8 Responses to “Lessons from a Worm”

1. Heaven is not the sky » Blog Archive » An important distinction Says:
   July 26th, 2006 at 12:53 pm

   [...] MikeGene over at Telic Thoughts gives a good example of an important distinction that is often overlooked. Mike quotes from an article by Nicholas J. Strausfeld, a professor of neurobiology from The University of Arizona. "When I looked at their brains, I was shocked because I didn't expect to see what I saw," said Nicholas J. Strausfeld of The University of Arizona in Tucson. "I just felt from their organization that these looked like spider brains, that they had more in common with spider brains than with other arthropod brains." [...]

Pingback by Heaven is not the sky » Blog Archive » An important distinction — July 26, 2006 @ 12:53 pm

2. Guts Says:
   July 26th, 2006 at 8:25 pm

   Mark Nutter:

   In the ID argument, things are held to be designed because they "look like" they were designed. But what does that mean, exactly? What, objectively speaking, are the qualities that make a thing "look like" it was designed? You just "know it when you see it." It's not really specific or measurable, it's more of a subjective perception.

   Actually thats simply not true. The similarities between biological systems and intelligently designed objects are quite measurable, for example, that both kinds of "machines" (molecular and human-engineered) are kinetically "out-of-equilibrium", they are constructions that have many parts with specific mechanical degrees of freedom. They are able to use energy to perform work (sometimes with amazing efficiency), create information, reversible, feedback control, signals, etc. The field of biological physics is based, at least in part if not entirely, on these kinds of measurments. There are many examples like this. Interesting that this idea actually goes back pretty far , to the seventeenth century, perhaps even further back.

Comment by Guts — July 26, 2006 @ 8:25 pm

3. Guts Says:
   July 27th, 2006 at 2:00 pm

   Mark Nutter:

   You can make comparisons between the structures on a human face and the pattern of light and dark on the moon, but that doesn't mean you've scientifically identified an actual connection between the two. There's a significant difference between analogy and correlation.

   Obviously if you only have one or a few characteristics for which to compare, then your comparison is simply a vague analogy/metaphor, even subjective. However, that is absolutely not what I showed, I didn't show just one or two characteristics that cannot be measured, or that is subjective, I showed many similarities that can be measured experimentally. What does it mean to "look designed", it means when you look at an intelligently designed object, and you look at something else that you don't know whether it is designed, you say "wow that looks designed because of a,b,c,x, y, z". There is no difference between me looking at the spider brain, and looking at another brain and saying, "wow that looks like a pre-spider brain because of a,b,c,x, y, z". The "a,b,c,x, y, z" is not subjective, as you claimed, it is measurable. The only thing that can establish an actual correlation is watching a videotape of the worm evolving into a spider-like organism and an intelligent designer designing bacterial flagella. However, there is structural and functional correspondance between the machines in nature and the machines that humans make, just as there is between the worm brain and the spider brain.

   Mark Nutter:

   You can compare points of similarity between things observed in nature and things known to have been designed by men, but the fact remains that relative to designedness (the key point here) there is no objectively measurable criterion for what it means to "look designed." You can, for instance, compare the DNA molecule to a spiral staircase, but does that mean that DNA was designed as a spiral staircase, or is that a manifestation of the electrostatic forces of attraction and repulsion that cause the atoms of a large molecule to assume a shape that balances attraction and repulsion?

   In this case, the techniques used in evolutionary biology and ID converge. In evolutionary biology you have two sequences, say, with some % similarity. The less similarity the two sequences have, the less confident you are in homology and vice versa. It's the same with the ID argument, if you want to compare DNA to an actual spiral stair-case (rather then just the spiral staircase pattern as the similarity you are pointing to) then that is like comparing two sequences with very low percent similarity. There is much greater similarity between the eubacterial flagellar motor and the one humans make, for the [measurable] reasons I explain above, and also according to experts in the field: "More so than other motors, the flagellum resembles a machine designed by a human" and "The flagellum functions in a similar way to a man-made machine but the diameter is only about 30 nanometers." (DeRosier and here, respectively). The similarity between the two kinds of "machines" have more things in common than DNA and a stair case, and thus one can build a hypothesis and draw tests from this similarity. If we found systems in the cell using DNA as an actual staircase much like humans do, then the "face on the moon" starts to come into view.

   Mark Nutter:

   That is, if a flagellum "looks like" a motor, it must be artificial, i.e. designed. However, to make only a binary comparison, to say a flagellum "looks like" a motor, does nothing for the ID argument unless one makes the additional connection "motor -> artificial."

   No, you're talking about proofs and must be's again. You keep doing that. The two situations are actually equivalent. What I do above, is I compare the machines in Biology directly to the machines we make. Both biological and human-engineered machines have specific characterisitics which can be compared and measured. And the conclusion is that there is less difference in say flagellum/human-made motor comparison than in the statistical chemical reaction in the gas phase/human-made motor comparison. You don't need to prove that there is such a connection in either the spider/worm case or in the flagellum/machine case in order to formulate a useful, predictive explanation for the similarities.

   Mark Nutter:

   The tertiary connection is the one that matters to the ID argument, and it's also the one which cannot be objectively measured, because that goes back to the question of what it is about the motor that "looks designed."

   What about the motor that looks designed is precisely what I described, the ability of motion with the participation of specific mechanical degrees of freedom that is determining their function, for example. It is important in both molecular and man made machines, and many experimental papers have been published on this subject.

   Mark Nutter:

   Now, one could argue that such "machines" are too simple, that to indicate design, a machine needs a certain minimum level of "machine-ness".

   And the person who would argue that would be absolutely correct.

   Mark Nutter:

   But this gets back to my original point: how does one objectively measure the "machine-ness" (or designed-ness) of a given structure or process? What units is this quality measured in?

   The same way that you measure the similarity between two sequences. Count. In the puller-levy analogy you describe, you are basically talking about the equivalent of how the best explanation for two sequences that are 80 percent similar, but very short, is mere coincidence not homology. The "face on the moon" so to speak. One can go through the physics of enzyme catalysis and list the similarities between human-engineered machines, for example, how the reaction mechanisms that are far from the state of equilibrium and close to it must be different. You can even go the other way, study human machines and look for those characteristics in biology, if you find more than you thought you would from say, a purely statistical process, you can then even predict that you have discovered a new molecular machine, ID can be scientifically useful! The more similarites you find, the more complexity you see, the stronger the inference to design.

   Mark Nutter:

   The whole question at issue here is whether complex, information-creating, work-performing, mechanical systems can arise spontaneously or whether they were designed.

   Yes that is the question, or more accurately, "can and did arise spontaneously", but you don't need to know the actual answer before proposing a testable one, if we already knew the answer there would be no need to make any comparisons, we can just move on to something else. The answer may even be a mesh between the two. You look at A and B, and you say A and B are similar therefore there might be a connection. Then you can draw additional detailed studies to test that prediction. Evolutionary biologists do this using similarity all the time. They do not prove the connection , they use it to draw tests. Entire models are sometimes even based soley on analogy. IDists use the same logic, well at least I do, and there is nothing superstitious about it. In other words, similarities with other things we happen to know were designed is precisely the definition of "looks designed". Being a rampant Poperian, I am not going to believe in my hypothesis, just use it for ideas for coming up with tests (Being human, its hard not to want to beleive them!). But if we start believing our hypotheses, and not testing them, then we are no better than those who are superstitious. No one knows whether these machines were actually designed or whether they arose spontaneously, all we can do is try to find the best way to figure it out. We do know however that intelligent beings regularly and easily generate machines of high complexity, but natural processes have a really hard time with it.

Comment by Guts — July 27, 2006 @ 2:00 pm

4. Guts Says:
   July 27th, 2006 at 9:03 pm

   Mark Nutter:

   Guts continues replying to me via comments in Telic Thoughts, and I suppose that's a good thing. (Anything to boost readership of my poor little blog, eh?)

   As if the dozen trackbacks you so generously leave on our blog every week isn't enough :mrgreen:. Fortunately you actually brought up a subject that interests me this week.

   Mark Nutter:

   Right away he set me up for a big disappointment:Darn! I thought for sure he was going to tell me what "looks designed" means, in objective, measurable terms, and then he goes and "defines" it in terms of a bunch of undefined variables. Too bad, I would love for somebody to specify, in concrete and measurable terms, exactly what the "a, b, c, x, y, z" of "looking designed" are. Oh well, maybe someday"¦

   Huh? I used undefined variables because I already specified concrete and measurable terms in both replies to you. That both kinds of "machines" (molecular and human-engineered) are kinetically "out-of-equilibrium", they are constructions that have many parts with specific mechanical degrees of freedom. They are able to use energy to perform work (sometimes with amazing efficiency), create information, reversible, etc.

   Mark Nutter:

   I never denied that there are measurable characteristics that can be found in common between two arbitrarily-chosen things. You can measure the roundness of the moon and you can measure the roundness of an orange, and you can compare the two in terms of those measurements and find that an orange is more like the moon than an apple is, for instance. But that's not the point. The point is, which characteristics are you comparing? You can't compare anything to the characteristics of "designedness," because as yet we have no objective, measurable standards for what the term "designedness" would mean.

   I already discussed this. If you have A as something very similar to B, not just somewhat similar or vaguely similar like only having the characteristic of "roundness", you can hypothesize a connection between them. This is done in both evolutionary biology and ID. You keep saying "designedness" as if it was some kind of vague concept. It isn't, we can observe intelligent design, we can even observe the mechanism of intelligent design, we can study it, taste it, eat it (not recommended from less experienced designers!). So we can compare stuff to it. One of the things we can compare to it is biological systems and it turns out there are many characteristics that are shared between biological systems, and designed objects.

   Mark Nutter:

   Yes, I'm not denying that you can make measurable comparisons between two different things; my point is that when you compare a biological structure to a "motor" or a "machine," you're comparing on the basis of its "motory-ness" or "machiny-ness," not its designedness.

   Actually, the very reason why DeRoseir et. al. says the flagellum looks like it was designed is because of it's machine-like nature. The reason why is because ID is the only "process" we readily observe building these type of things with these types of characteristics. He didn't say "it looks like it evolved by random mutation and natural selection".

   Mark Nutter:

   Remember, the issue in question is whether or not nature can spontaneously produce complex things with complex and efficient functions. Calling something "a machine" merely testifies that it is one of these complex things with complex functions; it tells us nothing about what the answer to the question might be (unless one is assuming one's conclusions).

   Actually yes it does, it does tells us what the answer to the question might be. We regularly and easily see how intelligent designers can generate such machines. Thus we are justified in taking this as axiomatic for further detailed study and hypotheses.

   Mark Nutter:

   Guts goes on to quibble (like so many Telic Thoughts folks!) about the fact that I said "must be" to mean "reasonably justifies drawing a conclusion that"¦" Honestly, I don't know why they're so anal-retentive about that; you'd think the idea of letting the data drive one's conclusions were some horrible heresy.

   But "reasonably justified conclusion" is not what you mean when it comes down to it, and you do it throughout your responses here. For example, when you ask why we wouldn't expect to see these patterns readily arise in nature spontaneously. The answer is, in a positive ID hypothesis, the mere possibility is not relevant. Heck, in a positive ID hypothesis, even if it was found that natural processes can regularly generate them like agents can it would still be irrelevant. Really all your saying here, in all your responses thus far, can be reduced to "but maybe it evolved! maybe it evolved!" but who cares? I'm not saying I know IDdidit, I'm saying I'm hypothesizing IDdidit based on these patterns and based on the observations of what generates these patterns, it's a reasonably justified conclusion, driven by available data.

   Mark Nutter:

   Fortunately, Guts doesn't just leave it there. He does address the issues (thanks Guts!):

   You're welcome.

   Mark Nutter:

   And I have no quibble with making measurable comparisons between the motory-ness of a flagellum and the motory-ness of an Evinrude. I'm merely pointing out that, if you want to know whether or not nature can spontaneously produce motors, this particular comparison is irrelevant.
   Yes, we know that some motors are designed. The question is, once you're done drawing analogies between motors and flagella, are there any specific characteristics of designedness itself which are comparable between the two systems?

   On this I agree. If you want to know whether machines can evolve through blind mechanisms, then it won't matter to you how closely they resemble designed machines. The same is true on the ID side, if you want to know if these things were designed, homology inferences won't matter to you. If you think they evolved and want to propose tests that it evolved then by all means, have at it. That you think it evolved however, and those tests that you propose that it evolved, is irrelevant to a positive argument for ID. ID does predict that it would be vastly improbable for blind forces to accomplish such design, so in that way, the negative argument of ID can also make predictions and be scientifically testable.

   However, the question of whether we can know what some characteristics of design is answered by studying, …the design! One way we can do this is to study a specific class of intelligent design, machines. Use these characteristics to find closely matching objects in life, and then in the process, you can discover even more molecular machines and thus this perspective does have value.

   Mark Nutter:

   It's really a simple exercise in logic: some animals are dogs, dogs have four legs, I see an animal with four legs, am I justified in concluding that it is a dog?

   Well no, but the fallacy here is that you are again thinking there are only some characteristics that these machines share, i.e. just four legs. You do this constantly in your last response as well. An animal can differ completely from a dog despite having four legs. The situation is more like dogs and wolves share many of the same characteristics, therefore, they may be connected.

   Spider brains and worm brains share many characteristics therefore they may be connected.

   All machines share many similar characteristics, therefore, they may be connected.

   Mark Nutter:

   In a valid scientific investigation, the predictions of a given hypothesis should arise logically and reasonably from the hypothesis itself. It's not enough to observe that both flagella and man-made motors have moving parts with limited degrees of freedom, and then claim that this pattern is one of the observable characteristics of designedness. What is the ID hypothesis, and why specifically does it predict that pattern, and not some other pattern?

   The ID hypothesis is that the designer has/had human-like advanced intelligence. One class of design that can be studied that are produced by human-like intelligence are…machines! One such characteristic of machines that I mentioned is that it has moving parts with limited degrees of freedom. If we find such a pattern in biology, we most likely have found a machine.

   Mark Nutter:

   And why does it predict that similar patterns will not also arise in nature, spontaneously?

   Because there's already a hypothesis that is considering that. Also, one of the reasons it is doubted is because machines have a way of conveying a kind of "forward-lookingness" of it's designer. There are actually many reasons why machine-like nature of an object conveys such signals of ID that are in many ways, (IMO) superior to chancy hypotheses, but I'm not really concerned here about that. Mostly I'm concerned with the "subjectiveness" you keep bringing up, the argument that the appearance of design of the flagellum because of it's machine-like complexity and similarity to intelligently designed machines is somehow not demonstrating how something can "look designed". It's uhh, interesting, or maybe I'm missing something subtle. I think the reason though, is that you are really hung up on that certainty thing.

   Mark Nutter:

   Also, how does this test work when applied to, say, Mt. Rushmore? The Golden Gate Bridge? A canoe? Is this really a characteristic of designedness, or a characteristic of "complex machiny-ness"?

   Like I said, complex machines are a class of design, there are many classes of design, for example, two distinct and unrelated systems using similar mechanisms, and that the similarity is largely conceptual. This phenonemon requires an explanation. The best explanation in my opinion is that of common design, a designer used the same "technique" to solve several problems. We can see this design characteristic in human design as well, like you'll probably see with several websites I've created. Again, there are characteristics that kind of go across the board, applies to all "design classes", but thats not really what i'm concerned with here.

   Mark Nutter:

   Guts goes on to make an argument that, frankly, I don't quite follow. He seems to be arguing from a subjective assessment of probabilities

   Actually, that statement I made has absolutely nothing to do with "subjective assessment of probabilities".

   Mark Nutter:

   There is a very great danger inherent in the practice of picking one's standards and criteria based on which ones will give a particular, desired result: you don't discover the truth that way, you only discover your own subjective beliefs. Arbitrarily picking characteristics that are already known to exist, and claiming these as the criteria for one's hypothesis, only masks a fundamental tautology.

   Agreed, but I have no idea how this is at all relevant, as I did absolutely nothing even remotely similar to this.

   Mark Nutter:

   That's all well and good, but you don't really test the ID alternative by picking out patterns in the observed data, arbitrarily (or presumptively) labelling them "predictions", and then drawing conclusions based on the fact that Hi Ho! these patterns do appear in the data.

   There is nothing arbitrary, nothing subjective, about which patterns I have picked out. I look at these patterns because it's what ID commonly and easily generates, and the patterns are specific, measurable, and experimentally testable.

Comment by Guts — July 27, 2006 @ 9:03 pm

5. Guts Says:
   July 28th, 2006 at 3:51 pm

   Mark Nutter:

   Notice the distinction (which Guts fails to make) between studying the characteristics of things which have been designed, and studying the characteristics that make up "designedness" itself.

   There is no difference. The way you learn about intelligent design is by studying intelligent design.

   Mark Nutter:

   We look at a staircase, knowing that it was designed, and then pick various attributes of stairs and call them "the characteristics of design." Then we look at a refrigerator, and it does not have those same characteristics. Does that mean it is not designed? Then we find a rock formation that has broken off in a series of parallel ledges, going up the side of the hill, in a manner very similar to a staircase. Does that mean it was designed?

   You keep making the same mistake. Lets say that we do find a rock formation that "looks like" a designed staircase. We then begin our measurements. Does each stair case match or at least closely match the size of a human foot so that one can easily stand on each step? If not are there signs that it at least once did? Is there some kind of "banister" type structure that will help us keep our balance as we walk up each step, like in human designs? As I said, the more % similarity to known human design, the greater the "looks designed" argument is. Also, just because some design classes don't fit others, doesn't mean we can't find some that do. So if we do happen to find a closed contained enclosure where the temperature is controlable but usually kept cold for various purposes may not yield any results by comparing it to a staircase , comparing it to a human designed refridgerator does yield results.

   Mark Nutter:

   What's missing is an explanation of why these particular characteristics should be distinctive of design. In other words, why should these particular characteristics appear in any designed system, and be absent from any non-designed system? What is it that makes these the characteristics of designedness, rather than being merely the characteristics of a particular system which we happen to know was designed?

   Uhh, those characteristics didn't just "poof" into existence once humans designed them. Their specific mechanical degrees of freedom are there by virtue of intelligent design, by virtue of their construction. Often in a machine, for example, the form and distribution of it's electric charge gives them their function. Machines are built precisely , they are digitally controlled, (i.e. they get instructions as encoded information). This characteristic is there by virtue of design, and it is measurable in both human-made design and molecular machines. I havn't even gotten into my favorite characteristics yet, but even design principles are virtually identical in both man made machines and molecular machines, in mitochondria for example, where some very complex reactions create a voltage difference, compare that to PEM fuel cells or hydroelectric dams. This princple didn't just "poof" into existence when the design was finished, it's there because the designer wanted it to be there and designed it so.

   Mark Nutter:

   To use my earlier example, what is it about four-leggedness that allows us to conclude that the four-legged animal in front of us is a dog?

   Why did you ignore my response?

   Mark Nutter:

   Only by assuming that all machines are designed can you assert that the characteristics of a machine are the characteristics of design.

   You keep saying the same thing over and over again but you don't ever explain what the logical fallacy is. It is in fact a reasonable and logical assumption. Just like the assumption that if an organism's sequences are very similar to a particular family of similar sequences, then they belong to that particular family, such as WD repeat sequences.

   Mark Nutter:

   This is flatly untrue, of course. We never observe bacterial flagella, or centrioles, or other natural systems, being formed by ID.

   But you know thats not what I said. I said we observe ID generating machine-like characteristics, the ones I've been listing since my first response to you, which is why DeRosier says "it looks like a machine designed by a human". Lets look closer at that quote:

   More so than other motors, the flagellum resembles a machine designed by a human (Figure 1a).

   If you actually look at Figure 1a, what does it say?

   (a)Schematic of the bacterial flagellum as a
   mechanical device. The parts thought to be
   responsible for torque generation are shown
   in thicker lines. They lie inside the cell except
   for the studs, which cross the membrane and
   are thought to be anchored to the peptidoglycan
   layer (PG). The filament or propeller lies
   outside the cell's inner (IM) and outer (OM)
   membranes and is about 10 mm long.
   (b) Image of the flagellum. The image is an
   average of about 100 individual electron micrographic
   images of a frozen-hydrated preparation
   of flagella. The bar corresponds to
   25 nm.
   (c) A color-coded copy of a slice through the
   cylindrically averaged flagellar structure. FliF,
   which forms the M ring, S ring, and socket,
   is shown in green. FliG, shown in blue, is
   attached to the cytoplasmic face of the M
   ring. FliM and FliN, shown in yellow, are
   thought to make up the C ring. The L and P
   rings are shown in pink, and the rod and the
   short stretch of hook are gray.

   "Mechanical device", "sockets", "rings". Obviously his reasoning here is the machine-like nature of the flagellum, that it looks and functions like human-engineered machines.

   Mark Nutter:

   What we observe happening in the present is nature producing these complex systems by natural, biochemical means, including the innovation of systems "designed" to resist antibiotic drugs, or to digest synthetic materials, or to perform other novel functions.

   What we don't see is them arising spontaneously through natural selection and random mutation from simpler precursors. They are constructed in factories much like machines we have are constructed in factories, the factories themselves function much like our own factories, with different compartments to keep various kinds of parts seperate, mechanisms also take various parts and attaches them to the correct assembly, etc.

   Mark Nutter:

   We observe humans creating similar systems by design, sure. The question is not whether some machines can be produced by design, the question is whether all machines must be the result of design. Simply assuming that all machines must be designed does not answer that question, it merely appeals to our ignorance of how nature works.

   No, it provides a useful and predictive starting point to conduct a scientific investigation.

   Mark Nutter:

   We don't yet understand how nature could spontaneously produce a machine, therefore we assume that it cannot, and draw a design inference because we've discarded natural causes due to our own ignorance.

   Why should we be forced to believe that nature can? Why not start a research program where we look for another answer? What is impossible about the hypothesis that intelligence designed the flagellum?

   Mark, do you think it's possible that the molecular machines in biology were intelligently designed?

   Mark Nutter:

   There is one area, at least, where Guts and I seem to agree: ID does not yet have any answers. It has some conjectures about what things might be answers, but looking at the qualities of machines tells us nothing about whether or not machines in nature were necessarily designed:

   Intelligently designed machines give us a good guide as to a possible cause of molecular machines precisely because they are so similar. It may not be necessarily so, but it is a reasonably justified conclusion driven by available data.

   Mark Nutter:

   Here I have no quibble at all, except perhaps that one need not even observe the qualities of a particular machine in order to suggest the possibility that intelligent design might produce machines with particular qualities.

   Actually, the only way one can know what qualities to look for is to observe them where you know intelligent design took place.

   Mark Nutter:

   Anybody can propose a conjecture about what might be the cause of something else. But that's what you do as Step Zero in the scientific method: proposing a conjectured cause. The scientific question is: does the evidence support the conclusion that a given machine is designed? For that question, ID has no answers, nor even a testable hypothesis

   That is utterly false. ID does have answers to that question, perhaps more elaborate then I described here, however, I'm concerned here with the "looks like" investigative technique employed by many IDists, i.e. "it looks designed" or "it looks like a machine designed by humans" therefore, "I should see some characteristics if actually does and it's not just my subjective opinion". But even this gives us tests to work with, one example can be found here where the "machine-like" quality lead to a prediction

   Enolase functions in the degradosome as a prong that plugs the degradosome into the glycolytic pathway so that ATP generated by pyruvate kinase is then quickly channeled to the helicase to fuel its unwinding activity.

   That is, the degradosome is a dynamic modular machine that literally is plugged in to turn it on. But it can also easily be unplugged to turn it off, which is why scientists don't pull out other glycolytic enzymes attached to enolase. The reversible nature of degradosome function makes it possible to regulate its activity. The nice thing about this hypothesis is that it explains why enolase is still functioning as a glycolytic enzyme. But it also means enolase is not an example of an alternative function.

   As you can see, knowing the characteristics of human designed machines can lead to fruitful hypotheses about various features of life.

   Mark Nutter:

   Contrary to what Guts claims, it's extremely relevant to consider all the alternatives before reaching a scientific conclusion.

   Ok please tell me how scientists have considered the design alternative before reaching the naturalistic conclusion. Darwinists do not consider any design alternative , they simply rule it out from the get go.

   Mark Nutter:

   Here's the situation expressed logically:

   If A, therefore C (e.g. if design, then complex motor)
   If B, therefore C (e.g. if nature, then complex motor)
   Given C (complex motor)
   Conclusion: A (design)

   Is this really "a reasonably justified conclusion"?

   No the logic is like this:

   There exists complex machines
   We do not see complex machines arise spontaneously.
   The only cause that we know for some complex machines is intelligent design
   Therefore it is reasonable to conclude that the machines in nature are also intelligently designed.

   That is the beginning of your investigation. You don't need to be certain about it, it doesn't have to be necessary ,in fact thats what makes it falsifiable.

   Mark Nutter:

   Guts is saying it's "reasonably justified" to conclude design based on observing characteristics and ignoring the possibility that other causes could also have produced those same characteristics.

   Precisely, "could have" is not the same as "did".

   Mark Nutter:

   It may be ok to disregard alternative explanations while exploring a particular hypothesis, but when it comes to drawing "reasonably justified" conclusions, you need to consider all the facts, not just the ones that support a particular conclusion.

   There are no "facts" that settle the question as to the spontaneous generation of complex machines.

   Me:

   The ID hypothesis is that the designer has/had human-like advanced intelligence. One class of design that can be studied that are produced by human-like intelligence are"¦machines! One such characteristic of machines that I mentioned is that it has moving parts with limited degrees of freedom. If we find such a pattern in biology, we most likely have found a machine.

   Mark Nutter:

   But the missing part, the part that prevents this from being a testable hypothesis, is the part about ""¦and not some other pattern?" Why, for instance, should we expect to find that a designed system will have moving parts (e.g. a motor), instead of lacking them (e.g. stairs, Mt. Rushmore, etc)?

   I already discussed this in my last response, so I'll simply repeat it here.Like I said, complex machines are a class of design, there are many classes of design, for example, two distinct and unrelated systems using similar mechanisms, and that the similarity is largely conceptual. This phenonemon requires an explanation. The best explanation in my opinion is that of common design, a designer used the same "technique" to solve several problems. We can see this design characteristic in human design as well, like you'll probably see with several websites I've created. Again, there are characteristics that kind of go across the board, applies to all "design classes", but thats not really what i'm concerned with here.

   Mark Nutter:

   This is still the same approach as the "seer" proving his psychic powers by saying "I knew it" after anything that happens.

   Actually if you take a look at each of the characteristics I listed , one can propose that a particular system they are studying is kinetically kept out of equilibrium, that it is reversible, etc, without knowing that first. If you do, most likely, you have found a machine never discovered before. Using the characteristics of human designed machines one can find new undiscovered machines in the cell, no pyschic powers necessary.

   Mark Nutter:

   This is even better, from my perspective. One of the characteristics of "designedness" is "forward-lookingness." Ok, so what objective, measurable characteristics define "forward-lookingness"? In other words, what measurable, concrete attributes are there in systems with "forward-lookingness" that are absent from systems without "forward-lookingness"?

   This has been elucidated by an oft cited "predictions list" at Talk.Origins:

   Because evolution has no foresight, and cannot plan for future functions, it would be extremely suspicious if biological molecular systems were efficiently designed. Again, this does not rule out complexity - merely efficiency of mechanism.

   Efficiency of mechanism of course, is measurable, and experimentally testable. That is just one of the many non-subjective tests of "forward-lookingness" that machines exhibit, and it also happens to be a characteristic shared by molecular machines and human designed machines (and thats no coincidence). Another is that each of the parts have specific degrees of freed determined by their construction which give them complex function which creates information.

   Mark Nutter:

   By the way, what I'm hung up on is letting the evidence dictate one's conclusions

   Then why are you saying "necessarily" "must be" "could have" as if those were actually relevant to a positive ID argument? Aren't you guys always complaining that ID is nothing but arguments against evolution? Then why do you keep asking me to argue against evolution?

   My response here pretty much covers the "gist" of your second posting, but I just wanted to correct some glaring mistakes in that second post:

   Mark Nutter:

   Guts doesn't like my "dogs have four legs" analogy because I only gave one characteristic (four-leggedness) whereas he gave several. I could just as easily give several characteristics of dogs, too, based on my observations

   This once again just ignores the argument that I'm actually making, and conjures up a straw man. I am not, for example, talking about "all four legged animals". I'm talking about much more characteristics than just four legs. I'm looking at two very similar "animals" with a plethora (cf three amigos) of similar characteristics: wolves and dogs. Or more specifically to my case: man made machines and molecular machines. The similarity in wolves and dogs suggests a connection, just as the similarity between molecular machines and man made machines suggest a connection. This has still not been addressed, strangely, it's been ignored.

   You do mention more similarites , but were you joking? That couldn't have been a serious response. Of course there are many animals that "bite" and have "one nose" and "ears", but be more descriptive with those characteristics, as I am when it comes to molecular machines and man made machines, and you wil begin to see distinguishing patterns .

   Mark Nutters:

   Are those characteristics the result of being designed, or are they the result of natural law preventing a machine from working unless it has those characteristics

   Actually many of those characteristics are what breaks the tendencies of natural law , for example, being kept kinetically out of equilibrium, or mastering the brownian storm because of the efficiency of your motor mechanism.

   Mark Nutter:

   He says they are the characteristics of a certain class of designed systems (namely, complex motors), but again, are these characteristics that any designed complex motor will have and any non-designed complex motor will lack?

   This question is loaded. There are actually no examples of "non-designed complex motors" or "designed molecular motors in life" simply because we do not know the origin of the motors we see in life. Because we do know that these motors are very similar to the motors that are intelligently designed, but not designed naturalistically, a reasonable hypothesis is that the motors in life are also designed.

   Mark Nutter:

   I don't think so. If a system has to "create information" in order to be a designed complex motor, I daresay that lets the flagellum out as a candidate for ID.

   This is simply false of course, oddly you give no justification for this assertion. So I'll let you in your next response, discuss this thoroughly, then I'll respond.

   Mark Nutter:

   What does "kinetically out of equilibrium" mean, and why would this condition not exist in an undesigned complex motor?

   Give me an example of an undesigned complex motor. You don't know what "kinetically out of equilibrium means? And yet you've been disagreeing with me for like what, three+ posts?

   Mark Nutter:

   Is it not redundant to say that a "complex" motor will have "many parts"?

   

   Mark Nutter:

   Why would a non-designed complex motor lack parts with degrees of freedom, and how could it direct energy towards the motor's function without this kind of constraint?

   Give me an example of a non-designed complex motor.

   Mark Nutter:

   What characteristics are included under the heading "etc."?

   Lets specifically discuss these characteristics first because you don't seem to have understood me.

   Mark Nutter:

   No doubt Guts will respond that the positive argument for ID doesn't care whether the constraints of natural law produce the very features that ID'ers attribute to design.

   No a positive argument wouldn't care about that unless there was proof that it did.

   Mark Nutter:

   And that's fine, they don't need to care. The only time you need to consider other possible sources for a set of characteristics is if you want to use them to justify an inference that such-and-such is more likely to be designed than undesigned. As long as you're content to merely speculate, you can ignore such considerations altogether. Just don't claim that you've found a theory that fits the facts better than evolutionary theory does.

   Ok please, with references to the peer reviewed journals followed by a complete discussion, show me which complex motor has arisen through the constraints of natural law spontaneously, and without input from intelligent design. Don't just assert or guess, explain it thoroughly. I can do the opposite pretty easily. If you can't do that as easily as I could, or at all even, then why is my conclusion not rationally justified and drive by availabe data?

Comment by Guts — July 28, 2006 @ 3:51 pm

6. Guts Says:
   July 28th, 2006 at 4:43 pm

   Mark Nutter:

   Guts responds to my last post(s) by repeating the same arguments I've already addressed. But he does make one statement I would like to explore in more detail.

   Actually, I did repeat some of the same arguments, but thats because you ignored my response (as you do here). But I also elaborated on them, and gave some new ones.

   Mark Nutter:

   Even intelligent design must conform itself to the constraints imposed by nature.

   Intelligent design also has the unique ability to resist the tendencies of nature, like defying gravity itself.

   Mark Nutter:

   Yes, ID can be a productive means, in terms of cognitive perceptions, for anticipating which solutions are likely to be functional and even efficient in nature. But this isn't the same as making testable predictions based on an ID hypothesis, because we're not talking about a prediction that will return one set of results in the case of a designed complex motor, and a measurably different set of results in the case of an undesigned complex motor.

   Please give me an example of an undesigned complex motor. The assumption that all complex motors are examples of intelligent design, based on rational conclusion driven by available data, is what one can use to make testable hypotheses.

   Mark Nutter:

   Our experience with the constraints imposed by nature is leading us to anticipate that similar configurations will work under similar conditions, but that's a reflection of the consistency of natural laws, and the need for even intelligent design to conform to those constraints. It's not a test of whether ID fits the facts better than natural alternatives.

   Then it should be very easy to, with references to the peer reviewed journals followed by a complete discussion, show me which complex motor has arisen through the constraints of natural law spontaneously, and without input from intelligent design. Don't just assert or guess, explain it thoroughly. I can do the opposite pretty easily. If you can't do that as easily as I could, or at all even, then why is my conclusion not rationally justified and driven by available data?

Comment by Guts — July 28, 2006 @ 4:43 pm

7. Guts Says:
   July 29th, 2006 at 9:11 pm

   It's rather strange that you titled this post "the scientific challenge" but in fact the actual science I requested is completely absent from this post.

   As an example, my question was:

   Ok please tell me how scientists have considered the design alternative before reaching the naturalistic conclusion. Darwinists do not consider any design alternative , they simply rule it out from the get go.

   All you do in your summary here is describe precisely how one can make predictions from ID theory (I was more specific in my former responses, such as with enolase, but of course, that was ignored). I want to see how Darwinists rule out Design alternatives. Here's a paper where you can show me an example of this:

   The cilium/flagellum is a sensory-motile organelle ancestrally present in eukaryotic cells. For assembly cilia universally rely on intraflagellar transport (IFT), a specialised bidirectional transport process mediated by the ancestral and conserved IFT complex. Based on the homology of IFT complex proteins to components of coat protein I (COPI) and clathrin-coated vesicles, we propose that the non- vesicular, membrane-bound IFT evolved as a specialised form of coated vesicle transport from a protocoatomer complex. IFT thus shares common ancestry with all protocoatomer derivatives, including all vesicle coats and the nuclear pore complex (NPC). This has major implications for the evolutionary origin of the cilium. First, it reinforces the tenet that duplication and divergence of pre-existing structures, rather than symbiosis, were the major themes during cilium evolution. Second, it suggests that the initial step in the autogenous origin of the cilium was the establishment of a membrane patch with transmembrane proteins transported by the ancestral vesicle-coating IFT complex. We propose a scenario for how the initial membrane patch gradually protruded to enhance exposure to the environment, then started to move, and finally compartmentalised to render receptor signalling and ciliary beating more efficient.

   Where is the design alternative definitively ruled out?

   Mark Nutter:

   Guts also criticizes my logic (without actually finding any fallacies or errors in it), and offers his own instead:

   That wasn't "your logic" that was an erroneous interpretation of the argument I'm using. Why would I bother refuting an argument that is falsely attributed to me?

   Mark Nutter:

   Point 2 however ("We do not see complex machines arise spontaneously") is a non-observation. If we don't see something, does that mean it does not exist, or merely that we fail to see it? Perhaps we're just not looking in the right place at the right time, or with the right equipment.

   Thats precisely what makes the hypothesis falsifiable.

   Mark Nutter:

   I would re-phrase this argument as:

   1. Complex machines exist.
   2. We know design can produce complex machines.
   3. We do not know whether or not other causes can produce complex machines.

   No, that would make the argument incomplete. It needs a number 4:

   "Because of (2) it is a reasonably justified conclusion that the complex machines in the cell were also designed". When you omitted (2) and rewrote (3), you made a completely different argument that I'm not using, it's called "a straw man".

   Instead of continuing to change my argument, why don't you address it?

   Mark Nutter:

   Now, to this reasoning, we can also add other observations, such as the fact that intelligent design requires the existence of an intelligent designer, and that in every known case of unquestioned intelligent design, there is independent evidence for the existence of the designer, as well as evidence related to the means by which the designer(s) implemented and produced the actual instances of each design.

   First even if true (which it isn't), that would be irrelevant to the hypothesis , as the independant evidence could be lost or simply not yet found (i.e. as could've been the case if the face on mars were actually a face), and thusly, the objection would be an "argument from ignorance" :grin:. Second, it has been shown that logical inferences are enough in science, for example here's a hypothesis about the origin of cells:here

   All life is organized as cells. Physical compartmentation from the environment and self-organization of
   self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter
   with such attributes would be life's most likely forebear.

   Basically they are proposing the hypothesis that the ancestor was membraneless, that the two domains (the bacteria and archaea) differentiated , they then developed their membranes independently and eukarotes originated via symbiosis with bacteria.

   If in order to simply base a hypothesis on known similarities that suggest connections (as I do as well), I need to show independant evidence of the connection (i.e. a designer and compartmentless ancestor) , where is that done in this peer-reviewed paper?

   Mark Nutter:

   I suspect Guts didn't understand what I was saying, since I'm pretty sure he's not suggesting that man-made machines violate the laws of nature.

   "Breaking the tendencies of natural law" doesn't mean violating the laws of nature.

   Mark Nutter:

   This is a telling response. If we do not know the origin of the motors we see in life, how do we know that none of them are examples of non-designed complex motors?

   We don't. We hypothesize that they aren't, and draw tests from this hypothesis until that hypothesis is falsified or verified. The only way to produce an example of an undesigned complex motor would be to show that it is in fact undesigned. There are no demonstrations of this. So it's up in the air. Right now, the only known cause of complex motors is intelligent design. This is not based on ignorance either, because there is no available data that is currently in our hands to be ignorant of. It is not possible to be ignorant of data that may in fact not exist.

   Mark Nutter:

   More importantly, how can you create a testable hypothesis of design if you are unable to describe and predict what the characteristics of an undesigned motor would be, observation or not?

   I discuss this a little more below but let me start with this: The prediction is that the characteristics of machines, lets take efficiency of mechanism for example, could not (in a statistical sense) arise from natural processes because they do not have foresight. A process that does not have foresight would improbably be able to foresee the need for a very efficient complex motor breaking water molecules and how to design the parts accordingly. Intelligent designers can.

   Mark Nutter:

   Part of testing is being able to tell the difference between what we should see if the hypothesis is true, and what we should see if it is not true. To admit that ID gives us no way to tell what an "undesigned complex motor" should look like is to admit that ID has no testable hypothesis about complex motors.

   That doesn't follow. I discussed this in my previous responses but let me do it again, the fact that you can't give me an example of a "known undesigned complex motor" to differentiate with "known designed motors" supports and strengenths the hypothesis, indeed, it is the basis for the hypothesis. It is question begging to say "what would a undesigned motor look like" because thats one of the investigation's questions, whether undesigned complex motors could even exist.

   One way to test whether undesigned complex motors could actually arise spontaneously, is to do something akin to Behe's flagellar test. Or perhaps less controversial, to show a homologous simpler ancestor that actually predates the flagellum. The great white hope was the t3ss but that went down in flames,just as ID predicts.

   The hypothesis however, is that the reason why we do see complex motors in life is because they were intelligently designed. If there was no intelligent design, we would see flotsam and jetsam, because that is more like what we would expect from natural processes, because that is in fact what we do see natural processes generate. Sloppy simplicity. In other words, if the objects in life did arise spontaneosly , they would look very different then what they actually look like, flagella for example wouldn't have a core number of parts needed for function across all lineages, they would be in all ways reducible and redundant and floppy. This is why some anti-IDists argue this (and another way in which this ID hypothesis about complex motors is empirically testable). Man made machines are not in all ways reducible and redundant, they are specific, precise, and all are IC. Floppy, simple, systems with 100% variable parts present no difficulty whatsoever to blind natural processes. Thats what was so interesting about Musgrave's error a while back, he argued that protein-protein interactions were simple and can be generated easily, however, upon closer inspection, and precisely as ID would predict, he was incorrect, but I digress.

   Still , in a purely positive ID argument, one that does not take alternatives into consideration unless absolutely proven, even "could have" arguments are irrelevant. One can propose a purely positive history of life based on ID. One can measure the relative usefulness of each hypothesis soley by it's track record, not by imaginative could have arguments.

   Mark Nutter:

   Guts does not understand why I think a flagellum fails to create information, so I'll just ask, by way of reply, what information a flagellum creates? If he means that the creation of information is necessary in order to specify a flagellum, then I've got all kinds of instances of nature spontaneously creating new information.For example, the information which specifies me as a unique biological individual

   But this once again begs the question. For example cell division is also very machine-like (it's even reversible). That information wouldn't even exist without this information creating machine. That is not an example of nature spontanesouly producing a machine that creates information such as that needed to specify the flagellum.

   I see a deeper flaw in your logic here though. Remember that the ID test functions much like a % sequence similarity analysis. You don't just take one characteristic, and proclaim you have shown how all the characteristics can be produced spontaneously.

   Mark Nutter:

   That's a good response, rhetorically speaking, since I can't describe the difference between a designed motor and an undesigned motor unless someone comes up with a concrete and measurable definition of what the characteristics of "designedness" are, so that I could say they were present in the designed motor, and absent from the undesigned motor.

   One cannot tell what is absent from an undesigned complex motor unless they actually had an undesigned complex motor. There are none. Thats a wierd response given that you actually liked one of my characteristics that somehow fit the made up word "designedness", and I actually showed how this characteristic can be measured.

Comment by Guts — July 29, 2006 @ 9:11 pm

8. Guts Says:
   July 30th, 2006 at 2:02 am

   New policy at TT, only 1 trackback per post, unless you're not Nutter.

Comment by Guts — July 30, 2006 @ 2:02 am

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