. 94

    This is why some of the most notable evolutionary biologists that have studied the process of speciation have been specialists in birds: Darwin himself (recall Darwin’s finches), Wallace (who discovered “Wallace’s Line” primarily by studying birds),and Ernst Mayr, who studied birds in the same biogeographic region as Wallace, but a half century later.

  95. 95

    Other specialists in the evolutionary biology of speciation have specialized in insects, which are also notable for having adaptations for flight. Such specialists would include: Darwin again (an obsessive collector of beetles and other insects), Wallace again (ditto), Charles Michener, Tom Seeley, Robert Trivers, Karl von Frisch (1973 Nobel Prize), William Wheeler, and Edward O. Wilson. The latter is also famous for having developed the theory of island biogeography (along with mathematician and theoretical biologist, Robert MacArthur) and synthesizing the emerging science of sociobiology.

  96. 96
    JohnADavison says:

    It is now apparent based on field observations (by the Grants) of natural hybridizations that all of Darwin’s precious finches are a single species.

    The real mystery is why didn’t Darwin or someone since domesticate the finches and test Darwin’s assumption that they were separate species? Finches are among the easiest birds to domesticate. The canary is a finch!

    I will tell you why the Darwinians refuse to test the hypothesis that Darwin’s finches are separate species. They are terrified of what their experiments might disclose. That is why and the only reason why. That is why they refuse to test any of their silly assumptions. In short they are not scientists. They are congenital mystics. They can’t help it. They were “born that way” just as William Wright’s book by that title clearly documents.

    Ernst Mayr, a hero to the Darwinian flock, actually described himself as a “dyed-in-the-wool Darwinian.”
    The Growth of Biolgical Thought, page 132.

    Isn’t “dyed-in-the-wool” synonymous with “born that way”? Of course it is!

    All enlightened Darwinians, if there are such, must realize that that “natural selection” is a total failure. That is why Paul Zachary Myers and Richard Dawkins have completely abandoned science to dedicate all their energies to the denigration of the only conceivable alternative to the aimless Darwinian model which is a creative role for some kind of higher power or powers. They don’t even mention the doctrine they silently defend because they realize it is undefensible.

    It is hard to believe isn’t it?

    Not at all. It has been going on for a century and a half. It is the biggest and most enduring hoax in the history of science.

    I love it so!

  97. 97
    JohnADavison says:

    [duplicate deleted per John A Davison’s request. Sal]

  98. 98
    JohnADavison says:

    Please delete my duplicated message.

  99. 99
    jerry says:

    John,

    Since birds have been brought up, I have a question or a couple of related questions. There are about 10,000 so called species of birds including the various varieties of finches you mentioned. Which means that this 10,000 is probably far less as other species may just be variations of each other. You also mention that a canary is a finch and our good friends cardinals and blue jays are in the same order.

    Now in canidae there are wolves and dogs and they can interbreed so essentially the various dog breeds and wolves are the same species. Would this be true for a lot of bird species such as the various finch type birds. Are they really just variants of each other? Or are they truly different species? I know they do not interbreed but could they be bred artificially.

    And if whatever number of species of birds there really are, how did they originate. Now traditional evolutionary biology will say by separation and natural selection within the separated gene pool.

    My general impression of most evolution is that a lot of it is what I call devolution or a narrowing of the gene pool over time within various sub populations along with an occasional mutation with the resulting array that we see today.

    Also finches seem to be within the order Passeriformes or song birds while wolves and dogs are within the family canidae. These are different classes but is the level on the taxonomy scale just reflect that there are more varieties of birds than mammals and thus have to be fit into different levels and that the levels do not really mean the same thing from class to class.

    Any thoughts on this. This is a lot but if you have time to answer some of these, I would be interested.

  100. 100
    Pendulum says:

    Dr. JAD @ 96,

    What species definition are you using here? Mayr’s definition only considers natural interbreeding, so what these multiple species would do in domestication is irrelevant.

  101. 101
    JohnADavison says:

    Evolution has been in large part a progressive loss of potential until today it is questionable if even natural speciation is still in progress.

    Theodosius Dobzhanky gave us an unambiguous definition of species. Two forms will be considered to be separate species when their progeny prove to be sterile. This definition may require an experimental test. While the two forms may not choose to interbreed, that certainly does not mean they should be regarded as distinct species. There are humans who might not choose to interbreed. Dobzhansky’s criterion requires, when necessary, artificial insemination. Darwinians are loathe to experiment for reasons I already stated.

    Quite independently, even natural speciation seems to have ceased. The important related point is that there is no reason to believe that any taxonomic category ever appeared gradually. If you examine the “transitional” forms you will discover that the paleontologists are forced to put each new discovery in a separate genus. That is especially evident in the horse series which terminated with the genus Equus. I know of not a single fossil or extant form that ever gradually assumed its final form.

    In a very real sense the genus, or kind, has been the most significant element in creative evolution. Both Julian Huxley and Robert Broom claimed that a new genus has not appeared in the last two million years. I have extended that conclusion to include experimentally verifiable species that satisfy Dobzhansky’s physiological criterion. I see no evidence that they are any longer being produced.

    I realize that my position is not popular with the establishment but that does not mean that it is not valid.

    Dobzhansky, a lifelong Darwinian, provided us with a sensible, physiologiocal criterion for speciation. All I am suggesting is that if we apply it, we might have to conclude, as I already have, that creative evolution is finished and that only extinction remains.

    Incidentally, as a young man, before leaving Russia for the New World, Dobzhansky was a student of Leo Berg. I believe that if Dobzhansky had remained in Russia, Darwinism would have died that much sooner.

    Whatever others may think and no matter how they may react here or elsewhere, the Darwinian scheme for evolution is a dismal failure. It, by its own assumptions, fails to qualify even as a working hypothesis.

  102. 102
    JohnADavison says:

    Since there seems to be a lull here, I remind the participants that in message #74 I challenged all to provide a single example in which “debate” served to resolve any issue scientific or otherwise. For the record, there has been no response.

    Actually, “debate” prevents resolution because it honors your opponent’s position even when that position is patently ridiculous as is the Godless, aimless model which still defines the basis of neoDarwinian gradualism, the only hypothesis in all of science which assumes that it is immune to the judgement of the experimental laboratory and the undeniable testimony of a largely discontinuous fossil record.

    “Any system that purports to account for evolution must involve a mechanism not mutational and aleatory.”
    Pierre Grasse, Evolution of Living Organisms, page 245, the sentence in his italics for emphasis.

    At present there are two such systems available, my Prescribed Evolutionary Hypothesis (PEH) and the closely related Universal Genome Hypothesis (UGH), neither of which can ever be reconciled with the Darwinian fairy tale.

    So don’t expect me to “debate.” It is waste of time. I am a physiologist who is interested in how things work. I return to Uncommon Descent in the same spirit I have entered all forums, to challenge all positions that I deem to be without foundation and to promote all that I feel is well founded science.

  103. 103
    iconofid says:

    JohnADavison “Since there seems to be a lull here, I remind the participants that in message #74 I challenged all to provide a single example in which “debate” served to resolve any issue scientific or otherwise. For the record, there has been no response.”

    It seems that you’re the only one who thinks the issue worth debating.

    Am I the only one laughing?

  104. 104
    Pendulum says:

    Thank you for clarifying the species concept you are using.

  105. 105
    jerry says:

    I agree with John, the issue isn’t worth debating because it is too one sided. For the 3 1/2 years I have been on this site I haven’t seen one coherent defense of the naturalist position on evolution. So John is right. The question is how was the design instantiated and when.

    No I am laughing too at the ineptness of the Darwinist who come here. There a pretty inept group.

  106. 106
    Pendulum says:

    Dr. JAD, thanks for clarifying you position.

  107. 107
    iconofid says:

    Jerry, by “issue”, I meant the issue of whether or not debate ever resolved anything. I was laughing because John, who says he’s not here to debate, seems to be the only one who wants to debate debate.

    As for what you’re talking about, and being of the “naturalist” tendency, I’ve never known anyone present convincing evidence of the existence of the non-natural.

    What have you got against people who look for natural explanations for natural phenomena? Surely you look for a material mechanical fault when your car breaks down, not gremlins?

    The question is how was the design instantiated and when.

    A very good question. We eagerly await the research and the results. And this will certainly involve debate amongst I.D.ers.

    In this case, I’ll certainly go with John. I predict no resolution.

    I may have it wrong, but doesn’t Dr Davison see design at the level of species? How near is that to your view?

  108. 108
    David Kellogg says:

    jerry [104],

    No I am laughing too at the ineptness of the Darwinist[s] who come here. The[y’]re a pretty inept group.

    Oh, I don’t know.

  109. 109
    jerry says:

    “I may have it wrong, but doesn’t Dr Davison see design at the level of species? How near is that to your view?”

    I do not think so but you should ask him. I am far from an expert on his beliefs except for our concurrence on the limitations of natural selection. The most over hyped concept in the history of science. I believe he thinks the design happened a long time ago. The birds could be descendant from an original gene pool from 60-80 million years ago but I have no idea what John thinks which is why I asked. The birds obviously contain a lot of variation. Where did that variation come from? That is the $million question.

    As for me, the issue is a mystery. I think that is the only honest answer there is. The one thing I believe is that design is very probable as some point because of the inadequacy of natural processes. What I think it is written all over this blog the last 3 1/2 years. I am not shy about saying what I believe.

  110. 110
    jerry says:

    David Kellogg,

    Maybe someone will surprise me some day. Remember they did find the black swan.

  111. 111
    JohnADavison says:

    Of course phylogeny is a mystery. So is ontogeny, the development of the individual. They are closely related phenomena which show many similarities.

    Both are predetermined, both are irreversible and both terminate never to be resumed. Death is the terminus of the individual and extinction the end of each species.

    I believe with Robert Broom that the entire sequence was planned millions of years ago and there is little we can do to modify the Plan, a word Broom capitalized. I also agree with Albert Einstein –

    “Everything is determined…by forces over which we have no control.”

    I wish he had used the past tense as I see no evidence for the supernatural at present even as I remain convinced that it must have played a role in the distant past.

    If we are planning on continuing to exist as a species we had better change our ways as we are on the road to extinction right along with all our fellow creatures and we are the primary cause. I hate being pessimistic and I hate being right.

  112. 112
    JohnADavison says:

    Meanwhile, this thread is headed for the bottom of the page where it will disappear into oblivion as threads here always do. MacNeill has decided I do not exist and so I find myself once again lecturing in an empty auditorium. This is not the first time this has happened, nor will it be the last.

    I remain open to any form of constructive dialogue here or anywhere else where I am permitted to speak.

    Let the record show that Allen MacNeill, like every other Darwinian I have ever encountered, is unwilling to respond to any challenge to the Darwinian fairy tale. He has deleted my benign comments at his blog and decided that I do not exist here.

    I see no reason to continue here. I have achieved my purpose which was to expose the Darwinian fantasy for what it always was, an obligatory ideology required by a congenital mentality unable to respond to the real world, a world every aspect of which was designed by one or more designers whose existence is no longer evident but whose past must never be denied.

    So I now return this thread to Allen MacNeill to do with what he has always done, which is to promote the most failed hypothesis in the history of science.

  113. 113
    crater says:

    John, maybe you could share with us a summary of your Perscribed Evolutionary Hypothesis?

  114. 114
    JohnADavison says:

    The 2005 PEH paper is available on the opening page of my weblog along with all of the rest of my published papers under the title of Evolutionary Works. It requires no further clarification. You can also find it under John A. Davison right here at Uncommon Descent. Check the sidebar.

  115. 115
    JohnADavison says:

    This thread is now on page 2 and as I predicted –

    “Out of sight, out of mind.”

    I love it so!

  116. 116
    jerry says:

    John,

    Since I too think that natural selection is effete in terms of evolution, it is hard to ask any pertinent questions. Obviously I do not have your experience which is why I hope you will give the more salient reasons that NS is worthless for the long haul. It makes it easier when we get someone new hear and rather than rehash the usual, it would be nice to point to a comprehensive analysis and tell them to come back when they are finished.

    The thread is open on my computer and all I have to do is press cmd R on my Mac and it updates. That is how I picked up your last comment. So you are not out of sight or out of mind.

  117. 117
    JohnADavison says:

    jerry,

    I have abandoned this thread to Allen MacNeill for greener pastures, some right here at Uncommon Descent! Look around.

  118. 118
    JohnADavison says:

    As a parting shot –

    http://jadavison.wordpress.com.....mment-1729

    #422

    Enjoy!

  119. 119
    jerry says:

    John,

    You have to understand that all the Darwinists or anti ID people who come here and probably any where cannot defend Darwinism. So they never try. There has been sort of a UD Challenge to anyone who could be the first to provide a coherent defense of Darwinism.

    No one has stepped up to the plate. So your statements asking for a dialogue will go unanswered since a dialogue requires two or more and the anti ID people never come forward. They are experts at deflection, nit picking, sniping from afar and changing the subject.

    Sorry to see you go. I have just read Allen’s long description of the Modern Evolutionary Synthesis and so far what Allen has written represents nothing ID can’t live with. I like what he has written but it just seems like genetics and micro evolution. Nothing controversial.

    I doubt Haldane’s observation about brothers and cousins. I can’t imagine a Darwinist dying for anything in this world. They are generally atheists and after dying, well there just isn’t anything there for them so why would they. They will become an extinct species because someone once said to me that if you are not willing to die for something then you will be eliminated by those who are willing.

    Come back when you can.

  120. 120
    ab says:

    Hi Jerry,

    I think John was specifically referring to this thread.

  121. 121
    scordova says:

    Thanks to all for commenting.

    I regret to inform you all that UD has just been subjected to a very large SPAM attack since this moring. The volume of the attack is so large that it is possible some of your comments might get deleted accidentally as we try to deal with the problem.

    At this point, I’m afraid I’m going to have to sign off monitoring the SPAM and moderation queues for the time being.

    As a result, you can keep trying to comment, but I cannot guarantee that the comments will get through.

    Thanks again to everyone who participated in this discussion.

  122. 122
    jerry says:

    ab,

    I am not sure what John means but on his blog he referred to Allen MacNeill’s write up on the Modern Synthesis which I read.

  123. 123
    JohnADavison says:

    I was referring to the most recent thread at Allen’s weblog. It is pure neoDarwinian pablum, none of which ever had anything to do with creative evolution. MacNeill is a “true believer” in the atheist Darwinian hoax and there is absolutely nothing that can be done for him. The sad part is the influence that zealots like Dawkins, Myers and MacNeill have had over the thousands of students that have passed through the portals of their curricula and their “groupthink” protectionist forums.

    The reality is that there is absolutely nothing in the selection/gradual/mutation model that ever played a role in speciation or in any other aspect of progressive evolution, a phenomenon of the distant past.

    The Darwinian fantasy has never had any validity as a working hypothesis and has now joined the Ether of Physics and the Phlogiston of Chemistry in the scrap heap of pseudoscience.

    Unlike the Salem witch trials which lasted only a few months, the Darwinian fantasy has persisted for 150 years. I am delighted to pronounce it dead and buried. It was always a monumental joke.

    “La commedia e finita”
    Paglacci

  124. 124
    JohnADavison says:

    Pagliacci

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