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Analogy, How Scientifically Powerful is It?

by Steve Petermann

I don't think there is any question that many ID claims rely heavily on arguments from analogy. Since the analogies drawn by ID proponents do have prima facie power (even Dawkins admits this: "Biology is the study of complicated things that give the appearance of having been designed for a purpose."), the question that remains is how much force this type of scientific reasoning carries. Typically ID critics attempt to play down the power of analogical arguments. Now clearly, use of analogy in a superficial way (if it looks like a duck, walks like a duck, and quacks like a duck, it's a duck) carries little force and can lead to false conclusions. To determine if it's really a duck a more in-depth probing should be required. Perhaps it's really a machine designed to simulate a duck but underneath the feathers it has a metallic frame, motors, gears, and levers. So what form of exploration and reasoning is required to validate the conclusion? Is there really something more than the utilization of analogy that can be employed to overcome the weakness of a prima facie claim? Or is analogy really the foundational engine driving reason and scientific validation? In other words, is it analogy "all the way down" If so then the question is not whether arguments from analogy are valid and powerful, but what analogical arguments are being made and how compelling are they?


To answer this question let's look at some science. Prominent neuroscientist and philosopher Paul Churchland looks at this very thing in his Engine of Reason, the Seat of the Soul. Now before someone thinks the reference to "soul" in the title indicates that Churchland is attempting some religious apologetics, think again. To the contrary Churchland is an eliminative materialist. However, his book does offer some very interesting research on how the brain works and how reasoning occurs. His model is a connectionist model illustrating how neural trajectories and multidimensional, neuronal activation vectors drive reason. I'll try to summarize his assertions as they apply to this topic.

First Churchland claims that as we experience life we develop "prototypical representations" of things. He uses face recognition as an example.

The brain seems to represent faces with a pattern of activations in a special cortical area somewhat farther along in the visual system(the occipito-temporal region), a pattern whose elements correspond to various canonical features or abstract "dimensions" of observed faces.

and

The human family displays a wonderful diversity of faces, but each one strikes out in its own idiosyncratic direction from what might be call the standard, average, or prototypical human face.

This provides for the ability to recognize a face as a face even if they have varying attributes. Then as new faces are experienced the activation matrix of the prototype is fine tuned and expanded.

Another interesting and important feature of neural networks is their ability to "fill in" missing information. He calls this vector completion. I'm sure everyone has had experiences where they seem to be able to recognize something from only a small part of the data. Activation vectors have this ability.

This ability to identify familiar faces correctly despite the loss of 20 percent of the information in the input vector illustrates a marvellous property of neural networks, a property with far-reaching consequences. This property is their capacity for what is called vector completion. Since the output layer identifies the input person correctly as Jane, it must be responding to a facial coding vector at the second layer that is very close to the proper coding point for Jane. At the least, the second-layer coding vector must be closer to Jane's point than to any other person's coding point, else the output layer could not have identified her correctly.

Apparently this ability is extremely important for creative thought. In fact, Churchland thinks it is vector completion (filling in) that is the basis of inductive inference.

What we have observed here, in the phenomenon of vector completion at layers two and three, is a primitive form of inductive inference. Indeed, it may be that vector completion is the basic form that inductive inference takes in living creatures in general.

Now prototypes shouldn't be thought of as some isolated neural representations. In fact they are interconnected with other prototypes. In neural networks activation vectors share neurons and connections with other activation vectors. According to Churchland that interconnectivity offers the ability for forming novel combinations of activations to create new "concepts". It is this ability that makes scientific progress possible. When the scientist is confronted with something new, certain sets of activation vectors are fired possibly in ways not activated before. This can account for the generation of new ideas and explanations.

To illustrate this Churchland uses an example of translating the observation of wave interference in a sea wall to the problem of the double slit experiment in quantum mechanics. Now the dynamics of a sea wall is observable.

seawall.jpg

When the double slit experiment is done, if the experimenter initially thinks that light is a particle, for very thin slits the pattern on the screen is puzzling. This is because instead of two very bright images there are several bright lines with the brightest in the center and the fainter ones on either side. This would be very puzzling but for the fact that a similar pattern can be observed with a sea wall. Since this prototype would already be in place in the scientist's mind, the analogy can be applied to what is unobservable and the idea that light can behave like waves emerges. This is a perfect example of the how the brain uses analogy to make scientific discoveries. Churchland states:

The prototype's novel application to optical phenomena is systematically vindicated by the prototype-driven experimental probing. The distribution of the bright and dark bands of light vary exactly as do the high- and low-amplitude water wave sites. What began as an analogically inspired guess quickly acquires the status of a confidently held theory. If the manipulative powers that characterized the original prototype carry over successfully into its new domain of deployment, wild horses will not stay our conviction that light must be waves.

Now ID critics might claim that analogical reasoning is only the starting point, could be fallacious, and must be validated by empirical data. Surely this is true. However, data is just data. It tells us nothing unless it is interpreted. But according to Churchland's model interpretation relies on analogy as well. It would seem that science is absolutely riddled with analogical thinking "all the way down". To strip analogical reasoning of its force both in the beginning of scientific investigation and its subsequent fleshing out would seem to hamstring it entirely. It appears that fundamentally the brain is an analogical machine, comparing observed patterns with prototypes and integrating them in new ways with other activation vectors. This in turn offers new creative possibilities for explanation (abduction?). One has to wonder what prototypes Darwinists are utilizing when they claim that complex biotic systems are the result of blind, non-intentional processes.

Now, if ID was to base its claims on superficial analogy, it would rightly be rejected or at least held under high suspicion. However, as biotic systems are probed at deeper and deeper levels, the analogies to design just keep popping up. In these systems we find prototypes of complex information, manufacturing, transport systems, signal transmission, sensors, error checking, redundancy, built-in-test, modularity, sequenced assembly instructions, timed activations, feedback systems, etc. The list goes on and on. The fact that these and many other features found in biology are analogous to design as humans know it, is evident in the engineering and teleological language that is used to characterize it. If analogical thinking is "all the way down" in how science is done, how many analogies does it take for the scientific community to finally agree that "it's designed" is worth exploring?

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This entry was posted on Tuesday, August 8th, 2006 at 7:08 pm and is filed under Intelligent Design, Nature of Science. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site. The trackback link is: http://telicthoughts.com/analogy-how-scientifically-powerful-is-it/trackback/

171 Responses to “Analogy, How Scientifically Powerful is It?”

  1. Bradford Says:
    August 8th, 2006 at 7:19 pm

    IDers are in good company when utilizing arguments from analogy. Darwin and his supporters since the Origin have used such arguments. They are used outside studies of natural history as well. When assessing competing arguments from anlogy the best fit becomes a guiding principle.

  2. Comment by Bradford — August 8, 2006 @ 7:19 pm

  3. Salvador T. Cordova Says:
    August 8th, 2006 at 7:40 pm

    It is not possible to do the work of science without using a language that is filled with metaphors. Virtually the entire body of modern science is an attempt to explain phenomena that cannot be experienced directly by human beings, by reference to forces and processes that we cannot perceive directly because they are to small, like molecules, or too vast, like the entire known universe, or the result of forces that our senses cannot detect, like electromagnetism, or the outcome of extremely complex interactions, like the coming into being of an organism from its conception as a fertilized egg. Such explanations, if they are to be not merely formal propositions, framed in an invented technical language, but are to appeal to the understanding of the world that we have gained through ordinary experience, must necessarily involve the use of metaphorical language.

    Richard Lewontin

    This question was of extreme interest recently : Evolution and Design

    Salvador

  4. Comment by Salvador T. Cordova — August 8, 2006 @ 7:40 pm

  5. Nick Matzke Says:
    August 8th, 2006 at 9:01 pm

    Petermann writes,

    I don't think there is any question that many ID claims rely heavily on arguments from analogy.

    But Michael Behe writes,

    "As I testified, the ID argument is an induction, not an analogy." (EvolutionNews.org, quoting Behe's response to Kitzmiller)

    Petermann writes,

    Typically ID critics attempt to play down the power of analogical arguments. Now clearly, use of analogy in a superficial way (if it looks like a duck, walks like a duck, and quacks like a duck, it's a duck) carries little force and can lead to false conclusions.

    But Michael Behe writes,

    The strong appearance of design allows a disarmingly simple argument: if it looks, walks and quacks like a duck, then, absent compelling evidence to the contrary, we have warrant to conclude it's a duck. Design should not be overlooked simply because it's so obvious. (Behe, "Design for Living", New York Times, February 7, 2005)

    Later,
    Nick

  6. Comment by Nick Matzke — August 8, 2006 @ 9:01 pm

  7. Daniel Says:
    August 8th, 2006 at 9:02 pm

    The difference, of course, is that biologists actually follow up such arguments from analogy with rigorous examination and experimentation, to see if initial analogies are superficial or not. I've never heard of an argument for Intelligent Design that does this.

    Case in point - Wells' "paper" on centrioles, where he describes centriole structure, then describes the structure of a rotor-driven turbine… end of story… it's a hollow argument.

    True, however, many analogies in biology, and science in general, are retained even if they're not completely accurate - largely for the purpose of simplifying an explanation into something more understandable to the non-expert. Oversimplification does happen, afterall.

    Anyway, as Sal mentions, yes, this topic did come up during the past month, and I've offered my own argument to Hannah (sorry for the shameless plug;-) )

  8. Comment by Daniel — August 8, 2006 @ 9:02 pm

  9. macht Says:
    August 8th, 2006 at 9:45 pm

    Nick,

    Do you agree with Petermann or Behe?

  10. Comment by macht — August 8, 2006 @ 9:45 pm

  11. Bradford Says:
    August 8th, 2006 at 10:06 pm

    Matzke: Typically ID critics attempt to play down the power of analogical arguments. Now clearly, use of analogy in a superficial way (if it looks like a duck, walks like a duck, and quacks like a duck, it's a duck) carries little force and can lead to false conclusions.

    There is no need to play down arguments from analogy. They are universal. Besides, anti-IDers have argued that even if it it looks designed beware that it is not; in effect it looks and walks like a duck but is not a duck. The alternative natural selection device is waived like a magic wand even when no plausible pathway is in evidence.

  12. Comment by Bradford — August 8, 2006 @ 10:06 pm

  13. MikeGene Says:
    August 8th, 2006 at 10:06 pm

    WARNING: In light of Nick Matzke's most recent detective work, the Management at Telic Thoughts is obliged to inform its readers that Steve Petermann failed to clear his blog with the "Conform to Everything Behe/Dembski/Johnson Said" Review Board. We are currently meeting to determine if Petermann will retract his blog. Stay Tuned.

  14. Comment by MikeGene — August 8, 2006 @ 10:06 pm

  15. Daniel Says:
    August 8th, 2006 at 10:14 pm

    Besides, anti-IDers have argued that even if it it looks designed beware that it is not; in effect it looks and walks like a duck but is not a duck. The alternative natural selection device is waived like a magic wand even when no plausible pathway is in evidence.

    No plausible pathway evidence for natural selection?!?!

  16. Comment by Daniel — August 8, 2006 @ 10:14 pm

  17. Bradford Says:
    August 8th, 2006 at 10:29 pm

    Besides, anti-IDers have argued that even if it it looks designed beware that it is not; in effect it looks and walks like a duck but is not a duck. The alternative natural selection device is waived like a magic wand even when no plausible pathway is in evidence.

    No plausible pathway evidence for natural selection?!?!

    Observable instances primarily involve unicellular organisms. If you have a plausible pathway to the first cell and an intelligible account of what was selected and why then kindly let us know.

  18. Comment by Bradford — August 8, 2006 @ 10:29 pm

  19. Daniel Says:
    August 8th, 2006 at 10:46 pm

    Bradford -
    That's not the same thing as natural selection or speciation, that's something called the "origin of life."

    If you want a plausible explanation for the origin of life, read up on the RNA World Hypothesis - a good starting point can be found here.

  20. Comment by Daniel — August 8, 2006 @ 10:46 pm

  21. Bradford Says:
    August 8th, 2006 at 11:07 pm

    That's not the same thing as natural selection or speciation, that's something called the "origin of life."

    If you want a plausible explanation for the origin of life, read up on the RNA World Hypothesis - a good starting point can be found here.

    I'm familar with the RNA world. It's weak, not plausible. Are you saying there is no selection process involved in OOL?

  22. Comment by Bradford — August 8, 2006 @ 11:07 pm

  23. great_ape Says:
    August 8th, 2006 at 11:26 pm

    Daniel, Daniel, you clearly haven't been following this saga for very long. You see, "evolutionary theory" and "origin of life" are utterly inseparable in the ID universe. Treating them as separable issues is something only biologists woud do, and as biologists have been thoroughly brainwashed by the materialistic darwinian paradigm, they are clearly not to be trusted in this matter. The structure of the typical ID/anti-ID exchange goes something like this: a) ID proponent makes some damning blanket assertion about evolution's inadequacy b) ID-proponent expresses disbelief and/or provides information contesting this assertion c) ID proponent changes topic to origin of life c) digression. Daniel, if you can't provide a thorough depiction of the origin of life, then evolutionary theory inevitably tumbles like the crude house of cards it most certainly is. Journals filled with research articles, museums filled with bones, virtual forests of phylogenetic trees…these ultimately amount to nothing if you can't tell me what happened billions of years ago to kick the whole thing off. Now get off your rump and dig up some *real* answers, won't you?
    Sorry, I digress….
    Analogical reasoning. After reading up on epistemology for a fashion, particularly as it regards to natural science, I was also left with a strong impression that analogy ran "all the way down." I had a vague sense that it provided a crucial link between deduction and induction. Trying to collect my thoughts and articulate this, however, proved more difficult that I had imagined. I did not realize churchland tried to tie analogical reasoning to neural nets and vectors, etc. Now I will certainly have to read the book to satisfy my curiosity. To think that I have been generally turned off by churchland because of his extreme materialism… And here I am inspired to read a book by churchland by an ID website.

    And they tell me I waste my time by frequenting these establishments…

  24. Comment by great_ape — August 8, 2006 @ 11:26 pm

  25. great_ape Says:
    August 8th, 2006 at 11:29 pm

    Oops. That was **evolution proponent** in step (b) of the above exchange. Freudian slip? Wait, never mind, Freud was a darwinist.

  26. Comment by great_ape — August 8, 2006 @ 11:29 pm

  27. Bradford Says:
    August 8th, 2006 at 11:37 pm

    Ape writes: Daniel, Daniel, you clearly haven't been following this saga for very long. You see, "evolutionary theory" and "origin of life" are utterly inseparable in the ID universe.

    You miss the point Ape. Whether they are separable areas of study is irrelevant to an intelligent inference. It is true that OOL is the embarassing relative in the Darwinian family best kept out of public view. However if an ID argument is based on the origin of life then bring the black sheep out.

    .

  28. Comment by Bradford — August 8, 2006 @ 11:37 pm

  29. bFast Says:
    August 8th, 2006 at 11:42 pm

    Behe, "the ID argument is an induction, not an analogy." Behe was big on using analogy to help explain the issue, vis-a-vis the famed mousetrap. He also uses analogy to help us wee mortals understand the specifics of the bacterial flagellum — rotor, stator, etc. However, though he uses analogy to clarify the problem presented to the evolutionary paradyme by the flagellum (etc), his case is not analogy. His case is simple — once you are one, two or three mutational steps away from a working flagellum, you have a pot of functionless genes. Event by event mutation, where each event produces something more useful than before will not get you to a flagellum. This is a simple argument. It is certainly falsifiable. And it is not by any means founded in analogy. I agree with Behe, this is induction, not analogy.

    Daniel, "If you want a plausible explanation for the origin of life, read up on the RNA World Hypothesis - a good starting point can be found here."

    I get board with the constant hooting that "we've (almost) done it" that the abiogeneis boys keep claiming. As far as I can tell, after listening to the chatter of biologists discussing rna world, self-replicating proteins etc., there are two vast gaps of knowledge in the OOL equation: how on earth did the first replicating, mutating, selecting molecule or set of molecules come together in the first place, and what plausible path did these primitive replicators find which led to DNA based life. Even if the former question were solved, the latter is huge!

    Recent research isn't helping any either. It seems that the simplest form of independant life is somewhat more complex than thought a couple of years ago. Further the eukaryotes don't seem to have evolved from the archae — ouch!

    In my experience, evolutionary biologists quickly dismiss the OOL equation by saying that OOL is not a question of evolution, but a quesiton of abiogeneis — it's not my field. This, as far as I am concerned is a major jam out.

  30. Comment by bFast — August 8, 2006 @ 11:42 pm

  31. Steve Petermann Says:
    August 8th, 2006 at 11:50 pm

    Hi Daniel,

    The difference, of course, is that biologists actually follow up such arguments from analogy with rigorous examination and experimentation, to see if initial analogies are superficial or not.

    First, I'm curious what analogies Darwinian biologists appeal to, to support their claim that evolution is blind and non-intentional. Also could you cite the rigorous examination and experimentation that they have employed to support that claim as well?

  32. Comment by Steve Petermann — August 8, 2006 @ 11:50 pm

  33. Nick Matzke Says:
    August 9th, 2006 at 12:08 am

    Nick,

    Do you agree with Petermann or Behe?

    Heck, I have no idea who to believe. Some time ago I decided that there was no "right" description of the ID argument (or the IC argument), because IDists are fatally inconsistent in their definitions and arguments. I generally think that the positive ID argument basically is an analogy argument, but there we have Behe, the leading ID advocate and more coherant than most, explicitly and vehemently denying it, and bashing Judge Jones for getting it wrong. There is nothing for me to do but shrug.

    You guys are the ID advocates, not me. Do you agree with Petermann or Behe?

  34. Comment by Nick Matzke — August 9, 2006 @ 12:08 am

  35. Steve Petermann Says:
    August 9th, 2006 at 12:10 am

    Hi Nick,

    There are all sorts of ways to formalize what happens in the brain. Terms like analogy, induction, abduction are abstractions for brain processes. Obviously these terms point to a complex of brain processes that result in an attempt to map unobservable reality to what we can observe. What Churchland and other neuroscientists have shown is that scientific reasoning is based on matching, mixing, and integrating prototypes developed from actual observations. These "analogical" processes are at the heart of scientific exploration. Churchland, in fact, conflates prototype matching, mixing, and integration with induction and abduction. The point is that attempts to deflate ID arguments from analogy, per se, also deflate scientific reasoning itself. If you have some other neurally based processes besides this to support the Darwinian claims I would like to hear them.

  36. Comment by Steve Petermann — August 9, 2006 @ 12:10 am

  37. macht Says:
    August 9th, 2006 at 12:58 am

    Nick Matzke yesterday:

    "Conveniently, TTers often put up posts more or less defending or promoting claims from the main ID blogs."

    Nick Matzke today:

    All those quotes from Petermann and Behe.

  38. Comment by macht — August 9, 2006 @ 12:58 am

  39. Nick Matzke Says:
    August 9th, 2006 at 1:19 am

    Macht, you might have a point if Petermann had said something like, "Arguments for ID are arguments from analogy. Behe prominently disagrees and the Discovery Institute has prominently cited his disagreement, but these people don't know what they are talking about when it comes to ID."

    Instead, the post didn't agree or disagree with the DI or Behe. This is fine. In my comment yesterday I said TT posts "often" defend these, not "always."

    Getting back to my original point: Petermann started off his post by saying,

    I don't think there is any question that many ID claims rely heavily on arguments from analogy.

    But I think I showed there is rather a large question on this point, at least according to the leading ID advocate. If you guys all think Behe is clearly wrong and Peterman is right, that's fine, say so, but otherwise Petermann's statement remains dubious.

  40. Comment by Nick Matzke — August 9, 2006 @ 1:19 am

  41. trrll Says:
    August 9th, 2006 at 1:40 am

    Analogy is simultaneously one of the most powerful modes of thought and one of its most catastrophic failure modes. When it works right, it yields powerful new abstractions. When it goes wrong, it yields delusions and sympathetic magic. It is clear that our minds are "wired" to think in terms of analogies, to such an extent that it does so even when we know intellectually that they is not valid, as when we see faces in clouds and wood grain.

    I think the role of analogy in thought is a lot like the role of mutation in natural selection. Our minds are constantly generating random linkages between different ideas. Most of these "conceptual mutations" are wrong, and are filtered out by neural selection mechanisms that discard analogies where the fit is too imperfect. But once in a while, such a link turns out to be strong enough to generate a fruitful hypothesis.

  42. Comment by trrll — August 9, 2006 @ 1:40 am

  43. Bradford Says:
    August 9th, 2006 at 1:44 am

    Matzke: But I think I showed there is rather a large question on this point, at least according to the leading ID advocate. If you guys all think Behe is clearly wrong and Peterman is right, that's fine, say so, but otherwise Petermann's statement remains dubious.

    What is the point of this other than to indicate there is a diversity of views among IDers? Opponents of ID do not always agree with each other either. It is not uncommon for people to come to the same conclusion from different vantage points.

  44. Comment by Bradford — August 9, 2006 @ 1:44 am

  45. Nick Matzke Says:
    August 9th, 2006 at 1:52 am

    Steve,

    In reply to your main points, IMHO:

    1. There is nothing intrinsically problematic about the generic practice of reasoning from analogy.

    2. I would agree that scientists and everyone else reason by analogy all the time.

    3. I would disagree that ID skeptics denigrate analogy arguments in general. In fact, I think leading evolution thinkers are often "better" at sophisticated analogy thinking than the average person or the average scientist. "Better" in the sense of (a) analogizing disparate biological phenomenon to each other and to other processes, often uncovering common patterns and causes, and (b) being keenly aware of the strengths and limitations of the analogies (and especially disanalogies). IMO Richard Dawkins is actually quite good at this when he is in his field (evolutionary zoology), and if one reads what Dawkins actually writes and not the standard IDists misrepresentations.

    4. Finally, I think you miss the real point ID skeptics make regarding ID and analogies, namely that major disanalogies between biological "design" and human design sink any easy inference from biology to ID. The Kitzmiller decision got it basically right IMO:

    Indeed, the assertion that design of biological systems can be inferred from the "purposeful arrangement of parts" is based upon an analogy to human design. Because we are able to recognize design of artifacts and objects, according to Professor Behe, that same reasoning can be employed to determine biological design. (18:116-17, 23:50 (Behe)). Professor Behe testified that the strength of the analogy depends upon the degree of similarity entailed in the two propositions; however, if this is the test, ID completely fails.

    Unlike biological systems, human artifacts do not live and reproduce over time. They are non-replicable, they do not undergo genetic recombination, and they are not driven by natural selection. (1:131-33 (Miller); 23:57-59 (Behe)). For human artifacts, we know the designer's identity, human, and the mechanism of design, as we have experience based upon empirical evidence that humans can make such things, as well as many other attributes including the designer's abilities, needs, and desires. (D-251 at 176; 1:131-33 (Miller); 23:63 (Behe); 5:55- 58 (Pennock)). With ID, proponents assert that they refuse to propose hypotheses on the designer's identity, do not propose a mechanism, and the designer, he/she/it/they, has never been seen. In that vein, defense expert Professor Minnich agreed that in the case of human artifacts and objects, we know the identity and capacities of the human designer, but we do not know any of those attributes for the designer of biological life. (38:44-47 (Minnich)). In addition, Professor Behe agreed that for the design of human artifacts, we know the designer and its attributes and we have a baseline for human design that does not exist for design of biological systems. (23:61-73 (Behe)). Professor Behe's only response to these seemingly insurmountable points of disanalogy was that the inference still works in science fiction movies. (23:73 (Behe)).

    There are some other major disanalogies between biology and human design, i.e.:

    * Pervasive correlated homologous features (=similarity not required by similarity in function)

    * Functions of biological "designs" vs. functions of human designs: Biological "designs" are limited to functions that are favored by natural selection or sexual selection. Human designs typically serve other functions, i.e., serving humans.

    Darwin and many major biologists since then have emphasized these points when pointing out why the argument to Design doesn't work — and notably, these specific disanalogies are just as pervasive and telling at the level of complex molecular adaptations. So IMO they must be met head on by anyone wishing to reinvigorate the ID argument.

  46. Comment by Nick Matzke — August 9, 2006 @ 1:52 am

  47. macht Says:
    August 9th, 2006 at 1:53 am

    I agree with you that there is no "right" description of ID because I don't think ID has been developed enough to make that claim. I tend to agree with Paul Nelson that ID right now is basically a bag of intuitions, with no strong, central theory. A lot of these intuitions are analogies. This isn't a problem in itself, however, since much of science is based on analogies. Heck, for a long time, much of physics was based on the analogy that reality was like a giant machine. Even now we talk about the mechanism by which evolution works.

    What ultimately will matter is if these intuitions will end up being useful for scientists in making predictions and provide them with testable hypotheses for research and not whether they are analogies or not.

  48. Comment by macht — August 9, 2006 @ 1:53 am

  49. Nick Matzke Says:
    August 9th, 2006 at 1:59 am

    What is the point of this other than to indicate there is a diversity of views among IDers?

    That is pretty much the opposite of what Petermann's opening post said — he didn't think there was "any question" about it.

    Not a huge point, I know, but it does show that either Petermann or Behe is pretty confused on this point.

  50. Comment by Nick Matzke — August 9, 2006 @ 1:59 am

  51. Guts Says:
    August 9th, 2006 at 2:28 am

    Unlike biological systems, human artifacts do not live and reproduce over time. They are non-replicable, they do not undergo genetic recombination, and they are not driven by natural selection. (1:131-33 (Miller); 23:57-59 (Behe)).

    I responded to this here. Needless to say, there are quite a few similarities that strengthen the design inference, there are no disanalogies that sever the link between biological machines and human made machines regardless of whether they confer a selective advantage. In fact, it is probably rare that a robust complex machine would not. For example, in many cases of human designs meant to evolve, it is clear that the machines front load their selective advantages. In other words, the properties that define a machine almost ensure that they would be fully used. The virtually identical properties of machines in biology and those that are designed by humans is quite demonstratable, contrary to the judge's assertions.

  52. Comment by Guts — August 9, 2006 @ 2:28 am

  53. great_ape Says:
    August 9th, 2006 at 2:31 am

    bradford: "You miss the point Ape. Whether they are separable areas of study is irrelevant to an intelligent inference. It is true that OOL is the embarassing relative in the Darwinian family best kept out of public view. However if an ID argument is based on the origin of life then bring the black sheep out."

    Yes, if the ID argument in question was in fact based on the origin of life, but all to often the argument isn't initially about origin of life at all. Case in point, above you were contesting the notion of natural mechanisms yielding the illusion of premeditated design when, in fact, there is no such design at all. That is not an origin of life issue, and it is one in which concrete responses via natural selection can be made: for example, the illusion of "design" in darwin's finches' beak morphology. The illusion would be that each species beak is designed a priori for its particular food source. Yet when Daniel asked you if you seriously thought natural selection offered no such pathways to apparent design, you shifted to origin of life, wherein there lies much safety and comfort. The same tactic has been invoked repeatedly iwith myself and others. Step 1: attack evolutionary theory at mutliple levels. Step 2: retreat to the murky waters of the primal soup. As I have stressed repeatedly, the overwhelming majority of the substance of modern evolutionary biology (i.e. what you'd read in the relevant modern journals), molecular evolution, population genetics, etc is not reliant on OOL whatsoever. It only requires that there *was* an OOL, however that may have happend. Clearly none of us is in disagreement about the fact that this event occurred. We ETs, however, have much more to say about what happened subsequent to that event, regarding common descent, phylogentic relationships, mechanisms of mutation and how changes come about, how allelic variation behaves under selection and under neutrality, etc. It is a rich and fruitful dimension of biology, and if tomorrow we discover OOL was initiated by the fiat of Zergon the galactic overlord, little about that body of knowledge would change. Unless, of course, Zergon was particularly deceitful in his machinations. But should that be the case, there would be much more important things to concern ourselves with.

  54. Comment by great_ape — August 9, 2006 @ 2:31 am

  55. Bradford Says:
    August 9th, 2006 at 6:15 am

    Ape: The illusion would be that each species beak is designed a priori for its particular food source. Yet when Daniel asked you if you seriously thought natural selection offered no such pathways to apparent design, you shifted to origin of life, wherein there lies much safety and comfort. The same tactic has been invoked repeatedly iwith myself and others. Step 1: attack evolutionary theory at mutliple levels. Step 2: retreat to the murky waters of the primal soup.

    I'm afraid you still don't get it. If an intelligent inference is established at the point of origins every biological event thereafter would be a by-product of intelligent design. It is true that beak changes can be explained without reference to intelligent input. That does not mean the origin of the initial genome, from which finch genomes descended, can be likewise explained. Similarly, once I click the post indicator on my screen this message will be transmitted. You can explain the physical dynamics of the transmission without referencing the alphanumeric and computer codes by which the intelligently formulated message is conveyed. Witnessing secondary effects from a code, initially generated by intelligence, can give one a false impression that a chain of events proceeded without intelligent input.

  56. Comment by Bradford — August 9, 2006 @ 6:15 am

  57. Daniel Says:
    August 9th, 2006 at 11:04 am

    Bradford,

    I'm familar with the RNA world. It's weak, not plausible. Are you saying there is no selection process involved in OOL?

    It's sure as hell more plausible than the creationist version of abiogenesis. And no, I'm not saying OOL does not involve selection, I'm saying it's not what one usually refers to when they discuss Natural Selection. In other words, if you're going to talk specifically about selection of early biotic chemistry processes, as opposed to natural selection in the broad sense, you should say so. (you made it sound as if you thought natural selection in the "microevolutionary" sense was nonsense, which would have been ridiculously silly)

    Great Ape,

    Daniel, Daniel, you clearly haven't been following this saga for very long.

    No, I haven't - I enjoy the conversations with some here, but dislike others, so I only stop in from time to time. However…

    That's nonsense. Of course it's all just one continuum of the history of life, just as the separation of "micro-" and "macro-" evolution isn't accurate. Still, one can conceptually talk about different stages of life's history, such as the OOL, the last universal common ancestor, the origin of the eukaryotic cell, the first multicellular organisms, the later bilaterian ancestor, the establishment of the modern animal phyla, and all the way down to modern speciation. You may not get the point, but Bradford does. Go consult with your fellow IDers about what is "utterly inseparable" in the ID universe.

    And the notion that IDers don't distinguish between OOL and later evolution is just silly. Have you forgotten how big a tent ID is, and how every one of you has a different explanation of how the Designer might have intervened in life???

    Daniel, if you can't provide a thorough depiction of the origin of life, then evolutionary theory inevitably tumbles like the crude house of cards it most certainly is.

    Does it now? LOL Have fun in "the ID universe," and contact me when you decide to rejoin the reality-based universe.

    bFast,

    I get board with the constant hooting that "we've (almost) done it" that the abiogeneis boys keep claiming.

    Putting words in my mouth? I didn't say "we've (almost) done it," I said there's a plausible explanation out there that makes a lot better sense than creationist abiogenesis. I have no idea what research will discover in the future, I'm talking about what biologists have already uncovered, and I'm not dismissing it as "not my field," either.

    Meanwhile, it's the ID community that's claiming "we've almost done it," (I'm sure you've read Nelson's recent article on this), which IDers and Creationists have been claiming since before Michael Denton's A Theory In Crisis.

    Steve Peterman:

    First, I'm curious what analogies Darwinian biologists appeal to, to support their claim that evolution is blind and non-intentional. Also could you cite the rigorous examination and experimentation that they have employed to support that claim as well?

    Analogies? Surely you've heard of The Blind Watchmaker, right? That's the first and perhaps most popular one that comes to mind. TBW itself is not a tour de force of evidence - it's more anectdotal and descriptive than analytical - but it's conceptually based upon valid evidence. As for experimentation, an example of that would be Cairns work on directed mutation.

    Now, those are just examples, which you asked for, mind you. I don't expect them to convince any of you of anything, only to reinforce my point that biologists use analogies for descriptive purposes as well, we just test them also, which IDers do not do (which the exception of Behe & Snokes, which didn't work out so well).

    So my points still stand - the use of analogy can be persuasive, biologists use them too, and yet biologists do not rely upon them (they test them).

  58. Comment by Daniel — August 9, 2006 @ 11:04 am

  59. bFast Says:
    August 9th, 2006 at 11:37 am

    Macht:

    What ultimately will matter is if these intuitions will end up being useful for scientists in making predictions and provide them with testable hypotheses for research and not whether they are analogies or not.

    I question the validitity of "being useful for scientists in making predictions and provide them with testable hypotheses for research." I have heard this statement a million times. It seems to me, however, that producing testable hypotheses is a means to the end, the end being truth. Though the scientific method will eventually self-correct, and truth will rise to the surface, it may do so by producing event discoveries like the big bang. Thought the big bang theory has caused lots of science to happen, the cause of the big bang has been absolutely impervious to exploration, and seems prepared to remain so. The big bang has produced the great "I don't know" wall. I suspect that bacterial flagellum may be the same kind of wall.

    In science's slow meandering towards truth, however, we create a serious problem. It seems that we believe that we know much more than we really do. Society accepts the current view of science as truth, and lives accordingly. The current "selfish gene" model of life produces, IMHO, a seriously undesireable sociological effect. I, therefore, vote to get science past its current perceveration as quickly as possible. Lets seriously accept the validity of the major falsification challenges to NDE, rather than worrying about what kind of science will result if we reject NDE.

  60. Comment by bFast — August 9, 2006 @ 11:37 am

  61. trrll Says:
    August 9th, 2006 at 11:39 am

    I'm afraid you still don't get it. If an intelligent inference is established at the point of origins every biological event thereafter would be a by-product of intelligent design.

    Scientists don't know how life began. There are a lot of ideas, many with some degree of experimental support, but no theory is so well supported that it is generally accepted as correct. From a scientific point of view, origin-of-life research has been very successful. One thing that nonscientists rarely understand is that to a scientist, it is more important for a theory to be fruitful–to lead to novel discoveries–than for it to be correct. And from a scientific standpoint, origin of life research has been quite successful, leading to discoveries in areas such as catalytic RNA, self-assembly of membranes, catalysis by random peptides, etc. And all of these discoveries are being made by the people who were flexible enough in their religious beliefs to be able to say, "Let's assume that if intelligent influence was involved, it was at a more basic level than this; how might life have formed without the need for outside interference?"

    But don't worry. If a natural origin of life is established, you can push back speculation of intelligent influence to the Big Bang. And if a natural origin of the Big Bang is established, you can push back speculation of intelligent influence to the nature of physical law. It's hard to imagine that science will ever explain everything so thoroughly that there is no conceivable role for an external intelligence. This is what enables the many biologists with strong religious beliefs to do research on things like evolution and a chemical origin of life–they say, "Let's suppose that God is very, very clever, clever enough to use natural mechanisms to accomplish what might at first glance seem to require a miracle. How might He have achieved this?"

  62. Comment by trrll — August 9, 2006 @ 11:39 am

  63. Steve Petermann Says:
    August 9th, 2006 at 11:40 am

    Nick,

    3. I would disagree that ID skeptics denigrate analogy arguments in general. In fact, I think leading evolution thinkers are often "better" at sophisticated analogy thinking than the average person or the average scientist. "Better" in the sense of (a) analogizing disparate biological phenomenon to each other and to other processes, often uncovering common patterns and causes, and (b) being keenly aware of the strengths and limitations of the analogies (and especially disanalogies). IMO Richard Dawkins is actually quite good at this when he is in his field (evolutionary zoology), and if one reads what Dawkins actually writes and not the standard IDists misrepresentations.

    If Darwinists are keen on using analogy, what analogies are they using to support the claim that evolution is blind and non-intentional? If as you say "scientists and everyone else reason by analogy all the time." then why not be upfront on these analogies? At least IDers offer their's up for critique and exploration. Since this should be critical to supporting a fundamental tenet of the Darwinian model, will you?

    4. Finally, I think you miss the real point ID skeptics make regarding ID and analogies, namely that major disanalogies between biological "design" and human design sink any easy inference from biology to ID.

    Well that's the task isn't it, to evaluate how well the analogies fit the current object of study. Analogies by their nature have both similarities and differences from what they are being compared to. In fact according to Churchland this is where scientific progress is made. In his wave inteference example there were major differences between the sea wall and quantum mechanics but the similarities (wave dynamics) were such that science was able to come up with a powerful explanation. This is how it should be with ID. While, as I pointed out, there are stunning functional similarities between biotic systems and engineered systems, there are also differences. The task, in my view, of ID research would be to carry the notion of design forward and see if it works. Of course before this can happen, scientists must accept that the analogies present are strong enough to warrant further exploration.

  64. Comment by Steve Petermann — August 9, 2006 @ 11:40 am

  65. Daniel Says:
    August 9th, 2006 at 11:55 am

    Steve,
    … I did respond, with a reference to the analogy of the blind watchmaker, and the experimentation of this model (specifically directed versus undirected mutation) by Cairns.

    But you hit the nail on the head in this last comment:

    The task, in my view, of ID research would be to carry the notion of design forward and see if it works.

    Indeed. Yet, IDers have yet to do this… and I don't see any reason to believe Nelson's recent claims of "secret ID research under way," nor of any conceivable way to actually test design experimentally.

  66. Comment by Daniel — August 9, 2006 @ 11:55 am

  67. great_ape Says:
    August 9th, 2006 at 12:05 pm

    "Does it now? LOL Have fun in "the ID universe," and contact me when you decide to rejoin the reality-based universe." –Daniel

    Daniel,
    Please revisit my initial post again when your reality-based universe includes the possibility of sarcasm. :wink:

  68. Comment by great_ape — August 9, 2006 @ 12:05 pm

  69. Daniel Says:
    August 9th, 2006 at 12:17 pm

    Great Ape,
    If you're original comment was sarcastic, then my apologies - I still don't quite see where you give it away as sarcasm, but that would help your post make much more sense indeed.

  70. Comment by Daniel — August 9, 2006 @ 12:17 pm

  71. macht Says:
    August 9th, 2006 at 12:29 pm

    bfast,

    I'm not at all convinced that science taking a "slow meandering towards truth." See, for example, here. Science is probably better described as giving us truthlike, not true. I think you'd also like Feyerabend's idea of the proliferation of theories.

  72. Comment by macht — August 9, 2006 @ 12:29 pm

  73. Nick Matzke Says:
    August 9th, 2006 at 12:36 pm

    If Darwinists are keen on using analogy, what analogies are they using to support the claim that evolution is blind and non-intentional? If as you say "scientists and everyone else reason by analogy all the time." then why not be upfront on these analogies?

    LOL. Ever heard of "the tree of life" A guy named Chuck made it the centerpiece of a little book back in 1859. Gould and others have since concluded that a bush is an even better analogy, with humans just a twig. Do I really have to do your thinking for you like this?

    (note that all the science of evolution says is that evolution works by certain specified natural processes, like the weather. You can call this "blind" and "unintentional" if you like, but only in the same way that the weather is "blind" and "unintentional". Science does not rule in or out the possibility that God is creating the world in every second of its existence, etc. More evolution 101…)

  74. Comment by Nick Matzke — August 9, 2006 @ 12:36 pm

  75. Nick Says:
    August 9th, 2006 at 12:36 pm

    (Not Matzke, in case there is any confusion over our log ins)

    If Darwinists are keen on using analogy, what analogies are they using to support the claim that evolution is blind and non-intentional?

    Gould used the analogies of a Drunkard's walk and Spandrels in a cathedral, but I'm not sure that they are exactly what you are looking for. In those cases, he was using the analogy as a teaching aid to help explain a concept rather than attempting to demostrate the validity of an evolutionary concept by analogy with something else.

  76. Comment by Nick — August 9, 2006 @ 12:36 pm

  77. macht Says:
    August 9th, 2006 at 12:50 pm

    Man, I need to reread what I write.

  78. Comment by macht — August 9, 2006 @ 12:50 pm

  79. Bradford Says:
    August 9th, 2006 at 12:59 pm

    Bradford,

    I'm familar with the RNA world. It's weak, not plausible. Are you saying there is no selection process involved in OOL?

    Daniel: It's sure as hell more plausible than the creationist version of abiogenesis.

    It's unclear exactly what you mean by creationist version of abiogenesis. Usually in these groups this codes for Genesis although strictly speaking creation indicates the action of a deity not a particular belief. In any case I would note that Genesis is not an empirical study. Are you saying that your faith is superior to my own?

  80. Comment by Bradford — August 9, 2006 @ 12:59 pm

  81. Bradford Says:
    August 9th, 2006 at 1:09 pm

    trrll: And from a scientific standpoint, origin of life research has been quite successful, leading to discoveries in areas such as catalytic RNA, self-assembly of membranes, catalysis by random peptides, etc. And all of these discoveries are being made by the people who were flexible enough in their religious beliefs to be able to say, "Let's assume that if intelligent influence was involved, it was at a more basic level than this; how might life have formed without the need for outside interference?"

    If you pour enough money and time into anything you will get some positive spin-offs. The resources would be better devoted to medical research.

    But don't worry. If a natural origin of life is established, you can push back speculation of intelligent influence to the Big Bang.

    I'm not a bit worried that OOL will be established. It is a search for a miracle disguised as science. Truthfully the concern is on your side of the aisle. It is why intelligence is denied irrespective of the degree of scientific evidence supporting a concept. That is the real lesson of abiogenesis.

  82. Comment by Bradford — August 9, 2006 @ 1:09 pm

  83. Steve Petermann Says:
    August 9th, 2006 at 1:18 pm

    Daniel,

    Analogies? Surely you've heard of The Blind Watchmaker, right? That's the first and perhaps most popular one that comes to mind. TBW itself is not a tour de force of evidence - it's more anectdotal and descriptive than analytical - but it's conceptually based upon valid evidence.

    [I didn't see this before I posted that you hadn't responded]

    But this is not an analogy of an observable. Surely this wouldn't qualify. What would be required is an observable analogy that things like the complexity we see in biotic system can be created through blind, non-intentional processes. Can you provide that type of analogy? You say its conceptually based on valid evidence. Please elaborate.

    As for experimentation, an example of that would be Cairns work on directed mutation.

    The fact that these bacteria can "directly" mutate says nothing about the underlying cause. In fact it could actually be an example of ID.

  84. Comment by Steve Petermann — August 9, 2006 @ 1:18 pm

  85. great_ape Says:
    August 9th, 2006 at 1:18 pm

    It is perhaps unfortunate the analogy has too often been drawn between the inability of evolution to "look ahead" and orient itself towards future goals per se and the sort of blindness of vision or forethought a person might have. For now, as a consequence, the rhetoric surrounding the evolution debate is filled with the imagery of a blind bumbling fool, one who lacks the capacity to accomplish much at all–at least a first impression. This is perhaps not the best imagery for natural selection and mutation, and it is one we should seek to remedy by providing more and more concrete examples of how RM+NS can be generative of new function and complexity. While the focus on the blindness analogy was important to counteract our natural inclination towards teleological thinking, it has perhaps come back to haunt us in the war of hearts and minds. Is there a better imagery out there, a better analogy?

  86. Comment by great_ape — August 9, 2006 @ 1:18 pm

  87. trrll Says:
    August 9th, 2006 at 1:21 pm

    If you pour enough money and time into anything you will get some positive spin-offs. The resources would be better devoted to medical research.

    That has not been my experience as a scientist. Some lines of inquiry turn out to be time and money pits. Others yield rich veins of discovery. Indeed, some of the discoveries of origin-of-life research–insights into things like catalysis and self-assembly–are already being applied to medical applications.

  88. Comment by trrll — August 9, 2006 @ 1:21 pm

  89. Steve Petermann Says:
    August 9th, 2006 at 1:23 pm

    Nick Matzke,

    LOL. Ever heard of "the tree of life" A guy named Chuck made it the centerpiece of a little book back in 1859. Gould and others have since concluded that a bush is an even better analogy, with humans just a twig. Do I really have to do your thinking for you like this?

    This may be an analogy of descent but what I'm asking for is an analogy that descent is blind and non-intentional. First you'd have to discover a non-intentional causal source and then show the analogy that it can produce the complexity we see. Can you provide that?

  90. Comment by Steve Petermann — August 9, 2006 @ 1:23 pm

  91. Joy Says:
    August 9th, 2006 at 1:25 pm

    Nick M.:

    Ever heard of "the tree of life" A guy named Chuck made it the centerpiece of a little book back in 1859. Gould and others have since concluded that a bush is an even better analogy, with humans just a twig. Do I really have to do your thinking for you like this?

    Tree of life… tree of… Oh, yeah! Now I remember where I heard that before! I thought a guy named Moses wrote about it in one of five not-so little books a long, long time ago. Now you tell me his real name was "Chuck" and he wrote it in 1859? Now I'm really confused… :roll:

  92. Comment by Joy — August 9, 2006 @ 1:25 pm

  93. Steve Petermann Says:
    August 9th, 2006 at 1:29 pm

    Hi Nick,

    Gould used the analogies of a Drunkard's walk and Spandrels in a cathedral, but I'm not sure that they are exactly what you are looking for. In those cases, he was using the analogy as a teaching aid to help explain a concept rather than attempting to demostrate the validity of an evolutionary concept by analogy with something else.

    What I am looking for is an analogy where some non-intentional causal source can create something like a flagellum. We already know that intelligent humans can create something like this. That's an observable analogy.

  94. Comment by Steve Petermann — August 9, 2006 @ 1:29 pm

  95. Daniel Says:
    August 9th, 2006 at 2:21 pm

    Bradford:

    It's unclear exactly what you mean by creationist version of abiogenesis. Usually in these groups this codes for Genesis although strictly speaking creation indicates the action of a deity not a particular belief. In any case I would note that Genesis is not an empirical study. Are you saying that your faith is superior to my own?

    I'm not distinguishing between YEC and OEC, I'm more specifically referring to the notion of special creation, which I contrasted here.

    However, I haven't said anything at all about my faith - as I usually do, I talk about the known science, and keep my personal religious views to myself and my family.

    Steve:

    But this is not an analogy of an observable. Surely this wouldn't qualify.

    Why not? The analogy is used differently, sure, but it's no less an analogy. Perhaps a more fitting analogy, which you seem to be asking for, is comparing the direction of evolution with a similar non-biotic system, such as comparing evolution and nat'l selection to the path a stream selects in going down a hill. Each functions as a process of choosing which way to go based upon the mode of least resistence at any given moment, with each decision influencing future decisions, as Descent With Modification does.

    The fact that these bacteria can "directly" mutate says nothing about the underlying cause. In fact it could actually be an example of ID.

    Go back and re-read the cited articles on Cairns. Although at first he thought he found evidence that organisms can direct mutational change, he later found out that this was incorrect: mutations have never successfully been found to be preferentially occuring in some genes over others, only the conservation (selection for or against) has been shown. Thus, you have it backwards: there cannot be an underlying cause for something that has no effect.

  96. Comment by Daniel — August 9, 2006 @ 2:21 pm

  97. Steve Petermann Says:
    August 9th, 2006 at 2:40 pm

    Daniel,

    Perhaps a more fitting analogy, which you seem to be asking for, is comparing the direction of evolution with a similar non-biotic system, such as comparing evolution and nat'l selection to the path a stream selects in going down a hill. Each functions as a process of choosing which way to go based upon the mode of least resistence at any given moment, with each decision influencing future decisions, as Descent With Modification does

    But streams don't create the complexity we see in biosystems. Since humans do, it would appear that ID analogies greatly trump yours. Churchland's example is very specific, not some vague notion like least resistance. Surely there is a better analogy to support the non-teleological aspect of what many think is such an enormously important theory.

  98. Comment by Steve Petermann — August 9, 2006 @ 2:40 pm

  99. Nick Says:
    August 9th, 2006 at 2:54 pm

    Steve:
    What I am looking for is an analogy where some non-intentional causal source can create something like a flagellum. We already know that intelligent humans can create something like this. That's an observable analogy.

    Ahh. In that case, I don't think you will find "Darwinists" relying on analogies in that way, and I don't see any particular value in searching for such an analogy.

  100. Comment by Nick — August 9, 2006 @ 2:54 pm

  101. Daniel Says:
    August 9th, 2006 at 3:04 pm

    True, the stream analogy is an over-simplification, biology is much more complex. And you're quite right in describing this complexity when you say in the concluding paragraph of your initial post, that analogies of design just keep popping up in biology. Biologists themselves frequently use the descriptive term "design" when describing structure and function in features of life - the difference lies in whether you're referring to a selected design or a chosen design. This is where the stream analogy comes in… does the stream select its path as it goes along, or does it chose the destination and then figure out how to get there?

    Clearly, there's a conspicuous absense of evidence for choice in the "design." In fact, evo-devo, molecular biology and computational biology are going a long way to explaining the acquisition of complexity in naturally selecting processes, lending greater creedence to the role of selection in the "design."

  102. Comment by Daniel — August 9, 2006 @ 3:04 pm

  103. Nick Says:
    August 9th, 2006 at 3:06 pm

    (not Matzke)
    To expand on my last comment:

    Various people have mentioned analogies that are used to help explain or teach different concepts in biology. But, what you seem to want is a system which generates complexity in the same undirected way as evolution and which can be used as an analogy for evolutionary biology. Problem is, the characteristics of living organisms that permit evolution seem to be unique to life. They are not shared by human designed machines, although hypothetical von neumann machines might share some of the relevant characteristics. Since nothing else shares the relevant characteristics of life, analogies will be of limited value for investigating evolution.

  104. Comment by Nick — August 9, 2006 @ 3:06 pm

  105. Daniel Says:
    August 9th, 2006 at 3:09 pm

    Nick,
    In the flagellum example, or any other example of apparent complexity in biology, I think you're forgetting the first thing that we (or at least I) learned way back in HS biology class: the prevailing method of studying biology since Darwin has been the elucidation of how structure and function influence each other.

    That groups like the Discovery Institute are perverting this incidental relationship between structure and function (aka design) to their own ends (inserting an unwarranted theoretical causation) is, to me, the part we should be arguing about.

  106. Comment by Daniel — August 9, 2006 @ 3:09 pm

  107. Guts Says:
    August 9th, 2006 at 3:17 pm

    Nick:

    Problem is, the characteristics of living organisms that permit evolution seem to be unique to life.

    Actually the Brandeis project showed pretty much artificial intelligent self-replication. The problem here though is that the motors and programs were intelligently designed, but the robots did in fact evolve on their own.

    The basic question here is whether systems that evolve, both biological and artificial, use highly complex devices and mechanisms to do so, and whether such things are generated by non-intentional processes. The situtation is that there exists systems with machine-like complexity for which we only observe one reliable cause, intelligence. This is enough to warrant an investigative hypothesis, with perhaps even simulations much like the Brandeis project.

  108. Comment by Guts — August 9, 2006 @ 3:17 pm

  109. Steve Petermann Says:
    August 9th, 2006 at 3:32 pm

    Nick,

    Ahh. In that case, I don't think you will find "Darwinists" relying on analogies in that way, and I don't see any particular value in searching for such an analogy.

    It's not a question of value. Apparently, according to Churchland, that is the way science proceeds and progresses. We start with observations that create prototypes. From there science can use those prototypes to explain other things. His wave interference story is an example. Apparently instead of Darwinists basing their claims on observations and the prototypes that get encoded in their neural networks, they dream up some prototype (non-intentional forces create biotic like complexity) out of thin air and then go forward. If that is the case then according to Churchland's model they are not doing science.

  110. Comment by Steve Petermann — August 9, 2006 @ 3:32 pm

  111. Joy Says:
    August 9th, 2006 at 3:33 pm

    Daniel:

    mutations have never successfully been found to be preferentially occuring in some genes over others, only the conservation (selection for or against) has been shown.

    Um… surely you didn't mean to say this, Daniel. I just did a search that returned 784,000 hits for "preferential mutation," and among these are entire genomics databases set up for identifying hot-spots, hypermutational triggers and preferential mutation types. Now there's lots of diseases in there so these aren't necessarily adaptive, but mutations do occur preferentially in many places on the genome, can occur in direct response to biochemical triggers, and can most certainly be preferential in TYPE (like G/C and such).

    Selection can only occur after mutation occurs, and some mutations are 'invisible' to selection. I know you know this, I was just pointing out that your absolute assertions have crossed into erroneous territory.

  112. Comment by Joy — August 9, 2006 @ 3:33 pm

  113. great_ape Says:
    August 9th, 2006 at 3:33 pm

    Perhaps two analogies are necessary. On the one hand, following Darwin, we can invoke the example of human selection (e.g. on dogs) for a diverse set of attributes, resulting in a wide range of doggy forms. Here the human serves as a simple proxy for natural selection. Like the natural environment, people choose what lineage will proliferate based on some character or set of characters. One must accept the notion that the whims of human choice in this matter are very much like the enivronmental "whims" prodded the development of species as a whole. They can change, and different environments will in effect have different selective pressures, just like the Scottish and the Danes had different selection regimes for their dogs.

    On the other hand, we have the titanic resources of space and time. As an example, the grand canyon can be carved by water. It seems incomprenhensible, but so is this stretch of time to us. ID will contend that carving a gorge is not equivalent to the complexity of the flagellum. No, not really, but the leap one must make from flowing water to carving the canyon is. We posit that *once set in motion* the same forces that generated diverse forms of dogginess, when coupled with the vast resources of time such as that which carved the grand canyon, can yield the flagellum and far more.

  114. Comment by great_ape — August 9, 2006 @ 3:33 pm

  115. Guts Says:
    August 9th, 2006 at 3:37 pm

    Daniel:

    mutations have never successfully been found to be preferentially occuring in some genes over others

    Actually there are examples of this, like here, Molecular Microbiology 52(3), 643-650, 2004 where increased mutations in genes that improve uptake of the scarce amino acid occurs in response to starvation.

  116. Comment by Guts — August 9, 2006 @ 3:37 pm

  117. Joy Says:
    August 9th, 2006 at 3:49 pm

    great_ape:

    On the other hand, we have the titanic resources of space and time. As an example, the grand canyon can be carved by water. It seems incomprenhensible, but so is this stretch of time to us. ID will contend that carving a gorge is not equivalent to the complexity of the flagellum. No, not really, but the leap one must make from flowing water to carving the canyon is.

    Quibble, please. The Grand Canyon is an overgrown ditch. It was created by water carrying away earth and rock that was there before the water started carving. If we were to apply your analogy to evolution, we'd have to suppose there existed some super-being at the beginning of space and time that got "whittled down" to humans and worms and bacteria here on planet earth.

    Since the planet we live on is purportedly just 4.5 billion years old, and because Darwinism/Neodarwinism asserts that life started out simple and got complex over time, the proper analogy would be if the ocean [water] built a nuclear submarine by collecting and assembling raw materials over a mere century.

  118. Comment by Joy — August 9, 2006 @ 3:49 pm

  119. Steve Petermann Says:
    August 9th, 2006 at 3:59 pm

    Hi great_ape,

    Perhaps two analogies are necessary. On the one hand, following Darwin, we can invoke the example of human selection (e.g. on dogs) for a diverse set of attributes, resulting in a wide range of doggy forms. Here the human serves as a simple proxy for natural selection.

    I agree that might be a viable analogy to build on.

    No, not really, but the leap one must make from flowing water to carving the canyon is. We posit that *once set in motion* the same forces that generated diverse forms of dogginess, when coupled with the vast resources of time such as that which carved the grand canyon, can yield the flagellum and far more.

    This one, on the other hand, should only provide prima facie evidence. If that's it, I can't see how that's enough to assert a prominent theory like neoDarwinism. Surely more should be required for the non-teleological aspects of Darwinian theory to be accepted and taught. Also you are assuming that the carving of the Grand Canyon was non-intentional. Perhaps this is really the work of a great artist. What analogy can you employ that it was done non-intentionally? This strikes at the heart of what I am saying. Where on earth would one find such an analogy.

  120. Comment by Steve Petermann — August 9, 2006 @ 3:59 pm

  121. Daniel Says:
    August 9th, 2006 at 3:59 pm

    Joy:

    I just did a search that returned 784,000 hits for "preferential mutation," and among these are entire genomics databases set up for identifying hot-spots, hypermutational triggers and preferential mutation types.

    Yes, I meant to say that.

    Mutational changes on the nucleotide base-pair level have never been shown to occur only in genes that need modification for survival. Go back and re-read the link on Cairns - he specifically showed that under stress conditions, cells mutate more rapidly. Initially, he thought this elevated mutational frequency was specific to a small subset of genes, which gave the impression of a directed mutagenesis at work on the cells' parts; this was disproven upon further work, which showed that all genes in those cells showed elevated mutational frequencies. The findings supported the conclusions that mutations themselves are not directional or preferential - but yes, the appearance of preferential change in the phenotype has been observed in a very large number of biology studies.

    So, just to clear up any misunderstandings about what you may think I meant (and sorry if I wasn't clear on it), I did mean that mutation is a neutral process, even if the appearance of phenotypic variation and selection are not neutral processes.

    Guts, same response (directing you to Cairns' work) for your comment: cellular stresses (such as nutrient starvation) results in elevated levels of mutations for all genes, not just those required for nutrient synthesis. … i.e., the dna mutations in that study occur neutrally, not preferentially or directionally.

  122. Comment by Daniel — August 9, 2006 @ 3:59 pm

  123. Guts Says:
    August 9th, 2006 at 4:03 pm

    Daniel:

    Guts, same response (directing you to Cairns' work) for your comment: cellular stresses (such as nutrient starvation) results in elevated levels of mutations for all genes, not just those required for nutrient synthesis. "¦ i.e., the dna mutations in that study occur neutrally, not preferentially or directionally.

    But thats not what my reference shows. I also direct you to the book in our side panel Evolution In Four Dimensions.

  124. Comment by Guts — August 9, 2006 @ 4:03 pm

  125. Daniel Says:
    August 9th, 2006 at 4:12 pm

    Guts,
    Interesting - and sorry, I skimmed over the paper you referenced a bit quick. I just printed it out and will read it thoroughly now, and get back to you.

    As for the book Evo in 4 dimentions, I'd heard of it, and recently put it on my amazon wishlist for future purchase. No idea when I'll get to it though… but the desciption seems to put it into line with Kirschner & Gerhart's Plausibility of Life and their thesis of "facilitated variation" - having read Jablonka and Lamb's book yourself, would you say that that is a fair characterization?

  126. Comment by Daniel — August 9, 2006 @ 4:12 pm

  127. Guts Says:
    August 9th, 2006 at 4:16 pm

    Yeah sounds about right, but I havn't read Plausibility yet.

  128. Comment by Guts — August 9, 2006 @ 4:16 pm

  129. Bradford Says:
    August 9th, 2006 at 4:45 pm

    Daniel: However, I haven't said anything at all about my faith - as I usually do, I talk about the known science, and keep my personal religious views to myself and my family.

    If you are talking about known science then science indicates cells come only from other cells. Asserting they result from unknown and unspecified pathways reflects a faith based belief.

  130. Comment by Bradford — August 9, 2006 @ 4:45 pm

  131. Daniel Says:
    August 9th, 2006 at 4:50 pm

    Guts,
    Looking now at Barbara Wright's minireview, which you linked to, it does indeed argue for the sort of stress-directed mutagenesis (SDM) which I am arguing against. In the Introduction, Wright fairly states the dilemna:

    The search for directed mutations has been stymied by the problem posed by Delbruck in (1946): if a mutation can only be observed under conditions that may cause it, as well as select it, how can we tell the difference? Does the stress cause the mutation before the mutant is selected? This conundrum has understandably led to confusion, controversy, and, by default, acceptance of the Dogma first articulated more than 100 years ago by Weismann (1893). Recent advances in this field reveal mechanisms by which a specific stress does in fact cause mutations in related genes, thus resolving the issue raised by Delbruck.

    However, Wright goes on to fail to demonstrate (or cite a study that demonstrated) the hypermutational rates exclusively in stress-response genes. Instead, her "evidences" of SDM appears to be referring to the observation of variatants and the fixation of mutations, much akin to K&G's "facilitated variation." And facilitated variation is a concept that is gaining quite a bit of ground in recent years.

    But Wright also correctly hints that we would have a hell of a time actually proving or disproving directed mutation, but that thus far the default has been to the undirected/random mutation conclusion. It's simply very difficult to identify mutations prior to their fixation.

    All of this is very much in line with the Cairns work that I cited upthread, as well - the notion of directed mutation has been an attractive idea since evolution and genetics first met, but it's an unproven concept.

  132. Comment by Daniel — August 9, 2006 @ 4:50 pm

  133. Daniel Says:
    August 9th, 2006 at 4:52 pm

    Bradford,
    If you wish to call my acceptance of scientific hypotheses belief, I object to that, but there's not much that I can do about it, is there? :roll:

  134. Comment by Daniel — August 9, 2006 @ 4:52 pm

  135. Guts Says:
    August 9th, 2006 at 4:58 pm

    Daniel:

    However, Wright goes on to fail to demonstrate (or cite a study that demonstrated) the hypermutational rates exclusively in stress-response genes.

    I'm not exactly sure what you mean. One of the studies she cited was this one:

    Adaptive mgl-regulatory mutations and genetic diversity evolving in glucose-limited Escherichia coli populations.

    Where they actually show where the majority of mutations occurred. But yeah I agree this is unproven, but thats not surprising in this field.

  136. Comment by Guts — August 9, 2006 @ 4:58 pm

  137. Bradford Says:
    August 9th, 2006 at 5:05 pm

    Bradford,
    If you wish to call my acceptance of scientific hypotheses belief, I object to that, but there's not much that I can do about it, is there?

    There is nothing special about a hypothesis. We're not referencing a theory. You are entitled to your beliefs but if you are going to assert an empirical claim based on them then be prepared to back it up.

  138. Comment by Bradford — August 9, 2006 @ 5:05 pm

  139. Daniel Says:
    August 9th, 2006 at 5:19 pm

    Guts,
    Just to double-check, I printed out Notley-McRobb & Ferenci (1999) also. A couple of things of note in that paper:
    1) They use samples of a bacterial population grown in a chemostat to establish their findings, meaning that they're looking only at allelic frequencies that occur in an appreciable percentage of the population. In other words, any mutation that occurs in less than ~5% of the population typically would be "invisible" to the researchers, and those that are "visible" involve only the mutations that have been fixed in at least a reasonable fraction of the bacterial population.

    2) The title and abstract itself (and data therein) claim only to have identified mutations in the mgl-regulatory system that confer adaptive advantage for glucose-limited environments, and the identification of diversity at loci involved in this regulatory system - nothing at all about genome-wide patterns of hypermutation that would settle the matter either way.

  140. Comment by Daniel — August 9, 2006 @ 5:19 pm

  141. Daniel Says:
    August 9th, 2006 at 5:24 pm

    Bradford,

    You are entitled to your beliefs but if you are going to assert an empirical claim based on them then be prepared to back it up.

    You think there's no empirical evidence for the plausibility of the RNA World Hypothesis?

    Please, it may be shocking to you, and objectionable to your religious convictions, but there IS a valid basis for accepting such a hypothesis that does not require blind faith in dogmatic scripture.

  142. Comment by Daniel — August 9, 2006 @ 5:24 pm

  143. Bradford Says:
    August 9th, 2006 at 6:00 pm